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$$$getRootComponent$$$() - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
Returns the root components.

A

A - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
a - Variable in class com.compomics.util.math.statistics.linear_regression.RegressionStatistics
a in y = a.x + b
A_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Identifier for an a ion.
A_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Identifier for an a ion.
aa - Variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
The amino acid that can generate this ion as single letter code.
AAIdentityFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
Feature based on an amino acid identity.
AAIdentityFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
Empty default constructor
AAIdentityFeatureAbsolute - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
An amino acid identity feature at a fixed position on the peptide sequence.
AAIdentityFeatureAbsolute() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
Empty default constructor
AAIdentityFeatureAbsolute(int, char) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
Constructor.
AAIdentityFeatureRelative - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
An amino acid identity feature at a position relative to the end of an ion on the peptide sequence.
AAIdentityFeatureRelative() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
Empty default constructor
AAIdentityFeatureRelative(int, char) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
Constructor.
aaIndex - Variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
The index on the sequence.
aaIndex - Variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
The index on the sequence.
AaMass - Class in com.compomics.util.gui
Displays the mass of a series of amino acids.
AaMass(Frame, boolean) - Constructor for class com.compomics.util.gui.AaMass
Creates a form AaMass.
AaOccurrence - Class in com.compomics.util.experiment.identification.protein_sequences
This class gathers statistics on the occurrence of amino acids in a fasta file.
AaOccurrence() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.AaOccurrence
Empty default constructor
AaOccurrence(int[]) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.AaOccurrence
Constructor.
AAPropertyFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
Feature based on an amino acid property.
AAPropertyFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
Empty default constructor
AAPropertyFeatureAbsolute - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
An amino acid property feature at a fixed position on the peptide sequence.
AAPropertyFeatureAbsolute() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
Empty default constructor
AAPropertyFeatureAbsolute(int, AminoAcid.Property) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
Constructor.
AAPropertyFeatureRelative - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
An amino acid property feature at a position relative to the end of an ion on the peptide sequence.
AAPropertyFeatureRelative() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
Empty default constructor
AAPropertyFeatureRelative(int, AminoAcid.Property) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
Constructor.
AAPropertyRelationshipFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Feature based on the relationship between two amino acid features.
AAPropertyRelationshipFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
Empty default constructor
AAPropertyRelationshipFeature(AAPropertyRelationshipFeature.Relationship, AAPropertyFeature, AAPropertyFeature) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
Constructor.
AAPropertyRelationshipFeature.Relationship - Enum in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
The different relationships implemented.
AASequenceFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
Feature based on the amino acid properties of a sequence.
AASequenceFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
Empty default constructor
AASequenceFeature.Function - Enum in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
The different functions implemented to compare the amino acid features.
AASequenceImpl - Class in com.compomics.util.protein
This class represents a sequence for a protein or peptide.
AASequenceImpl(String) - Constructor for class com.compomics.util.protein.AASequenceImpl
Constructor that allows the initialization of the sequence with a String variable representing that sequence.
AASequenceImpl(String, Vector) - Constructor for class com.compomics.util.protein.AASequenceImpl
Constructor that allows the initialization of the sequence with a String variable representing that sequence and a Vector of Modification instances.
AaSubstitutionMatrix - Class in com.compomics.util.experiment.biology.variants
Matrix of amino acid substitutions.
AaSubstitutionMatrix() - Constructor for class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Empty default constructor
AaSubstitutionMatrix(String, String) - Constructor for class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Constructor.
AaSubstitutionMatrixTableModel - Class in com.compomics.util.gui.variants.aa_substitutions
Table model to display the content of an amino acid substitution matrix.
AaSubstitutionMatrixTableModel() - Constructor for class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
Empty default constructor
AaSubstitutionMatrixTableModel(AaSubstitutionMatrix, boolean) - Constructor for class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
Constructor.
ABBREVIATION - Variable in enum com.compomics.util.experiment.units.StandardUnit
The abbreviated name of the unit.
abort() - Method in class com.compomics.util.io.ftp.FTP
Send Abort command.
AbstractIdentificationParametersCli - Class in com.compomics.cli.identification_parameters
This class serves as a base for the implementation of IdentificationParametersCLI in specific tools.
AbstractIdentificationParametersCli() - Constructor for class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
 
ACC_NUMPRESS_LINEAR - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
 
ACC_NUMPRESS_PIC - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
 
ACC_NUMPRESS_SLOF - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
 
accept(File, String) - Method in class com.compomics.software.autoupdater.JarFileFilter
 
accept(File) - Method in class com.compomics.util.io.file.filefilters.DatFileFilter
Accept all directories, *.dat files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.DtaFileFilter
Accept all directories, *.dta files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.FastaFileFilter
Accept all directories, *.fasta files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.JpegFileFilter
Accept all directories, *.jpeg files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.MgfFileFilter
Accept all directories, *.mgf files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.Ms2FileFilter
Accept all directories, *.ms2 files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.MzDataFileFilter
Accept all directories, and *.mzData files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.MzMlFileFilter
Accept all directories, and *.mzML files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.MzXmlFileFilter
Accept all directories, and *.mzXML files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.OmxFileFilter
Accept all directories, *.omx files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.OutFileFilter
Accept all directories, *.out files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.PdfFileFilter
Accept all directories, *.pdf files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.PeffFileFilter
Accept all directories, *.peff files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.PepXmlFileFilter
Accept all directories, *.pep.xml, *.pepxml and *.xml files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.PklFileFilter
Accept all directories, *.pkl files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.PklSpoFileFilter
Accept all directories, *.pkl.spo files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.PkxFileFilter
Accept all directories, *.pkx files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.PngFileFilter
Accept all directories, *.png files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.ProtXmlFileFilter
Accept all directories, *.prot.xml, *.protxml and *.xml files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.SequestParamsFileFilter
Accept all directories, sequest.params files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.SvgFileFilter
Accept all directories, *.svg files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.TiffFileFilter
Accept all directories, *.tiff files.
accept(File) - Method in class com.compomics.util.io.file.filefilters.XmlFileFilter
Accept all directories, *.xml files.
accept(File, String) - Method in class com.compomics.util.io.file.FilenameExtensionFilter
Tests if a specified file should be included in a file list.
accept(File) - Method in class com.compomics.util.io.file.FilenameExtensionFilter
 
AccessionMetaData - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
Accession meta data.
AccessionMetaData() - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData
Empty default constructor.
AccessionMetaData(AccessionMetaData) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData
Copy constructor
AccessionMetaData(String) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData
Constructor.
AccessionMetaData(String, int, int, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData
Constructor.
ACE_K_126 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for lysine acetylation (PMID: 18338905).
ACE_K_143 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for lysine acetylation (PMID: 18338905).
acquire(long) - Method in class com.compomics.util.threading.ObjectMutex
Acquire function for the given key.
acquire(String) - Method in class com.compomics.util.threading.ObjectMutex
Acquire function for the given key.
acquire() - Method in class com.compomics.util.threading.SimpleSemaphore
Acquires.
add(AaSubstitutionMatrix) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Adds the content of a substitution matrix in this matrix.
addAddendum(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method allows the addition of an addendum to the list.
addAdditionalDataset(double[], double[], Color, Color) - Method in class com.compomics.util.gui.spectrum.ChromatogramPanel
Adds an additional profileChromatogram dataset to be displayed in the same Chromatogram Panel.
addAdditionalDataset(String, Integer, Color, Color, int) - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
Adds an additional isotopic distribution dataset to be displayed in the same panel.
addAdditionalDataset(double[], double[], Color, Color) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Adds an additional spectrum dataset to be displayed in the same Spectrum Panel.
addAdditionalMirroredDataset(double[], double[], Color, Color) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Adds an additional mirrored spectrum dataset to be displayed in the same Spectrum Panel.
addAll(ModificationtableContent) - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Add all.
addAll(ModificationScoring) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Adds all scores from another score if better.
addAmbiguousModificationSites(int, HashMap<Integer, HashSet<String>>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Adds a group of modifications to the mapping of ambiguous sites.
addAminoAcidAfter(Character) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Adds an amino acid to the list of allowed amino acids after the cleavage site.
addAminoAcidBefore(Character) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Adds an amino acid to the list of allowed amino acids before the cleavage site.
addAminoAcidSequence(AminoAcidSequence) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Adds a sequence of amino acids to the tag.
addAutomaticDeNovoSequencing(Peptide, IonMatch[], int, int, int, boolean, boolean, boolean, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.
addAutomaticDeNovoSequencing(Peptide, IonMatch[], int, int, int, boolean, boolean, double, double, boolean, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
addAutomaticDeNovoSequencing(Peptide, IonMatch[], int, int, int, boolean, boolean, double, double, boolean, boolean, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
addAutomaticDeNovoSequencing(Tag, IonMatch[], int, int, int, boolean, boolean, boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.
addAutomaticDeNovoSequencing(Tag, IonMatch[], int, int, int, boolean, boolean, double, double, boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
addAutomaticDeNovoSequencing(Tag, IonMatch[], int, int, int, boolean, boolean, double, double, ArrayList<float[]>, boolean, boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
addAutomaticDeNovoSequencing(Peptide, IonMatch[], int, int, int, boolean, boolean, double, double, ArrayList<float[]>, boolean, boolean, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags.
addAutomaticDeNovoSequencing(Peptide, IonMatch[], int, int, int, boolean, boolean, double, double, float, float, ArrayList<float[]>, boolean, boolean, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags.
addAutomaticDeNovoSequencing(Tag, IonMatch[], int, int, int, boolean, boolean, double, double, float, float, ArrayList<float[]>, boolean, boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add reference areas annotating the de novo tags.
addBlock(PdbBlock) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Add a block.
addColumn(ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
addConfidentModificationSite(String, int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Adds a confident modification site.
addContactGroup(ContactGroup) - Method in class com.compomics.util.pride.PrideObjectsFactory
Adds a contact group in the PRIDE objects.
addDomain(String, String) - Method in class com.compomics.util.experiment.biology.genes.go.GoDomains
Adds a go domain to the mapping.
addElement(MolecularElement, Integer) - Method in class com.compomics.util.protein.MolecularFormula
Method to add MolecularElements to this formula
addElementsPanel() - Method in class com.compomics.util.gui.atoms.AtomChainDialog
Add a new atom panel.
addEnzyme(Enzyme) - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Adds an enzyme in the factory.
addEnzyme(Enzyme) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Adds an enzyme.
addException(long) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Adds an exception.
addExportFeature(String, ExportFeature) - Method in class com.compomics.util.io.export.ExportScheme
Adds an export feature to the desired section.
addExportScheme(ExportScheme) - Method in interface com.compomics.util.io.export.ExportFactory
Adds an export scheme to the map of user schemes.
addFeature(Ms2pipFeature) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
Adds a feature to the map.
addFileToZip(File, ZipOutputStream, WaitingHandler, long) - Static method in class com.compomics.util.io.compression.ZipUtils
Adds a new file to the zip stream.
addFileToZip(File, ZipOutputStream) - Static method in class com.compomics.util.io.compression.ZipUtils
Adds a new file to the zip stream.
addFileToZip(String, File, ZipOutputStream, WaitingHandler, long) - Static method in class com.compomics.util.io.compression.ZipUtils
Adds a new file to the zip stream.
addFilter(Integer, String) - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
Adds a filter.
addFixedModification(Modification) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Adds a fixed modification.
addFolderContent(ArchiveOutputStream, File, WaitingHandler) - Static method in class com.compomics.util.io.compression.TarUtils
Add content to the tar file.
addFolderToZip(String, ZipOutputStream) - Static method in class com.compomics.util.io.compression.ZipUtils
Adds a new entry to the zip file corresponding to a new folder.
addFoundCharges(HashSet<Integer>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Adds a new charge to the list of found charges.
addFraction(String) - Method in class com.compomics.util.experiment.identification.Identification
Adds a fraction, fractions correspond to the PSM files names.
addFragmentIonTypeMarkers(HashMap<IonMatch, ArrayList<XYZDataPoint>>, JFreeChart, boolean) - Static method in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Adds interval markers for all the fragment ion types.
addGoLink(String) - Method in class com.compomics.util.gui.genes.GeneDetailsDialog
Returns the GO accession number as a web link to the given GO term at QuickGO.
addHidingFilter(MatchFilter) - Method in class com.compomics.util.gui.filtering.FilterParameters
Adds a hiding filter (previous filter with same name will silently be overwritten).
addIdentificationParameters(IdentificationParameters) - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Adds the given identification parameters to the factory.
addInstrument(Instrument) - Method in class com.compomics.util.pride.PrideObjectsFactory
Adds a instrument in the PRIDE objects.
addIntensity(int, Integer, int, double) - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Add intensity.
addIonType(Ion.IonType, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Adds a new ion type and subtype to annotate.
addIonType(Ion.IonType) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Adds a new ion type to annotate.
addIonType(Ion.IonType, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Adds a new ion type and subtype to annotate.
addIonType(Ion.IonType) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Adds a new ion type to annotate.
addLine(ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
addListeners() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method adds the event listeners to the panel.
addManualValidation(long) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Adds a manually validated Match.
addMass(int, double) - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
Add a mass for this glycan.
addMassGap(double) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Adds a mass gap to the tag.
addMirroredSpectrum(double[], double[], double, String, String, boolean, Color, Color) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Add a mirrored spectrum (or chromatogram).
addMissingPrecursorCharges(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
Add missing precursor charges.
addMissingSpectrumTitles(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
Adds missing spectrum titles.
addModification(Modification) - Method in class com.compomics.util.protein.AASequenceImpl
This method adds a modification to the list of modifications.
addModificationPattern(Modification) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Adds a modification pattern for bitwise pattern search.
addModificationScoring(String, ModificationScoring) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Adds a scoring result for the modification of interest.
addModificationSite(int, ArrayList<Character>) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Adds a list of modifications to one of the amino acid pattern.
addMolecularFormula(MolecularFormula) - Method in class com.compomics.util.protein.MolecularFormula
Method to add whole formulas to this formula
addMouseListenerToHeaderInTable(JTable) - Method in class com.compomics.util.sun.TableSorter
 
addNeutralLoss(NeutralLoss) - Static method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Adds a neutral loss to the class static map.
addNeutralLoss(NeutralLoss) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Adds a neutral loss.
addNeutralLoss(NeutralLoss) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Adds a neutral loss.
addNeutralLoss(NeutralLoss, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Adds a new neutral loss to the map.
addNeutralLoss(String, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Adds a new neutral loss to the map.
addNeutralLoss(NeutralLoss) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Adds a neutral loss.
addObject(long, Object) - Method in class com.compomics.util.db.object.ObjectsCache
Adds an object to the cache.
addObject(long, Object, boolean, boolean) - Method in class com.compomics.util.db.object.ObjectsCache
Adds an object to the cache.
addObject(IdentificationFeaturesCache.ObjectType, long, Object) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Adds an object in the cache.
addObject(long, Object) - Method in class com.compomics.util.experiment.identification.Identification
Adds an object into the database.
addObjects(HashMap<Long, Object>) - Method in class com.compomics.util.db.object.ObjectsCache
Adds an object to the cache.
addObjects(HashMap<Long, Object>, boolean, boolean) - Method in class com.compomics.util.db.object.ObjectsCache
Adds an object to the cache.
addObjects(HashMap<Long, Object>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification
Adds a list of objects into the database.
addPatientInformation(PatientInformation, Comparable) - Method in class com.compomics.util.experiment.patient.Patient
Adds patient information,
addPeptideAssumption(int, PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Add a hit.
addPeptideMatch(long, PeptideMatch) - Method in class com.compomics.util.experiment.identification.Identification
Adds a peptide match.
addPeptideMatches(HashMap<Long, Object>) - Method in class com.compomics.util.experiment.identification.Identification
Adds a peptide match.
addPeptideMatchKey(long) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Add a subordinated peptide key.
addPeptideMatchKeys(long[]) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Add a subordinated peptide key.
addPeptideNormalisationFactor(String, double) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Adds a peptide normalization factor.
addProteinMatch(long, ProteinMatch) - Method in class com.compomics.util.experiment.identification.Identification
Adds a protein match.
addProteinMatches(HashMap<Long, Object>) - Method in class com.compomics.util.experiment.identification.Identification
Adds a protein match.
addProteinNormalisationFactor(String, double) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Adds a protein normalization factor.
addProtocol(Protocol) - Method in class com.compomics.util.pride.PrideObjectsFactory
Adds a protocol in the PRIDE objects.
addPsmNormalisationFactor(String, double) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Adds a PSM normalization factor.
addReferenceAreaXAxis(ReferenceArea) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Add a x-axis reference area.
addReferenceAreaYAxis(ReferenceArea) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Add a y-axis reference area.
addReferenceGroup(ReferenceGroup) - Method in class com.compomics.util.pride.PrideObjectsFactory
Adds a reference group in the PRIDE objects.
addRefinementFixedModification(Modification) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Adds a fixed refinement modification.
addRefinementVariableModification(Modification) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Adds a variable refinement modification.
addReporterIon(ReporterIon) - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Adds a reporter ion to the class static map.
addReporterIon(ReporterIon) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Adds a reporter ion.
addRestrictionAfter(Character) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Adds an amino acid to the list of forbidden amino acids after the cleavage site.
addRestrictionBefore(Character) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Adds an amino acid to the list of forbidden amino acids before the cleavage site.
addSample(Sample) - Method in class com.compomics.util.pride.PrideObjectsFactory
Adds a sample in the PRIDE objects.
addScore(Integer, Integer) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Adds a score for a given algorithm to the scoring preferences.
addScrollListeners(JTable, JScrollPane, JScrollBar) - Static method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Add scroll bar and mouse wheel listeners.
addSelectedCharge(int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Add a charge to take into account when annotating the spectrum.
addSeparator() - Method in class com.compomics.util.io.export.ExportWriter
Adds a separator.
addSeparator(WorkbookStyle) - Method in class com.compomics.util.io.export.ExportWriter
Adds a separator.
addSeparator(WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
addSeparator(WorkbookStyle) - Method in class com.compomics.util.io.export.writers.TextWriter
 
addShortcutAtDeskTop(MavenJarFile) - Method in class com.compomics.software.autoupdater.FileDAO
Add desktop shortcut.
addShortcutAtDeskTop(MavenJarFile, String) - Method in class com.compomics.software.autoupdater.FileDAO
Adds a shortcut to the desktop.
addSortListener(JTable, ProgressDialogX) - Static method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Convenience method adding a row sorter listener to the given JTable.
addSpectrum(String, String, ArrayList<PeptideAssumption>, ArrayList<TreeMap<Double, HashMap<Integer, Double>>>, PeptideSpectrumAnnotator) - Method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Adds a peptide-spectrum match to the file.
addSpectrum(String, Spectrum) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileWriter
Adds a spectrum to the file.
addSpectrumMatches(HashMap<Long, Object>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification
Adds a spectrum matches into the database.
addSpectrumMatchKey(long) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Add a spectrum match key.
addSpectrumPanelListener(SpectrumPanelListener) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method registers the specified SpectrumPanelListener with this instance and notifies it of all future events.
addStarringFilter(MatchFilter) - Method in class com.compomics.util.gui.filtering.FilterParameters
Adds a starring filter (previous filter with same name will silently be overwritten).
addSubstitution(Character, Character) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Adds a possible substitution.
addTagAssumption(int, TagAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Add a hit.
addToZip(File, ZipOutputStream) - Static method in class com.compomics.util.io.compression.ZipUtils
Adds a new file to the zip stream.
addToZip(File, ZipOutputStream, WaitingHandler, long) - Static method in class com.compomics.util.io.compression.ZipUtils
Adds a new file to the zip stream.
addToZip(File, String, ZipOutputStream) - Static method in class com.compomics.util.io.compression.ZipUtils
Adds a new file to the zip stream.
addToZip(File, String, ZipOutputStream, WaitingHandler, long) - Static method in class com.compomics.util.io.compression.ZipUtils
Adds a new file to the zip stream.
addUrParam(UrParameter) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Adds a user refinement parameter.
addUserAdvocate(String) - Static method in class com.compomics.util.experiment.identification.Advocate
Adds a user advocate and returns it.
addUserModification(Modification) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Adds a new user modification.
addVariableModification(ModificationMatch) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Adds a modification to one of the amino acid sequence.
addVariableModification(ModificationMatch) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Adds a modification match.
addVariableModification(Modification) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Adds a variable modification.
addWaitingActionListener(WaitingActionListener) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Adds a waiting action listener.
addWaitingActionListener(WaitingActionListener) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Adds a waiting action listener.
addXYZDataSeries(HashMap<IonMatch, ArrayList<XYZDataPoint>>) - Method in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Adds the provided data series to an XYZ data set.
adjustmentValueChanged(AdjustmentEvent) - Method in class com.compomics.util.gui.TableScrollBarListener
 
Advocate - Class in com.compomics.util.experiment.identification
The advocate of a hit can be a search engine, a sequencing algorithm, a rescoring algorithm, etc.
Advocate() - Constructor for class com.compomics.util.experiment.identification.Advocate
Empty default constructor
advocate - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
The advocate supporting this assumption.
Advocate.AdvocateType - Enum in com.compomics.util.experiment.identification
The different types of advocates.
Alanine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Alanine.
Alanine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
Constructor.
ALANINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Alanine immonium ion.
AlgorithmParametersDialog - Interface in com.compomics.util.gui.parameters.identification
Interface for an algorithm settings dialog.
align(Collection<Integer>, Collection<Integer>) - Static method in class com.compomics.util.experiment.identification.modification.ModificationSiteMapping
Aligns two series of integer, minimizing the distance between them and excluding outliers.
alignAll(Collection<Integer>, Collection<Integer>) - Static method in class com.compomics.util.experiment.identification.modification.ModificationSiteMapping
Aligns two series of integer, minimizing the distance between them.
alignAll(HashMap<Integer, ArrayList<Integer>>) - Static method in class com.compomics.util.experiment.identification.modification.ModificationSiteMapping
Aligns a series of integer on possible targets maximizing the number of matched targets.
AlignedListCellRenderer - Class in com.compomics.util.gui.renderers
ListCellRenderer with alignment functionality.
AlignedListCellRenderer() - Constructor for class com.compomics.util.gui.renderers.AlignedListCellRenderer
Empty default constructor
AlignedListCellRenderer(int) - Constructor for class com.compomics.util.gui.renderers.AlignedListCellRenderer
Creates a new AlignedListCellRenderer
AlignedTableCellRenderer - Class in com.compomics.util.gui.renderers
TableCellRenderer with alignment functionality.
AlignedTableCellRenderer() - Constructor for class com.compomics.util.gui.renderers.AlignedTableCellRenderer
Empty default constructor
AlignedTableCellRenderer(int) - Constructor for class com.compomics.util.gui.renderers.AlignedTableCellRenderer
Creates a new AlignedTableCellRenderer
AlignedTableCellRenderer(int, Color) - Constructor for class com.compomics.util.gui.renderers.AlignedTableCellRenderer
Creates a new AlignedTableCellRenderer
AlignmentBlock - Class in com.compomics.util.pdbfinder.das.readers
AlignmentBlock.
AlignmentBlock() - Constructor for class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Empty default constructor
AlignmentBlock(int, int, int, int, String, String) - Constructor for class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Constructor.
allSubstitutions - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Substitution matrix allowing all substitutions.
allVariants - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Current storing of all variant operations.
allXcomponents - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Information about all component where the Xs belong to.
allXMassDiffs - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
The all X mass differences.
alphaLevel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The opacity of the spectra.
AlternateRowColoursJTable - Class in com.compomics.util
This class provides a simple extension on a JTable, allowing even and uneven rows to have different colours.
AlternateRowColoursJTable() - Constructor for class com.compomics.util.AlternateRowColoursJTable
Default empty constructor.
AlternateRowColoursJTable(int, int) - Constructor for class com.compomics.util.AlternateRowColoursJTable
Creates a new AlternateRowColoursJTable.
AlternateRowColoursJTable(TableModel, TableColumnModel) - Constructor for class com.compomics.util.AlternateRowColoursJTable
Creates a new AlternateRowColoursJTable.
AlternateRowColoursJTable(TableModel) - Constructor for class com.compomics.util.AlternateRowColoursJTable
Creates a new AlternateRowColoursJTable.
AlternateRowColoursJTable(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class com.compomics.util.AlternateRowColoursJTable
Creates a new AlternateRowColoursJTable.
AlternateRowColoursJTable(Vector, Vector) - Constructor for class com.compomics.util.AlternateRowColoursJTable
Creates a new AlternateRowColoursJTable.
AlternateRowColoursJTable(Object[][], Object[]) - Constructor for class com.compomics.util.AlternateRowColoursJTable
Creates a new AlternateRowColoursJTable.
ambiguousChar - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
If original character was B, J, X, Z.
AmbiguousSequenceIterator - Class in com.compomics.util.experiment.identification.protein_sequences
Iterator going through the possible sequences of a sequence containing combinations of amino acids.
AmbiguousSequenceIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.AmbiguousSequenceIterator
Empty default constructor
AmbiguousSequenceIterator(char[], int) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.AmbiguousSequenceIterator
Constructor.
AmbiguousSequenceIterator(String, int) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.AmbiguousSequenceIterator
Constructor.
AmbiguousSequenceIterator(String) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.AmbiguousSequenceIterator
Constructor.
AMINO_ACID_STRINGS - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
The amino acid one letter codes as string array.
AminoAcid - Class in com.compomics.util.experiment.biology.aminoacids
Class representing amino acids.
AminoAcid() - Constructor for class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Empty default constructor.
aminoAcid - Variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
The amino acid targeted represented as single letter code.
AminoAcid.Property - Enum in com.compomics.util.experiment.biology.aminoacids
Properties of the amino acids.
aminoAcidCombinations - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
The amino acid combinations.
AminoAcidPattern - Class in com.compomics.util.experiment.biology.aminoacids.sequence
An amino acid pattern is a sequence of amino acids.
AminoAcidPattern() - Constructor for class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Creates a blank pattern.
AminoAcidPattern(AminoAcidPattern) - Constructor for class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Creates a pattern from another pattern.
AminoAcidPattern(ArrayList<String>) - Constructor for class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Convenience constructor giving a list of targeted residues as input.
AminoAcidPatternDialog - Class in com.compomics.util.gui
This dialog allows the design and test of amino acid patterns.
AminoAcidPatternDialog(Frame, AminoAcidPattern, boolean) - Constructor for class com.compomics.util.gui.AminoAcidPatternDialog
Creates a new AminoAcidPatternDialog.
aminoAcidProperty - Variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
The property of the amino acids to consider.
aminoAcidProperty - Variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
The property of the amino acids to consider.
aminoAcids - Variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
Amino acids that are likely to induce this loss.
aminoAcidScores - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
The individual amino acid scores.
AminoAcidSequence - Class in com.compomics.util.experiment.biology.aminoacids.sequence
This class represents a series of amino acids with associated modifications.
AminoAcidSequence() - Constructor for class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Creates a blank sequence.
AminoAcidSequence(String) - Constructor for class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Constructor taking a sequence of amino acids as input.
AminoAcidSequence(String, ModificationMatch[]) - Constructor for class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Constructor taking a sequence of amino acids as input.
AminoAcidSequence(AminoAcidSequence) - Constructor for class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Creates a sequence from another sequence.
AminoAcidSubstitution - Class in com.compomics.util.experiment.biology.variants
Class representing an amino acid substitution.
AminoAcidSubstitution() - Constructor for class com.compomics.util.experiment.biology.variants.AminoAcidSubstitution
Empty default constructor
AminoAcidSubstitution(char, char) - Constructor for class com.compomics.util.experiment.biology.variants.AminoAcidSubstitution
Constructor.
AMU - Static variable in class com.compomics.util.experiment.Constants
The atomic mass unit in kg.
AMU_NO_EXP - Static variable in class com.compomics.util.experiment.Constants
The atomic mass unit without exponent.
ANALYSIS_SECTION - Static variable in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Key for the analysis section.
andromeda - Static variable in class com.compomics.util.experiment.identification.Advocate
The Andromeda search engine.
AndromedaIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This IdfileReader reads identifications from an Andromeda result file.
AndromedaIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
Default constructor for the purpose of instantiation.
AndromedaIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
Constructor for an Andromeda result file reader.
AndromedaParameters - Class in com.compomics.util.parameters.identification.tool_specific
The Andromeda specific parameters.
AndromedaParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Constructor.
AndromedaParameters.AndromedaDecoyMode - Enum in com.compomics.util.parameters.identification.tool_specific
The available decoy modes.
AndromedaParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the Andromeda specific settings.
AndromedaParametersDialog(Frame, AndromedaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
Creates a new AndromedaParametersDialog with a frame as owner.
AndromedaParametersDialog(Dialog, Frame, AndromedaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
Creates a new AndromedaParametersDialog with a dialog as owner.
annotate(SpectrumAnnotation, Graphics, HashMap<String, Integer>, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method attempts to find the specified SpectrumAnnotation in the current peak list and if so, annotates it correspondingly on the screen.
ANNOTATED_STATUS - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This status indicates that annotation (if present) will be displayed, while limiting the user to zooming in/out.
annotateHighestPeak - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If more than one peak is within the accuracy range of an annotation setting this to true will always select the most intense of possible peaks.
annotatePeaks(Graphics, Vector, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Annotate the annotated peaks.
AnnotationParameters - Class in com.compomics.util.experiment.identification.spectrum_annotation
This class contains the spectrum annotation parameters.
AnnotationParameters() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Constructor.
AnnotationParameters(SearchParameters) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Constructor setting preferences from search parameters.
AnnotationParameters.IntensityThresholdType - Enum in com.compomics.util.experiment.identification.spectrum_annotation
Enum of the types of intensity thresholds available.
AnnotationParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
A simple dialog for setting the spectrum annotation preferences.
AnnotationParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog
Empty default constructor
AnnotationParametersDialog(Frame, AnnotationParameters, double, HashSet<String>, ArrayList<Integer>, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog
Creates a new AnnotationPreferencesDialog with a frame as owner.
AnnotationParametersDialog(Dialog, Frame, AnnotationParameters, double, HashSet<String>, ArrayList<Integer>, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog
Creates a new AnnotationPreferencesDialog with a dialog as owner.
AplFileWriter - Class in com.compomics.util.experiment.io.mass_spectrometry.apl
This class writes spectrum files in Andromeda Peak List (APL) format.
AplFileWriter() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.apl.AplFileWriter
Empty default constructor
AplFileWriter(File) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.apl.AplFileWriter
Constructor.
append(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Appends another pattern at the end of this pattern.
append(AtomImpl) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Appends an atom to the chain of atoms.
append(AtomImpl, int) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Appends an atom to the chain of atoms.
append(File, File) - Static method in class com.compomics.util.io.IoUtil
Appends the content of a file to another.
appendAscii(String) - Method in class com.compomics.util.io.ftp.FTP
APPEND (with create) to a file to the FTP server in Ascii mode.
appendBinary(String) - Method in class com.compomics.util.io.ftp.FTP
APPEND (with create) to a file to the FTP server in Binary mode.
appendColumns(DoubleMatrix) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
appendCTerm(AminoAcidSequence) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Appends another sequence at the end of this sequence.
appendCTerm(String) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Appends a series of unmodified amino acids to the sequence.
appendDecoySequences(File, File, FastaParameters, WaitingHandler) - Static method in class com.compomics.util.experiment.io.biology.protein.converters.DecoyConverter
Appends decoy sequences to the provided FASTA file.
appendLines(DoubleMatrix) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
appendNTerm(AminoAcidSequence) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Appends another sequence at the beginning of this sequence keeping the original order.
appendNTerm(String) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Appends a series of unmodified amino acids to the beginning sequence keeping the original order.
appendReport(String, boolean, boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
appendReport(String, boolean, boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
appendReport(String, boolean, boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
appendReport(String, boolean, boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
appendReport(String, boolean, boolean) - Method in interface com.compomics.util.waiting.WaitingHandler
Append text to the report.
appendReportEndLine() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
appendReportEndLine() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
appendReportEndLine() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
appendReportEndLine() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
appendReportEndLine() - Method in interface com.compomics.util.waiting.WaitingHandler
Append a new line to the report.
appendReportNewLineNoDate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
appendReportNewLineNoDate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
appendReportNewLineNoDate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
appendReportNewLineNoDate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
appendReportNewLineNoDate() - Method in interface com.compomics.util.waiting.WaitingHandler
Append two tabs to the report.
appendSuffix(String, String) - Static method in class com.compomics.util.io.IoUtil
Appends a suffix to a file name before the file extension.
appendTaggedResidue(StringBuilder, char, String, String, String, String, ModificationParameters, boolean, boolean) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns the single residue as a tagged string (HTML color or PTM tag).
appendTaggedResidue(StringBuilder, char, String, ModificationParameters, int, boolean, boolean) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Appends the single residue as a tagged string (HTML color or PTM tag).
appRunningIntoConda(String) - Static method in class com.compomics.software.CompomicsWrapper
Check if the application with name condaAppName is running in a Conda environment.
AQUA - Static variable in class com.compomics.util.AlternateRowColoursJTable
A rather pronounced AQUA colour (r=183, g=222, b=232).
areNeutralLossesSequenceAuto() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns whether neutral losses are considered only for amino acids of interest or not.
Arginine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Arginine.
Arginine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
Constructor.
ARGININE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Arginine immonium ion.
array - Variable in class com.compomics.util.TempByteArray
The byte array.
ARRAYS_MAP - Static variable in class com.compomics.util.experiment.identification.utils.ModificationUtils
Map of arrays for C-term.
ArrayUtil - Class in com.compomics.util
Utility functions to work with arrays.
ArrayUtil() - Constructor for class com.compomics.util.ArrayUtil
 
AscendingIntensityComparator - Static variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
This comparator compares two Peak instances on ascending intensity.
AscendingMzComparator - Static variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
This comparator compares two Peak instances on ascending m/z value.
ascii() - Method in class com.compomics.util.io.ftp.FTP
Set transfer type to 'A' (ascii transfer).
asGenericHeader() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the header in generic format.
asLong(String) - Static method in class com.compomics.util.experiment.personalization.ExperimentObject
Creating a unique 64 bit hash key from the original key of arbitrary length.
asMgf(String, Spectrum) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileWriter
Returns the spectrum as an mgf bloc.
asMgf(String, Spectrum, TreeMap<String, String>) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileWriter
Returns the spectrum as an mgf bloc.
Asparagine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Asparagine.
Asparagine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
Constructor.
ASPARAGINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Asparagine immonium ion.
ASPARTIC_ACID - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Aspartic acid immonium ion.
AsparticAcid - Class in com.compomics.util.experiment.biology.aminoacids.impl
Aspartic Acid.
AsparticAcid() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
Constructor.
asSequence(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the component of the amino acid pattern at the given index.
asSequence() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
 
asSequence() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
 
asSequence() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the tag as intelligible sequence of tag components.
asSequence() - Method in interface com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
Returns the tag component as String like a peptide sequence.
assignSample(String, String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Assign a sample to an ion referenced by its static index.
asStringBuilder() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the sequence represented by this amino acid pattern in a new string builder.
AssumptionFilter - Class in com.compomics.util.experiment.identification.filtering
Peptide Assumption filter.
AssumptionFilter() - Constructor for class com.compomics.util.experiment.identification.filtering.AssumptionFilter
Constructor.
AssumptionFilter(String) - Constructor for class com.compomics.util.experiment.identification.filtering.AssumptionFilter
Constructor.
AssumptionFilter(String, String) - Constructor for class com.compomics.util.experiment.identification.filtering.AssumptionFilter
Constructor.
AssumptionFilter(String, String, String, String, String) - Constructor for class com.compomics.util.experiment.identification.filtering.AssumptionFilter
Constructor.
AssumptionFilterItem - Enum in com.compomics.util.experiment.identification.filtering.items
Enum of the different items an assumption filter can filter on.
Atom - Class in com.compomics.util.experiment.biology.atoms
This interface contains information about atoms.
Atom() - Constructor for class com.compomics.util.experiment.biology.atoms.Atom
Empty default constructor
AtomChain - Class in com.compomics.util.experiment.biology.atoms
A chain of atoms.
AtomChain() - Constructor for class com.compomics.util.experiment.biology.atoms.AtomChain
Creates an empty atom chain.
atomChain - Variable in class com.compomics.util.experiment.biology.ions.Ion
The atomic composition of the ion.
AtomChainDialog - Class in com.compomics.util.gui.atoms
AtomChainDialog.
AtomChainDialog(JDialog, AtomChain, AtomChain, boolean) - Constructor for class com.compomics.util.gui.atoms.AtomChainDialog
Creates a new dialog.
AtomChainDialog(Frame, AtomChain, AtomChain, boolean) - Constructor for class com.compomics.util.gui.atoms.AtomChainDialog
Creates a new dialog.
AtomImpl - Class in com.compomics.util.experiment.biology.atoms
Class for a specific atom.
AtomImpl() - Constructor for class com.compomics.util.experiment.biology.atoms.AtomImpl
Empty default constructor.
AtomImpl(String, Integer) - Constructor for class com.compomics.util.experiment.biology.atoms.AtomImpl
Constructor.
AtomImpl(Atom, Integer) - Constructor for class com.compomics.util.experiment.biology.atoms.AtomImpl
Constructor.
AtomPanel - Class in com.compomics.util.gui.atoms
Panel for selecting atoms.
AtomPanel(AtomChainDialog, Atom, int, int, int, boolean) - Constructor for class com.compomics.util.gui.atoms.AtomPanel
Creates a new AtomPanel.
AVERAGE - Static variable in interface com.compomics.util.interfaces.Modification
Constant to indicate the position of the average mass in the mass array.
Avogadro - Static variable in class com.compomics.util.experiment.Constants
The Avogadro constant.
AVOGADRO_NO_EXP - Static variable in class com.compomics.util.experiment.Constants
The Avogadro constant without exponent.

B

B - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
B - Class in com.compomics.util.experiment.biology.aminoacids.impl
Asn or Asp: Asx (Mascot).
B() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.B
Constructor.
b - Variable in class com.compomics.util.math.statistics.linear_regression.RegressionStatistics
b in y = a.x + b
B_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Identifier for a b ion.
B_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Identifier for a b ion.
BackgroundSpeciesDialog - Class in com.compomics.util.gui.parameters.identification.advanced
Dialog for editing the background species.
BackgroundSpeciesDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog
Empty default constructor
BackgroundSpeciesDialog(JFrame, GeneParameters, FastaSummary) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog
Creates a new GenePreferencesDialog with a frame as owner.
BackgroundSpeciesDialog(JDialog, Frame, GeneParameters, FastaSummary) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog
Creates a new GenePreferencesDialog with a dialog as owner.
BareBonesBrowserLaunch - Class in com.compomics.util.examples
Class that makes it possible to open a URL in the default browser.
BareBonesBrowserLaunch() - Constructor for class com.compomics.util.examples.BareBonesBrowserLaunch
Empty default constructor
BasicMathFunctions - Class in com.compomics.util.math
Class used to perform basic mathematical functions.
BasicMathFunctions() - Constructor for class com.compomics.util.math.BasicMathFunctions
Empty default constructor.
BIG_ENDIAN_LABEL - Static variable in class com.compomics.util.BinaryArrayImpl
Defines the valid String indicating big endian byte order.
BigFunctions - Class in com.compomics.util.math
Functions operating with BigDecimal objects.
BigFunctions() - Constructor for class com.compomics.util.math.BigFunctions
Empty default constructor
BigMathUtils - Class in com.compomics.util.math
Utils for the manipulation of big numbers.
BigMathUtils() - Constructor for class com.compomics.util.math.BigMathUtils
Empty default constructor
binary() - Method in class com.compomics.util.io.ftp.FTP
Set transfer type to 'I' (binary transfer).
BinaryArrayImpl - Class in com.compomics.util
Persistence independent object model implementation class:
BinaryArrayImpl() - Constructor for class com.compomics.util.BinaryArrayImpl
Default constructor with protected access.
BinaryArrayImpl(String, long, String, String) - Constructor for class com.compomics.util.BinaryArrayImpl
Creates an instance of this BinaryArray object, setting all fields as per description below.
BinaryArrayImpl(double[], String) - Constructor for class com.compomics.util.BinaryArrayImpl
Constructor that allows the creation of a BinaryArray object using an array of double values.
BinaryArrayImpl(float[], String) - Constructor for class com.compomics.util.BinaryArrayImpl
Constructor that allows the creation of a BinaryArray object using an array of float values.
BinningFilter - Class in com.compomics.util.math.statistics.linear_regression.filters
Filters by binning.
BinningFilter() - Constructor for class com.compomics.util.math.statistics.linear_regression.filters.BinningFilter
Empty default constructor
BinomialDistribution - Class in com.compomics.util.math.statistics.distributions
Implementation of a binomial distribution.
BinomialDistribution() - Constructor for class com.compomics.util.math.statistics.distributions.BinomialDistribution
Empty default constructor
BinomialDistribution(int, double) - Constructor for class com.compomics.util.math.statistics.distributions.BinomialDistribution
Constructor.
BIOMART_ENSEMBL_FILENAME - Static variable in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
The name of the Ensembl BioMart datasets file.
BIOMART_ENSEMBL_GENOME_FILENAME - Static variable in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
The name of the Ensembl Genome BioMart datasets file.
BiomartMapping - Class in com.compomics.util.experiment.biology.taxonomy.mappings
Mapping of the species to BioMart dataset.
BiomartMapping() - Constructor for class com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
Constructor.
BlobObject - Class in com.compomics.util.db.object.objects
Class used to store entire objects in the database as a blob.
BlobObject(Object) - Constructor for class com.compomics.util.db.object.objects.BlobObject
Constructor.
BlobObject() - Constructor for class com.compomics.util.db.object.objects.BlobObject
Constructor.
BlobObject(byte[]) - Constructor for class com.compomics.util.db.object.objects.BlobObject
Constructor.
BoxedObject<K> - Class in com.compomics.util.general
Convenience class allowing the boxing of an object.
BoxedObject() - Constructor for class com.compomics.util.general.BoxedObject
Constructor.
BoxedObject(K) - Constructor for class com.compomics.util.general.BoxedObject
Constructor.
BUFFER_LENGTH - Static variable in class com.compomics.util.io.compression.GzUtils
The length of the character buffer to use.
BUFFER_SIZE - Static variable in class com.compomics.util.io.compression.TarUtils
The buffer size.
BUFFER_SIZE - Static variable in class com.compomics.util.io.compression.ZipUtils
The buffer size.
BugReport - Class in com.compomics.util.gui.error_handlers
A simple bug report dialog.
BugReport(JFrame, LastSelectedFolder, String, String, String, String, String, File) - Constructor for class com.compomics.util.gui.error_handlers.BugReport
Creates a new BugReport dialog.
BugReport(JDialog, LastSelectedFolder, String, String, String, String, String, File) - Constructor for class com.compomics.util.gui.error_handlers.BugReport
Creates a new BugReport dialog.
builder - Variable in class com.compomics.util.io.json.JsonMarshaller
GsonBuilder that can be used to append interfaces so the parser knows how to handle them.
buildPeptidesAndProteins(SpectrumMatch, SequenceMatchingParameters, SequenceProvider, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideAndProteinBuilder
Creates the peptides and protein instances based on the given spectrum match.
byonic - Static variable in class com.compomics.util.experiment.identification.Advocate
The Byonic search engine integrated in the Byonic protein metrics interface.
ByteArrayRenderer - Class in com.compomics.util.gui.renderers
ByteArrayRenderer.
ByteArrayRenderer() - Constructor for class com.compomics.util.gui.renderers.ByteArrayRenderer
Empty default constructor
BYTES_TO_HOLD_DOUBLE - Static variable in class com.compomics.util.BinaryArrayImpl
Defines the number of bytes required in an UNENCODED byte array to hold a dingle double value.
BYTES_TO_HOLD_FLOAT - Static variable in class com.compomics.util.BinaryArrayImpl
Defines the number of bytes required in an UNENCODED byte array to hold a single float value.

C

C - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
C - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The carbon atom.
C3H9N - Static variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
C3H9N loss.
C_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Identifier for a c ion.
C_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Identifier for a c ion.
C_TERM_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
 
Ca - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The Calcium atom.
CacheElement - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
The cache element.
CacheElement(Double, String, Double, ArrayList<MatrixContent>) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.CacheElement
Constructor.
Calcium - Class in com.compomics.util.experiment.biology.atoms.impl
The calcium atom.
Calcium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Calcium
Constructor.
calculate() - Method in class com.compomics.util.general.IsotopicDistribution
This method will do the calculations
calculate() - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
This method will do the calculations
calculateMass(String) - Method in class com.compomics.util.general.MassCalc
This method attempts to calculate the mass of a chemical formula.
call() - Method in class com.compomics.cli.enzymes.EnzymesCLI
Calling this method will run the process.
call() - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
 
call() - Method in class com.compomics.cli.modifications.ModificationsCLI
Calling this method will run the process.
call() - Method in class com.compomics.cli.paths.PathSettingsCLI
Sets the path settings and returns null.
canceled() - Method in class com.compomics.util.gui.file_handling.FileDisplayDialog
Returns if the dialog was canceled by the user.
cancelPressed() - Method in interface com.compomics.util.waiting.WaitingActionListener
Method called whenever the user pressed cancel.
canReverse() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Indicates whether the tag can be reversed (ie if termini are mass gaps with mass ≥ water).
Carbon - Class in com.compomics.util.experiment.biology.atoms.impl
Carbon.
Carbon() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Carbon
Constructor
catchException(Exception) - Method in class com.compomics.util.exceptions.ExceptionHandler
Catches an exception and informs the user.
catchException(Exception) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
This method is called whenever an exception is encountered in a separate thread.
cd(String) - Method in class com.compomics.util.io.ftp.FTP
CD to a specific directory on a remote FTP server.
cdup() - Method in class com.compomics.util.io.ftp.FTP
Go up one directory on remote system.
CH4OS - Static variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
CH4OS loss.
changeRepresentativeSite(String, String, int, int, int, ModificationProvider) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Changes the representative site for a given ambiguously localized modification in all maps.
CHAR_BUFFER_SIZE - Static variable in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
The size of the char buffer to use when copying files.
character - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Character which was chosen.
charAt(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns the amino acid at the given index on the sequence in its single letter code.
Charge - Class in com.compomics.util.experiment.biology.ions
This class contains convenience methods for the handling of charges.
Charge() - Constructor for class com.compomics.util.experiment.biology.ions.Charge
Empty default constructor.
charge - Variable in class com.compomics.util.experiment.identification.matches.IonMatch
The inferred charge of the ion.
chargeValidated(Ion, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns a boolean indicating whether the given charge can be found on the given fragment ion.
checkDuplicateTitles() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns if the spectra should be checked for duplicate titles or not.
checkForNewDeployedVersion(String, MavenJarFile, URL, String, boolean, boolean, boolean, Image, Image, boolean) - Static method in class com.compomics.software.CompomicsWrapper
Check if a newer version of the tool is deployed in the Maven repository, and closes the tool if the user decided to update.
checkForNewVersion(String, String, String) - Static method in class com.compomics.software.CompomicsWrapper
Deprecated.
use the Maven repository option instead: checkForNewDeployedVersion
checkForNewVersion(String, String, String, boolean, String, String) - Static method in class com.compomics.software.CompomicsWrapper
Deprecated.
use the Maven repository option instead: checkForNewDeployedVersion
checkIfURLExists(String, String, String) - Static method in class com.compomics.util.io.IoUtil
Check if a given URL exists.
checkJavaVersion(String) - Static method in class com.compomics.software.CompomicsWrapper
Checks if the user is running Java 64 bit and shows a warning if not, and shows a dialog with a warning and a link to the JavaTroubleShooting page if not.
checkMgfSize() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns if the mgf should be checked for size.
checkModel() - Method in class com.compomics.util.sun.TableSorter
 
checkModificationPattern(PeptideProteinMapping) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Checking if peptide-protein should be discarded due to pattern modification conflict.
checkPeakPicking() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns if the spectra should be checked for peak picking or not.
checkProbabilityRange(double) - Static method in class com.compomics.util.math.BasicMathFunctions
Checks that a probability is between 0 and 1 and throws an IllegalArgumentException otherwise.
checkProbabilityRangeInPercent(double) - Static method in class com.compomics.util.math.BasicMathFunctions
Checks that a probability is between 0 % and 100 % and throws an IllegalArgumentException otherwise.
ChromatogramPanel - Class in com.compomics.util.gui.spectrum
This class provides a JPanel that can display a profileChromatogram.
ChromatogramPanel() - Constructor for class com.compomics.util.gui.spectrum.ChromatogramPanel
Empty default constructor
ChromatogramPanel(double[], double[]) - Constructor for class com.compomics.util.gui.spectrum.ChromatogramPanel
This constructor creates a ChromatogramPanel based on the passed parameters.
ChromatogramPanel(double[], double[], String, String) - Constructor for class com.compomics.util.gui.spectrum.ChromatogramPanel
This constructor creates a ChromatogramPanel based on the passed parameters.
ChromatogramPanel(double[], double[], String, String, Integer) - Constructor for class com.compomics.util.gui.spectrum.ChromatogramPanel
This constructor creates a ChromatogramPanel based on the passed parameters.
ChromatogramPanel(double[], double[], String, String, Integer, boolean) - Constructor for class com.compomics.util.gui.spectrum.ChromatogramPanel
This constructor creates a ChromatogramPanel based on the passed parameters.
clear() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Clears the filter items.
clear() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Clears the parameters.
clearAllScores() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Clears all scores.
clearCache() - Method in class com.compomics.util.db.object.ObjectsCache
Clears the cache.
clearCharges() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Clears the selected charges.
clearEnzymes() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Clears the enzymes set including specificity and missed cleavages.
clearFactory() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Clears the factory getInstance() needs to be called afterwards.
clearFixedModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Clears fixed modifications.
clearFoundCharges() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Clears the found charges.
clearIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Clears the ion types annotated.
clearIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Clears the ion types annotated.
clearNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Clears the considered neutral losses.
clearNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Clears the mapping.
clearNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Clears the considered neutral losses.
clearParametersMap() - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Clears the loaded parameters.
clearRefinementModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Clears refinement modifications.
clearScores(Integer) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Clears the score for the given algorithm.
clearSpectrumCounting() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Clears the spectrum counting data in cache.
clearVariableModifications() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Clears the variable modifications.
clearVariableModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Clears variable modifications.
clearVariantMatches() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Clears the list of imported variant matches.
cleave(Protein) - Method in class com.compomics.util.protein.DualEnzyme
This method is the focus of the Enzyme instance.
cleave(Protein) - Method in class com.compomics.util.protein.Enzyme
This method is the focus of the Enzyme instance.
cleave(Protein, int, int) - Method in class com.compomics.util.protein.Enzyme
This method is the focus of the Enzyme instance.
cleave(Protein) - Method in class com.compomics.util.protein.RegExEnzyme
 
CliLogger - Class in com.compomics.software.log
Simple logger.
CliLogger(File) - Constructor for class com.compomics.software.log.CliLogger
Constructor.
CliLogger(File, String, String) - Constructor for class com.compomics.software.log.CliLogger
Constructor.
clone() - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
 
clone() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
 
clone() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
 
clone() - Method in interface com.compomics.util.experiment.filtering.Filter
Clones the filter.
clone() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
 
clone() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Clones the modification match into a new match with the same attributes.
clone() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Creates a new peptide draft with the same attributes as this one.
clone() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Clones the settings.
clone() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
 
clone() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
 
clone() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method provides a deep copy of the Header instance.
clone(DigestionParameters) - Static method in class com.compomics.util.parameters.identification.search.DigestionParameters
Clones the given parameters.
clone() - Method in class com.compomics.util.protein.DualEnzyme
Provides a cloned version of this DualEnzyme.
clone() - Method in class com.compomics.util.protein.Enzyme
This method returns a deep copy of the current Enzyme.
clone() - Method in class com.compomics.util.protein.ModificationImplementation
Override of the clone method.
clone() - Method in class com.compomics.util.protein.ModificationTemplate
Override of the clone method.
clone() - Method in class com.compomics.util.protein.RegExEnzyme
 
close() - Method in class com.compomics.software.log.CliLogger
 
close(boolean) - Method in class com.compomics.util.db.object.ObjectsDB
Closes the db connection.
close(boolean) - Method in class com.compomics.util.experiment.identification.Identification
Closes the database connection.
close() - Method in class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
Closes the iterator.
close() - Method in class com.compomics.util.experiment.io.biology.protein.iterators.HeaderIterator
Closes the iterator.
close() - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
 
close() - Method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
 
close() - Method in class com.compomics.util.experiment.io.mass_spectrometry.apl.AplFileWriter
 
close() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileIterator
 
close() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
close() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileWriter
 
close() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileIterator
 
close() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileWriter
 
close() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
close() - Method in interface com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
 
close() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator
 
close() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
 
close() - Method in class com.compomics.util.general.FileLoggerImplementation
This method closes the stream to the output file.
close() - Method in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
 
close() - Method in class com.compomics.util.io.export.ExportWriter
Writes the content in cache and closes the connection to the file.
close() - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
close() - Method in class com.compomics.util.io.export.writers.TextWriter
 
close() - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
 
close() - Method in class com.compomics.util.io.flat.readers.SimpleGzReader
 
close() - Method in class com.compomics.util.io.flat.readers.SimpleTextReader
 
close() - Method in interface com.compomics.util.io.flat.SimpleFileReader
 
close() - Method in class com.compomics.util.io.flat.SimpleFileWriter
 
closeBuffer(MappedByteBuffer) - Static method in class com.compomics.util.io.IoUtil
Attempts at closing a buffer.
closeServer() - Method in class com.compomics.util.io.ftp.FTP
Issue the QUIT command to the FTP server and close the connection.
closeWhenComplete(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Set if the dialog is to be closed when the process is complete.
CmsFileIterator - Class in com.compomics.util.experiment.io.mass_spectrometry.cms
Iterator for a Compomics Mass Spectrometry (cms) file.
CmsFileIterator(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileIterator
Constructor.
CmsFileReader - Class in com.compomics.util.experiment.io.mass_spectrometry.cms
Reader for Compomics Mass Spectrometry (cms) files.
CmsFileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
Constructor allocating for single thread usage.
CmsFileUtils - Class in com.compomics.util.experiment.io.mass_spectrometry.cms
Utils to store ms files.
CmsFileUtils() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileUtils
 
CmsFileWriter - Class in com.compomics.util.experiment.io.mass_spectrometry.cms
Writer for cms files.
CmsFileWriter(File) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileWriter
Constructor.
CmsFolder - Class in com.compomics.util.experiment.io.mass_spectrometry.cms
Placeholder for the temp folder to use for cms files.
CmsFolder() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFolder
 
color2Hex(int) - Static method in class com.compomics.util.Util
Converts a color to hex format for use in HTML tags.
color2Hex(Color) - Static method in class com.compomics.util.Util
Converts a color to hex format for use in HTML tags.
ColorAdapter - Class in com.compomics.util.io.json.adapter
ColorAdapter required to avoid illegal reflective access warnings.
ColorAdapter() - Constructor for class com.compomics.util.io.json.adapter.ColorAdapter
 
columnPermutation(int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
ColumnTypeConverter - Class in com.compomics.util.db
This class converts column types into Strings representing corresponding Java types.
ColumnTypeConverter() - Constructor for class com.compomics.util.db.ColumnTypeConverter
Empty default constructor
com.compomics.cli.enzymes - package com.compomics.cli.enzymes
Command line for the handling of enzymes.
com.compomics.cli.fasta - package com.compomics.cli.fasta
Command line for the handling of fasta files.
com.compomics.cli.identification_parameters - package com.compomics.cli.identification_parameters
Command line for the handling of identification parameters.
com.compomics.cli.modifications - package com.compomics.cli.modifications
Command line for the handling of modifications.
com.compomics.cli.paths - package com.compomics.cli.paths
Command line for the handling of paths.
com.compomics.cli.peptide_mapper - package com.compomics.cli.peptide_mapper
Command line for PeptideMapper.
com.compomics.scripts_marc - package com.compomics.scripts_marc
 
com.compomics.software - package com.compomics.software
Convenience classes for command line usage of compomics-utilities tools.
com.compomics.software.autoupdater - package com.compomics.software.autoupdater
Classes related to auto updating compomics-utilities tools.
com.compomics.software.cli - package com.compomics.software.cli
Convenience classes for the handling of command lines.
com.compomics.software.dialogs - package com.compomics.software.dialogs
Dialogs for starting compomics-utilities tools and setting their Java options.
com.compomics.software.log - package com.compomics.software.log
Classes related to software log.
com.compomics.software.settings - package com.compomics.software.settings
Settings for compomics-utilities tools.
com.compomics.software.settings.gui - package com.compomics.software.settings.gui
GUI settings for compomics-utilities tools.
com.compomics.util - package com.compomics.util
General utilities classes.
com.compomics.util.db - package com.compomics.util.db
Database related classes.
com.compomics.util.db.components - package com.compomics.util.db.components
Database related components.
com.compomics.util.db.interfaces - package com.compomics.util.db.interfaces
Database related interfaces.
com.compomics.util.db.object - package com.compomics.util.db.object
This package contains the classes relative to the object database.
com.compomics.util.db.object.objects - package com.compomics.util.db.object.objects
This package contains classes of objects that can be stored in the database.
com.compomics.util.enumeration - package com.compomics.util.enumeration
Enumeration used by compomics-utilities.
com.compomics.util.examples - package com.compomics.util.examples
Examples of how the compomics-utilities library can can be used by other projects.
com.compomics.util.exceptions - package com.compomics.util.exceptions
Classes for the handling of exceptions.
com.compomics.util.exceptions.exception_handlers - package com.compomics.util.exceptions.exception_handlers
Implementations of the ExceptionHandler interface.
com.compomics.util.experiment - package com.compomics.util.experiment
Gene factory classes.
com.compomics.util.experiment.biology.aminoacids - package com.compomics.util.experiment.biology.aminoacids
The amino acid classes.
com.compomics.util.experiment.biology.aminoacids.impl - package com.compomics.util.experiment.biology.aminoacids.impl
The amino acid implementations.
com.compomics.util.experiment.biology.aminoacids.sequence - package com.compomics.util.experiment.biology.aminoacids.sequence
Classes related to the handling of protein sequences.
com.compomics.util.experiment.biology.atoms - package com.compomics.util.experiment.biology.atoms
The atom classes.
com.compomics.util.experiment.biology.atoms.impl - package com.compomics.util.experiment.biology.atoms.impl
Atoms implementations.
com.compomics.util.experiment.biology.enzymes - package com.compomics.util.experiment.biology.enzymes
Classes related to enzymes.
com.compomics.util.experiment.biology.genes - package com.compomics.util.experiment.biology.genes
Classes related to genes.
com.compomics.util.experiment.biology.genes.ensembl - package com.compomics.util.experiment.biology.genes.ensembl
Classes for the handling of Ensembl data.
com.compomics.util.experiment.biology.genes.go - package com.compomics.util.experiment.biology.genes.go
Classes for the handling of GO terms.
com.compomics.util.experiment.biology.ions - package com.compomics.util.experiment.biology.ions
Experiment classes related to ions.
com.compomics.util.experiment.biology.ions.impl - package com.compomics.util.experiment.biology.ions.impl
Ion implementations.
com.compomics.util.experiment.biology.modifications - package com.compomics.util.experiment.biology.modifications
 
com.compomics.util.experiment.biology.proteins - package com.compomics.util.experiment.biology.proteins
Classes related to proteins.
com.compomics.util.experiment.biology.taxonomy - package com.compomics.util.experiment.biology.taxonomy
Classes related to species and taxonomy.
com.compomics.util.experiment.biology.taxonomy.mappings - package com.compomics.util.experiment.biology.taxonomy.mappings
Classes related to species mapping.
com.compomics.util.experiment.biology.variants - package com.compomics.util.experiment.biology.variants
Experiment classes related to variants.
com.compomics.util.experiment.biology.variants.amino_acids - package com.compomics.util.experiment.biology.variants.amino_acids
Type of implemented variants.
com.compomics.util.experiment.filtering - package com.compomics.util.experiment.filtering
Filtering classes.
com.compomics.util.experiment.identification - package com.compomics.util.experiment.identification
Experiment classes related to identifications.
com.compomics.util.experiment.identification.amino_acid_tags - package com.compomics.util.experiment.identification.amino_acid_tags
Amino Acid Tag classes.
com.compomics.util.experiment.identification.features - package com.compomics.util.experiment.identification.features
Classes for the generation of identification features.
com.compomics.util.experiment.identification.filtering - package com.compomics.util.experiment.identification.filtering
Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.filtering.items - package com.compomics.util.experiment.identification.filtering.items
Items used by the filters to filter on.
com.compomics.util.experiment.identification.identification_parameters - package com.compomics.util.experiment.identification.identification_parameters
Parameters settings for the spectrum identification algorithms.
com.compomics.util.experiment.identification.matches - package com.compomics.util.experiment.identification.matches
Experiment classes related to matches.
com.compomics.util.experiment.identification.matches_iterators - package com.compomics.util.experiment.identification.matches_iterators
Identification match iterators.
com.compomics.util.experiment.identification.modification - package com.compomics.util.experiment.identification.modification
Modification mapping and localization.
com.compomics.util.experiment.identification.modification.mapping - package com.compomics.util.experiment.identification.modification.mapping
Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.scores - package com.compomics.util.experiment.identification.modification.scores
PTM scores.
com.compomics.util.experiment.identification.peptide_fragmentation - package com.compomics.util.experiment.identification.peptide_fragmentation
Peptide fragment intensities.
com.compomics.util.experiment.identification.peptide_fragmentation.models - package com.compomics.util.experiment.identification.peptide_fragmentation.models
Predictors for peptide fragment intensities.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration - package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
This package contains the classes needed to configure the ms2pip features.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features - package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
This package contains features implemented for ms2pip.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic - package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
This package contains generic features implemented for ms2pip.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation - package com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation
This package contains the classes needed to generate ms2pip features.
com.compomics.util.experiment.identification.peptide_inference - package com.compomics.util.experiment.identification.peptide_inference
Classes related to peptide inference.
com.compomics.util.experiment.identification.peptide_shaker - package com.compomics.util.experiment.identification.peptide_shaker
Experiment classes used in PeptideShaker calculations.
com.compomics.util.experiment.identification.protein_inference - package com.compomics.util.experiment.identification.protein_inference
Classes related to protein inference.
com.compomics.util.experiment.identification.protein_inference.fm_index - package com.compomics.util.experiment.identification.protein_inference.fm_index
Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.protein_sequences - package com.compomics.util.experiment.identification.protein_sequences
Protein sequence handling related classes.
com.compomics.util.experiment.identification.protein_sequences.digestion - package com.compomics.util.experiment.identification.protein_sequences.digestion
This package contains classes used to digest protein sequences into peptides.
com.compomics.util.experiment.identification.protein_sequences.digestion.iterators - package com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
This package contains implementations of the SequenceIterator interface.
com.compomics.util.experiment.identification.psm_scoring - package com.compomics.util.experiment.identification.psm_scoring
Main PSM scoring class.
com.compomics.util.experiment.identification.psm_scoring.psm_scores - package com.compomics.util.experiment.identification.psm_scoring.psm_scores
Main PTM scoring classes.
com.compomics.util.experiment.identification.spectrum_annotation - package com.compomics.util.experiment.identification.spectrum_annotation
Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators - package com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators - package com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.experiment.identification.spectrum_assumptions - package com.compomics.util.experiment.identification.spectrum_assumptions
Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.identification.utils - package com.compomics.util.experiment.identification.utils
This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.identification.validation - package com.compomics.util.experiment.identification.validation
Experiment classes related to identification matches validation.
com.compomics.util.experiment.io.biology.protein - package com.compomics.util.experiment.io.biology.protein
Experiment IO classes for biological resources.
com.compomics.util.experiment.io.biology.protein.converters - package com.compomics.util.experiment.io.biology.protein.converters
Fasta file converters.
com.compomics.util.experiment.io.biology.protein.iterators - package com.compomics.util.experiment.io.biology.protein.iterators
Fasta file iterators.
com.compomics.util.experiment.io.identification - package com.compomics.util.experiment.io.identification
Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders - package com.compomics.util.experiment.io.identification.idfilereaders
Experiment classes related to reading search engine files.
com.compomics.util.experiment.io.identification.writers - package com.compomics.util.experiment.io.identification.writers
Writer for identification results.
com.compomics.util.experiment.io.mass_spectrometry - package com.compomics.util.experiment.io.mass_spectrometry
Classes for the handling of mass spectrometry files.
com.compomics.util.experiment.io.mass_spectrometry.apl - package com.compomics.util.experiment.io.mass_spectrometry.apl
Classes for the handling of Andromeda peak list (apl) files.
com.compomics.util.experiment.io.mass_spectrometry.cms - package com.compomics.util.experiment.io.mass_spectrometry.cms
Classes for the handling of Compomics mass spectrometry (cms) files.
com.compomics.util.experiment.io.mass_spectrometry.mgf - package com.compomics.util.experiment.io.mass_spectrometry.mgf
Classes for the handling of mgf files.
com.compomics.util.experiment.io.mass_spectrometry.ms2 - package com.compomics.util.experiment.io.mass_spectrometry.ms2
Classes for the handling of ms2 files.
com.compomics.util.experiment.io.mass_spectrometry.mzml - package com.compomics.util.experiment.io.mass_spectrometry.mzml
Classes for the handling of mzml files.
com.compomics.util.experiment.io.parameters - package com.compomics.util.experiment.io.parameters
Experiment IO classes relative to the handling of parameters.
com.compomics.util.experiment.io.temp - package com.compomics.util.experiment.io.temp
Experiment IO classes relative to the handling of temporary files.
com.compomics.util.experiment.mass_spectrometry - package com.compomics.util.experiment.mass_spectrometry
Experiment classes related to mass spectrometry.
com.compomics.util.experiment.mass_spectrometry.indexes - package com.compomics.util.experiment.mass_spectrometry.indexes
Classes related to the indexing of spectra.
com.compomics.util.experiment.mass_spectrometry.proteowizard - package com.compomics.util.experiment.mass_spectrometry.proteowizard
Package containing the classes used to interact with ProteoWizard.
com.compomics.util.experiment.mass_spectrometry.spectra - package com.compomics.util.experiment.mass_spectrometry.spectra
Experiment classes related to spectra.
com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser - package com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser
Package containing the classes used to interact with ThermoRawFileParser.
com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui - package com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui
Package containing the GUI classes used to interact with ThermoRawFileParser.
com.compomics.util.experiment.mass_spectrometry.utils - package com.compomics.util.experiment.mass_spectrometry.utils
Utility classes for mass spectrometry.
com.compomics.util.experiment.normalization - package com.compomics.util.experiment.normalization
Classes related to quantification values normalization.
com.compomics.util.experiment.patient - package com.compomics.util.experiment.patient
Experiment classes related to patent information.
com.compomics.util.experiment.personalization - package com.compomics.util.experiment.personalization
Experiment customization classes.
com.compomics.util.experiment.quantification - package com.compomics.util.experiment.quantification
Experiment classes related to quantification.
com.compomics.util.experiment.quantification.reporterion - package com.compomics.util.experiment.quantification.reporterion
Experiment classes related to reporter ions.
com.compomics.util.experiment.quantification.spectrumcounting - package com.compomics.util.experiment.quantification.spectrumcounting
Experiment classes related to spectrum counting.
com.compomics.util.experiment.refinement_parameters - package com.compomics.util.experiment.refinement_parameters
Experiment classes related to specific parametrization of experiment objects.
com.compomics.util.experiment.units - package com.compomics.util.experiment.units
Unit related classes.
com.compomics.util.general - package com.compomics.util.general
General, top-level tasks that are used throughout the other packages in the util section.
com.compomics.util.general.servlet - package com.compomics.util.general.servlet
Servlet representation of the classes from the general utilities package (com.compomics.util.general)
com.compomics.util.gui - package com.compomics.util.gui
Basic GUI classes.
com.compomics.util.gui.atoms - package com.compomics.util.gui.atoms
Atoms GUI dialogs.
com.compomics.util.gui.enzymes - package com.compomics.util.gui.enzymes
Dialogs for enzymes.
com.compomics.util.gui.error_handlers - package com.compomics.util.gui.error_handlers
Help handlers.
com.compomics.util.gui.error_handlers.notification - package com.compomics.util.gui.error_handlers.notification
Notification dialogs.
com.compomics.util.gui.events - package com.compomics.util.gui.events
GUI event classes.
com.compomics.util.gui.export.graphics - package com.compomics.util.gui.export.graphics
Exporting of graphics.
com.compomics.util.gui.export.report - package com.compomics.util.gui.export.report
Report editor GUI.
com.compomics.util.gui.file_handling - package com.compomics.util.gui.file_handling
GUI related file filters.
com.compomics.util.gui.filtering - package com.compomics.util.gui.filtering
GUI filters.
com.compomics.util.gui.genes - package com.compomics.util.gui.genes
Dialogs for the handling of genes.
com.compomics.util.gui.interfaces - package com.compomics.util.gui.interfaces
GUI related interfaces.
com.compomics.util.gui.isotopic_calculator - package com.compomics.util.gui.isotopic_calculator
GUI class for the Isotopic Distribution calculator.
com.compomics.util.gui.modification - package com.compomics.util.gui.modification
PTM GUI dialogs.
com.compomics.util.gui.parameters - package com.compomics.util.gui.parameters
GUI classes for parameters, settings and preferences.
com.compomics.util.gui.parameters.identification - package com.compomics.util.gui.parameters.identification
GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.gui.parameters.identification.advanced - package com.compomics.util.gui.parameters.identification.advanced
Dialogs for advanced identification parameters.
com.compomics.util.gui.parameters.identification.algorithm - package com.compomics.util.gui.parameters.identification.algorithm
Search algorithm settings dialogs.
com.compomics.util.gui.parameters.identification.pride - package com.compomics.util.gui.parameters.identification.pride
Dialogs for pride reprocessing parameters.
com.compomics.util.gui.parameters.identification.search - package com.compomics.util.gui.parameters.identification.search
Dialogs for search parameters.
com.compomics.util.gui.parameters.proteowizard - package com.compomics.util.gui.parameters.proteowizard
Package containing the GUI classes used to interact with ProteoWizard.
com.compomics.util.gui.parameters.tools - package com.compomics.util.gui.parameters.tools
GUI classes for parameters, settings and preferences used in tools.
com.compomics.util.gui.protein - package com.compomics.util.gui.protein
GUI class related to protein sequence formatting.
com.compomics.util.gui.renderers - package com.compomics.util.gui.renderers
GUI renderer classes.
com.compomics.util.gui.spectrum - package com.compomics.util.gui.spectrum
Spectrum and Chromatogram visualization GUI classes.
com.compomics.util.gui.tablemodels - package com.compomics.util.gui.tablemodels
Self updating table model classes.
com.compomics.util.gui.utils - package com.compomics.util.gui.utils
GUI utilities classes.
com.compomics.util.gui.utils.user_choice - package com.compomics.util.gui.utils.user_choice
GUI utils allowing the user to choose something.
com.compomics.util.gui.utils.user_choice.list_choosers - package com.compomics.util.gui.utils.user_choice.list_choosers
Implementations of the ListChooser.
com.compomics.util.gui.variants.aa_substitutions - package com.compomics.util.gui.variants.aa_substitutions
GUI classes relative to amino acid substitution.
com.compomics.util.gui.waiting.waitinghandlers - package com.compomics.util.gui.waiting.waitinghandlers
Waiting handler classes.
com.compomics.util.interfaces - package com.compomics.util.interfaces
Interfaces for the more specific implementations in the util package.
com.compomics.util.io - package com.compomics.util.io
Classes related to input/output.
com.compomics.util.io.compression - package com.compomics.util.io.compression
Classes related to file compression.
com.compomics.util.io.compression.SectionGzWriter - package com.compomics.util.io.compression.SectionGzWriter
Package for writing gzfiles with multiple sections.
com.compomics.util.io.export - package com.compomics.util.io.export
Classes related to exporting reports.
com.compomics.util.io.export.features - package com.compomics.util.io.export.features
Classes related to exporting Reporter features.
com.compomics.util.io.export.features.peptideshaker - package com.compomics.util.io.export.features.peptideshaker
Package containing classes listing the possible export features for PeptideShaker.
com.compomics.util.io.export.features.reporter - package com.compomics.util.io.export.features.reporter
Package containing classes listing the possible export features for Reporter.
com.compomics.util.io.export.styles - package com.compomics.util.io.export.styles
Export styles.
com.compomics.util.io.export.writers - package com.compomics.util.io.export.writers
Export writer.
com.compomics.util.io.export.xml - package com.compomics.util.io.export.xml
Convenience classes for xml exports.
com.compomics.util.io.file - package com.compomics.util.io.file
Classes related to the handling of files.
com.compomics.util.io.file.filefilters - package com.compomics.util.io.file.filefilters
Classes related to file filters.
com.compomics.util.io.flat - package com.compomics.util.io.flat
Export of flat files.
com.compomics.util.io.flat.readers - package com.compomics.util.io.flat.readers
 
com.compomics.util.io.ftp - package com.compomics.util.io.ftp
Classes related to the handling of FTP.
com.compomics.util.io.json - package com.compomics.util.io.json
Classes related to the handling of json files.
com.compomics.util.io.json.adapter - package com.compomics.util.io.json.adapter
JSON adapter classes.
com.compomics.util.io.json.marshallers - package com.compomics.util.io.json.marshallers
JSON marshaller classes.
com.compomics.util.junit - package com.compomics.util.junit
Custom classpath related test class.
com.compomics.util.math - package com.compomics.util.math
Basic match functions.
com.compomics.util.math.clustering - package com.compomics.util.math.clustering
Basic clustering functions.
com.compomics.util.math.clustering.settings - package com.compomics.util.math.clustering.settings
Settings for the clustering.
com.compomics.util.math.matrix - package com.compomics.util.math.matrix
Double matrix classes.
com.compomics.util.math.roc - package com.compomics.util.math.roc
ROC curve calculation.
com.compomics.util.math.statistics - package com.compomics.util.math.statistics
Math classes related to statistics.
com.compomics.util.math.statistics.distributions - package com.compomics.util.math.statistics.distributions
Math classes related to distributions.
com.compomics.util.math.statistics.linear_regression - package com.compomics.util.math.statistics.linear_regression
Classes to perform linear regressions.
com.compomics.util.math.statistics.linear_regression.filters - package com.compomics.util.math.statistics.linear_regression.filters
Implementation of algorithms performing linear regression.
com.compomics.util.math.statistics.linear_regression.regressions - package com.compomics.util.math.statistics.linear_regression.regressions
Filters to apply prior to a linear regression.
com.compomics.util.memory - package com.compomics.util.memory
Memory management.
com.compomics.util.messages - package com.compomics.util.messages
Classes related to sending messages to the user.
com.compomics.util.nucleotide - package com.compomics.util.nucleotide
Useful objects for modeling and handling nucleotides.
com.compomics.util.parameters - package com.compomics.util.parameters
Utilities parameters.
com.compomics.util.parameters.identification - package com.compomics.util.parameters.identification
Identification parameters.
com.compomics.util.parameters.identification.advanced - package com.compomics.util.parameters.identification.advanced
Advanced Identification parameters.
com.compomics.util.parameters.identification.search - package com.compomics.util.parameters.identification.search
Identification parameters relative to the search.
com.compomics.util.parameters.identification.tool_specific - package com.compomics.util.parameters.identification.tool_specific
Parameters settings for the search algorithms.
com.compomics.util.parameters.peptide_shaker - package com.compomics.util.parameters.peptide_shaker
PeptideShaker parameters.
com.compomics.util.parameters.quantification.spectrum_counting - package com.compomics.util.parameters.quantification.spectrum_counting
Spectrum counting parameters.
com.compomics.util.parameters.searchgui - package com.compomics.util.parameters.searchgui
SearchGUI parameters.
com.compomics.util.parameters.tools - package com.compomics.util.parameters.tools
Tool parameters.
com.compomics.util.pdbfinder - package com.compomics.util.pdbfinder
Classes for mapping between UniProt accession numbers and PDB structures.
com.compomics.util.pdbfinder.das.readers - package com.compomics.util.pdbfinder.das.readers
Classes for aligning and annotating PDB files when mapped to UniProt accession numbers.
com.compomics.util.pdbfinder.pdb - package com.compomics.util.pdbfinder.pdb
Classes for parsing PDB files.
com.compomics.util.pride - package com.compomics.util.pride
Objects related to mapping to PRIDE.
com.compomics.util.pride.prideobjects - package com.compomics.util.pride.prideobjects
Objects related to mapping experiment annotation to PRIDE.
com.compomics.util.pride.prideobjects.webservice - package com.compomics.util.pride.prideobjects.webservice
Classes for validating PRIDE web service queries.
com.compomics.util.pride.prideobjects.webservice.file - package com.compomics.util.pride.prideobjects.webservice.file
Classes for validating PRIDE web service file types.
com.compomics.util.pride.prideobjects.webservice.query - package com.compomics.util.pride.prideobjects.webservice.query
Classes for validating PRIDE web service filters.
com.compomics.util.pride.validation - package com.compomics.util.pride.validation
Classes for validating PRIDE XML files.
com.compomics.util.protein - package com.compomics.util.protein
Classes concerning useful Objects and their operations for modeling and handling proteins.
com.compomics.util.sun - package com.compomics.util.sun
Classes related to Java's Swing library.
com.compomics.util.threading - package com.compomics.util.threading
Classes related to maps.
com.compomics.util.waiting - package com.compomics.util.waiting
Waiting handler interfaces.
comet - Static variable in class com.compomics.util.experiment.identification.Advocate
The Comet search engine, free version of Sequest.
CometParameters - Class in com.compomics.util.parameters.identification.tool_specific
The Comet specific parameters.
CometParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.CometParameters
Constructor.
CometParameters.CometOutputFormat - Enum in com.compomics.util.parameters.identification.tool_specific
The available output formats.
CometParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the Comet specific settings.
CometParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
Empty default constructor
CometParametersDialog(Frame, CometParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
Creates a new CometSettingsDialog with a frame as owner.
CometParametersDialog(Dialog, Frame, CometParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
Creates a new CometSettingsDialog with a dialog as owner.
command - Variable in class com.compomics.util.io.ftp.FTP
The last command issued.
commandLineDefaultOption - Static variable in enum com.compomics.util.io.export.ExportFormat
The default export format to use for command line exports.
CommandLineExceptionHandler - Class in com.compomics.util.exceptions.exception_handlers
Exception handler for command line processes.
CommandLineExceptionHandler() - Constructor for class com.compomics.util.exceptions.exception_handlers.CommandLineExceptionHandler
Constructor.
commandLineOption - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
The command line option name.
CommandLineParser - Class in com.compomics.util.general
This class provides a generic interface for the parsing of command-line arguments, options and flags.
CommandLineParser(String[]) - Constructor for class com.compomics.util.general.CommandLineParser
The constructor requires the caller to provide it with a command line arguments String[] that will be the basis of the parsing.
CommandLineParser(String[], String[]) - Constructor for class com.compomics.util.general.CommandLineParser
This constructor requests the command-line String[] as well as a String[] with a list of options which in turn take a parameter.
CommandLineUtils - Class in com.compomics.software.cli
This class groups some convenience methods for the use of compomics tools in command line.
CommandLineUtils() - Constructor for class com.compomics.software.cli.CommandLineUtils
 
CommandParameter - Class in com.compomics.software.cli
Convenience methods for the validation of command line parameters.
CommandParameter() - Constructor for class com.compomics.software.cli.CommandParameter
 
comment - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
Character to start the comment lines.
commit() - Method in class com.compomics.util.db.object.ObjectsDB
Committing all changes into the database.
comparatorsMap - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
Map of the comparators to use.
compare(String, String) - Method in class com.compomics.software.autoupdater.CompareVersionNumbers
 
compare(String, String) - Method in class com.compomics.util.CompareVersionNumbers
 
compare(int, int) - Method in class com.compomics.util.sun.TableSorter
 
compareRowsByColumn(int, int, int) - Method in class com.compomics.util.sun.TableSorter
 
compareTo(WaveletTree.HuffmanNode) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree.HuffmanNode
 
compareTo(Object) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Method that compares an IsotopicDistributionSpectrum
compareTo(Object) - Method in class com.compomics.util.protein.ModificationImplementation
Compares this object with the specified object for order.
compareTo(Object) - Method in class com.compomics.util.protein.ModificationTemplate
Compares this object with the specified object for order.
CompareVersionNumbers - Class in com.compomics.software.autoupdater
Class for comparing tool version numbers.
CompareVersionNumbers() - Constructor for class com.compomics.software.autoupdater.CompareVersionNumbers
 
CompareVersionNumbers - Class in com.compomics.util
Comparator for tool version numbers.
CompareVersionNumbers() - Constructor for class com.compomics.util.CompareVersionNumbers
Empty default constructor
ComplementaryIonAminoAcidFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Feature based on the amino acid properties of the complementary ion.
ComplementaryIonAminoAcidFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
Empty default constructor
ComplementaryIonAminoAcidFeature(AminoAcid.Property, AASequenceFeature.Function) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
Constructor.
ComplementaryIonFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Feature based on a property of the complementary ion.
ComplementaryIonFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
Empty default constructor
ComplementaryIonFeature(IonFeature.Property) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
Constructor.
complementarySeries - Variable in enum com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator.IonSeries
The complementary ion index as listed in the PeptideFragmentIon class.
CompomicsTools - Enum in com.compomics.util.enumeration
This enum types all computational omics tools and libraries that make use of the utilities library.
CompomicsWrapper - Class in com.compomics.software
A general wrapper for compomics tools.
CompomicsWrapper() - Constructor for class com.compomics.software.CompomicsWrapper
Constructor.
computeMappingRanges(double) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Compute mapping ranges.
computeMassTolerance(double, double) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Compute the inverse mass value.
computeMassValue(double, double) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Compute the mass value.
computeMolecularWeight(String) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
Returns the protein's molecular weight.
concatenate(ArrayList<String>) - Static method in class com.compomics.software.cli.CommandLineUtils
Returns the list of arguments as space separated string for the command line.
concatenate(String[]) - Static method in class com.compomics.software.cli.CommandLineUtils
Returns the list of arguments as space separated string for the command line.
concatenate(char[], char[], int) - Static method in class com.compomics.util.ArrayUtil
Appends the second array to the first array.
concatenate(double[], double[], int) - Static method in class com.compomics.util.ArrayUtil
Appends the second array to the first array.
concatenate(byte[], byte[], int) - Static method in class com.compomics.util.ArrayUtil
Convenience method to merge two byte arrays.
concatenate(Collection<T>...) - Static method in class com.compomics.util.StreamUtil
Returns a concatenation of the streams of the given collections.
condition - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
Description of the condition to meet to pass the filter.
CONFIDENT - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Index for a confident assignment.
configurationFileName - Static variable in class com.compomics.software.settings.UtilitiesPathParameters
Default name for the path configuration file.
Connectable - Interface in com.compomics.util.interfaces
This interface describes the behaviour for classes that can accept an incoming DB connection.
ConnectionDialog - Class in com.compomics.util.gui.utils
This class implements a dialog to gather all information concerning a DB connection.
ConnectionDialog() - Constructor for class com.compomics.util.gui.utils.ConnectionDialog
Empty default constructor
ConnectionDialog(JFrame, Connectable, String, String) - Constructor for class com.compomics.util.gui.utils.ConnectionDialog
This constructor takes as arguments the parent JFrame and a title for the dialog.
ConnectionDialog(JFrame, Connectable, String, Properties) - Constructor for class com.compomics.util.gui.utils.ConnectionDialog
This constructor takes as arguments the parent JFrame and a title for the dialog.
Constants - Class in com.compomics.util.experiment
Convenience class listing constants used throughout the library.
Constants() - Constructor for class com.compomics.util.experiment.Constants
Empty default constructor
construct() - Method in class com.compomics.util.sun.SwingWorker
Compute the value to be returned by the get method.
Constructors - Class in com.compomics.util.db.components
This class will generate the code for a default and full constructor for a DBAccessor, defined by the metadata passed in via the constructor.
Constructors() - Constructor for class com.compomics.util.db.components.Constructors
Empty default constructor
Constructors(DBMetaData) - Constructor for class com.compomics.util.db.components.Constructors
This constructor takes care of generating the code that represents the constructor for a DBAccessor for the given metadata.
Contact - Class in com.compomics.util.pride.prideobjects
An object for storing Contact details.
Contact() - Constructor for class com.compomics.util.pride.prideobjects.Contact
Empty default constructor
Contact(String, String, String) - Constructor for class com.compomics.util.pride.prideobjects.Contact
Create a new Contact object.
ContactGroup - Class in com.compomics.util.pride.prideobjects
An object for storing ContactGroup details.
ContactGroup() - Constructor for class com.compomics.util.pride.prideobjects.ContactGroup
Empty default constructor
ContactGroup(ArrayList<Contact>, String) - Constructor for class com.compomics.util.pride.prideobjects.ContactGroup
Create a new ContactGroup object.
contains(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the pattern contains a subsequence of amino acids.
contains(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the pattern contains a subsequence of amino acids.
contains(long) - Method in class com.compomics.util.experiment.identification.Identification
Checks if database contains a certain object.
contains(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns a boolean indicating whether a protein was found in this protein match.
contains(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Indicates whether the modification is contained in the profile, looking into all modifications (fixed, variable and refinement)
contains(String) - Method in class com.compomics.util.protein.AASequenceImpl
This method reports whether a certain residu (or fixed sequence String) is found in the current sequence.
containsDecoys() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Returns true if the FASTA file contains decoys.
containsForbiddenCharacter(String) - Static method in class com.compomics.util.Util
Indicates whether a string contains characters forbidden in file names.
containsLoss(String) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Returns a boolean indicating whether a loss is implemented in the mapping.
containsModification(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns a boolean indicating whether the Modification is loaded in the factory.
containsModification(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Indicates whether a modification has been already scored.
containsPeptide(long) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns a boolean indicating whether a peptide was found in this protein match.
containsSpectrum(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns a boolean indicating whether the spectrum title is implemented in this index.
controlSocket - Variable in class com.compomics.util.io.ftp.FTP
Socket for communicating commands with the server.
convertBooleanToInteger(Boolean) - Static method in class com.compomics.util.Util
Converts a boolean value to the corresponding integer value, 0 for false and 1 for true.
convertFile(File, File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.biology.protein.converters.GenericFastaConverter
Appends decoy sequences to the provided FASTA file.
convertPridePtm(String, ModificationParameters, ArrayList<String>, boolean) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Tries to convert a PRIDE Modification to utilities Modification name, and add it to the modification profile.
convertSearchGUIFile(String[]) - Static method in class com.compomics.cli.peptide_mapper.PeptideMapperCLI
 
convertTypes(int[], int[]) - Static method in class com.compomics.util.db.ColumnTypeConverter
This method converts coded SQL columntypes into the corresponding Java objects (whose names are given int the String[] elements).
Copper - Class in com.compomics.util.experiment.biology.atoms.impl
The copper atom.
Copper() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Copper
Constructor.
copyFile(File, File) - Static method in class com.compomics.util.io.IoUtil
Copy the content of a file to another.
copyFile(File, File, boolean) - Static method in class com.compomics.util.io.IoUtil
Copy the content of one file to another.
coss - Static variable in class com.compomics.util.experiment.identification.Advocate
The CompOmics Spectral Searching (COSS) engine.
CossIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This IdfileReader reads identifications from a COSS tsv result file.
CossIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
Default constructor for the purpose of instantiation.
CossIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
Constructor for a COSS tsv result file reader.
CossIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
Constructor for a COSS tsv result file reader.
createDefaultGeneMappingFilesGeneric(String, File, File, boolean) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Copies the given gene mapping files to the gene mappings folder.
createDefaultTableHeader() - Method in class com.compomics.util.gui.modification.ModificationTable
 
createDefaultTableHeader() - Method in class com.compomics.util.gui.spectrum.FragmentIonTable
 
createDesktopShortcut(MavenJarFile, String, String, boolean) - Method in class com.compomics.software.autoupdater.FileDAO
Creates a new Desktop Shortcut to the Maven jar file, atm windows only.
createDesktopShortcut(MavenJarFile, String, String, boolean) - Method in class com.compomics.software.autoupdater.GUIFileDAO
Creates a new Desktop Shortcut to the Maven jar file, atm windows only.
createDesktopShortcut(MavenJarFile, String, String, boolean) - Method in class com.compomics.software.autoupdater.HeadlessFileDAO
Creates a new Desktop Shortcut to the Maven jar file, atm windows only.
createImageIcon(String) - Static method in class com.compomics.util.io.file.filefilters.FileFilterUtils
Returns an ImageIcon, or null if the path was invalid.
createIntermediateScoreMap() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Instantiates the intermediate scores map if null.
createLessTable() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Create the less table.
createOptionsCLI(Options) - Static method in enum com.compomics.cli.enzymes.EnzymesCLIParams
Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in enum com.compomics.cli.fasta.FastaParametersCLIParams
Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
Provides the options left to the user.
createOptionsCLI(Options) - Method in class com.compomics.cli.identification_parameters.IdentificationParametersCLI
 
createOptionsCLI(Options) - Static method in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in enum com.compomics.cli.modifications.ModificationsCLIParams
Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in enum com.compomics.cli.paths.PathSettingsCLIParams
Creates the options for the command line interface based on the possible values.
createPeptideFilter() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Creates a new peptide filter.
createProteinFilter() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Creates a new protein filter.
createPsmFilter() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Creates a new PSM filter.
createWaveletTreeHuffman(byte[], WaitingHandler, WaveletTree.HuffmanNode) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Create wavelet tree huffman.
CTERM - Static variable in class com.compomics.util.protein.Enzyme
 
cTermCorrection - Variable in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
The mass to add to the C-terminal gap so that is corresponds to a peptide fragment.
cTermCorrection - Variable in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
The mass to add to the C-terminal gap so that is corresponds to a peptide fragment.
CTERMINAL - Static variable in class com.compomics.util.protein.DualEnzyme
The code for C-terminal position in the resultant peptide.
CTERMINUS - Static variable in interface com.compomics.util.interfaces.Modification
The residue code for the C-terminus.
CTERMTRUNC - Static variable in class com.compomics.util.protein.Protein
The code for an C-terminal truncation.
Cu - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The Copper atom.
CURRENT_VERSION - Static variable in class com.compomics.util.parameters.identification.IdentificationParameters
Currently supported version number.
currentGraphicsPanelType - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Sets the current GraphicsPanel type, default to centroid spectrum.
currentPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The current padding (distance between the axes and the border of the panel).
currentVersion - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
Current version of the features.
CvTerm - Class in com.compomics.util.pride
A simple CvTerm object.
CvTerm() - Constructor for class com.compomics.util.pride.CvTerm
Empty default constructor
CvTerm(String, String, String, String) - Constructor for class com.compomics.util.pride.CvTerm
Create a new CV term.
cwd(String) - Method in class com.compomics.util.io.ftp.FTP
Change working directory to a specific directory on a remote FTP server.
Cysteine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Cysteine.
Cysteine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
Constructor.
CYSTEINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Cysteine immonium ion.

D

D - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
DasAlignment - Class in com.compomics.util.pdbfinder.das.readers
DasAlignment.
DasAlignment() - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAlignment
Empty default constructor
DasAlignment(JsonObject) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAlignment
Constructor.
DasAnnotationServerAlingmentReader - Class in com.compomics.util.pdbfinder.das.readers
DasAnnotationServerAlingmentReader.
DasAnnotationServerAlingmentReader() - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader
Empty default constructor.
DasAnnotationServerAlingmentReader(String) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader
Creates a new reader for a json string.
DasAnnotationServerResultReader - Class in com.compomics.util.pdbfinder.das.readers
DasAnnotationServerResultReader
DasAnnotationServerResultReader() - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
Empty default constructor
DasAnnotationServerResultReader(String) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
Creates a new reader for an XML string.
DasFeature - Class in com.compomics.util.pdbfinder.das.readers
DasFeature.
DasFeature() - Constructor for class com.compomics.util.pdbfinder.das.readers.DasFeature
Empty default constructor
DasFeature(String) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasFeature
Constructor.
dat - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
DAT - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
DATA_SECTION - Static variable in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Key for the data section.
databaseType - Variable in class com.compomics.util.experiment.io.biology.protein.FastaSummary
The database type occurrence in the FASTA file.
dataMissingAtRow(int) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Calling this method indicates that data is missing at the given row.
DataRoc - Class in com.compomics.util.math.roc
This class can be used to draw roc curves from experimental data.
DataRoc() - Constructor for class com.compomics.util.math.roc.DataRoc
Empty default constructor
DataRoc(ArrayList<Double>, ArrayList<Double>, DataRoc.RocInterpolation) - Constructor for class com.compomics.util.math.roc.DataRoc
Constructor.
DataRoc.RocInterpolation - Enum in com.compomics.util.math.roc
Enum listing the possible ways of interpolating points on the ROC.
dataSetCounter - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The number of datasets currently displayed in the panel.
dataSetCounterMirroredSpectra - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The number of mirrored datasets currently displayed in the panel.
DateChooser - Class in com.compomics.util.gui.utils
This class provides a simple date chooser.
DateChooser() - Constructor for class com.compomics.util.gui.utils.DateChooser
Empty default constructor
DateChooser(JFrame) - Constructor for class com.compomics.util.gui.utils.DateChooser
Creates a new DataChooser object.
DateChooser(JFrame, Calendar) - Constructor for class com.compomics.util.gui.utils.DateChooser
This constructor takes the parent JFRame for this dialog, as well as a reference parameter for the selected date.
DatFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.dat files.
DatFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.DatFileFilter
Empty default constructor
DBAccessor - Class in com.compomics.util.db
This class represents an accessor class' sourcecode as generated by the DBAccessorGenerator class.
DBAccessor() - Constructor for class com.compomics.util.db.DBAccessor
Empty default constructor
DBAccessor(DBMetaData, String, boolean) - Constructor for class com.compomics.util.db.DBAccessor
This constructor creates all code for the accessor, based on the specified metadata.
DBAccessorGenerator - Class in com.compomics.util.db
This class generates an Object that can be used for access to a given table in a JDBC accessible RDBMS.
DBAccessorGenerator() - Constructor for class com.compomics.util.db.DBAccessorGenerator
Default constructor.
DBElement - Interface in com.compomics.util.db.interfaces
This interface indicates that the implementing class can be stored, manipulated and deleted in a permanent storage (typically a RDBMS).
DBMetaData - Class in com.compomics.util.db
This class wraps the metadata retrieved from a table on the DB.
DBMetaData() - Constructor for class com.compomics.util.db.DBMetaData
Empty default constructor
DBMetaData(String, String[], int[], int[]) - Constructor for class com.compomics.util.db.DBMetaData
Constructor that allows the specification of table name, column names and column types.
DBMetaData(String, String[], int[], int[], String[]) - Constructor for class com.compomics.util.db.DBMetaData
Constructor that allows the specification of table name, column names and column types and the primary key columns..
DBMetaData(String, Vector, Vector, Vector) - Constructor for class com.compomics.util.db.DBMetaData
Constructor that allows the specification of table name, column names and column types.
DBMetaData(String, Vector, Vector, Vector, Vector) - Constructor for class com.compomics.util.db.DBMetaData
Constructor that allows the specification of table name, column names, column types, column sizes and the primary key columns.
DbMutex - Class in com.compomics.util.db.object
Placeholder for the db mutex.
DbMutex() - Constructor for class com.compomics.util.db.object.DbMutex
 
dbMutex - Static variable in class com.compomics.util.db.object.DbMutex
The db mutex.
DBResultSet - Class in com.compomics.util.db
This class wraps a DB resultset in an 'offline' object.
DBResultSet() - Constructor for class com.compomics.util.db.DBResultSet
Default constructor, just creates an empty resultset.
DBResultSet(ResultSet) - Constructor for class com.compomics.util.db.DBResultSet
This constructor takes a ResultSet from which the data is read.
DBResultSet(ResultSet, boolean) - Constructor for class com.compomics.util.db.DBResultSet
This constructor takes a ResultSet from which the data is read.
decode(String, byte[]) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Convenience function for decoding binary data encoded by MSNumpress.
decodeFixedPoint(byte[]) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Decode fixed point.
decodeLinear(byte[], int, Double[]) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Decodes data encoded by encodeLinear.
decodePic(byte[], int, Double[]) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Decodes data encoded by encodePic Result vector guaranteedly shorter than twice the data length (in nbr of values).
decodeSlof(byte[], int, Double[]) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Decodes data encoded by encodeSlof.
DECOY_FLAGS - Static variable in class com.compomics.util.experiment.io.biology.protein.FastaParameters
The decoy flags used to infer the FASTA parameters.
DECOY_SEPARATORS - Static variable in class com.compomics.util.experiment.io.biology.protein.FastaParameters
The decoy separators used to infer the FASTA parameters.
DecoyConverter - Class in com.compomics.util.experiment.io.biology.protein.converters
This class appends decoy sequences to the given FASTA file.
DecoyConverter() - Constructor for class com.compomics.util.experiment.io.biology.protein.converters.DecoyConverter
Empty default constructor.
decreaseIndent() - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Decreases the indent counter.
decreseDepth() - Method in class com.compomics.util.io.export.ExportWriter
Notifies the writer that data of a lower hierarchical depth will be written, e.g.
decreseDepth() - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
decreseDepth() - Method in class com.compomics.util.io.export.writers.TextWriter
 
DEFAULT_COLUMN_SEPARATOR - Static variable in class com.compomics.util.Util
Default column separator for text files.
DEFAULT_HEADER - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
The standard format.
DEFAULT_NON_VISIBLE_MARKER_ALPHA - Static variable in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
The default non-visible alpha level.
DEFAULT_SEPARATOR - Static variable in class com.compomics.util.io.IoUtil
Default separator for tabular files.
DEFAULT_STRING_MATCHING - Static variable in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Default string matching.
DEFAULT_VISIBLE_MARKER_ALPHA - Static variable in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
The default visible alpha level.
defaultModsSorted - Variable in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Set to true if the default mods are sorted alphabetically.
defaultMutationMatrices - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Returns the implemented default substitution matrices.
DefaultOutputLoggerImplementation - Class in com.compomics.util.general
This class implements a default logger (for debugging purposes).
DefaultOutputLoggerImplementation() - Constructor for class com.compomics.util.general.DefaultOutputLoggerImplementation
Default constructor.
DefaultOutputLoggerImplementation(PrintStream, PrintStream) - Constructor for class com.compomics.util.general.DefaultOutputLoggerImplementation
Constructor that takes two PrintStreams to output to.
defaultPath - Static variable in class com.compomics.software.settings.UtilitiesPathParameters
Replacement for the path when not available.
defaultPrecursorCharges - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The precursor charges to inspect by default.
DefaultSpectrumAnnotation - Class in com.compomics.util.gui.spectrum
This class provides a default implementation of the SpectrumAnnotation interface.
DefaultSpectrumAnnotation() - Constructor for class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
Empty default constructor
DefaultSpectrumAnnotation(double, double, Color, String) - Constructor for class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
Constructor creating a DefaultSpectrumAnnotation object.
DefaultStyle - Class in com.compomics.util.io.export.styles
Default style for Excel sheets.
DefaultStyle() - Constructor for class com.compomics.util.io.export.styles.DefaultStyle
Empty default constructor.
delay(long) - Method in class com.compomics.scripts_marc.Dummy
 
delete(Connection) - Method in interface com.compomics.util.db.interfaces.Deleteable
This method will physically delete the implemented object's data from the persistent store.
delete(String) - Method in class com.compomics.util.io.ftp.FTP
Delete the specified file from the ftp server file system.
Deleteable - Interface in com.compomics.util.db.interfaces
This interface indicates that the implementing class can be deleted from permanent storage.
DeleteableCode - Class in com.compomics.util.db.components
This class generates the code to make a DBAccessor class an implementation of the Deleteable interface.
DeleteableCode() - Constructor for class com.compomics.util.db.components.DeleteableCode
Empty default constructor
DeleteableCode(DBMetaData) - Constructor for class com.compomics.util.db.components.DeleteableCode
This constructor will generate the code to make the DBAccessor an implementation of the Deleteable interface, based on the specified metadata.
deleteContactGroup(ContactGroup) - Method in class com.compomics.util.pride.PrideObjectsFactory
Delete the given contact group.
deleteDir(File) - Static method in class com.compomics.util.io.IoUtil
Deletes all files and subdirectories under dir and dir itself.
deleteInstrument(Instrument) - Method in class com.compomics.util.pride.PrideObjectsFactory
Delete the given instrument.
deleteProtocol(Protocol) - Method in class com.compomics.util.pride.PrideObjectsFactory
Delete the given protocol.
deleteReferenceGroup(ReferenceGroup) - Method in class com.compomics.util.pride.PrideObjectsFactory
Delete the given reference group.
deleteSample(Sample) - Method in class com.compomics.util.pride.PrideObjectsFactory
Delete the given sample.
deleteTempFiles - Variable in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
If true, temp files are deleted upon completion.
deleteTempFolders() - Static method in class com.compomics.util.experiment.io.temp.TempFilesManager
Deletes the temp folders created.
Deletion - Class in com.compomics.util.experiment.biology.variants.amino_acids
Class representing an amino acid deletion.
Deletion() - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Deletion
Empty default constructor
Deletion(char) - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Deletion
Constructor.
DELIMITER - Static variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Character defining as delimiter between protein sequences.
deltaMassWindow - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
DescendingIntensityComparator - Static variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
This comparator compares two Peak instances on descending intensity.
description - Variable in enum com.compomics.cli.enzymes.EnzymesCLIParams
Explanation for the CLI parameter.
description - Variable in enum com.compomics.cli.fasta.FastaParametersCLIParams
Explanation for the CLI parameter.
description - Variable in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Explanation for the CLI parameter.
description - Variable in enum com.compomics.cli.modifications.ModificationsCLIParams
Explanation for the CLI parameter.
description - Variable in enum com.compomics.cli.paths.PathSettingsCLIParams
The description of the command line option.
description - Variable in enum com.compomics.util.experiment.biology.modifications.ModificationType
The description of the type.
description - Variable in enum com.compomics.util.experiment.filtering.FilterItemComparator
The description to use.
description - Variable in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
The description of the filtering item.
description - Variable in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
The description of the filtering item.
description - Variable in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
The description of the filtering item.
description - Variable in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
The description of the filtering item.
description - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
Description of the filter.
description - Variable in enum com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
The description of the error type.
description - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature.Property
The description of the option.
description - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature.Property
The description of the option.
description - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature.Property
The description of the option.
description - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.PeptideFragmentationModel
The description of the option.
description - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
Short description of the score.
description - Variable in enum com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters.IntensityThresholdType
The description of the threshold.
description - Variable in enum com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator.TiesResolution
The description.
description - Variable in enum com.compomics.util.experiment.io.identification.MzIdentMLVersion
The description of the option.
description - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
A brief description of the filter.
description - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
A brief description of the format.
description - Variable in enum com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
A brief description of the format.
description - Variable in enum com.compomics.util.io.export.ExportFormat
Description of the format.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
The description of the feature.
description - Variable in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
The description of the feature.
description - Variable in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
The description.
description - Variable in enum com.compomics.util.parameters.peptide_shaker.ProjectType
The description of the option.
description - Variable in enum com.compomics.util.parameters.searchgui.OutputParameters
The description of the option.
deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class com.compomics.util.io.json.adapter.InterfaceAdapter
 
determineColorOfPeak(String) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Deprecated.
it is advised to use methods based on the ion type rather than on the peak label
determineDefaultFragmentIonColor(Ion, boolean) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Returns the peak color to be used for the given peak label.
determineFragmentIonColor(Ion, boolean) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Returns the peak color to be used for the given peak label according to the color map.
determineFragmentIonColor(String) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Deprecated.
use the method based on the Ion class instead
DEUTEROACETYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.impl.Glycan
Final index for deuteroacetylated masses.
DEUTEROMETHYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.impl.Glycan
Final index for deuteromethylated masses.
DI_METHYL_R_112 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for di-methylation of R (PMID: 16335983).
DI_METHYL_R_115 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for di-methylation of R (PMID: 16335983).
DI_METHYL_R_157 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for di-methylation of R (PMID: 16335983).
digest(String, int, Integer, Integer) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Digests a protein sequence in a list of expected peptide sequences.
digest(String, int, Double, Double) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Digests a protein sequence in a list of expected peptide sequences.
DigestionParameters - Class in com.compomics.util.parameters.identification.search
This class groups the parameters for the digestion of proteins.
DigestionParameters() - Constructor for class com.compomics.util.parameters.identification.search.DigestionParameters
Constructor for empty parameters.
DigestionParameters.CleavageParameter - Enum in com.compomics.util.parameters.identification.search
Enum for the different types of digestion.
DigestionParameters.Specificity - Enum in com.compomics.util.parameters.identification.search
Enum for the different types of enzyme specificity.
dir() - Method in class com.compomics.util.io.ftp.FTP
Folder-list files on a remote FTP server.
direcTag - Static variable in class com.compomics.util.experiment.identification.Advocate
The DirecTag sequencing algorithm.
DirecTagIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
An identification file reader for Direct tag results.
DirecTagIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Default constructor for the purpose of instantiation.
DirecTagIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Constructors, parses a file.
DirecTagParameters - Class in com.compomics.util.parameters.identification.tool_specific
The DirecTag specific parameters.
DirecTagParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Constructor.
DirecTagParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for editing the DirecTag advanced settings.
DirecTagParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
Empty default constructor
DirecTagParametersDialog(Frame, DirecTagParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
Creates a new DirecTagSettingsDialog with a frame as owner.
DirecTagParametersDialog(Dialog, Frame, DirecTagParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
Creates a new DirecTagSettingsDialog with a dialog as owner.
disconnect() - Method in class com.compomics.util.io.ftp.FTPDownloader
Disconnect from the FTP server.
Distribution - Interface in com.compomics.util.math.statistics
This class represents a statistical distribution model like a Gaussian distribution.
DistributionRoc - Class in com.compomics.util.math.roc
This class can be used to draw roc curves from experimental data.
DistributionRoc() - Constructor for class com.compomics.util.math.roc.DistributionRoc
Empty default constructor
DistributionRoc(Distribution, Distribution) - Constructor for class com.compomics.util.math.roc.DistributionRoc
Constructor.
doGet(HttpServletRequest, HttpServletResponse) - Method in class com.compomics.util.general.servlet.MassCalcServlet
Override of parent class, implemented here as a simple forward to the 'doPost' method.
doPost(HttpServletRequest, HttpServletResponse) - Method in class com.compomics.util.general.servlet.MassCalcServlet
Override of parent class; this method handles post requests, and through forwarding also get requests.
DOUBLE_PRECISION - Static variable in class com.compomics.util.BinaryArrayImpl
Defines the valid String indicating the correct precision for encoded doubles.
DoubleMatrix - Class in com.compomics.util.math.matrix
Implementation of a matrix for double objects.
DoubleMatrix() - Constructor for class com.compomics.util.math.matrix.DoubleMatrix
 
DoubleMatrix(int) - Constructor for class com.compomics.util.math.matrix.DoubleMatrix
 
DoubleMatrix(DoubleMatrix) - Constructor for class com.compomics.util.math.matrix.DoubleMatrix
 
DOUBTFUL - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Index for a doubtful assignment.
downloadFile(String, File) - Method in class com.compomics.util.io.ftp.FTPDownloader
Download the given file from the FTP server.
downloadGeneMappings(String, String, String, String, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Download the gene mappings.
downloadGeneSequences(File, String, String, String, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Download the gene sequences mappings.
downloadGoMappings(String, String, String, boolean, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Download the GO mappings.
downloadLatestVersion(String, String, String, File, URL, String, boolean, boolean, Image, Image, boolean) - Static method in class com.compomics.software.CompomicsWrapper
Check if a newer version of the tool is deployed in the Maven repository, and closes the tool if the user decided to update.
DownloadLatestZipFromRepo - Class in com.compomics.software.autoupdater
Download the latest zip file from the repository.
DownloadLatestZipFromRepo() - Constructor for class com.compomics.software.autoupdater.DownloadLatestZipFromRepo
 
downloadLatestZipFromRepo(URL, String) - Static method in class com.compomics.software.autoupdater.DownloadLatestZipFromRepo
Downloads the latest deploy from the genesis Maven repository of the artifact of the jarPath, starts it without arguments and removes the old jar if there was an update.
downloadLatestZipFromRepo(URL, String, boolean, boolean, boolean, WaitingHandler) - Static method in class com.compomics.software.autoupdater.DownloadLatestZipFromRepo
Downloads the latest deploy from the genesis Maven repository of the artifact and starts it without arguments.
downloadLatestZipFromRepo(URL, String, boolean, String[], boolean, boolean, WaitingHandler) - Static method in class com.compomics.software.autoupdater.DownloadLatestZipFromRepo
Downloads the latest zip archive of the jar in the URL from the genesis Maven repository.
downloadLatestZipFromRepo(URL, String, boolean, boolean, String[], URL, WaitingHandler) - Static method in class com.compomics.software.autoupdater.DownloadLatestZipFromRepo
Downloads the latest zip archive of the jar in the URL from a given jarRepository.
downloadLatestZipFromRepo(URL, String, boolean, String, String[], URL, boolean, boolean, WaitingHandler) - Static method in class com.compomics.software.autoupdater.DownloadLatestZipFromRepo
Retrieves the latest version of a Maven jar file from a Maven repository, also checks if the environment is headless or not.
downloadLatestZipFromRepo(URL, String, boolean, String, String[], URL, boolean, boolean, FileDAO, WaitingHandler) - Static method in class com.compomics.software.autoupdater.DownloadLatestZipFromRepo
Retrieves the latest version of a Maven jar file from a Maven repository.
downloadLatestZipFromRepo(File, String, String, String, String, String[], URL, boolean, boolean, FileDAO, WaitingHandler) - Static method in class com.compomics.software.autoupdater.DownloadLatestZipFromRepo
Retrieves the latest version of a Maven jar file from a Maven repository.
downloadMapping(String) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
Downloads the mapping for the given species name from UniProt and saves it to the mapping file.
downloadMappings(WaitingHandler, Integer) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Try to download the gene and GO mappings for the currently selected species.
downloadPeptideShaker() - Method in class com.compomics.software.dialogs.PeptideShakerSetupDialog
Download PeptideShaker.
downloadSearchGUI() - Method in class com.compomics.software.dialogs.SearchGuiSetupDialog
Download SearchGUI.
downloadTaxonomyFile(File) - Static method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
Downloads the UniProt taxonomy mapping to the given file.
drawAxes(Graphics, double, double, int, double, double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method draws the axes and their labels on the specified Graphics object, taking into account the padding.
drawDaisyChain(Graphics, Vector, Vector, int, int, Vector, Vector, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Draw daisy chains.
drawFilledPolygon(Graphics) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method draws filled polygons for all of the peaks for all datasets in the current x-axis range on the panel.
drawLabel() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns true if the label is to be drawn, false otherwise.
drawMeasurementLine(int, int, int, int, Graphics, Color, int, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method draws a line, measuring the distance between two points in real mass units.
drawMirroredPeaks(Graphics) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method draws all of the peaks for all datasets in the current x-axis range on the panel.
drawOnTop() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns true if the area is to be drawn in front of the data, false otherwise.
drawPeaks(Graphics) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method draws all of the peaks for all datasets in the current x-axis range on the panel.
drawXAxisReferenceAreas(Graphics, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Draws the x-axis reference areas if any.
drawXTags(Graphics, int, int, int, int, int) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method draws tags on the X axis.
drawYAxisReferenceAreas(Graphics, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Draws the y-axis reference areas if any.
drawYTags(Graphics, int, int, int, int) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method draws tags on the Y axis.
dropDottedLine(int, int, int, Graphics, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method drops a dotted line from the specified total height to the top of the indicated point.
dta - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
DTA - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
DtaFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.dta files.
DtaFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.DtaFileFilter
Empty default constructor
DualEnzyme - Class in com.compomics.util.protein
This class implements an enzyme with a dual specificity; the N-terminus of a resultant peptide will have certain residue, the C-terminus will have another, eg.
DualEnzyme() - Constructor for class com.compomics.util.protein.DualEnzyme
Empty default constructor
DualEnzyme(String, String, String, String, String, int) - Constructor for class com.compomics.util.protein.DualEnzyme
This constructor allows you to specify all the information for this enzyme plus the number of missed cleavages that this instance will allow.
DualEnzyme(String, String, String, String, String) - Constructor for class com.compomics.util.protein.DualEnzyme
This constructor allows you to specify all the information for this enzyme.
Dummy - Class in com.compomics.scripts_marc
 
Dummy() - Constructor for class com.compomics.scripts_marc.Dummy
 
dummy - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Dummy scores.
dummy - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
An empty parameter used for instantiation.
DummyFrame - Class in com.compomics.util.gui
A simple class used to be able to show a JDialog without a parent frame in the OS task bar.
DummyFrame(String, String) - Constructor for class com.compomics.util.gui.DummyFrame
Constructor.
DummyFrame(String, Image) - Constructor for class com.compomics.util.gui.DummyFrame
Constructor.
DummyParameters - Class in com.compomics.util.experiment.io.parameters
Dummy parameters used to retrieve the parameters type and version.
DummyParameters() - Constructor for class com.compomics.util.experiment.io.parameters.DummyParameters
Empty default constructor
dumpToDB() - Method in class com.compomics.util.db.object.ObjectsDB
Triggers a dump of all objects within the cache into the database.
Duration - Class in com.compomics.util.waiting
Class used to measure duration of a process.
Duration() - Constructor for class com.compomics.util.waiting.Duration
Constructor for an empty instance.
Duration(long, long) - Constructor for class com.compomics.util.waiting.Duration
Constructor.

E

E - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
E - Static variable in class com.compomics.util.math.BigMathUtils
Big decimal value of E.
edited - Variable in class com.compomics.util.db.object.ObjectsCache.ObjectsCacheElement
The edited state.
editFilter(Filter) - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Edits the given filter.
ElementaryElement - Class in com.compomics.util.experiment.biology.atoms
This class can be used to retrieve elementary elements like a neutron.
ElementaryElement() - Constructor for class com.compomics.util.experiment.biology.atoms.ElementaryElement
Empty default constructor.
ElementaryIon - Class in com.compomics.util.experiment.biology.ions.impl
This class represents an elementary ion.
ElementaryIon() - Constructor for class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
Empty default constructor
ElementaryIon(String, double, int) - Constructor for class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
Constructor.
EMPTY - Static variable in class com.compomics.util.experiment.identification.utils.ModificationUtils
Empty array for no result.
EmptyCollections - Class in com.compomics.util.gui.utils
This class contains empty collections that can be used for empty results without creating new objects.
EmptyCollections() - Constructor for class com.compomics.util.gui.utils.EmptyCollections
Empty default constructor
emptyDir(File) - Static method in class com.compomics.util.io.IoUtil
Deletes all files and subdirectories under dir.
emptyInternalCaches() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
the sequence is kept in different formats internally.
emptyIntSet - Static variable in class com.compomics.util.gui.utils.EmptyCollections
Convenience result of an empty set.
emptyIntTreeSet - Static variable in class com.compomics.util.gui.utils.EmptyCollections
Convenience result of an empty set.
emptyStringSet - Static variable in class com.compomics.util.gui.utils.EmptyCollections
Convenience result of an empty set.
emptyStringTreeSet - Static variable in class com.compomics.util.gui.utils.EmptyCollections
Convenience result of an empty set.
encode(double[], String) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Encode.
encodeFixedPoint(double, byte[]) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Encode fixed point.
encodeInt(long, byte[], int) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
This encoding works on a 4 byte integer, by truncating initial zeros or ones.
encodeLinear(double[], int, byte[], double) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Encodes the doubles in data by first using a - lossy conversion to a 4 byte 5 decimal fixed point repressentation - storing the residuals from a linear prediction after first to values - encoding by encodeInt (see above) The resulting binary is maximally dataSize * 5 bytes, but much less if the data is reasonably smooth on the first order.
encodePic(double[], int, byte[]) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Encodes ion counts by simply rounding to the nearest 4 byte integer, and compressing each integer with encodeInt.
encodeSlof(double[], int, byte[], double) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Encodes ion counts by taking the natural logarithm, and storing a fixed point representation of this.
ENCODING - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
Encoding for the file, cf the second rule.
ENCODING - Static variable in class com.compomics.util.io.IoUtil
Default encoding, cf the second rule.
ENCODING - Static variable in class com.compomics.util.Util
Default encoding, cf the second rule.
end() - Method in class com.compomics.util.waiting.Duration
Sets the end time to the system current time in milliseconds.
ENSEMBL_GENOME_SPECIES - Static variable in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
The names of the Ensembl genome species files.
ENSEMBL_SPECIES - Static variable in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
The names of the Ensembl species files.
EnsemblGenomesSpecies - Class in com.compomics.util.experiment.biology.taxonomy.mappings
This class provides information about the species mapping in Ensembl Genomes (Bacteria, Fungi, Metazoa, Plants, Protists).
EnsemblGenomesSpecies() - Constructor for class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
Constructor.
EnsemblGenomesSpecies.EnsemblGenomeDivision - Enum in com.compomics.util.experiment.biology.taxonomy.mappings
Enum of the different Ensembl genome divisions.
ensemblName - Variable in enum com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies.EnsemblGenomeDivision
The name in the Ensembl mapping file.
EnsemblSpecies - Class in com.compomics.util.experiment.biology.taxonomy.mappings
Mapping of the Ensembl species.
EnsemblSpecies() - Constructor for class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
Constructor.
ensemblType - Variable in enum com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies.EnsemblGenomeDivision
The schema name for XML queries.
EnsemblVersion - Class in com.compomics.util.experiment.biology.genes.ensembl
Class for the handling of Ensembl versions.
EnsemblVersion() - Constructor for class com.compomics.util.experiment.biology.genes.ensembl.EnsemblVersion
Empty default constructor
ENTIRELY_NOT_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
 
Enzyme - Class in com.compomics.util.experiment.biology.enzymes
This class models an enzyme.
Enzyme() - Constructor for class com.compomics.util.experiment.biology.enzymes.Enzyme
Empty default constructor.
Enzyme(String) - Constructor for class com.compomics.util.experiment.biology.enzymes.Enzyme
Constructor for an Enzyme.
Enzyme - Class in com.compomics.util.protein
This class implements the functionality for an Enzyme.
Enzyme() - Constructor for class com.compomics.util.protein.Enzyme
Empty default constructor
Enzyme(String, String, String, String) - Constructor for class com.compomics.util.protein.Enzyme
This constructor requires that you specify all the information for this enzyme.
Enzyme(String, String, String, String, int) - Constructor for class com.compomics.util.protein.Enzyme
This constructor allows you to specify all the information for this enzyme plus the number of missed cleavages that this instance will allow.
Enzyme(Enzyme, int) - Constructor for class com.compomics.util.protein.Enzyme
Creates a new Enzyme from a com.compomics.util.experiment.biology.Enzyme enzyme and the maximum number of missed cleavages.
EnzymeFactory - Class in com.compomics.util.experiment.biology.enzymes
This factory will load enzymes from a JSON file and provide them on demand as a standard class.
enzymeLoaded(String) - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Indicates whether an enzyme is loaded in the factory.
enzymeMapping(DigestionParameters) - Static method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Tries to map the utilities enzyme in the digestion preferences to the enzymes supported by MyriMatch.
EnzymeParametersDialog - Class in com.compomics.util.gui.parameters.identification.pride
Simple dialog for mapping a PRIDE enzyme to a utilities enzyme.
EnzymeParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.pride.EnzymeParametersDialog
Empty default constructor
EnzymeParametersDialog(Frame, boolean, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.pride.EnzymeParametersDialog
Creates a new EnzymeSelectionDialog with a frame as owner.
EnzymeParametersDialog(Dialog, Frame, boolean, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.pride.EnzymeParametersDialog
Creates a new EnzymeSelectionDialog with a dialog as owner.
EnzymeParametersDialog(JDialog, boolean, String) - Constructor for class com.compomics.util.gui.parameters.identification.pride.EnzymeParametersDialog
Creates a new EnzymeSelectionDialog.
EnzymesCLI - Class in com.compomics.cli.enzymes
Command line to manage the enzymes.
EnzymesCLI(EnzymesCLIInputBean) - Constructor for class com.compomics.cli.enzymes.EnzymesCLI
Constructor.
EnzymesCLIInputBean - Class in com.compomics.cli.enzymes
This class parses the parameters from an EnzymeCLI.
EnzymesCLIInputBean(CommandLine) - Constructor for class com.compomics.cli.enzymes.EnzymesCLIInputBean
Parses all the arguments from a command line.
EnzymesCLIParams - Enum in com.compomics.cli.enzymes
Enum class specifying the EnzymesCLI parameters.
EnzymesDialog - Class in com.compomics.util.gui.enzymes
Dialog for the Enzymes.
EnzymesDialog(Frame, boolean) - Constructor for class com.compomics.util.gui.enzymes.EnzymesDialog
Creates a new EnzymesDialog.
equals(Object) - Method in class com.compomics.util.BinaryArrayImpl
Performs equals methods dependent on values of instance variables and class of Object o.
equals(Object) - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
equals(Enzyme) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Returns true of the two enzymes are identical.
equals(FastaParameters) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
 
equals(Object) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
 
equals(IdentificationAlgorithmParameter) - Method in interface com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter
Indicates whether another identificationAlgorithmParameter has the same parameters.
equals(DoubleMatrix) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
equals(GeneParameters) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Compares these preferences to other preferences.
equals(IdMatchValidationParameters) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Returns true if the objects have identical settings.
equals(ModificationLocalizationParameters) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Returns true if the objects have identical settings.
equals(ProteinInferenceParameters) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns true if the objects have identical settings.
equals(PsmScoringParameters) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Returns true if the objects have identical settings.
equals(IdentificationParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns true if the identification parameter objects have identical settings.
equals(ModificationParameters) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns true of the two profiles are identical.
equals(SearchParameters) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns true if the search parameter objects have identical settings.
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
 
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
 
equals(Object) - Method in class com.compomics.util.protein.ModificationImplementation
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class com.compomics.util.protein.ModificationTemplate
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class com.compomics.util.protein.Protein
This method will check equality between this object and another Protein instance.
error(SAXParseException) - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Receive notification of a recoverable error.
establishConnection() - Method in class com.compomics.util.db.object.ObjectsDB
Establishes connection to the database.
estimateAACoverage(long, boolean) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns amino acid coverage of this protein by enzymatic or non-enzymatic peptides only in an array where the index of the best validation level of every peptide covering a given amino acid is given.
estimateDensityFunction(Double[]) - Method in class com.compomics.util.math.statistics.distributions.NormalKernelDensityEstimator
Estimate the density function.
estimateDensityFunction(double[]) - Method in class com.compomics.util.math.statistics.distributions.NormalKernelDensityEstimator
Estimate the density function.
estimateScalingFactors(Identification, Metrics, SequenceProvider, IdentificationFeaturesGenerator, WaitingHandler, ExceptionHandler, ProcessingParameters) - Method in class com.compomics.util.experiment.quantification.spectrumcounting.ScalingFactorsEstimators
Estimates the scaling factors and stores them in the given metrics.
estimateSpectrumCounting(Identification, SequenceProvider, long, SpectrumCountingParameters, int, IdentificationParameters) - Static method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the spectrum counting index based on the project settings.
estimateTheoreticMass(ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Estimates the theoretic mass of the peptide.
ExcelWriter - Class in com.compomics.util.io.export.writers
ExportWriter for the export to Excel files.
ExcelWriter() - Constructor for class com.compomics.util.io.export.writers.ExcelWriter
Empty default constructor.
ExcelWriter(File) - Constructor for class com.compomics.util.io.export.writers.ExcelWriter
Constructor.
exception - Variable in class com.compomics.cli.peptide_mapper.MappingWorker
 
exceptionCaught - Variable in class com.compomics.util.exceptions.ExceptionHandler
List of caught exceptions.
ExceptionHandler - Class in com.compomics.util.exceptions
Interface for the general handling of exceptions.
ExceptionHandler() - Constructor for class com.compomics.util.exceptions.ExceptionHandler
Empty default constructor
exceptions - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
The exceptions to the rule.
excludeNullValues(Double[]) - Method in class com.compomics.util.math.statistics.distributions.NormalKernelDensityEstimator
Exclude null values from an array of double.
existsExtensionNotCaseSensitive(File) - Static method in class com.compomics.util.io.IoUtil
Checks if the given file exists with the extension in another case and returns it.
exp(BigDecimal, MathContext) - Static method in class com.compomics.util.math.BigFunctions
Returns the value of the exponential of the given BigDecimal using the given MathContext.
expBD(BigDecimal, MathContext) - Static method in class com.compomics.util.math.BigFunctions
Returns the value of the exponential of the given BigDecimal using the given MathContext.
ExperimentObject - Class in com.compomics.util.experiment.personalization
This abstract class provides customization facilities.
ExperimentObject() - Constructor for class com.compomics.util.experiment.personalization.ExperimentObject
Empty default constructor
Export - Class in com.compomics.util
Includes export to figure formats for Components and JFreeCharts.
Export() - Constructor for class com.compomics.util.Export
Empty default constructor
exportChart(JFreeChart, Rectangle, File, ImageType) - Static method in class com.compomics.util.Export
Exports the contents of a JFreeChart to an svg, png, pdf etc.
exportComponent(Component, Rectangle, File, ImageType) - Static method in class com.compomics.util.Export
Exports the contents of a Component to an svg, png, pdf etc.
ExportFactory - Interface in com.compomics.util.io.export
An export factory manages and generates reports.
ExportFeature - Interface in com.compomics.util.io.export
This interface represents an export feature.
ExportFormat - Enum in com.compomics.util.io.export
Enum of the different formats available for the exports.
exportFormat - Variable in class com.compomics.util.io.export.ExportWriter
The format of the export.
ExportFormatSelectionDialog - Class in com.compomics.util.gui
Simple dialog for selecting the format type to export to.
ExportFormatSelectionDialog(JFrame, boolean) - Constructor for class com.compomics.util.gui.ExportFormatSelectionDialog
Create and open a new ExportFormatSelectionDialog.
ExportFormatSelectionDialog(JDialog, boolean) - Constructor for class com.compomics.util.gui.ExportFormatSelectionDialog
Create and open a new ExportFormatSelectionDialog.
ExportGraphicsDialog - Class in com.compomics.util.gui.export.graphics
Simple dialog for selecting the image type to export a graphics element to.
ExportGraphicsDialog(JFrame, Image, Image, boolean, Component, LastSelectedFolder) - Constructor for class com.compomics.util.gui.export.graphics.ExportGraphicsDialog
Create and open a new ExportGraphicsDialog.
ExportGraphicsDialog(JFrame, Image, Image, boolean, ChartPanel, LastSelectedFolder) - Constructor for class com.compomics.util.gui.export.graphics.ExportGraphicsDialog
Create and open a new ExportPlot dialog.
ExportGraphicsDialog(JDialog, Image, Image, boolean, Component, LastSelectedFolder) - Constructor for class com.compomics.util.gui.export.graphics.ExportGraphicsDialog
Create and open a new ExportGraphicsDialog.
ExportGraphicsDialog(JDialog, Image, Image, boolean, ChartPanel, LastSelectedFolder) - Constructor for class com.compomics.util.gui.export.graphics.ExportGraphicsDialog
Create and open a new ExportPlot dialog.
ExportScheme - Class in com.compomics.util.io.export
This class allows creating a standard output scheme.
ExportScheme() - Constructor for class com.compomics.util.io.export.ExportScheme
Empty default constructor
ExportScheme(String, boolean, HashMap<String, ArrayList<ExportFeature>>, String, boolean, boolean, int, boolean, boolean, boolean, String) - Constructor for class com.compomics.util.io.export.ExportScheme
Constructor.
ExportScheme(String, boolean, ArrayList<String>, HashMap<String, ArrayList<ExportFeature>>, String, boolean, boolean, int, boolean, boolean, boolean) - Constructor for class com.compomics.util.io.export.ExportScheme
Constructor.
ExportScheme(String, boolean, HashMap<String, ArrayList<ExportFeature>>, String, boolean, boolean, int, boolean, boolean, boolean) - Constructor for class com.compomics.util.io.export.ExportScheme
Constructor.
ExportWriter - Class in com.compomics.util.io.export
The export writer will write the output in the desired export format.
ExportWriter() - Constructor for class com.compomics.util.io.export.ExportWriter
Empty default constructor.
ExtendedPeptide - Class in com.compomics.util.experiment.identification.protein_sequences.digestion
This class packages together a peptide, its fixed modifications and its position on the protein.
ExtendedPeptide() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.ExtendedPeptide
Empty default constructor
ExtendedPeptide(Peptide, int, String[]) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.ExtendedPeptide
Constructor.
EXTENSION - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileUtils
The file extension for cms files.
extension - Variable in enum com.compomics.util.io.export.ExportFormat
The extension to use for this format.
extension - Static variable in class com.compomics.util.pride.PrideObjectsFactory
The extension to use when saving objects.
EXTENSIONS - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
The file extension for mgf files.
EXTENSIONS - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileUtils
The file extension for mzml files.
extractAndUpdatePathOptions(String[]) - Static method in class com.compomics.cli.paths.PathSettingsCLI
If the arguments contains changes to the paths these arguments will be extracted and the paths updated, before the remaining non-path options are returned for further processing.
extractFile(File, WaitingHandler) - Static method in class com.compomics.util.io.compression.TarUtils
Extracts files from a tar.
extractFile(File, File, WaitingHandler) - Static method in class com.compomics.util.io.compression.TarUtils
Extracts files from a tar.

F

F - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
F - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The Fluorine atom.
factorial(int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns n! as a long.
factorial(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns n!/k!, an error is thrown if it cannot fit in a long.
factorial(BigInteger) - Static method in class com.compomics.util.math.BigFunctions
Returns n! as BigInteger.
factorial(BigInteger, BigInteger) - Static method in class com.compomics.util.math.BigFunctions
Returns n!/k! as BigInteger.
factorialDouble(int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns n! as a double.
factorialDouble(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns n!/k! as double.
fadeIn(JDialog) - Static method in class com.compomics.util.gui.utils.SwingUtils
Creates an animation to fade the dialog opacity from 0 to 1.
fadeIn(JDialog, int, float) - Static method in class com.compomics.util.gui.utils.SwingUtils
Creates an animation to fade the dialog opacity from 0 to 1.
fadeInAndOut(JDialog) - Static method in class com.compomics.util.gui.utils.SwingUtils
Creates an animation to fade the dialog opacity from 0 to 1, wait at 1 and then fade to 0.
fadeInAndOut(JDialog, int, float, int) - Static method in class com.compomics.util.gui.utils.SwingUtils
Creates an animation to fade the dialog opacity from 0 to 1, wait at 1 and then fade to 0 and dispose.
fadeOut(JDialog) - Static method in class com.compomics.util.gui.utils.SwingUtils
Creates an animation to fade the dialog opacity from 1 to 0.
fadeOut(JDialog, int, float) - Static method in class com.compomics.util.gui.utils.SwingUtils
Creates an animation to fade the dialog opacity from 1 to 0, and then dispose.
FAS - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
fas - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
FASTA - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
fasta - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
fastaFile - Variable in class com.compomics.util.experiment.io.biology.protein.FastaSummary
The file this summary represents.
FastaFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.fasta files.
FastaFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.FastaFileFilter
Empty default constructor
FastaIterator - Class in com.compomics.util.experiment.io.biology.protein.iterators
Iterator for a FASTA file.
FastaIterator(File) - Constructor for class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
Constructor without sanity check.
FastaIterator(File, boolean) - Constructor for class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
Constructor.
FastaMapper - Interface in com.compomics.util.experiment.identification.protein_inference
Interface for a class mapping peptides and tags to a protein.
FastaParameters - Class in com.compomics.util.experiment.io.biology.protein
The parameters used to parse a FASTA file.
FastaParameters() - Constructor for class com.compomics.util.experiment.io.biology.protein.FastaParameters
Empty default constructor.
FastaParametersCLIParams - Enum in com.compomics.cli.fasta
Command line parameters for the FASTA files.
FastaParametersDialog - Class in com.compomics.util.gui.protein
A dialog for advanced database settings.
FastaParametersDialog(Frame, FastaParameters, boolean) - Constructor for class com.compomics.util.gui.protein.FastaParametersDialog
Creates a new FractionSettingsDialog with a frame as owner.
FastaParametersDialog(Dialog, Frame, FastaParameters, boolean) - Constructor for class com.compomics.util.gui.protein.FastaParametersDialog
Creates a new FractionSettingsDialog with a dialog as owner.
FastaParametersInputBean - Class in com.compomics.cli.fasta
This class gathers command line parameters for the parsing of FASTA files.
FastaParametersInputBean(CommandLine, File, WaitingHandler) - Constructor for class com.compomics.cli.fasta.FastaParametersInputBean
Parses all the arguments from a command line.
FastaSummary - Class in com.compomics.util.experiment.io.biology.protein
This class parses a FASTA file and gathers summary statistics.
FastaSummary() - Constructor for class com.compomics.util.experiment.io.biology.protein.FastaSummary
Empty default constructor.
FastaSummary(String, String, String, File, TreeMap<String, Integer>, HashMap<ProteinDatabase, Integer>, int, int, long) - Constructor for class com.compomics.util.experiment.io.biology.protein.FastaSummary
Constructor.
fastaTag - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
Tag for the fasta file.
fatalError(SAXParseException) - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Receive notification of a non-recoverable error.
fatalError(IOException) - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
This is a extension method to the #fatalError(SAXParseException) method to allow the handling of IOExceptions.
Fe - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The Iron atom.
FeaturesGenerator - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation
This class computes the ms2PIP features from a peptide.
FeaturesGenerator() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation.FeaturesGenerator
Empty default constructor
FeaturesGenerator(FeaturesMap) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation.FeaturesGenerator
Constructor.
FeaturesMap - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
This class contains a map of selected features indexed by category.
FeaturesMap() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
Constructor.
FeaturesMapManager - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
This class is used to manage the features maps.
FeaturesMapManager() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMapManager
Empty default constructor
FeedBack - Class in com.compomics.util.messages
This class is used to report a message to the user.
FeedBack() - Constructor for class com.compomics.util.messages.FeedBack
Empty default constructor
FeedBack(FeedBack.FeedBackType, String, ArrayList<String>, String) - Constructor for class com.compomics.util.messages.FeedBack
Creates a new report for the user.
FeedBack.FeedBackType - Enum in com.compomics.util.messages
The supported report types.
FILE_GET - Static variable in class com.compomics.util.io.ftp.FTP
Pre-defined state.
FILE_PUT - Static variable in class com.compomics.util.io.ftp.FTP
Pre-defined state.
FileAdapter - Class in com.compomics.util.io.json.adapter
This class is intended to avoid the default behavior of the GSON parser to append the current path to the absolute path of a file.
FileAdapter() - Constructor for class com.compomics.util.io.json.adapter.FileAdapter
Empty default constructor.
FileAndFileFilter - Class in com.compomics.util.gui.file_handling
Store the selected file and the file type description.
FileAndFileFilter() - Constructor for class com.compomics.util.gui.file_handling.FileAndFileFilter
Empty default constructor
FileAndFileFilter(File, FileFilter) - Constructor for class com.compomics.util.gui.file_handling.FileAndFileFilter
Create a new FileAndFileFilter object.
FileChooserUtil - Class in com.compomics.util.gui.file_handling
This class contains utilities functions for the file choosers.
FileChooserUtil() - Constructor for class com.compomics.util.gui.file_handling.FileChooserUtil
 
FileDAO - Class in com.compomics.software.autoupdater
FileDAO file access.
FileDAO() - Constructor for class com.compomics.software.autoupdater.FileDAO
 
FileDisplayDialog - Class in com.compomics.util.gui.file_handling
Dialog for showing a list of selected files with the option to remove files from the list.
FileDisplayDialog(JFrame, ArrayList<File>, boolean) - Constructor for class com.compomics.util.gui.file_handling.FileDisplayDialog
Creates a new FileSelectionDialog.
FileDisplayDialog(JDialog, ArrayList<File>, boolean) - Constructor for class com.compomics.util.gui.file_handling.FileDisplayDialog
Creates a new FileSelectionDialog.
fileExists(String, String) - Static method in class com.compomics.software.cli.CommandParameter
Returns true if the argument can be parsed as a file and the file exists.
fileExists(String, String, HashSet<String>) - Static method in class com.compomics.software.cli.CommandParameter
Returns true if the argument can be parsed as a file, the file exists and is in the specified format.
FileFilterUtils - Class in com.compomics.util.io.file.filefilters
Organizes the file filters.
FileFilterUtils() - Constructor for class com.compomics.util.io.file.filefilters.FileFilterUtils
Empty default constructor
FileLoggerImplementation - Class in com.compomics.util.general
This class implements the Logger interface for logging to a file.
FileLoggerImplementation(String) - Constructor for class com.compomics.util.general.FileLoggerImplementation
This constructor takes the name for the log file and sets a default timestamp format: "dd/MM/yyyy - HH:mm:ss".
FileLoggerImplementation(String, String) - Constructor for class com.compomics.util.general.FileLoggerImplementation
This constructor takes the name for the log file and the timestamp format.
fileName - Static variable in class com.compomics.util.pride.PtmToPrideMap
The name of the file to save.
fileNameEnding - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
The file name ending of the format.
fileNameEnding - Variable in enum com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
The file name ending of the format.
FilenameExtensionFilter - Class in com.compomics.util.io.file
This class will implement a FilenameFilter that filters on the extension of files.
FilenameExtensionFilter() - Constructor for class com.compomics.util.io.file.FilenameExtensionFilter
Empty default constructor
FilenameExtensionFilter(String) - Constructor for class com.compomics.util.io.file.FilenameExtensionFilter
This constructor takes an extension to filter on.
FilenameExtensionFilter(String, String) - Constructor for class com.compomics.util.io.file.FilenameExtensionFilter
This constructor takes an extension to filter on.
FileSelectionDialog - Class in com.compomics.util.gui.file_handling
A simple dialog for selecting between different files.
FileSelectionDialog(JFrame, ArrayList<File>, String) - Constructor for class com.compomics.util.gui.file_handling.FileSelectionDialog
Creates a new FileSelection dialog.
FileSelectionDialog(JDialog, ArrayList<File>, String) - Constructor for class com.compomics.util.gui.file_handling.FileSelectionDialog
Creates a new FileSelection dialog.
FileSystemAccessor - Class in com.compomics.util.io.file
This class serves as a fast OS independent access point to the file system.
FileSystemAccessor() - Constructor for class com.compomics.util.io.file.FileSystemAccessor
Empty constructor.
FileType - Enum in com.compomics.util.pride.prideobjects.webservice.file
An enum of the possible file types for the PRIDE file type options.
Filter - Interface in com.compomics.util.experiment.filtering
Generic interface for a filter.
filterAnnotations(Vector<SpectrumAnnotation>, HashMap<Ion.IonType, HashSet<Integer>>, ArrayList<NeutralLoss>, boolean, boolean, boolean) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Deprecated.
used only in demo classes
FilterDialog - Class in com.compomics.util.gui.filtering
Dialog to edit identification matches filters.
FilterDialog(JDialog, MatchFilter, ArrayList<String>) - Constructor for class com.compomics.util.gui.filtering.FilterDialog
Creates and displays a new dialog.
filterExists(String) - Method in class com.compomics.util.gui.filtering.FilterParameters
Returns a boolean indicating whether the name of this filter is already taken or not.
FilterItem - Interface in com.compomics.util.experiment.filtering
Interface for an item used for filtering.
FilterItemComparator - Enum in com.compomics.util.experiment.filtering
Comparators for filter items.
FilterParameters - Class in com.compomics.util.gui.filtering
This class groups the display filter preferences.
FilterParameters() - Constructor for class com.compomics.util.gui.filtering.FilterParameters
Constructors.
filterTable() - Method in class com.compomics.util.gui.XYPlottingDialog
Filters the selected values table according to the currently selected values and the current data filters.
filterType - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
The type of filter.
finalize() - Method in class com.compomics.util.general.FileLoggerImplementation
Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.
finalize() - Method in class com.compomics.util.gui.JTableForDB
Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.
finalizeFile() - Method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Finalizes the writing of the mzIdentML file.
findDeltaMassMatches(double, double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method attempts to find a list of known mass deltas, corresponding with the specified x value in the given window.
FindPdbForUniprotAccessions - Class in com.compomics.util.pdbfinder
Maps UniProt protein accession numbers to PDB file IDs.
FindPdbForUniprotAccessions() - Constructor for class com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
Empty default constructor
FindPdbForUniprotAccessions(String, WaitingHandler) - Constructor for class com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
Constructor.
finished() - Method in class com.compomics.util.sun.SwingWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
firstIndex(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the first index where the amino acid pattern is found.
firstIndex(AminoAcidSequence, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the first index where the amino acid pattern is found.
firstIndex(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the first index where the amino acid pattern is found.
firstIndex(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the first index where the amino acid pattern is found.
firstIndex(AminoAcidPattern, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the first index where the amino acid pattern is found in the given pattern.
firstIndex(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns the first index where the amino acid sequence is found in the given sequence.
fixedModifications - Variable in class com.compomics.util.experiment.identification.protein_sequences.digestion.ExtendedPeptide
The fixed modifications of the peptide.
Flamable - Interface in com.compomics.util.interfaces
This interface describes the behaviour for classes that can handle unrecoverable errors and exceptions, thrown by child threads etc.
FlamableJFrame - Class in com.compomics.util.gui
FlamableJFrame.
FlamableJFrame() - Constructor for class com.compomics.util.gui.FlamableJFrame
Wrapper constructor for that of the superclass.
FlamableJFrame(String) - Constructor for class com.compomics.util.gui.FlamableJFrame
Wrapper constructor for that of the superclass.
FlamableJFrame(GraphicsConfiguration) - Constructor for class com.compomics.util.gui.FlamableJFrame
Wrapper constructor for that of the superclass.
FlamableJFrame(GraphicsConfiguration, String) - Constructor for class com.compomics.util.gui.FlamableJFrame
Wrapper constructor for that of the superclass.
flanking(PeptideProteinMapping, FastaMapper) - Method in class com.compomics.cli.peptide_mapper.MappingWorker
 
FLOAT_PRECISION - Static variable in class com.compomics.util.BinaryArrayImpl
Defines the valid String indicating the correct precision for encoded floats.
floorDouble(double, int) - Static method in class com.compomics.util.Util
Floors a double value to the wanted number of decimal places.
Fluorine - Class in com.compomics.util.experiment.biology.atoms.impl
The fluorine atom.
Fluorine() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Fluorine
Constructor.
FMIndex - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
The FM index.
FMIndex() - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Empty default constructor.
FMIndex(File, FastaParameters, WaitingHandler, boolean, PeptideVariantsParameters, SearchParameters) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Constructor.
FMIndex(File, FastaParameters, WaitingHandler, boolean, IdentificationParameters) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Constructor.
fmIndexPosition - Variable in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
The position in the FM index.
fmol - Static variable in class com.compomics.util.experiment.units.Units
Femtomol.
FolderMonitor - Class in com.compomics.util.io.file
This class will monitor a specified folder for activity.
FolderMonitor() - Constructor for class com.compomics.util.io.file.FolderMonitor
Empty default constructor
FolderMonitor(File, long, int, HashMap) - Constructor for class com.compomics.util.io.file.FolderMonitor
This constructor allows the creation of a FolderMonitor that will take care of performing a specified action, with the specified parameters, whenever a new file is found.
FolderMonitor(File, long, int, HashMap, Logger) - Constructor for class com.compomics.util.io.file.FolderMonitor
This constructor allows the creation of a FolderMonitor that will take care of performing a specified action, with the specified parameters, whenever a new file is found.
FolderMonitor(File, long, String, int, HashMap) - Constructor for class com.compomics.util.io.file.FolderMonitor
This constructor allows the creation of a FolderMonitor for the specified filtered files that will take care of performing a specified action, with the specified parameters, whenever a new file is found.
FolderMonitor(File, long, String, int, HashMap, Logger) - Constructor for class com.compomics.util.io.file.FolderMonitor
This constructor allows the creation of a FolderMonitor for the specified filtered files that will take care of performing a specified action, with the specified parameters, whenever a new file is found.
FORBIDDEN_CHARACTER - Static variable in class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
Character forbidden in protein sequences, will be removed.
FORBIDDEN_CHARACTERS - Static variable in class com.compomics.util.Util
Forbidden characters in file names.
formatProteinSequence() - Method in class com.compomics.util.examples.UtilitiesDemo
Formats the protein sequence such that both the covered parts of the sequence and the peptide selected in the peptide table is highlighted, and any modifications and variants of a PEFF file.
formatProteinSequence(JEditorPane, String, int[], TreeMap<String, String>, HashMap<String, Color>, boolean, boolean, boolean) - Static method in class com.compomics.util.gui.protein.ProteinSequencePane
Formats the protein sequence such that the covered parts of the sequence is highlighted.
formatProteinSequence(JEditorPane, String, int[]) - Static method in class com.compomics.util.gui.protein.ProteinSequencePane
Formats the protein sequence such that the covered parts of the sequence is highlighted.
formatProteinSequence(JEditorPane, String, int, int, int[]) - Static method in class com.compomics.util.gui.protein.ProteinSequencePane
Formats the protein sequence such that the covered parts of the sequence is highlighted.
formatProteinSequence(JEditorPane, String, ArrayList<Integer>, ArrayList<Integer>, int[]) - Static method in class com.compomics.util.gui.protein.ProteinSequencePane
Formats the protein sequence such that both the covered parts of the sequence and the peptide selected in the peptide table is highlighted.
formatProteinSequence(JEditorPane, String, int, int, int[], TreeMap<String, String>, HashMap<String, Color>) - Static method in class com.compomics.util.gui.protein.ProteinSequencePane
Formats the protein sequence such that both the covered parts of the sequence and the peptide selected in the peptide table is highlighted.
formatTable() - Method in class com.compomics.util.gui.utils.user_choice.list_choosers.ModificationChooser
 
formatTable() - Method in class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
 
formatTable() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
Formats the table.
FORMATTER - Static variable in class com.compomics.software.cli.CommandLineUtils
The format to use for string output.
FORMYL_K - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for formylation of K (PMID: 24895383).
ForwardIonAminoAcidFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Feature based on the amino acid properties of the forward ion.
ForwardIonAminoAcidFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
Empty default constructor
ForwardIonAminoAcidFeature(AminoAcid.Property, AASequenceFeature.Function) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
Constructor.
ForwardIonFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Feature based on a property of the forward ion.
ForwardIonFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
Empty default constructor
ForwardIonFeature(IonFeature.Property) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
Constructor.
forwardSeries - Variable in enum com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator.IonSeries
The forward ion index as listed in the PeptideFragmentIon class.
FractionParameters - Class in com.compomics.util.parameters.identification.advanced
Settings for the handling of fractions.
FractionParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.FractionParameters
Constructor.
FractionParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
FractionSettingsDialog.
FractionParametersDialog(Frame, FractionParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.FractionParametersDialog
Creates a new FractionSettingsDialog with a frame as owner.
FractionParametersDialog(Dialog, Frame, FractionParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.FractionParametersDialog
Creates a new FractionSettingsDialog with a dialog as owner.
fractions - Variable in class com.compomics.util.experiment.identification.IdentificationKeys
The names of the spectrum files (without extensions) that were used for the PSMs.
FragmentAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
Annotator for b and y ions without neutral losses.
FragmentAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotator
Empty default constructor
FragmentAnnotator(Peptide, String[], SimplePeptideAnnotator.IonSeries) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotator
Constructor.
FragmentAnnotator(Peptide, String[], SimplePeptideAnnotator.IonSeries, boolean, boolean) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotator
Constructor.
FragmentAnnotatorNL - Class in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
A fragment annotator for peptide fragment ions with neutral losses.
FragmentAnnotatorNL() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotatorNL
Empty default constructor
FragmentAnnotatorNL(Peptide, String[], SimplePeptideAnnotator.IonSeries, boolean) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotatorNL
Constructor.
FragmentAnnotatorNL(Peptide, String[], SimplePeptideAnnotator.IonSeries, boolean, boolean, boolean) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotatorNL
Constructor.
FragmentationMethod - Enum in com.compomics.util.experiment.mass_spectrometry
Enum for the different fragmentation methods.
fragmentFactory - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The Fragment factory which will generate the fragment ions.
FragmentIonTable - Class in com.compomics.util.gui.spectrum
Creates a fragment ion table with the detected fragment ions.
FragmentIonTable() - Constructor for class com.compomics.util.gui.spectrum.FragmentIonTable
Empty default constructor
FragmentIonTable(Peptide, ArrayList<IonMatch[]>, HashSet<Integer>, NeutralLossesMap, boolean, boolean, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Constructor for class com.compomics.util.gui.spectrum.FragmentIonTable
Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.
FragmentIonTable(Peptide, ArrayList<IonMatch[]>, ArrayList<Spectrum>, HashSet<Integer>, NeutralLossesMap, boolean, boolean, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Constructor for class com.compomics.util.gui.spectrum.FragmentIonTable
Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type.
FragmentIonTableCellRenderer - Class in com.compomics.util.gui.renderers
A cell renderer to use for the FragmentIonTable making it possible to highlight certain cells.
FragmentIonTableCellRenderer() - Constructor for class com.compomics.util.gui.renderers.FragmentIonTableCellRenderer
Empty default constructor
FragmentIonTableCellRenderer(ArrayList<Integer>, Color, Color) - Constructor for class com.compomics.util.gui.renderers.FragmentIonTableCellRenderer
Creates a new FragmentIonTableCellRenderer.
FragmentItensityPredictor - Class in com.compomics.util.experiment.identification.peptide_fragmentation
Predictor for the peptide fragment intensity.
FragmentItensityPredictor() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.FragmentItensityPredictor
Empty default constructor
FragmentItensityPredictor(PeptideFragmentationModel) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.FragmentItensityPredictor
Constructor.
FrameExceptionHandler - Class in com.compomics.util.exceptions.exception_handlers
Handles exception for a given application and displays warnings using dialogs.
FrameExceptionHandler() - Constructor for class com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler
Empty default constructor
FrameExceptionHandler(JFrame, String) - Constructor for class com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler
Constructor.
fromJson(Class, String) - Method in class com.compomics.util.io.json.JsonMarshaller
Convert from JSON to object.
fromJson(Class, File) - Method in class com.compomics.util.io.json.JsonMarshaller
Convert from JSON to object.
fromJson(Class, URL) - Method in class com.compomics.util.io.json.JsonMarshaller
Convert from JSON to object.
fromJson(Type, String) - Method in class com.compomics.util.io.json.JsonMarshaller
Convert from JSON to object.
fromJson(Type, File) - Method in class com.compomics.util.io.json.JsonMarshaller
Convert from JSON to object.
fromJson(Type, URL) - Method in class com.compomics.util.io.json.JsonMarshaller
Convert from JSON to object.
FTP - Class in com.compomics.util.io.ftp
This class was modified from a source found on the net (java.sun.com, search in developer section on 'FtpProtocolException PORT').
FTP() - Constructor for class com.compomics.util.io.ftp.FTP
Empty default constructor
FTP(String) - Constructor for class com.compomics.util.io.ftp.FTP
Constructor for an FTP client connected to host host.
FTP(String, int) - Constructor for class com.compomics.util.io.ftp.FTP
Constructor for an FTP client connected to host host and port port.
FTP_PORT - Static variable in class com.compomics.util.io.ftp.FTP
FTP port to use for connection.
FTP_TO_SPECIFIED_DESTINATION - Static variable in class com.compomics.util.io.file.FolderMonitor
 
FTPClient - Class in com.compomics.util.io.ftp
This class implements a 'directory listener' to listen for new files and ftp them to a remote FTP server.
FTPClient() - Constructor for class com.compomics.util.io.ftp.FTPClient
Empty default constructor
FTPClient(String, String, String) - Constructor for class com.compomics.util.io.ftp.FTPClient
Constructor that takes the three parameters necessary for the FTP connection.
FtpConnectionException - Exception in com.compomics.util.io.ftp
This class handles an FTP connection exception.
FtpConnectionException() - Constructor for exception com.compomics.util.io.ftp.FtpConnectionException
Empty default constructor
FTPDownloader - Class in com.compomics.util.io.ftp
A simple FTP file downloader.
FTPDownloader() - Constructor for class com.compomics.util.io.ftp.FTPDownloader
Empty default constructor
FTPDownloader(String) - Constructor for class com.compomics.util.io.ftp.FTPDownloader
Set up an anonymous FTP connection (without protocol commands printed).
FTPDownloader(String, boolean) - Constructor for class com.compomics.util.io.ftp.FTPDownloader
Set up an anonymous FTP connection.
FTPDownloader(String, String, String, boolean) - Constructor for class com.compomics.util.io.ftp.FTPDownloader
Set up an FTP connection.
FtpLoginException - Exception in com.compomics.util.io.ftp
This class handles an FTP login exception.
FtpLoginException() - Constructor for exception com.compomics.util.io.ftp.FtpLoginException
Empty default constructor
FtpProtocolException - Exception in com.compomics.util.io.ftp
This class handles an FTP protocol exception.
FtpProtocolException() - Constructor for exception com.compomics.util.io.ftp.FtpProtocolException
Empty default constructor
FULL_NAME - Variable in enum com.compomics.util.experiment.units.StandardUnit
The full name of the unit.
fullName - Variable in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
The full name of the database.
FULLY_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
 
function - Variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
The function used to compare the amino acid properties.

G

G - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
GATHER_FILES_FOR_PICKUP - Static variable in class com.compomics.util.io.file.FolderMonitor
 
GENE_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
The suffix to use for files containing gene mappings.
GeneDetailsDialog - Class in com.compomics.util.gui.genes
This dialog displays the gene details associated to a protein match.
GeneDetailsDialog(Frame, ProteinMatch, GeneMaps, ProteinDetailsProvider) - Constructor for class com.compomics.util.gui.genes.GeneDetailsDialog
Creates a new GeneDetailsDialog.
GeneMapping - Class in com.compomics.util.experiment.biology.genes.ensembl
Class for the handling of gene mappings.
GeneMapping() - Constructor for class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
Constructor.
GeneMaps - Class in com.compomics.util.experiment.biology.genes
The gene maps for a given project.
GeneMaps() - Constructor for class com.compomics.util.experiment.biology.genes.GeneMaps
Creates new maps.
GeneParameters - Class in com.compomics.util.parameters.identification.advanced
Contains methods for downloading gene and GO mappings.
GeneParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.GeneParameters
Create a new GenePreferences object.
GeneParameters(GeneParameters) - Constructor for class com.compomics.util.parameters.identification.advanced.GeneParameters
Creates new gene preferences based on a GenePreferences object.
GeneParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
Dialog for editing the Gene Mapping Preferences.
GeneParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
Empty default constructor
GeneParametersDialog(JFrame, GeneParameters, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
Creates a new GenePreferencesDialog with a frame as owner.
GeneParametersDialog(JDialog, Frame, GeneParameters, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
Creates a new GenePreferencesDialog with a dialog as owner.
generateDecoy() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns whether a decoy database shall be created and searched against.
generateQuery() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Returns a boolean indicating whether a blast query shall be generated.
GeneratorException - Exception in com.compomics.util.db
This class wraps all exception that can occur while generating code.
GeneratorException() - Constructor for exception com.compomics.util.db.GeneratorException
Empty default constructor
GeneratorException(String) - Constructor for exception com.compomics.util.db.GeneratorException
This constructor creates an exception with just a message.
GeneratorException(String, Exception) - Constructor for exception com.compomics.util.db.GeneratorException
This constructor creates an exception with a message and a nested exception.
GenericFastaConverter - Class in com.compomics.util.experiment.io.biology.protein.converters
This converter writes a FASTA file with standardized headers.
GenericFastaConverter() - Constructor for class com.compomics.util.experiment.io.biology.protein.converters.GenericFastaConverter
 
genericMzId - Static variable in class com.compomics.util.experiment.identification.Advocate
Advocate type for mzId files where no software is annotated.
get() - Method in class com.compomics.util.sun.SwingWorker
Return the value created by the construct method.
getAaAfter(Peptide, String, int, int, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the amino acids before the given peptide as a string.
getAaAfter(Peptide, int, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.
getAaBefore(Peptide, String, int, int, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.
getAaBefore(Peptide, int, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.
getAACoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates the validation level of every amino acid in the given protein.
getAaIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
Returns the index on the sequence.
getAaIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
Returns the index on the sequence.
getAaNumber(int) - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Returns the 1 based index of the amino acid which generated this ion.
getAaSubstitutionMatrix() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns the amino acid substitution matrix to use.
getAaTargeted() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the map of targeted amino acids.
getAbbreviatedFASTAHeader() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method returns an abbreviated version of the Header, suitable for inclusion in FASTA formatted files.
getAbbreviatedFASTAHeader(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method returns an abbreviated version of the Header, suitable for inclusion in FASTA formatted files.
getAbbreviatedFASTAHeaderWithAddenda() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method returns an abbreviated version of the Header, suitable for inclusion in FASTA formatted files.
getAbbreviation() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
Returns the abbreviated name of the unit.
getAbsoluteError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the absolute matching error in Da.
getAbsoluteError(int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the absolute matching error in Da after isotope removal.
getAbsoluteFilePath() - Method in class com.compomics.software.autoupdater.MavenJarFile
Returns the absolute file path.
getAccession() - Method in class com.compomics.util.experiment.biology.proteins.Protein
Getter for the protein accession.
getAccession() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the accession.
getAccession() - Method in class com.compomics.util.pride.CvTerm
Returns the accession.
getAccessionOrRest() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the accession or if this is null the rest.
getAccessions() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns the accessions of the proteins in this match.
getAccessions() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getAccessions() - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
 
getAccessions() - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
Returns all accessions loaded in the provider.
getAccountedNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Returns an arraylist of the names of the implemented neutral losses.
getActicationType() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Returns the activation type.
getAddenda() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method allows the caller to retrieve all addenda for the current header, or 'null' if there aren't any.
getAdvocate(int) - Static method in class com.compomics.util.experiment.identification.Advocate
Returns the advocate corresponding to the given index.
getAdvocate(String) - Static method in class com.compomics.util.experiment.identification.Advocate
Returns the advocate with the given name.
getAdvocate() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Get the used advocate.
getAdvocateColorMap() - Static method in class com.compomics.util.experiment.identification.Advocate
Returns the advocate color map.
getAdvocateFromFile(String) - Static method in class com.compomics.util.experiment.identification.Advocate
Deprecated.
no longer used
getAdvocates() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns the advocates supporting hits for this spectrum.
getAdvocates() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Returns the advocates with a specific scoring.
getAdvocateToolTipMap() - Static method in class com.compomics.util.experiment.identification.Advocate
Returns the advocate tool tip map.
getAlgorithm() - Method in interface com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter
Returns the identification algorithm.
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
 
getAlgorithm() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
 
getAlgorithmDeltaPEP() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the difference in identification algorithm level PEP with the next best peptide assumption with sequence difference for the given search engine.
getAlgorithms() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the algorithms for which specific parameters are stored.
getAlgorithmSpecificParameters() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the algorithm specific parameters in a map: algorithm as indexed in the Advocate class > parameters.
getAlignmentBlocks() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Returns the alignment blocks.
getAlignNonConfidentModifications() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Indicates whether the non confidently localized modifications should be aligned on the confident sites.
getAllAlignments() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader
Get all alignments in the json string.
getAllFeatures() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
Get all features in the XML string.
getAllIsotopicElements(Class, Logger) - Static method in class com.compomics.util.general.IsotopicElement
Static method that gives all the isotopicElements from the isotopicElement.txt file
getAllModifications(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns a set of the names of all modifications found on a peptide.
getAllModifications(Tag, ModificationParameters, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns a set of the names of all modifications found on a tag.
getAllModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns a list of all searched modifications.
getAllModificationTitles() - Static method in class com.compomics.util.protein.ModificationFactory
This method returns all modification titles known to the Factory.
getAllNotFixedModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns a list of all searched modifications but the fixed ones.
getAllocatedBytes() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Computes the number of allocated bytes.
getAllocatedBytes() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Returns the number of bytes for the allocated arrays.
getAllocatedBytes() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Returns the number of bytes for the allocated arrays.
getAllPeptideAssumptions(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns all peptide assumptions for the specified search engine indexed by their score.
getAllPeptideAssumptions() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns a stream of all peptide assumptions
getAllPossibleSequences() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns all possible sequences which can be obtained from the targeted amino acids.
getAllProperties() - Method in interface com.compomics.util.db.interfaces.DBElement
This method will return a HashMap with all the properties for this DBElement.
getAllPtmLocations() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the sites of all localized PTMs.
getAllReferenceAreasXAxis() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns all the x-axis references areas as a hashmap, with the labels as the keys.
getAllReferenceAreasYAxis() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns all the y-axis references areas as a hashmap, with the labels as the keys.
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.It is very important to close the file reader after creation.
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
 
getAllSpectrumMatches(SpectrumProvider, WaitingHandler, SearchParameters, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
 
getAllTableColumns() - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
Returns all the table columns, both visible and hidden.
getAllTableColumns() - Method in class com.compomics.util.gui.XYPlottingDialog
 
getAllTagAssumptions(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns all tag assumptions for the specified search engine indexed by their score.
getAllTagAssumptions() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns a stream of all tag assumptions
getAlpha() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Get the alpha level (transparency).
getAlphaLevel() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the alpha level.
getAmbiguityKey() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the ambiguity key.
getAmbiguouslyLocalizedModifications() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns a list of modifications presenting at least an ambiguous site.
getAmbiguousModificationsAtRepresentativeSite(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns the ambiguous modification assignments registered at the given representative site in a map: secondary site > modifications.
getAmbiguousModificationSiteNumber(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns a summary of the number of modifications present on the sequence ambiguously assigned to an amino acid grouped by representative site followed by secondary ambiguous sites.
getAmbiguousModificationSiteNumber(IdentificationMatch, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns a summary of the number of modifications present on the sequence ambiguously assigned to an amino acid grouped by representative site followed by secondary ambiguous sites.
getAmbiguousModificationSites(IdentificationMatch, String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns a list of the modifications present on the sequence ambiguously assigned to an amino acid grouped by representative site followed by secondary ambiguous sites.
getAmbiguousModificationSites(IdentificationMatch, String, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns a list of the modifications present on the sequence ambiguously assigned to an amino acid grouped by representative site followed by secondary ambiguous sites.
getAmbiguousModificationsSites(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns the ambiguous modification sites registered for the given modification.
getAminoAcid(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the amino acid corresponding to the letter given.
getAminoAcid(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the amino acid corresponding to the single letter code given.
getAminoAcid() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
Returns the amino acid targeted represented as single letter code.
getAminoAcidAfter() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Getter for the amino acids potentially following the cleavage.
getAminoAcidAt(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns the amino acid at the given index on the sequence.
getAminoAcidBefore() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Getter for the amino acids potentially preceding the cleavage.
getAminoAcidCombinations(int) - Static method in class com.compomics.util.experiment.identification.TagFactory
Returns all the amino acid combinations for a given tag length.
getAminoAcidFeature1() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
Returns the first amino acid feature.
getAminoAcidFeature2() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
Returns the second amino acid feature.
getAminoAcidFromGeneticCode(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the amino acid from the standard genetic code.
getAminoAcidPatternFromString(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Parses the amino acid pattern from the given string as created by the toString() method.
getAminoAcidPatternFromString(String, int) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Parses the amino acid pattern from the given string as created by the toString() method.
getAminoAcidProperties() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
 
getAminoAcidProperties() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.MultipleAAPropertyFeature
Returns the amino acid properties to consider.
getAminoAcidProperty() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
 
getAminoAcidProperty() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
 
getAminoAcidProperty() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.SingleAAPropertyFeature
Returns the amino acid property to consider.
getAminoAcids() - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Convenience method returning an array of all implemented amino acids represented by their singe letter code.
getAminoAcidsAtTarget() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the targeted amino acids at position "target".
getAminoAcidsAtTargetSet() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns a set containing the amino acids at target.
getAminoAcidScores() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the amino acid scores.
getAminoAcidsList() - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Convenience method returning an arrayList of all implemented amino acids.
getAnnotationIntensityLimit() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the intensity percentile to consider for annotation.
getAnnotationParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the annotation parameters used for identification.
getAnnotationSettings() - Method in class com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog
Returns the annotation settings as set by the user.
getApplicationFolder(CompomicsTools) - Method in class com.compomics.util.io.PropertiesManager
Get the application folder that contains the appropriate properties.
getAreaColor() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Get the area color.
getAreaUnderCurveColors() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the list of colors used for the datasets.
getArray(int) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns an array containing only the given index.
getArtifactId() - Method in class com.compomics.software.autoupdater.MavenJarFile
Returns the artifact id.
getAs() - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns a histogram of the as found in the previously interpolated scores.
getAscii(String) - Method in class com.compomics.util.io.ftp.FTP
GET a file from the FTP server in Ascii mode.
getAssayCount(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns the assay count for a given project.
getAssayDetail(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns the assay details for a given assay.
getAssayDetailList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
Convert from JSON to a list of AssaytDetails.
getAssayDetails(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns the assay details for a given project.
getAssayFileCount(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of file details for a given assay.
getAssayFileDetails(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of file details for a given assay.
getAssembly(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
Returns the Ensembl assembly corresponding to the given NCBI taxon.
getAssembly(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
Returns the Ensembl assembly corresponding to the given NCBI taxon.
getAsStringPattern(SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the amino acid pattern as case insensitive pattern for String matching.
getAssumptionFilter() - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
Returns the filter used to filter at the assumption level.
getAtom(String) - Static method in class com.compomics.util.experiment.biology.atoms.Atom
Returns the atom corresponding to the given short name.
getAtom() - Method in class com.compomics.util.gui.atoms.AtomPanel
Returns the currently selected atom.
getAtomChain(String) - Static method in class com.compomics.util.experiment.biology.atoms.AtomChain
Returns an atom chain from the input as string.
getAtomChain() - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Returns the atom chain as a list of AtomImpl.
getAtomChainAdded() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the atom chain added.
getAtomChainAdded() - Method in class com.compomics.util.gui.atoms.AtomChainDialog
Returns the added atom chain as edited by the user.
getAtomChainRemoved() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the atom chain removed.
getAtomChainRemoved() - Method in class com.compomics.util.gui.atoms.AtomChainDialog
Returns the removed atom chain as edited by the user.
getAtomicComposition() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the atomic composition.
getAtomSymbol() - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
Returns the atom symbol as specified in the Atom class.
getAuc() - Method in class com.compomics.util.math.roc.DataRoc
 
getAuc() - Method in class com.compomics.util.math.roc.DistributionRoc
 
getAuc() - Method in interface com.compomics.util.math.statistics.ROC
Returns an estimation of the area under the curve.
getAutoUpdate() - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Indicates whether the gene mappings should be automatically updated.
getAverageMassDelta(String) - Method in interface com.compomics.util.interfaces.Modification
This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue.
getAverageMassDelta(String) - Method in class com.compomics.util.protein.ModificationImplementation
This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue.
getAverageMassDelta(String) - Method in class com.compomics.util.protein.ModificationTemplate
This method returns a double with the average mass difference conferred on the sequence by this modification for the specified residue.
getBackedUpModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns the modifications backed-up as a map.
getBackgroundPeakWidth() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the current width of the background peaks.
getBackgroundSpecies() - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Returns the taxon of the species selected as background species.
getBase64String() - Method in class com.compomics.util.BinaryArrayImpl
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the basicity according to PMID 14730315.
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getBasicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getBatchSize() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the batch size.
getBestPeptideAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Getter for the best peptide assumption.
getBestTagAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Getter for the best tag assumption.
getBin(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the bin corresponding to the given m/z.
getBinary(String) - Method in class com.compomics.util.io.ftp.FTP
GET a file from the FTP server in Binary mode.
getBinaryDataAsNumberArray(String, MzmlFileIterator.Precision, byte[]) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator
Retrieve the binary data as an array of numeric values.
getBinMax() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the highest bin.
getBinMin() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the lowest bin.
getBinnedCumulativeProbability(double) - Method in class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
Get the binned cumulative probability.
getBinnedCumulativeProbabilityLog(double) - Method in class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
Get the binned logged cumulative probability.
getBins() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
Returns the bins in the map.
getBins() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the bins in the map as a list.
getBiomartEnsemblGenomeMappingFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Ensembl Genome BioMart file.
getBiomartEnsemblMappingFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Ensembl BioMart file.
getBiomartMapping() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the BioMart mapping.
getBlob - Variable in class com.compomics.util.db.object.objects.BlobObject
Object representation of the blob.
getBlob() - Method in class com.compomics.util.db.object.objects.BlobObject
Returns the byte representation of the object.
getBlock() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Returns the block.
getBlocks() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Returns the blocks.
getBlockSequence(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Get the blocked sequence.
getBorderColor() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns the border color.
getBorderWidth() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns the border width.
getBs() - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns a histogram of the bs found in the previously interpolated scores.
getCacheSize() - Method in class com.compomics.util.db.object.ObjectsCache
Returns the cache size in number of objects.
getCategories() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
Returns the different categories of the features in this map.
getCategoriesAsString() - Static method in enum com.compomics.util.experiment.biology.modifications.ModificationCategory
Returns all of the modification category options as a string.
getCategory() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the modification category.
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
 
getCategory() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
 
getCategory() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
Returns the category of the feature.
getCharacterInfo(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Returns the character and rank at a given index.
getCharge() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Getter for the charge
getCharge() - Method in interface com.compomics.util.interfaces.SpectrumFile
This method reports on the charge of the precursor ion.
getChargeAsFormattedString(int) - Static method in class com.compomics.util.experiment.biology.ions.Charge
Returns the charge as a string of + or -.
getChargePrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the pride CV term for the ion match charge.
getChartPanel() - Method in class com.compomics.util.gui.spectrum.IntensityHistogram
Returns the chart panel.
getChartPanel() - Method in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Returns the chart panel.
getChartPanel() - Method in class com.compomics.util.gui.spectrum.MassErrorPlot
Returns the chart panel.
getChartPanel() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the chart panel.
getChoice() - Method in class com.compomics.util.gui.SampleSelection
Getter for the users choice.
getChromosome(String) - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
Returns the chromosome for a given gene.
getChromosome(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the chromosome corresponding to a given gene name.
getClassInCache(Class) - Method in class com.compomics.util.db.object.ObjectsCache
Returns the class type of the objects in cache.
getClassObjectIDs(Class) - Method in class com.compomics.util.db.object.ObjectsDB
Returns an iterator of all objects of a given class.
getClassObjectIDs(Class, String) - Method in class com.compomics.util.db.object.ObjectsDB
Returns an iterator of all objects of a given class.
getClassObjects(Class) - Method in class com.compomics.util.experiment.identification.Identification
Returns the keys of the objects of the given class,
getClassObjects(Class, String) - Method in class com.compomics.util.experiment.identification.Identification
Returns the keys of the objects of the given class,
getClassSizeMultiplier() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the intensity class size multiplier.
getCleavage(int) - Method in class com.compomics.util.protein.DualEnzyme
This method returns the residues that are used for cleavage at the respective locations.
getCleavage() - Method in class com.compomics.util.protein.DualEnzyme
Simple getter for the cleavable residues of the Enzyme.
getCleavage() - Method in class com.compomics.util.protein.Enzyme
Simple getter for the cleavagable residues of the Enzyme.
getCleavage() - Method in class com.compomics.util.protein.RegExEnzyme
 
getCleavageParameter() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Returns the cleavage parameters.
getCleavageParameters(int) - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
Returns the cleavage parameter of the given index.
getClipNtermMethionine() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns if the starting methionine peptides will be included both with and without the starting M.
getClusterMembers(int) - Method in class com.compomics.util.math.clustering.KMeansClustering
Get the sample names of all the members in the given cluster.
getClusterMembersData(int) - Method in class com.compomics.util.math.clustering.KMeansClustering
Returns a hashmap with the values for the members in the given cluster.
getCmsFilePath(File, File) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
Returns the path of the cms file expected for the given mass spectrometry file and cms folder.
getCmsFilePaths() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getCmsFilePaths() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getCmsFilePaths() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the absolute path to the cms file indexed by ms file name without file extension.
getCode() - Method in interface com.compomics.util.interfaces.Modification
This method returns the short code for the modification, eg.
getCode() - Method in class com.compomics.util.protein.ModificationImplementation
This method returns the short code for the modification, eg.
getCode() - Method in class com.compomics.util.protein.ModificationTemplate
This method returns the short code for the modification, eg.
getCodedColumnType(String) - Method in class com.compomics.util.db.DBMetaData
This method returns the coded column type for the specified column.
getCodedColumnType(int) - Method in class com.compomics.util.db.DBMetaData
This method returns the coded columntype for the specified column index.
getCodedColumnTypes() - Method in class com.compomics.util.db.DBMetaData
This method reports on all the coded column types.
getColor(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the color used to code the given modification.
getColor() - Method in class com.compomics.util.experiment.identification.Advocate
Returns the color of the advocate.
getColor() - Method in interface com.compomics.util.gui.interfaces.SpectrumAnnotation
This method returns the color for the annotation.
getColor() - Method in class com.compomics.util.gui.protein.ModificationProfile
Returns the PTM color.
getColor() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
This method returns the color for the annotation.
getColor(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns the color used to code the given modification.
getColor(int) - Static method in class com.compomics.util.Util
Returns the color object corresponding to the given rgb representation.
getColors() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns the modification colors as a map.
getColummnNames() - Method in class com.compomics.util.gui.XYPlottingDialog
Return the column names.
getColumn(int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getColumnClass(int) - Method in class com.compomics.util.db.DBResultSet
Returns Object.class regardless of columnIndex.
getColumnClass(int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
 
getColumnClass(int) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
 
getColumnClass(int) - Method in class com.compomics.util.sun.TableMap
 
getColumnCount() - Method in class com.compomics.util.db.DBMetaData
This method returns the column count for this table.
getColumnCount() - Method in class com.compomics.util.db.DBResultSet
This method reports on the number of columns in the resultset.
getColumnCount() - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
 
getColumnCount() - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
 
getColumnCount() - Method in class com.compomics.util.sun.TableMap
 
getColumnName(int) - Method in class com.compomics.util.db.DBMetaData
This method returns the name of the specified column.
getColumnName(int) - Method in class com.compomics.util.db.DBResultSet
Returns a default name for the column using spreadsheet conventions: A, B, C, ...
getColumnName(int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
 
getColumnName(int) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
 
getColumnName(int) - Method in class com.compomics.util.sun.TableMap
 
getColumnNames() - Method in class com.compomics.util.db.DBMetaData
This method reports on all the column names.
getColumnNames() - Method in class com.compomics.util.db.DBResultSet
This method reports on all the columnn ames.
getColumns() - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getColumnSize(String) - Method in class com.compomics.util.db.DBMetaData
This method returns the column size for the specified column.
getColumnSize(int) - Method in class com.compomics.util.db.DBMetaData
This method returns the column size for the specified column index.
getColumnSizes() - Method in class com.compomics.util.db.DBMetaData
This method reports on all the column sizes.
getCombination(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the number of k-combinations in a set of n elements.
getCombination(BigInteger, BigInteger) - Static method in class com.compomics.util.math.BigFunctions
Returns the number of k-combinations in a set of n elements as a big decimal.
getCombinationDouble(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the number of k-combinations in a set of n elements.
getCombinations() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the amino acids combinations which might represent this amino acid.
getCombinations(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns a list of all combinations which can be created from a sequence when expanding ambiguous amino acids like Xs.
getCommandLineArgument(ArrayList<File>) - Static method in class com.compomics.software.cli.CommandLineUtils
Returns the list of file as argument for the command line.
getCommandLineArgument(File) - Static method in class com.compomics.software.cli.CommandLineUtils
Returns the file as argument for the command line.
getCommandLineDescription() - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
Returns the different options as command line description.
getCommandLineDescription() - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
Returns the different options as command line description.
getCommandLineOption() - Static method in enum com.compomics.util.io.export.ExportFormat
Returns the command line description when the format is used as command line argument.
getCommandLineOptions() - Static method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
Returns the different implemented scores as list of command line option.
getCommandLineOptions() - Static method in enum com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters.IntensityThresholdType
Returns the different intensity threshold types as command line options description.
getCommandLineOptions() - Static method in enum com.compomics.util.experiment.io.identification.MzIdentMLVersion
Returns a string describing the different options.
getCommandLineOptions() - Static method in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
Returns the different matching types as command line options description.
getCommandLineOptions() - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
Convenience method returning all possibilities in a command line option description format.
getCommonName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
Returns the common name corresponding to the given NCBI taxon.
getCommonName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
Returns the common name corresponding to the given NCBI taxon.
getComparatorForItem(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns the comparator set for a given filtering item.
getComplementaryIonsFeatures(Peptide, int, int, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation.FeaturesGenerator
Returns the ms2pip features for the complementary ions of the given peptide at the given charge.
getComplementMzTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the complement m/z tolerance.
getComplementScoreWeight() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the complement score weight.
getComposition() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
The composition of the loss.
getComputeExactPValues() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the exact p-values are to be computed.
getComputeSpScore() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true of the SP score is to be computed.
getComputeXCorr() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns true if a Sequest-like cross correlation score will be calculated for the top ranking hits in each spectrum’s result set.
getConcatenatTargetDecoy() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the target and decoy results are to be concatenated.
getCondition() - Method in interface com.compomics.util.experiment.filtering.Filter
Returns a description of the condition to match for the filter to validate.
getCondition() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
 
getConfidence() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the confidence.
getConfidenceLevel(int) - Static method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Convenience method returning the given confidence level as a string.
getConfidenceMargin() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Returns the margin to the threshold to use as factor of the resolution.
getConfidenceThreshold() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns the confidence below which a peptide is considered absent.
getConfident() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Returns a boolean indicating whether the modification is confidently localized on the sequence.
getConfidentlyLocalizedModifications() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns a list of modifications presenting at least a confident site.
getConfidentModificationsAt(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns the main potential modifications at the given amino acid index.
getConfidentModificationSites(IdentificationMatch, String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns a summary of all modifications present on the sequence confidently assigned to an amino acid.
getConfidentModificationSites(IdentificationMatch, String, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns a summary of the modifications present on the peptide sequence confidently assigned to an amino acid with focus on given list of modifications.
getConfidentModificationSitesNumber(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of confidently localized variable modifications.
getConfidentModificationSitesNumber(IdentificationMatch, ArrayList<String>) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of confidently localized variable modifications.
getConfidentPtmLocations() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the confidently and very confidently localized PTMs.
getConfidentSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns a list of all confident modification sites.
getConfidentSitesForModification(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns the confident sites for the given modification.
getConsecutiveIonProbability() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the consecutive ion probability.
getContactGroups() - Method in class com.compomics.util.pride.PrideObjectsFactory
Returns the contact groups.
getContacts() - Method in class com.compomics.util.pride.prideobjects.ContactGroup
Returns the contacts.
getContent() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the content of this tag as a list.
getContentPane() - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
This methods gives a JPanel holding everything from this frame
getControlSamples() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Returns the indexes of the samples labeled as control.
getConvertedColumnType(String) - Method in class com.compomics.util.db.DBMetaData
This method returns the converted column type for the specified column.
getConvertedColumnType(int) - Method in class com.compomics.util.db.DBMetaData
This method returns the converted columntype for the specified column index.
getConvertedColumnTypes() - Method in class com.compomics.util.db.DBMetaData
This method reports on all the converted column types.
getCopyRight() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the copyright.
getCoreHeader() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method reports on the core information for the header, which is comprised of the ID and the accession String:
getCorrelation(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the population Pearson correlation r between series1 and series2.
getCoverableAA(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns an array of the likelihood to find identify a given amino acid in the protein sequence.
getCoveredAminoAcids(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence.
getCreationTime() - Method in class com.compomics.util.experiment.ProjectParameters
 
getCtermAsString(boolean, int, String[]...) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the C-terminal annotation as string.
getCTerminal(boolean, ModificationParameters, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the C-terminal tag of this tag as a string for sequence display.
getCTerminalGap() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the C-terminal gap of the tag.
getcTermModification() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the C-term modification.
getCtermModification(PeptideDraft, String, int) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns the c-terminal modification for the given peptide draft.
getCTermTruncatedProtein(int) - Method in class com.compomics.util.protein.Protein
This method truncates the sequence for this protein on the C-terminus to the requested size.
getCTermTruncatedSequence(int) - Method in class com.compomics.util.protein.AASequenceImpl
This method will return an AASequenceImpl that represents a C-terminal truncation of the current sequence.
getCumulativeProbabilityAt(double) - Method in interface com.compomics.util.math.statistics.Distribution
Returns the cumulative density function value at a given position.
getCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
 
getCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
 
getCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
 
getCurrentAdded() - Method in class com.compomics.util.db.object.ObjectsDB
Getter for the current number of added objects.
getCurrentAnnotation(String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
 
getCurrentAnnotation(String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
 
getCurrentAnnotation(String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the currently matched ions with the given settings using the intensity filter.
getCurrentAnnotation(String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the currently matched ions with the given settings.
getCurrentEnsemblVersion(EnsemblGenomesSpecies.EnsemblGenomeDivision) - Static method in class com.compomics.util.experiment.biology.genes.ensembl.EnsemblVersion
Returns the current Ensembl version number.
getCurrentlyLoadedPeptide() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the currently inspected peptide.
getCurrentlyLoadedSpectrumFile() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the file of the spectrum currently inspected.
getCurrentlyLoadedSpectrumTitle() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the title of the spectrum currently inspected.
getCurrentPeptideKey() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns the current peptide key.
getCurrentProteinKey() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns the current protein key.
getCurrentVennDiagramType() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the current Venn diagram type.
getCvTerm() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Returns the CV term associated with this enzyme.
getCVTerm(String) - Method in class com.compomics.util.pride.PtmToPrideMap
Returns the CV term corresponding to the given PTM name.
getCvTerms() - Method in class com.compomics.util.pride.prideobjects.Instrument
Returns the CV terms.
getCvTerms() - Method in class com.compomics.util.pride.prideobjects.Protocol
Returns the CV terms.
getCvTerms() - Method in class com.compomics.util.pride.prideobjects.Sample
Returns the CV terms.
getDaltonDifference() - Method in class com.compomics.util.general.IsotopicElement
Getter for the dalton difference with the natural form of this element
getData() - Method in class com.compomics.util.db.DBResultSet
This method reports on the data stored in the resultset.
getData() - Method in class com.compomics.util.gui.renderers.ByteArrayRenderer
This method returns the data that is currently cached by the renderer.
getDatabaseDirectory() - Method in class com.compomics.util.experiment.identification.Identification
Returns the database directory.
getDatabaseType() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the database type as inferred from the header structure.
getDatabaseTypeAsString(ProteinDatabase) - Static method in class com.compomics.util.experiment.io.biology.protein.Header
Convenience method returning the database name as a String.
getDatabaseTypesAsString() - Static method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the implemented database types as an array of String.
getDataEndian() - Method in class com.compomics.util.BinaryArrayImpl
Returns the endian value of the binary array (mzData element .../data/endian).
getDataFilters() - Method in class com.compomics.util.gui.XYPlottingDialog
Return the data filters.
getDataFormats(Boolean, Boolean) - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
Returns a list of formats.
getDataLength() - Method in class com.compomics.util.BinaryArrayImpl
Returns the length of the binary array (mzData element .../data/length).
getDataPrecision() - Method in class com.compomics.util.BinaryArrayImpl
Returns the precision of the binary array (mzData element .../data/precision).
getDataset(String) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
Returns the Ensembl dataset for the given assembly.
getDaTolerance(double, double) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the absolute tolerance in Dalton corresponding to the relative tolerance in ppm at the given reference mass.
getDB() - Method in class com.compomics.util.db.object.ObjectsDB
Getter for the persistence manager.
getDbFile() - Method in class com.compomics.util.db.object.ObjectsDB
Getter for the database file.
getDbFolder() - Method in class com.compomics.util.db.object.ObjectsDB
Getter for the database folder.
getDbFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the last used database folder.
getDbSummaryFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the folder where FASTA files summary statistics are stored.
getDecodedByteArray() - Method in class com.compomics.util.BinaryArrayImpl
Returns the contents of the binary array decoded using the Base64 algorithm.
getDeconvolutionIntensityRatio() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the deconvolution intensity ratio.
getDeconvolutionMassTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the deconvolution mass tolerance.
getDeconvolutionMassToleranceType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the deconvolution mass tolerance type.
getDecoyAccessions() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getDecoyAccessions() - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
 
getDecoyAccessions() - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
Returns the decoy accessions.
getDecoyFlag() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Returns the decoy flag.
getDecoyFormat() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the decoy format.
getDecoyMode() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the decoy mode.
getDecoyParameters(FastaParameters) - Static method in class com.compomics.util.experiment.io.biology.protein.converters.DecoyConverter
Returns the FASTA parameters of the target-decoy database based on the parameters of the target database.
getDecoySeed() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the decoy seed.
getDecoysInFirstBin() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Returns the minimal number of decoys to include in a bin to set the bin size of the score histogram.
getDecoySummary(File, FastaSummary) - Static method in class com.compomics.util.experiment.io.biology.protein.converters.DecoyConverter
Returns the FASTA summary of the target-decoy database based on the summary of the target database.
getDecoyType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the decoy type.
getDecreasingScore(Peptide, int, String, String, Spectrum, IdentificationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, PeptideSpectrumAnnotator, int) - Method in class com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
Scores the match between the given peptide and spectrum using the given score.
getDefaultColor(String) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns a default color based on the modification name.
getDefaultCVTerm(String) - Static method in class com.compomics.util.pride.PtmToPrideMap
Deprecated.
use the getCvTerm method for the PTM instead
getDefaultDescription() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Indicates whether the description is automatically generated.
getDefaultExportFolder() - Method in class com.compomics.util.gui.VennDiagramDialog
 
getDefaultFeaturesMap() - Static method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMapManager
Returns the default features map used in the c implementation, see https://github.com/mvaudel/ms2pip_c.
getDefaultInstruments() - Static method in class com.compomics.util.pride.prideobjects.Instrument
Returns a list of predefined instruments.
getDefaultLosses(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the possible neutral losses expected by default for a given peptide.
getDefaultLosses(Tag, ModificationParameters, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
Returns the possible neutral losses expected by default for a given tag.
getDefaultLosses(SpectrumIdentificationAssumption, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the possible neutral losses expected by default for a given peptide.
getDefaultModifications() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the names of the default modifications.
getDefaultModificationsOrdered() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the alphabetically (case insensitive) ordered names of the default modifications.
getDefaultNeutralLosses() - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
Returns the default neutral losses.
getDefaultParameters() - Static method in class com.compomics.util.parameters.identification.search.DigestionParameters
Returns default digestion parameters.
getDefaultPeptideFDR() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Returns the default peptide FDR.
getDefaultProteinFDR() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Returns the default protein FDR.
getDefaultProtocols() - Static method in class com.compomics.util.pride.prideobjects.Protocol
Returns a list of default protocols.
getDefaultPsmFDR() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Returns the default PSM FDR.
getDefaultReference(String, String, int) - Static method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Returns the default reference for an identification.
getDefaultReferences() - Static method in class com.compomics.util.pride.prideobjects.ReferenceGroup
Returns the default references.
getDefaultSamples() - Static method in class com.compomics.util.pride.prideobjects.Sample
Returns a list of default samples.
getDefaultScores() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Returns the default scores.
getDefaultSequenceMatching() - Static method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns default preferences from amino acid matching.
getDeisotopingMode() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the deisotoping flag value.
getDeletedAminoAcid() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Deletion
 
getDeltaMass(double, boolean, int, int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the precursor mass error (in ppm or Da).
getDeltaMassWindow() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Get the size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
getDeltaPEP() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the difference in identification algorithm level PEP with the next best peptide assumption with sequence difference across all search engines.
getDeltaScore(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the delta score at a given site.
getDeNovoCharge() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the charge to use for the fragment ions in the de novo sequencing.
getDeNovoGuiPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the path to the DeNovoGUI installation.
getDescendingCumulativeProbabilityAt(double) - Method in interface com.compomics.util.math.statistics.Distribution
Returns the cumulative density function value at a given position when starting from the high values.
getDescendingCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
 
getDescendingCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
 
getDescendingCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
 
getDescription() - Method in interface com.compomics.software.settings.PathKey
Returns the description of the path.
getDescription() - Method in enum com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey
 
getDescription() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Returns the description of the cleavage of this enzyme.
getDescription() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Returns the description of this substitution matrix.
getDescription() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Deletion
 
getDescription() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Insertion
 
getDescription() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
 
getDescription() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Swap
 
getDescription() - Method in interface com.compomics.util.experiment.biology.variants.Variant
Returns the description of the variant as string.
getDescription() - Method in interface com.compomics.util.experiment.filtering.Filter
Returns a description for the filter.
getDescription() - Method in interface com.compomics.util.experiment.filtering.FilterItem
Returns a description of the item.
getDescription() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
 
getDescription() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
 
getDescription() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
 
getDescription() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
 
getDescription() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
 
getDescription() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
 
getDescription() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
Returns the description of the feature.
getDescription(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getDescription() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Returns the description for this database.
getDescription() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the description.
getDescription(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
Returns the description of the protein with the given accession.
getDescription() - Method in class com.compomics.util.experiment.patient.PatientInformation
Returns the description of the information.
getDescription() - Method in interface com.compomics.util.io.export.ExportFeature
Returns the description of the feature.
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
 
getDescription() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
 
getDescription() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
 
getDescription() - Method in class com.compomics.util.io.file.filefilters.DatFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.DtaFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.FastaFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.JpegFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.MgfFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.Ms2FileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.MzDataFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.MzMlFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.MzXmlFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.OmxFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.OutFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.PdfFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.PeffFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.PepXmlFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.PklFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.PklSpoFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.PkxFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.PngFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.ProtXmlFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.SequestParamsFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.SvgFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.TiffFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.filefilters.XmlFileFilter
The description of the filter.
getDescription() - Method in class com.compomics.util.io.file.FilenameExtensionFilter
 
getDescription() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the description of the parameters.
getDescriptionProteinName() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the protein name as inferred from the description.
getDescriptionShort() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the short description.
getDestinationFile() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Returns the file where to save the identification parameters.
getDestinationFile() - Method in class com.compomics.util.io.ftp.FTP
This method reports on the destinationfile currently used in transfer.
getDetector() - Method in class com.compomics.util.pride.prideobjects.Instrument
Returns the instrument detector.
getDeterminant() - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getDifference() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Returns the difference.
getDifference() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Returns the difference.
getDifferenceToMonoisotopic(int) - Method in class com.compomics.util.experiment.biology.atoms.Atom
Returns the mass difference between the given isotope and the monoisotopic mass.
getDigestionParameters() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the digestion preferences.
getDigestionType() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the enzyme digestion type.
getDiscardLowQualitySpectra() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Returns a boolean indicating whether low quality spectra shall be discarded.
getDisplayedTips() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the list of displayed tips.
getDisplayName() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
Returns the name to display, e.g.
getDisplayProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
getDisplayProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
getDisplayProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
getDisplayProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
getDisplayProgress() - Method in interface com.compomics.util.waiting.WaitingHandler
Returns if the waiting handler is to show the progress for the current process or not.
getDissociationType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the dissociation type.
getDivision(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
Returns the division corresponding to the given NCBI taxon.
getDoi() - Method in class com.compomics.util.pride.prideobjects.Reference
Returns the Digital Object Identifier (DOI) of the reference.
getDoPrecursorDeconvolution() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if precursor deconvolution is to be carried out.
getDoubleArray() - Method in class com.compomics.util.BinaryArrayImpl
Checks if all the necessary information is provided and then converts the decoded binary array into an array of double values (that for example could be used to draw a spectra).
getDoubleChargeWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the window size for doubly charged ions.
getDoubleListFromString(String, String) - Static method in class com.compomics.software.cli.CommandLineUtils
Parses a list of doubles from a command line option.
getDScoreThreshold() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Returns the D-score threshold.
getDSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns a set of sites where a D-score is available
getDuplicatedSpectrumTitles() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns a map of the duplicated spectrum titles, can be null.
getDuration() - Method in class com.compomics.util.waiting.Duration
Returns the duration in milliseconds.
getDynamicRange() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the dynamic range for spectrum filtering.
getElement() - Method in class com.compomics.util.general.IsotopicElement
Getter for the MolecularElement
getElement() - Method in exception com.compomics.util.general.UnknownElementMassException
Simple getter for the element variable.
getElementCount(MolecularElement) - Method in class com.compomics.util.protein.MolecularFormula
Getter for the count of a specific element
getEMail() - Method in class com.compomics.util.pride.prideobjects.Contact
Returns the contact e-mail.
getEnd() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Get the end value.
getEnd() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the end.
getEndBlock() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Returns the block end.
getEndLocation() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method reports on the end index of the header.
getEndPosition() - Method in class com.compomics.util.pdbfinder.das.readers.StartEndPosition
Returns the end position.
getEndProtein() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Returns the protein end.
getEnsemblAccession(String) - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
Returns the Ensembl accession for a given gene.
getEnsemblAssembly(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Ensembl assembly to use for the given taxon.
getEnsemblDataset(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Ensembl dataset to use for the given taxon.
getEnsembleSpecies() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns a map of the species in Ensembl.
getEnsemblGenomeDivisionFromName(String) - Static method in enum com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies.EnsemblGenomeDivision
Returns the EnsemblGenomeDivision corresponding to the given Ensembl name.
getEnsemblGenomesSpecies() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Ensembl genome species mapping.
getEnsemblGenomesSpeciesFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Ensembl genome species file.
getEnsemblId(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the Ensembl ID corresponding to the given gene name.
getEnsemblSchemaName(EnsemblGenomesSpecies.EnsemblGenomeDivision) - Static method in class com.compomics.util.experiment.biology.genes.ensembl.EnsemblVersion
Returns the name of the Ensembl schema for BioMart queries.
getEnsemblSpecies() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Ensembl species mapping.
getEnsemblSpeciesFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Ensembl species file.
getEnsemblSpeciesVersions(File) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Gets the information contained into the Ensembl species file.
getEnsemblVersion(Integer) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Returns the Ensembl version for a given species.
getEnsemblVersionFromFile(File, String) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Gets the Ensembl version of a given species from a file.
getEnsemblVersionsFile() - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Returns the Ensembl version file.
getEnsemblVersionsMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the Ensembl version map.
getEntitiesForPoint(int, int) - Method in class com.compomics.util.gui.VennDiagramPanel
Returns a list of the entities at the given x, y view location.
getEntitiesForPoint(int, int) - Method in class com.compomics.util.gui.XYPlottingDialog
Returns a list of the entities at the given x, y view location.
getEnzyme(String) - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Returns the enzyme corresponding to the given name.
getEnzyme() - Method in class com.compomics.util.gui.parameters.identification.pride.EnzymeParametersDialog
Returns the selected enzyme.
getEnzyme(String) - Method in class com.compomics.util.io.MascotEnzymeReader
This method will return a copy of an Enzyme instance for the given name, or 'null' if the enzyme was not found in the current list.
getEnzymeNames() - Method in class com.compomics.util.io.MascotEnzymeReader
This method reports on all the known names for enzymes in this reader.
getEnzymes() - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Get the imported enzymes.
getEnzymes() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Returns the enzymes used for digestion in a list.
getEnzymeToAdd() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
Returns the enzyme to add.
getEnzymeToRemove() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
Returns the name of the enzyme to remove.
getEnzymeType() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the enzyme type.
getError(boolean, int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the error.
getError(boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the error.
getErrorKeys() - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Returns a list containing the keys of the paths where the tool is not able to write.
getErrorMargin() - Method in interface com.compomics.util.gui.interfaces.SpectrumAnnotation
This method returns the allowed error margin (both sides) for the M/Z of the annotation (eg., 0.1 means an allowed interval of [M/Z-0.1, M/Z+0.1].
getErrorMargin() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
This method returns the allowed error margin (both sides) for the M/Z of the annotation (eg., 0.1 means an allowed interval of [M/Z-0.1, M/Z+0.1].
getErrors() - Method in class com.compomics.util.pride.validation.PrideXmlValidator
Returns the XML validation error object.
getErrorsAsList() - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Returns the errors as a list.
getErrorsAsString() - Method in class com.compomics.util.pride.validation.PrideXmlValidator
Returns the errors formatted as s single string.
getErrorsFormattedAsHTML() - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Returns the errors formatted as HTML.
getErrorsFormattedAsPlainText() - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Returns the errors formatted as plain text.
getEValueMap(ArrayList<Double>) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the e-value corresponding to a list of scores in a map.
getEValueMap(ArrayList<Double>, boolean) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the e-value corresponding to a list of scores in a map.
getEvenRowColor() - Method in class com.compomics.util.AlternateRowColoursJTable
This method returns the Color used for the even numbered rows, or 'null' if the default JTable background color is maintained for these rows.
getExceptions() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns the exceptions to the rule.
getExceptionType(Exception) - Static method in class com.compomics.util.exceptions.ExceptionHandler
Returns the exception type.
getExpectedIons(SpecificAnnotationParameters, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the expected ions in a map indexed by the possible charges.
getExpectedIons(SpecificAnnotationParameters, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the expected ions in a map indexed by the possible charges.
getExpectedIons(SpecificAnnotationParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the expected ions in a map indexed by the possible charges.
getExpectedModifications(double, ModificationParameters, Peptide, double, SequenceProvider, SequenceMatchingParameters, SearchParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns the expected modifications for a given modification mass indexed by site.
getExpectedVariableModifications(SearchParameters) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the expected variable modifications given the search parameters.
getExperiment_type() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Returns the experiment type.
getExperimentType() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Returns the experiment type.
getExportFeatures(String, boolean) - Method in interface com.compomics.util.io.export.ExportFactory
Returns the export features implemented for the given section.
getExportFeatures(boolean) - Method in interface com.compomics.util.io.export.ExportFeature
Returns a list of all implemented export features.
getExportFeatures(String) - Method in class com.compomics.util.io.export.ExportScheme
Returns the export features to be included in the given section.
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
 
getExportFeatures(boolean) - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
 
getExportFormat() - Method in class com.compomics.util.io.export.ExportWriter
Returns the export of the format.
getExportScheme(String) - Method in interface com.compomics.util.io.export.ExportFactory
Returns the export scheme indexed by the given name.
getExportWriter(ExportFormat, File, String, int, boolean) - Static method in class com.compomics.util.io.export.ExportWriter
Returns an export writer for the desired format.
getExtension() - Method in enum com.compomics.util.enumeration.ImageType
Returns the extension.
getExtension() - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
Returns the extension of the file for which this IdfileReader can be used.
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
 
getExtension() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
 
getExtension(File) - Static method in class com.compomics.util.io.file.filefilters.FileFilterUtils
Get the extension of a file.
getExtension(File) - Static method in class com.compomics.util.io.IoUtil
Returns the extensions of a file.
getExtension(String) - Static method in class com.compomics.util.io.IoUtil
Returns the extensions of a file name.
getFactorialsCache() - Static method in class com.compomics.util.math.BasicMathFunctions
Returns factorial 0 to 20 in an array.
getFastaParameters() - Method in class com.compomics.cli.fasta.FastaParametersInputBean
Returns the FASTA parameters as parsed from the command line.
getFastaParameters() - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
Returns the FASTA parameters.
getFastaParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the FASTA processing parameters.
getFastaSettings() - Method in class com.compomics.util.gui.protein.FastaParametersDialog
Returns the FASTA settings as set by the user.
getFastIndexFolderName() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the name of the FASTA index folder.
getFeature() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
Returns the peptide feature;
getFeatureFamily() - Method in interface com.compomics.util.io.export.ExportFeature
Returns the family type of this export feature.
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
 
getFeatureFamily() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
 
getFeatureId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the feature ID.
getFeatureLabel() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the feature label.
getFeatures(String) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
Returns the features in the map for the given category.
getFeed(String, String, ArrayList<String>) - Static method in class com.compomics.util.messages.FeedBack
Creates a feed object.
getFeed(String, String) - Static method in class com.compomics.util.messages.FeedBack
Creates a general feed with no key word.
getFile() - Method in class com.compomics.util.gui.file_handling.FileAndFileFilter
Returns the file.
getFileDetailList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
Convert from JSON to a list of FileDetails.
getFileFilter() - Method in class com.compomics.util.gui.file_handling.FileAndFileFilter
Returns the file filter.
getFileIn() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
Returns the file provided as input.
getFileIn() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
Returns the file provided as input.
getFileName() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the name of the indexed file.
getFilename() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Getter for the filename
getFilename() - Method in interface com.compomics.util.interfaces.SpectrumFile
This method reports on the filename for the file.
getFileName(String) - Static method in class com.compomics.util.io.IoUtil
An OS independent getName alternative.
getFileName(File) - Static method in class com.compomics.util.io.IoUtil
An OS independent getName alternative.
getFileName() - Method in class com.compomics.util.io.PklFile
 
getFileName() - Method in interface com.compomics.util.pride.PrideObject
Returns the name to use when serializing the object.
getFileName() - Method in class com.compomics.util.pride.prideobjects.Contact
 
getFileName() - Method in class com.compomics.util.pride.prideobjects.ContactGroup
 
getFileName() - Method in class com.compomics.util.pride.prideobjects.Instrument
 
getFileName() - Method in class com.compomics.util.pride.prideobjects.Protocol
 
getFileName() - Method in class com.compomics.util.pride.prideobjects.Reference
 
getFileName() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
 
getFileName() - Method in class com.compomics.util.pride.prideobjects.Sample
 
getFilenameExtensionLowerCase(String) - Static method in class com.compomics.util.io.IoUtil
Returns the given file name with lower-case extension.
getFileOut() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
Returns the file provided as output.
getFileOut() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
Returns the file provided as output.
getFilePaths() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getFilePaths() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getFilePaths() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the absolute path to the original mass spec file containing the spectra in a map indexed by file name without file extension.
getFileReader(File) - Method in class com.compomics.util.experiment.io.identification.IdfileReaderFactory
This method returns the proper identification file reader depending on the format of the provided file.
getFileReader(File) - Static method in interface com.compomics.util.io.flat.SimpleFileReader
Returns a file reader, text or gz, according to the extension of the file.
getFiles(String, ArrayList<String>) - Static method in class com.compomics.software.cli.CommandLineUtils
Returns a list of files as imported from the command line option.
getFileSize(URL) - Static method in class com.compomics.util.io.IoUtil
Returns the size of the file located at the given URL.
getFilter(Integer) - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
Returns the filter designed by the given number.
getFilter(String) - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
Returns the filter designed by the given name.
getFilter() - Method in class com.compomics.util.gui.filtering.FilterDialog
Returns the filter as set by the user.
getFilter() - Method in class com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog
Returns the id filter as set by the user.
getFilteredInput(ArrayList<Double>, ArrayList<Double>, double) - Static method in class com.compomics.util.math.statistics.linear_regression.filters.ProbabilityFilter
Returns a list containing first the filtered xs and then the filtered ys.
getFilteredInputFixedBins(ArrayList<Double>, ArrayList<Double>, int) - Static method in class com.compomics.util.math.statistics.linear_regression.filters.BinningFilter
Returns a list containing first the filtered xs and then the filtered ys.
getFilteredInputFixedBinsSize(ArrayList<Double>, ArrayList<Double>, int) - Static method in class com.compomics.util.math.statistics.linear_regression.filters.BinningFilter
Returns a list containing first the filtered xs and then the filtered ys.
getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
 
getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns the filter item corresponding to the given name.
getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.PeptideFilter
 
getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.ProteinFilter
 
getFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
 
getFilters() - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
Returns the index of the filters selected.
getFiltersMap() - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
Returns the filters map, filter index - value.
getFixedAaModifications() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the modifications at specific amino acids.
getFixedModificationAtAa(char) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns the fixed modification that can be found at the given amino acid.
getFixedModifications(boolean, boolean, ModificationParameters, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns the fixed modifications for this sequence based on the given modification parameters.
getFixedModifications(ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the fixed modifications for this peptide based on the given modification parameters.
getFixedModifications() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the fixed modifications for the peptide.
getFixedModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns the searched fixed modifications names.
getFixedModificationsAsString(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the peptide modifications as a string.
getFixedVariants() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
returns the fixed variants
getFlags() - Method in class com.compomics.util.general.CommandLineParser
This method will report on all flags that have been found, or return an empty String[] if none were present.
getFlanking() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Return whether the flanking amino acids of a mapped peptide are to be reported.
getFontSize() - Method in class com.compomics.util.gui.VennDiagramPanel
Get the font size.
getFontSizeLegend() - Method in class com.compomics.util.gui.VennDiagramPanel
Get the font size for the legend.
getForeignAccession() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the foreign accession.
getForeignDescription() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the foreign description.
getForeignID() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the foreign ID.
getFormat() - Method in class com.compomics.util.gui.ExportFormatSelectionDialog
Returns the selected format.
getFormatFromCommandLineOption(String) - Static method in enum com.compomics.util.io.export.ExportFormat
Returns the export format designed by the given command line option.
getForwardIons() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the forward ions searched as list of integers as indexed in the FragmentIon class.
getForwardIonsFeatures(Peptide, int, int, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation.FeaturesGenerator
Returns the ms2pip features for the forward ions of the given peptide at the given charge.
getForwardStart(String) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).
getFoundCharges() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the found charges.
getFoundModifications() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the variable modifications found in the currently loaded dataset.
getFoundModifications() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the names of the variable modifications found in the dataset.
getFractionConfidence(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the fraction confidence.
getFractionMolecularWeightRanges() - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
Returns the user provided molecular weight ranges for the fractions.
getFractionOfPeaksForChargeEstimation() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the fraction of peaks to be retained for charge >1 estimation.
getFractionParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the fraction parameters.
getFractionPEP(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the fraction pep.
getFractionPEP() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the fraction pep map.
getFractionPsmMatches() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the list of fraction PSM matches.
getFractions() - Method in class com.compomics.util.experiment.identification.Identification
Returns the fractions.
getFractions() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Return the fractions where this match was found.
getFractionScore(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the fraction score.
getFractionScore() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Return the fractions where this match was found.
getFractionSettings() - Method in class com.compomics.util.gui.parameters.identification.advanced.FractionParametersDialog
Returns the fraction settings as set by the user.
getFractionValidatedPeptides(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Get the number of validated peptides in the given fraction.
getFractionValidatedSpectra(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Get the number of validated spectra in the given fraction.
getFragmentAccuracyType() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the fragment accuracy type.
getFragmentationMethod() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the fragmentation method used.
getFragmentationMethod() - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
Returns the fragmentation method.
getFragmentationModel() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Returns the name of the fragmentation model.
getFragmentationRule() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the fragmentation rule.
getFragmentationTerminus() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the fragmentation terminus.
getFragmentationType() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Return the fragmentation ID.
getFragmentBinOffset() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the fragment ion bin offset.
getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the fragment ion accuracy.
getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Returns the fragment ion accuracy.
getFragmentIonAccuracy() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the MS2 ion m/z tolerance.
getFragmentIonAccuracyInDa(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the fragment ion accuracy in Da.
getFragmentIonAccuracyInDa(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Returns the fragment ion accuracy in Da.
getFragmentIonAccuracyInDaltons() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the absolute fragment ion tolerance in Dalton.
getFragmentIonAccuracyInDaltons(double) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the absolute fragment ion tolerance in Dalton.
getFragmentIons(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.ions.IonFactory
This method returns all the theoretic ions expected from a peptide.
getFragmentIons(Peptide, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.ions.IonFactory
This method returns the theoretic ions expected from a peptide.
getFragmentIons(Tag, ModificationParameters, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.ions.IonFactory
This method returns the theoretic ions expected from a tag.
getFragmentIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the type of peptide fragment ions annotated.
getFragmentIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Returns the type of peptide fragment ions annotated.
getFullFilePath(String) - Static method in class com.compomics.util.junit.TestCaseLM
This method finds a file from the current classpath and attempts to reconstruct its full filename.
getFullHeaderWithAddenda() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method reports on the full header, with the addenda (if present).
getFullName() - Method in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
Returns the full name of the database, null if not set.
getFullName() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
Returns the full name of the unit.
getFunction() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
Returns the function used to compare the amino acid properties.
getGeneMappingFile(String) - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Returns the gene mapping file.
getGeneMappingFolder() - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Returns the path to the folder containing the gene mapping files.
getGeneMaps(GeneParameters, FastaSummary, SequenceProvider, ProteinDetailsProvider, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Returns the gene maps for the given proteins.
getGeneName(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getGeneName() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the gene name.
getGeneName(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
Returns the gene name for the given protein.
getGeneNameToAccession() - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
Returns the gene name to protein accession map.
getGeneNameToChromosome() - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
Returns the gene name to chromosome map.
getGeneNameToChromosomeMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the gene name to chromosome map.
getGeneNameToEnsemblIdMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the gene name to Ensembl ID map.
getGeneParameters() - Method in class com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog
Returns the gene preferences.
getGeneParameters() - Method in class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
Returns the gene preferences.
getGeneParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the gene parameters.
getGeneratedKeys() - Method in interface com.compomics.util.db.interfaces.Persistable
This method will return the automatically generated key for the insert if one was triggered, or 'null' otherwise.
getGenericIon(Ion.IonType, int, NeutralLoss[]) - Static method in class com.compomics.util.experiment.biology.ions.Ion
Convenience method returning a generic ion based on the given ion type.
getGenericIon(Ion.IonType, int) - Static method in class com.compomics.util.experiment.biology.ions.Ion
Convenience method returning a generic ion based on the given ion type without neutral losses.
getGoAccession(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the GO Term accession corresponding to the given name.
getGoAccessionLink(String) - Method in class com.compomics.util.gui.genes.GeneDetailsDialog
Returns the GO accession number as a web link to the given GO term at QuickGO.
getGoAccessions(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Returns the GO accessions linked to a given protein accession.
getGoAccessionToProteinMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the GO to protein accession map.
getGoDomainsFile() - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Returns the GO domains file.
getGoMappingFile(String) - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Returns the GO mapping file.
getGoNamesForProtein(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the go terms names for a protein accession.
getGoNamesMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the GO accession to names map.
getGoNamesMap() - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Returns the GO accession to name map.
getGoTermsForProtein(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the go terms accessions for a protein accession.
getGoToProteinMap() - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Returns the GO to protein accession map.
getGPtmCategories() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the modification categories to include in the G-PTM search.
getGravy() - Method in class com.compomics.util.protein.AASequenceImpl
This method gets the GRAVY score (Kyte & Doolittle) from the cache, or, if it isn't cached, reconstructs it.
getGroupId() - Method in class com.compomics.software.autoupdater.MavenJarFile
Returns the group id.
getGroupNames() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns a standard map of the group names.
getGuiOptions() - Static method in enum com.compomics.util.parameters.peptide_shaker.ProjectType
Returns the different options as they should be displayed on the GUI.
getHeader() - Static method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
IdentificationParametersCLI header message when printing the usage.
getHeader() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData
Returns the parsed header.
getHeader(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getHeader(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
 
getHeader(String) - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
Returns the FASTA header of the protein as found in the FASTA file.
getHeader() - Method in class com.compomics.util.nucleotide.NucleotideSequence
This method reports on the nucleotide header.
getHeader() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Returns the header.
getHeader() - Method in class com.compomics.util.protein.Protein
This method reports on the header for the current protein.
getHeaderAsString() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData
Returns the header string representation.
getHeaderHeight() - Method in class com.compomics.util.io.export.styles.DefaultStyle
 
getHeaderHeight() - Method in interface com.compomics.util.io.export.WorkbookStyle
Returns the height of a header row.
getHeaderStyle() - Method in class com.compomics.util.io.export.styles.DefaultStyle
 
getHeaderStyle(int) - Method in class com.compomics.util.io.export.styles.DefaultStyle
 
getHeaderStyle() - Method in interface com.compomics.util.io.export.WorkbookStyle
Returns the standard cell style of a header.
getHeaderStyle(int) - Method in interface com.compomics.util.io.export.WorkbookStyle
Returns the standard cell style of a header at the given hierarchical depth.
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the helicity according to PMID 14730315.
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getHelicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getHidden() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns whether a match is hidden or not.
getHighestIntensity() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Method that find the intensity of the most intense peak
getHighestIntensity() - Method in interface com.compomics.util.interfaces.SpectrumFile
This method returns the intensity of the highest intensity peak in this spectrum.
getHighestVersionNumber() - Method in class com.compomics.software.autoupdater.MetaDataXMLParser
Returns the highest version number.
getHighIntensityCutOff() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the high intensity cut-off as percentage of the most intense ion peak.
getHistogram(int, Integer, int, int) - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Get histogram.
getHitListLength() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the length of the hit list for OMSSA.
getHitListLength() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Returns the length of the hit list.
getHomeFolder() - Static method in class com.compomics.util.io.file.FileSystemAccessor
Returns the user home folder.
getHtmlTooltip() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns information about the modification as an HTML tooltip.
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the hydrophobicity according to PMID 14730315.
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getHydrophobicity() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getIconMap(Class) - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns the default map of icons for the validation levels.
getId() - Method in interface com.compomics.software.settings.PathKey
Returns the id of the path.
getId() - Method in enum com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey
 
getId(String, boolean) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
Returns the NCBI taxon corresponding to the given species name.
getId() - Method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
Returns the id number of the score.
getID() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the ID.
getId() - Method in class com.compomics.util.experiment.patient.Patient
Returns the patient id,
getId() - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Returns the id of the object.
getIdentificationAlgorithmParameter(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the algorithm specific parameters, null if not found.
getIdentificationCharge() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the charge used for identification.
getIdentificationFeaturesCache() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the identification features cache.
getIdentificationFile() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the identification file.
getIdentificationKeys() - Method in class com.compomics.util.experiment.identification.Identification
Returns the identification keys.
getIdentificationParameters() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Returns the identification parameters.
getIdentificationParameters(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Returns the identification parameters corresponding to the given name.
getIdentificationParameters() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
Returns the identification parameters as set by the user.
getIdentificationParameters() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
Returns the selected identification parameters.
getIdentificationParameters(File) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
Loads the identification parameters from a file.
getIdentificationParameters(File) - Static method in class com.compomics.util.parameters.identification.search.SearchParameters
Loads the identification parameters from a file.
getIdentificationParametersFile(String) - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Returns the identification parameters corresponding to the given name.
getIdentifier() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns the reference identifier.
getIdentityMatrix(int) - Static method in class com.compomics.util.math.matrix.DoubleMatrix
 
getIdMatchValidationPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
Returns the validation settings as set by the user.
getIdValidationParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the identification matches validation parameters.
getImmoniumIon(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Returns the immonium ion corresponding to the given subtype.
getImmoniumIon(char) - Static method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Returns the immonium ion produced by the given amino acid.
getImplementedAtoms(boolean) - Static method in class com.compomics.util.experiment.biology.atoms.Atom
Returns an array of implemented atoms indicated by their short name.
getImplementedIons() - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Returns a set of possible subtypes.
getImplementedIonTypes() - Static method in class com.compomics.util.experiment.biology.ions.Ion
Returns the implemented ion types.
getImplementedIsotopes() - Method in class com.compomics.util.experiment.biology.atoms.Atom
returns an unsorted list of isotopes for which a mass is available relative to the monoisotopic peak (+1 for carbon 13).
getImplementedSections() - Method in interface com.compomics.util.io.export.ExportFactory
Returns the implemented sections.
getIndentString() - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Returns the indent string to use, e.g.
getIndex(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns an index for the amino acid excluding combinations.
getIndex() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Returns the index of a reporter ion.
getIndex() - Method in class com.compomics.util.experiment.identification.Advocate
Returns the index of the advocate.
getIndex() - Method in class com.compomics.util.experiment.identification.IdentificationMethod
returns the index of the identification method
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
 
getIndex() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
 
getIndex() - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
Returns an integer unique to this class.
getIndex() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Returns the index on the protein.
getIndex() - Method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns the index associated to this possibility.
getIndex(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the index corresponding to the desired spectrum.
getIndexedVariableModifications() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns the variable modifications indexed by site.
getIndexedVariableModifications() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the variable modifications indexed by site.
getIndexes(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the indexes where the amino acid pattern was found in the input.
getIndexes(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the indexes where the amino acid pattern was found in the input.
getIndexes(String, String) - Static method in class com.compomics.util.Util
Returns at which indexes a small string can be found in a big string.
getIndexOnProtein() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the peptide index on the protein.
getInferred() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Returns a boolean indicating whether the modification is inferred from another peptide.
getInitiatorMethionineBehavior() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the initiator methionine behavior.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
Returns the user selection as Andromeda parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
Returns the user selection as Comet parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
Returns the DirecTag parameters as set by the user.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
Returns the user selection as MetaMorpheus parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
Returns the user selection as MS Amanda parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
Returns the user selection as MS-GF+ parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
Returns the user selection as MyriMatch parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
Returns the Novor parameters as set by the user.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
Returns the user selection as OMSSA parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
Returns the PepNovo+ parameters as set by the user.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
Returns the user selection as Tide parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
Returns the user selection as X!tandem parameters object.
getInputFile() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Returns the input parameters file.
getInputFile() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the spectrum file name as found in the parameters section.
getInsertedAminoAcid() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Insertion
 
getInstance() - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Static method to get an instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
Static method which returns the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Static method to get the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Static method returning the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Static method to get the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.io.identification.IdfileReaderFactory
A static method to retrieve the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
Constructor for the factory.
getInstance() - Static method in class com.compomics.util.io.PropertiesManager
Get the singleton instance to access properties of Computational Omics tools.
getInstance() - Static method in class com.compomics.util.pride.PrideObjectsFactory
Method returning the instance of the factory.
getInstitution() - Method in class com.compomics.util.pride.prideobjects.Contact
Returns the instituition.
getInstrumentID() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Return the instrument ID.
getInstrumentID() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Return the instrument ID.
getInstruments() - Method in class com.compomics.util.pride.PrideObjectsFactory
Returns the instruments.
getIntegerListFromString(String, String) - Static method in class com.compomics.software.cli.CommandLineUtils
Parses a list of integers from a command line option.
getIntegerParameter(String) - Method in class com.compomics.util.experiment.ProjectParameters
 
getIntensities(int, Integer, int) - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Get intensity.
getIntensity(Ion) - Static method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.SequestFragmentationModel
Returns the intensity expected for the given ion.
getIntensity() - Static method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.UniformFragmentation
Returns a default intensity of 1.0.
getIntensity() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Getter for the precursor intensity (here always zero)
getIntensity() - Method in interface com.compomics.util.interfaces.SpectrumFile
This method reports on the intensity of the precursor ion.
getIntensityAtP(double) - Method in class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
Returns the intensity at a given upper tail cumulative probability.
getIntensityCutOffIncrement() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the intensity cut-off increment.
getIntensityLimit(Spectrum, AnnotationParameters.IntensityThresholdType, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
Returns the limit in intensity according to the given threshold.
getIntensityPrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the pride CV term for the ion match intensity.
getIntensityScoreWeight() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the intensity score weight.
getIntensityThresholdType() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the intensity threshold type.
getIntensityValues() - Method in class com.compomics.util.io.PklFile
 
getIntentisy(Ion) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.FragmentItensityPredictor
Returns the intensity expected for the given peak.
getIntermediateScore(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the desired intermediate score.
getIntermediateScores() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the intermediate scores map.
getInterpolation(ArrayList<Double>, Double, Double) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the interpolation of a list of hyperscores using a linear interpolation of the form result = a * log(score) + b.
getInterpolation(double, double, double) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the interpolated value for a given score in log.
getInterpolationValues(int[], boolean) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the interpolation values for the given scores in the form {a, b}.
getInterpolationValues(HashMap<Integer, Integer>, boolean) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the interpolation values for the given score histogram in the form {a, b}.
getIonAtRow(int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
Returns the ion type at the given row.
getIonMassErrorPrideCvTerm(int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the pride CV term for the ion match error.
getIonMatches(SpectrumIndex, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotator
Returns the ions matched in the given spectrum at the given charge.
getIonMatches(SpectrumIndex, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotatorNL
Returns the ions matched in the given spectrum at the given charge.
getIonMatches(SpectrumIndex) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
Returns the ions matched in the given spectrum.
getIonMatches(SpectrumIndex, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.PrecursorAnnotator
Returns the ions matched in the given spectrum at the given charge.
getIonMatches(SpectrumIndex) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ReporterIonAnnotator
Returns the ions matched in the given spectrum.
getIonMatches(SpectrumIndex, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
Returns the ion matches for the given spectrum.
getIons() - Static method in class com.compomics.util.parameters.identification.search.SearchParameters
Getter for the list of ion symbols used.
getIonType(String) - Static method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Returns the ion index corresponding to the given symbol in the drop down menu.
getIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the type of ions annotated.
getIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Returns the map of ions to annotate.
getIsotope() - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
Returns the isotope, 0 for monoisotope.
getIsotope() - Method in class com.compomics.util.gui.atoms.AtomPanel
Returns the currently selected isotope.
getIsotopeCorrection() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the isotope correction setting.
getIsotopeMass(int) - Method in class com.compomics.util.experiment.biology.atoms.Atom
Returns the mass corresponding to the given isotope number.
getIsotopeMzTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the deisotoping m/z tolerance.
getIsotopeNumber(Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
Returns the isotope number corresponding to the given rounded mass.
getIsotopeNumber(int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the distance in number of neutrons between the experimental mass and theoretic mass, image of the isotope number: 1 typically indicates C13 isotope.
getIsotopeNumber(double, int, int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the precursor isotope number according to the number of protons.
getIsotopicDistribution() - Method in class com.compomics.util.protein.AASequenceImpl
This method gives the IsotopicDistribution for the sequence
getItem(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
Returns the item designated by the given name.
getItem(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
Returns the item designated by the given name.
getItem(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
Returns the item designated by the given name.
getItem(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
Returns the item designated by the given name.
getItemsNames() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns the name of the items used to filter.
getIterativeReplaceEvalue() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the e-value threshold to use to replace a hit for the iterative search.
getIterativeSequenceEvalue() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the e-value threshold to use to consider a sequence for the iterative search.
getIterativeSpectrumEvalue() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the e-value threshold to use consider a spectrum for the iterative search.
getiXAxisMax() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the maximum value of the x-axis.
getiXAxisMin() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the minimum value of the x-axis.
getiYAxisMax() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the maximum value of the y-axis.
getiYAxisMin() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the minimum value of the y-axis.
getJarFilePath() - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
Returns the path to the jar file.
getJarFilePath() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersCLI
Returns the path to the jar file.
getJarFilePath() - Method in class com.compomics.cli.paths.PathSettingsCLI
Returns the path to the jar file.
getJarFilePath(String, String) - Static method in class com.compomics.software.CompomicsWrapper
Returns the path to the jar file.
getJarPath() - Method in class com.compomics.software.autoupdater.MavenJarFile
Returns the path to the jar file.
getJavaHome() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the Java Home folder.
getJavaHomeAndOptions(String) - Method in class com.compomics.software.CompomicsWrapper
Returns an array list containing the Java home plus any parameters to the JVM.
getJOptionEditorPane(String) - Static method in class com.compomics.util.gui.JOptionEditorPane
Returns a JEditorPane with HTML support to be used in a JOptionsPane.
getJsonStringFromFile(File) - Method in class com.compomics.util.io.json.JsonMarshaller
Convert JSON string from file.
getKeepTerminalAminoAcids() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the option for keeping the terminal amino acids when generating the decoys.
getKey() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the reference key of a peptide.
getKey(String, ModificationMatch[]) - Static method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the reference key of a peptide.
getKey() - Method in class com.compomics.util.experiment.identification.IdentificationMatch
Returns the key of a match.
getKey() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
 
getKey() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
 
getKey(String, String) - Static method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns a key to use for the spectrum match based on the file where the spectrum was found and its title.
getKey() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
 
getKeyFromId(String) - Static method in enum com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey
Returns the key from its id.
getKeysInBackend() - Method in class com.compomics.util.db.object.ObjectsDB
Returns the keys in backend set.
getKeyToPathMap() - Method in class com.compomics.software.settings.gui.PathParametersDialog
Returns the path settings in a map: key | path.
getKeyWords() - Method in class com.compomics.util.messages.FeedBack
Returns the key words for this report.
getKnownMassDeltas() - Static method in class com.compomics.util.gui.spectrum.GraphicsPanel
Get all the known mass deltas (if any).
getLabel() - Method in interface com.compomics.util.gui.interfaces.SpectrumAnnotation
This method returns the label for the annotation.
getLabel() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
This method returns the label for the annotation.
getLabel() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns the label.
getLabelColor() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns the label color.
getLabelWidth() - Static method in class com.compomics.util.gui.TableProperties
Returns the label width for the sparklines.
getLastHeader() - Method in class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
Returns the header corresponding to the last protein.
getLastModified() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns when the file was last modified.
getLastSelectedFolder() - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
Returns the last selected folder.
getLastSelectedFolder() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Returns the last selected folder.
getLastSelectedFolder(String) - Method in class com.compomics.util.io.file.LastSelectedFolder
Returns the last selected folder according to the given use case.
getLastSelectedFolder() - Method in class com.compomics.util.io.file.LastSelectedFolder
Returns the last selected folder according to the given use case.
getLastSelectedFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the last selected folder.
getLatestVersionNumberFromRemoteRepo(URL) - Static method in class com.compomics.software.autoupdater.WebDAO
Fetches the latest Maven deployed version from a Maven built repository.
getLatinName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
Returns the Latin name corresponding to the given NCBI taxon.
getLatinName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the Latin name of the species corresponding to the given taxon according to the UniProt mapping.
getLeadingAccession() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns the leading accession for this match.
getLegendDatasetAFourWay() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the legend location of dataset A in a four way Venn diagram.
getLegendDatasetAThreeWay() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the legend location of Dataset A in a three way Venn diagram.
getLegendDatasetBFourWay() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the legend location of dataset B in a four way Venn diagram.
getLegendDatasetBThreeWay() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the legend location of dataset B in a three way Venn diagram.
getLegendDatasetCFourWay() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the legend location of dataset C in a four way Venn diagram.
getLegendDatasetCThreeWay() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the legend location of dataset C in a three way Venn diagram.
getLegendDatasetDFourWay() - Method in class com.compomics.util.gui.VennDiagramPanel
Returns the legend location of dataset D in a four way Venn diagram.
getLength() - Method in class com.compomics.util.experiment.biology.proteins.Protein
Returns the number of amino acids in the sequence.
getLength() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
 
getLength() - Method in interface com.compomics.util.interfaces.Sequence
This method reports on the length of the current sequence.
getLength() - Method in class com.compomics.util.nucleotide.NucleotideSequence
This method reports on the length of the sequence for the current nucleotide sequence.
getLength() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
This method reports on the length of the current sequence.
getLength() - Method in class com.compomics.util.protein.AASequenceImpl
This method reports on the length of the current sequence.
getLength() - Method in class com.compomics.util.protein.Protein
This method reports on the length of the sequence for the current protein.
getLengthDiff() - Method in class com.compomics.util.experiment.identification.matches.PeptideVariantMatches
Returns the length difference induced by the variants.
getLengthInAminoAcid() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the amino acid length of the tag when mass gaps are considered like one amino acid
getLetter() - Method in class com.compomics.util.experiment.biology.atoms.Atom
Returns the symbol for the atom.
getLicense() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the license information of this file.
getLimitX() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns the maximal share of X's a match can contain, range [0.0-1.0].
getLine(int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getLinearRegression(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.linear_regression.regressions.MedianRegression
Returns a robust linear regression based on the median of statistics.
getLinearRegression(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.linear_regression.regressions.SimpleLinearRegression
Returns a simple linear regression.
getLines() - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getLink() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the link.
getLinkHref() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the linkHref.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class com.compomics.util.gui.renderers.AlignedListCellRenderer
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
 
getLn10(MathContext) - Static method in class com.compomics.util.math.BigMathUtils
Returns the value of ln(10) according to the mathContext.
getLocalizationConfidence(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the confidence of the PTM localization.
getLocalPrideFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the local PRIDE folder.
getLocation() - Method in interface com.compomics.util.interfaces.Modification
This method returns the location of the modification in the sequence.
getLocation() - Method in class com.compomics.util.protein.ModificationImplementation
This method returns the location of the modification in the sequence.
getLocationToDownloadOnDisk(String) - Method in class com.compomics.software.autoupdater.FileDAO
Try to find an at least somewhat sane location to download files to.
getLocationToDownloadOnDisk(String) - Method in class com.compomics.software.autoupdater.GUIFileDAO
Try to find an at least somewhat sane location to download files to.
getLocationToDownloadOnDisk(String) - Method in class com.compomics.software.autoupdater.HeadlessFileDAO
Try to find an at least somewhat sane location to download files to.
getLogFolder() - Method in class com.compomics.cli.paths.PathSettingsCLIInputBean
Returns the folder where to save the log files.
getLogIntensityAtP(double) - Method in class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
Returns the log10 intensity at a given upper tail cumulative probability.
getLongestAminoAcidSequence() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the longest amino acid sequence contained in this tag.
getLossesMass(NeutralLoss[]) - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
Convenience summing the masses of various neutral losses.
getLowerClearMzRange() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the lower mass value for the clear mz range.
getLowerPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Returns the lower precursor mass.
getLowIntensityCutOff() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the low intensity cut-off as percentage of the most intense ion peak.
getMagicNumber() - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileUtils
Returns the magic number of currently supported CMS files.
getMainTitle() - Method in class com.compomics.util.io.export.ExportScheme
Returns the main title of the report.
getMainTitleRowHeight() - Method in class com.compomics.util.io.export.styles.DefaultStyle
 
getMainTitleRowHeight() - Method in interface com.compomics.util.io.export.WorkbookStyle
Returns the row height for the main title.
getMainTitleStyle() - Method in class com.compomics.util.io.export.styles.DefaultStyle
 
getMainTitleStyle() - Method in interface com.compomics.util.io.export.WorkbookStyle
Returns the cell style for the main title.
getManualValidation() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns the manually validated items.
getManualValidation() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Indicates whether the match validation was manually inspected.
getMap() - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Get the map.
getMass() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
 
getMass() - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Returns the mass of the atomic chain as sum of the individual atoms.
getMass() - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
Returns the mass of the atom.
getMass() - Method in class com.compomics.util.experiment.biology.atoms.ElementaryElement
Returns the mass of the element.
getMass(int) - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
Get the glycan mass.
getMass() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Returns the mass of the neutral loss, from the atomic composition if available, from the mass field otherwise.
getMass() - Method in class com.compomics.util.experiment.biology.ions.NeutralLossCombination
Returns the mass of this combination.
getMass() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Getter for the mass difference induced by this modification.
getMass() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the mass, does not attempt to estimate it.
getMass(ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the mass, estimates it if not done before.
getMass() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
 
getMass() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the mass of the tag.
getMass(boolean, boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the theoretic mass of the tag, eventually without terminal gaps.
getMass() - Method in interface com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
Returns the mass of the tag component.
getMass(String, IdfileReader, SearchParameters, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
Returns the mass indicated by the identification algorithm for the given modification.
getMass() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the mass.
getMass(int) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
Returns the mass associated with the given bin, the middle of the bin.
getMass(int) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the mass associated with the given bin, the middle of the bin.
getMass(int) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
Returns the mass of the compound with the given charge.
getMass(int) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
Returns the mass of the precursor with the given charge.
getMass() - Method in interface com.compomics.util.interfaces.Sequence
This method will return the mass for the sequence.
getMass() - Method in class com.compomics.util.nucleotide.NucleotideSequence
This method returns the nucleotide sequence weight in Da.
getMass() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
This method will return the mass for the sequence.
getMass() - Method in class com.compomics.util.protein.AASequenceImpl
This method calculates the mass for the current sequence.
getMass() - Method in class com.compomics.util.protein.Protein
This method returns the protein weight in Da.
getMassAnalyzer() - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
Returns the mass analyzer.
getMassAndromeda(String, ModificationProvider, SearchParameters) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
Returns the mass indicated by the Andromeda for the given modification.
getMassByMass(String) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
Returns the mass indicated by the identification algorithm for the given modification.
getMassByName(String, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
Returns the mass indicated by the identification algorithm for the given modification.
getMassDelta(String, int) - Method in class com.compomics.util.protein.ModificationImplementation
This method returns the mass delta for the specified residue, measured either monoisotopically or averaged.
getMassDelta(String, int) - Method in class com.compomics.util.protein.ModificationTemplate
This method returns the mass delta for the specified residue, measured either monoisotopically or averaged.
getMassDiffAcceptorType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the mass difference acceptor type.
getMassErrorDistribution(String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the precursor mass error distribution of validated peptides in a spectrum file.
getMassGap() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Returns the mass gap comprised in this ion.
getMassOmssa(String, ModificationProvider, SearchParameters) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
Returns the mass indicated by the OMSSA for the given modification.
getMassShift() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the m/z shift applied to the fragment ions.
getMassShiftCTerm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the C-terminal m/z shift applied to all reverse ions.
getMassShiftNTerm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the N-terminal m/z shift applied to all forward ions.
getMatchingAminoAcid(char, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns a matching amino acid using the given preferences.
getMatchingKey() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the key accounting for sequence matching preferences
getMatchingKey(SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns a unique key for the peptide when considering the given matching preferences.
getMatchingPeaks(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the peaks matching the given m/z.
getMatchingSequence(String, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the matching sequence of a given sequence.
getMatchingSpectra(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
Returns a list containing the precursors matching the given m/z.
getMatchingType(int) - Static method in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
Returns the matching type corresponding to the given index.
getMatchKey(Ion, int) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the key for the ion match uniquely representing a peak annotation.
getMatchKey(Ion, int, IonMatchKeysCache) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the key for the ion match uniquely representing a peak annotation.
getMatchKey(int, int, int, String, int) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the key based on the different attributes of a match.
getMatchKey(Ion, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.IonMatchKeysCache
Returns the key for the ion match uniquely representing a peak annotation.
getMatchValidationLevel() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the validation level of the match.
getMatchValidationLevel(String) - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns the match validation level associated to a given name.
getMatchValidationLevel(int) - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns the match validation level associated to a given index.
getMatchValidationLevel() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Returns the lowest validation level considered as an integer as indexed in the MatchValidationLevel enum.
getMavenJarFileFromFolderWithArtifactId(File, String) - Method in class com.compomics.software.autoupdater.FileDAO
Fetches a Maven built jar file from a folder for the given artifact id (e.g peptideshaker or ms-lims).
getMaxCharge() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the maximal charge among found charges.
getMaxCharge() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the maximal charge found in the mgf file.
getMaxChargeSearched() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the maximal charge searched.
getMaxCombinations() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the maximal number of combinations.
getMaxDynamicMods() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the maximum number of dynamic mods.
getMaxDynamicMods() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the maximum number of variable modifications.
getMaxEValue() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the maximal e-value searched for.
getMaxEValue() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the maximal e-value searched for.
getMaxExp(MathContext) - Static method in class com.compomics.util.math.BigFunctions
Returns the estimated maximal value exp can be calculated on according to the mathContext.
getMaxFragmentCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the maximum fragment ion charge.
getMaxFragmentCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the maximal fragment charge.
getMaxFragmentPerSeries() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the maximal number of fragments to retain per series.
getMaxFragmentSize() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the max fragmentation size.
getMaxHeterozygousVariants() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the max heterozygous variants.
getMaxHitsPerSpectrumPerCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the maximal number of hits searched per spectrum and per charge.
getMaximum() - Method in interface com.compomics.util.interfaces.Monitorable
This method reports on the total amount steps the task can take before completion.
getMaximum() - Method in class com.compomics.util.io.file.MonitorableFileInputStream
This method reports on the maximum scale for the monitor.
getMaximum() - Method in class com.compomics.util.io.file.MonitorableInputStream
This method reports on the total amount of bytes that can be read from the monitored InputStream.
getMaximumExpectationValueRefinement() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the maximum expectation value to use for refinement.
getMaximumValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
Returns the current maximum value for the progressbar.
getMaxIndex() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the maximal index where amino acids are found.
getMaxIntensity() - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Returns the max intensity.
getMaxIntensity() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the maximum precursor intensity in this file.
getMaxIntensity() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Returns the max intensity value.
getMaxIsotopes() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns the maximal number of isotopes allowed (inclusive).
getMaxIsotopicCorrection() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the maximal isotopic correction.
getMaxIterations() - Method in class com.compomics.util.math.clustering.KMeansClustering
Returns the maximum number of iterations.
getMaxLoadedProteins() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum number of proteins loaded into memory.
getMaxLoadedSpectra() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum number of spectra loaded into memory.
getMaxMass() - Method in class com.compomics.util.gui.events.RescalingEvent
Returns the maximum mass.
getMaxMissedCleavages() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns the maximum number of missed cleavages.
getMaxModificationIsoforms() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the max modification isoforms.
getMaxModifications() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum number of modifications per peptide.
getMaxModificationSites() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum number of modifications sites per modification per peptide.
getMaxModsForPeptide() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the max mods for peptide.
getMaxMW() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the molecular weight of the fattest protein in the dataset.
getMaxMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the maximum m/z in this file.
getMaxMz() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
Returns the maximal m/z encountered among the precursors.
getMaxMz() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Returns the max mz value.
getMaxMzDeviation() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns the maximal m/z deviation allowed.
getMaxMzLadders() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the maximal m/z ladder length.
getMaxNeutralLosses() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum number of water and ammonia losses per peptide.
getMaxNeutralLossesPerModification() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum number identical modification specific losses per peptide.
getMaxNPeptides() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the maximal number of peptides among the proteins of the dataset.
getMaxNPsms() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the the maximal number of PSMs among the proteins of the dataset.
getMaxNSpectra() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the maximum number of spectra accounted by a single peptide Match all found in a protein match.
getMaxNumberOfModifications() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the maximal number of modifications.
getMaxPadding() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the max padding (distance between the axes and the border of the panel).
getMaxPeakCount() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the maximum peak count in this file.
getMaxPeakCount() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the maximum peak count.
getMaxPeakCount() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the max peak count.
getMaxPepLength() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the maximum peptide length.
getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum peptide length.
getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the maximal peptide length allowed.
getMaxPeptideLengthNoEnzyme() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the maximal peptide length to use when searching with no enzyme.
getMaxPeptideMass() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the maximal peptide mass.
getMaxPeptidePrecursorErrorDa() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Return the max peptide precursor mass error in Dalton.
getMaxPeptidePrecursorErrorPpm() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the max peptide precursor mass error in ppm.
getMaxPrecInt(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getMaxPrecInt() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getMaxPrecInt(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getMaxPrecInt() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getMaxPrecInt(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the maximum precursor intensity in a given file.
getMaxPrecInt() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the maximum precursor intensity among all files.
getMaxPrecMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getMaxPrecMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getMaxPrecMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getMaxPrecMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getMaxPrecMz(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the maximum precursor m/z in a given file.
getMaxPrecMz() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the maximum precursor m/z among all files.
getMaxPrecRT(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getMaxPrecRT() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getMaxPrecRT(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getMaxPrecRT() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getMaxPrecRT(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the maximum precursor RT in a given file.
getMaxPrecRT() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the maximum precursor RT among all files.
getMaxPrecursorAdjustment() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the maximum precursor adjustment.
getMaxPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the maximum precursor mass.
getMaxPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the maxPrecursorMass precursor mass.
getMaxPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the maxPrecursorMass precursor mass.
getMaxPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
getMaxPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
getMaxPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
getMaxPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
getMaxPrimaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
Returns the max primary progress counter.
getMaxProteinAccessionLength() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the max protein accession length.
getMaxProteinAveragePrecursorIntensity() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the maximum protein average precursor intensity.
getMaxProteinSummedPrecursorIntensity() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the maximum summed protein precursor intensity.
getMaxPtmsPerTagPeptide() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns the maximum number of PTMs to consider when mapping tags to protein sequences.
getMaxRank() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum rank.
getMaxRT() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the maximal RT in this file.
getMaxSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
getMaxSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
getMaxSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
getMaxSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
getMaxSecondaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
Returns the max secondary progress counter.
getMaxSpectrumChargeRange() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the maximum charge added when the charge is missing for a given spectrum.
getMaxSpectrumCount() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns the maximal amount of PSMs for the peptides in the current peptide list.
getMaxSpectrumCounting() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the maximal spectrum counting value of the proteins of the dataset.
getMaxSpectrumMz() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the max spectrum m/z to search for.
getMaxTagCount() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the maximum number of tags per spectrum to be generated.
getMaxTagPrecursorErrorDa() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Return the max tag precursor mass error in Dalton.
getMaxTagPrecursorErrorPpm() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the max tag precursor mass error in ppm.
getMaxValidatedPeptidesPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the maximum validated peptides at the fraction level.
getMaxValidatedSpectraPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the maximum validated spectra at the fraction level.
getMaxValueForProbability(double) - Method in interface com.compomics.util.math.statistics.Distribution
The value after which the density function will be smaller than p.
getMaxValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
 
getMaxValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
 
getMaxValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
 
getMaxVariableModifications() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the maximum number of variable modifications per peptide.
getMaxVariableModificationsPerPeptide() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the maximum number of variable modifications allowed on a single peptide.
getMaxVariableModificationsPerTypePerPeptide() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the maximum number of variable modifications of each modification type allowed on a single peptide.
getMaxVariableMods() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the maximum number of variable modifications per peptide.
getMaxXAxisValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method reports on the largest x-axis value in the point collection across all datasets.
getMaxXsInSequence() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns the maximal number of Xs to account for in a sequence.
getMDScore(ArrayList<SpectrumIdentificationAssumption>, Peptide, ArrayList<String>, SequenceMatchingParameters, Integer) - Static method in class com.compomics.util.experiment.identification.modification.scores.MDScore
Returns the MD score for the given peptide in a spectrum match.
getMean() - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
Returns the mean of the distribution.
getMedianValue(HashMap<Double, Integer>) - Static method in class com.compomics.util.math.HistogramUtils
Returns the median of a histogram.
getMedianValue(HashMap<Double, Integer>, int) - Static method in class com.compomics.util.math.HistogramUtils
Returns the median of a histogram.
getMeek() - Method in class com.compomics.util.protein.AASequenceImpl
This method will return an estimated 'net' HPLC retention time for the sequence based on the table by Meek.
It does NOT take a t0 value, specific to a setup, into account.
getMemoryParameter() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the upper memory limit in MB.
getMemoryShare() - Method in class com.compomics.util.db.object.ObjectsCache
Returns the share of heap size which can be used before emptying the cache.
getMendianA() - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the rounded median of the as found in the previously interpolated scores.
getMendianB() - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the rounded median of the bs found in the previously interpolated scores.
getMessage() - Method in exception com.compomics.util.db.GeneratorException
This method returns a String with the description for this exception.
getMessage() - Method in class com.compomics.util.messages.FeedBack
Returns the message.
getMessages() - Method in class com.compomics.util.io.StreamGobbler
Returns the messages.
getMethod() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the method.
getMethodId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the method ID.
getMethods() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
Returns the methods implemented in the factory.
getMethodsNames() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
Returns the name of the methods present in the factory.
getMethodsNamesAsArray() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
Returns the methods names as array.
getMethodUsed() - Method in class com.compomics.util.experiment.quantification.Quantification
getter for the method used
getMetrics() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the metrics.
getMetricsPrefix() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
Returns the metrics prefix.
getMgfFileName(String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
Returns the name of the mgf file corresponding to the given Andromeda file name.
getMgfFileName(String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
Returns the spectrum file name.This method assumes that the PepNovo output file is the mgf file name + ".out"
getMgfFileName(String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
Returns the spectrum file name.This method assumes that the pNovo output file is the mgf file name + ".pnovo.txt"
getMgfFileName(String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
Returns the spectrum file name.
getMgfIndex(File) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
Returns the index of all spectra in the given mgf file.
getMgfIndex(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
Returns the index of all spectra in the given MGF file.
getMgfMaxSize() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the max mgf file size before splitting.
getMgfNSpectra() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Get the max number of spectra in an mgf file.
getMH() - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
Returns the PepNovo mH.
getMinAllowedIntensityRatioToBasePeak() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the minimum allowed intensity ratio to base peak.
getMinAminoAcidScore() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns the minimum amino acid score.
getMinAnnotatedPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the minimal number of annotated peaks a peptide should have.
getMinChargeSearched() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the minimal charge searched.
getMinCtermMass() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns the minimal mass to consider for a c-terminus.
getMinFragmentMz() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the minimal fragment m/z.
getMinimalChargeForMultipleChargedFragments() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.
getMinimalLocalizationConfidence() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the minimal confidence among the PTM sites of this scoring.
getMinimumValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
Returns the current minimum value for the progressbar.
getMinIndex() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the minimal index where amino acids are found.
getMinIsotopes() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns the minimal number of isotopes allowed (inclusive).
getMinIsotopicCorrection() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the minimal isotopic correction.
getMinMass(char[]) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns the minimal mass that an amino acid sequence can have taking into account ambiguous amino acids.
getMinMass() - Method in class com.compomics.util.gui.events.RescalingEvent
Returns the minimum mass.
getMinMissedCleavages() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns the minimum number of missed cleavages.
getMinMz() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
Returns the minimal m/z encountered among the precursors.
getMinMz() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Returns the min mz value.
getMinPeakIntensity() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the minimum peak intensity.
getMinPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the minimum number of peaks.
getMinPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the minimal number of peaks a spectrum should contain.
getMinPeaksPerSpectrum() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the minimal number of peaks per spectrum.
getMinPepLength() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns the maximal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Sets the minimal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the minimum peptide length.
getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the minimum peptide length.
getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Sets the minimal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Sets the minimal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the minimal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Sets the minimal peptide length allowed.
getMinPeptideLengthNoEnzyme() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the minimal peptide length to use when searching with no enzyme.
getMinPrecMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getMinPrecMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getMinPrecMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getMinPrecMz() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getMinPrecMz(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the minimum precursor m/z in a given file.
getMinPrecMz() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the minimum precursor m/z among all files.
getMinPrecPerSpectrum() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the minimal number of precursors per spectrum.
getMinPrecursorAdjustment() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the minimum precursor adjustment.
getMinPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the minimum precursor mass.
getMinPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the minimum precursor mass.
getMinPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the minimum precursor mass.
getMinPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the minimal precursor mass.
getMinRT() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the minimum RT in this file.
getMinSpectrumChargeRange() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the minimum charge added when the charge is missing for a given spectrum.
getMinSpectrumMz() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Return the min spectrum m/z to search for.
getMinSpectrumPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the min number of peaks in a spectrum.
getMinTagLength() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns the minimum tag length.
getMinTerminiCleavages() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the minimum number of termini cleavages.
getMinus1() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Returns the isotopic correction factor at -1 Da.
getMinus2() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Returns the isotopic correction factor at -2 Da.
getMinValueForProbability(double) - Method in interface com.compomics.util.math.statistics.Distribution
The value before which the density function will be smaller than p.
getMinValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
 
getMinValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
 
getMinValueForProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
 
getMinVariantDepth() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the min variant depth.
getMinXAxisValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method reports on the smallest x-axis value in the point collection across all datasets.
getMiscleavages() - Method in class com.compomics.util.protein.Enzyme
Simple getter for the number of allowed missed cleavages for the Enzyme.
getMissedCleavages() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the number of missed cleavages.
getModel() - Method in class com.compomics.util.sun.TableMap
 
getModification(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
 
getModification(String) - Method in interface com.compomics.util.experiment.biology.modifications.ModificationProvider
Returns the modification with the given name name.
getModification() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Getter for the theoretic PTM name.
getModification(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns the back-ed up modification with the given name.
getModification(String, int) - Static method in class com.compomics.util.protein.ModificationFactory
This method will return a Modification instance from a title.
getModification(String, String, int) - Static method in class com.compomics.util.protein.ModificationFactory
This method takes a code and a residue (the residue for the N-terminus is NTERMINUS and for the C-terminus CTERMINUS!) and converts this into a Modification instance if possible.
getModificationLocalizationParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the modification localization scoring parameters.
getModificationMass(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns the mass corresponding to a given modification.
getModificationName(double, Peptide, int) - Method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Returns the name of the modification corresponding to he given modification mass at the given site on the given peptide.
getModificationName(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the name of the modification indexed by the given index.
getModificationName(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the name of the modification indexed by the given index.
getModificationParameters() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the modification settings.
getModificationPattern(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns the modification pattern that is targeted by the given modification.
getModificationPlotData(Peptide, Modification, int, String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Returns the modification plot series in the JFreechart format for one PSM.
getModificationProfile() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
Returns the modification profile corresponding to the input by the user.
getModifications() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the names of all imported Modifications.
getModifications(ModificationCategory...) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the names of all modifications in the given categories.
getModifications() - Method in class com.compomics.util.protein.AASequenceImpl
Simple getter for the modifications.
getModificationsAtRepresentativeSite(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns the modifications which have a representative ambiguous site at the given site.
getModificationScoring(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns the modification scoring for the desired modification (null if none found).
getModificationsForPsiAccession(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns an array list of the utilities modification names mapping to the given PSI-MOD accession number.
getModificationTableContent(PeptideAssumption, Modification, int, String, String, Spectrum, AnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Get the table content.
getModificationToAdd() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
Returns the modification to add.
getModificationToRemove() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
Returns the name of the modification to remove.
getModificationType() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the modification type.
getModifiedAaIndex(int, int) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the index of a modification on the amino acid sequence.
getModifiedSequence(IdentificationMatch, String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the match sequence annotated with modifications.
getModifiedSequence() - Method in class com.compomics.util.protein.AASequenceImpl
This method will return the sequence with annotated modifications.
getModPeptidesAreDifferent() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if modified peptides are considered different.
getMolecularFormula() - Method in class com.compomics.util.protein.AASequenceImpl
This method calculates the molecular formula based on the sequence
getMonoisotopicAtomChain() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the monoisotopic atom chain representing this amino acid.
getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the mass of the amino acid.
getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.atoms.Atom
Returns the monoisotopic mass.
getMonoisotopicMassDelta(String) - Method in interface com.compomics.util.interfaces.Modification
This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue.
getMonoisotopicMassDelta(String) - Method in class com.compomics.util.protein.ModificationImplementation
This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue.
getMonoisotopicMassDelta(String) - Method in class com.compomics.util.protein.ModificationTemplate
This method returns a double with the monoisotopic mass difference conferred on the sequence by this modification for the specified residue.
getMonoisotopicPrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the precursor mass is monoisotopic, false if average.
getMsConvertParameters() - Method in class com.compomics.util.gui.parameters.proteowizard.MsConvertParametersDialog
Returns the parameters as created by the user.
getMsFileIterator(File, WaitingHandler) - Static method in interface com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
Returns the file reader for the given mass spectrometry file based on its extension.
getMsFormat() - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
Returns the format to convert to.
getMyriMatchFormat() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Get the MyriMatch enzyme format.
getMZ() - Method in interface com.compomics.util.gui.interfaces.SpectrumAnnotation
This method returns the M/Z of the feature to annotate.
getMZ() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
This method returns the M/Z of the feature to annotate.
getMz(int) - Method in class com.compomics.util.protein.AASequenceImpl
This method calculates the mass over charge ratio for a given charge for the current sequence.
getMzBinOffset() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the m/z bin offset.
getMzBinWidth() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the m/z bin width.
getMzErrorType(int) - Static method in enum com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
Returns the error type corresponding to the given index.
getMzFidelityScoreWeight() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the mzFidelity score weight.
getMzIdentMLVersion(int) - Static method in enum com.compomics.util.experiment.io.identification.MzIdentMLVersion
Returns the mzIdentML format corresponding to the given index.
getMzidOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the mzid output is to be created.
getMZPrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the pride CV term for the ion match m/z.
getMzValues() - Method in class com.compomics.util.io.PklFile
 
getnAaDeletions() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns the number of amino acid deletions allowed.
getnAaInsertions() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns the number of amino acid insertions allowed.
getnAaSubstitutions() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns the number of amino acid substitutions allowed.
getnAaSwap() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns the number of amino acid swaps allowed.
getName() - Method in class com.compomics.util.db.object.ObjectsDB
Returns the database name.
getName() - Method in enum com.compomics.util.enumeration.CompomicsTools
Getter for the name of the tool or library.
getName() - Method in class com.compomics.util.experiment.biology.atoms.Atom
Returns the name of the atom.
getName() - Method in class com.compomics.util.experiment.biology.atoms.ElementaryElement
Returns the name of the element.
getName() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Get the enzyme name.
getName() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
 
getName() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
 
getName() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
 
getName() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
 
getName() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
 
getName() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
 
getName() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
This method returns the name of the reporter ion.
getName() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
 
getName() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the name of the ion.
getName() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Getter for the modification name.
getName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
Returns the name corresponding to the given NCBI taxon.
getName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the name of the species corresponding to the given taxon according to the UniProt mapping.
getName() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Returns the name of this substitution matrix.
getName() - Method in interface com.compomics.util.experiment.filtering.Filter
Returns the name of the filter.
getName() - Method in interface com.compomics.util.experiment.filtering.FilterItem
Returns the name of the item.
getName() - Method in class com.compomics.util.experiment.identification.Advocate
Returns the name of the advocate.
getName() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
 
getName() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
 
getName() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
 
getName() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
 
getName() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
 
getName() - Method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
Returns the name of the score.
getName() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the name of the inspected protein.
getName() - Method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns the name of this possibility.
getName() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Returns the name of the database.
getName() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Returns the name of the reagent.
getName() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns the name of the method.
getName() - Method in class com.compomics.util.io.export.ExportScheme
Returns the name of the scheme.
getName() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the name of the parameters.
getName() - Method in class com.compomics.util.pride.CvTerm
Returns the name.
getName() - Method in class com.compomics.util.pride.prideobjects.Contact
Returns the contact name.
getName() - Method in class com.compomics.util.pride.prideobjects.ContactGroup
Returns the contact group name.
getName() - Method in class com.compomics.util.pride.prideobjects.Instrument
Returns the instrument name.
getName() - Method in class com.compomics.util.pride.prideobjects.Protocol
Returns the protocol name.
getName() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
Returns the references group name.
getName() - Method in class com.compomics.util.pride.prideobjects.Sample
Returns the name of the sample.
getNameForGoTerm(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the name of a GO term.
getNameWithGapAndNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Returns the name with number and mass gap.
getNameWithNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Returns the name with number.
getNameWithNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Returns the name with number.
getnAnnotatedMostIntensePeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the minimal number of annotated most intense peaks.
getNCleavageSites(String, ArrayList<Enzyme>) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
Returns the number of cleavage sites.
getnClusters() - Method in class com.compomics.util.math.clustering.settings.KMeansClusteringSettings
Returns the number of clusters to use.
getNColumns() - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getNConfidentPeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of confident peptides for a given protein match.
getNConfidentProteins() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of confident proteins.
getnConfidentProteins() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the number of confident proteins.
getNConfidentSpectra(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of confident spectra for a given protein match.
getNConfidentSpectraForPeptide(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of confident spectra for a given peptide match.
getNEnzymaticTermini(Peptide, String) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the maximal number of termini for the given peptide on the given protein.
getNEnzymaticTermini(int, int, String, Enzyme) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the number of enzymatic termini for the given peptide coordinates and enzyme on this protein.
getNestedException() - Method in exception com.compomics.util.db.GeneratorException
This method returns the nested exception for this exception, or 'null' if none is present.
getNeutralLoss(String) - Static method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Returns the neutral loss associated to the given name in the static map of the class.
getNeutralLossCombination() - Method in class com.compomics.util.experiment.biology.ions.NeutralLossCombination
Returns the neutral losses in this combination.
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the possible neutral losses of this ion type.
getNeutralLosses(ModificationParameters) - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
Returns a list containing the default neutral losses and the losses found in the given modifications.
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the neutral losses possibly encountered with this modification.
getNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the considered neutral losses.
getNeutralLossesAsString() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the neutral loss (if any), the empty string if no loss.
getNeutralLossesAsString(NeutralLoss[]) - Static method in class com.compomics.util.experiment.biology.ions.Ion
Returns the neutral loss (if any), the empty string if no loss.
getNeutralLossesCombinations(HashSet<String>) - Method in class com.compomics.util.experiment.biology.ions.IonFactory
Returns the possible neutral losses combinations as array of arrays of neutral losses.
getNeutralLossesMap() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Returns the map of neutral losses to annotate.
getNeutronMassMultiple(int) - Static method in class com.compomics.util.experiment.biology.atoms.ElementaryElement
Returns the mass of the neutron multiplied by i.
getNeutronThreshold() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the mass after which exact neutron mass should be considered in the calculation.
getNew() - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
 
getNew() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns a new empty filter.
getNew() - Method in class com.compomics.util.experiment.identification.filtering.PeptideFilter
 
getNew() - Method in class com.compomics.util.experiment.identification.filtering.ProteinFilter
 
getNew() - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
 
getNextFeature() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
Get the next feature in the XML string.
getNextHeader(WaitingHandler) - Method in class com.compomics.util.experiment.io.biology.protein.iterators.HeaderIterator
Returns the next header.Null if none.
getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionCombinationIterator
 
getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionIterator
 
getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeCombinationIterator
 
getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeIterator
 
getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificCombinationIterator
 
getNextPeptide() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificIterator
 
getNextPeptide() - Method in interface com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator
Returns the next peptide that can be generated from the iterator.
getNextProtein() - Method in class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
 
getNextProtein() - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinIterator
Returns the next protein.
getNextSequence() - Method in class com.compomics.util.experiment.identification.protein_sequences.AmbiguousSequenceIterator
Returns the next sequence, null if none.
getnFeatures() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
Returns the number of features in the map.
getNLines() - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getNmissedCleavages(String) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Returns the number of missed cleavages in an amino acid sequence.
getNMissedCleavages(Enzyme) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the number of missed cleavages using the specified enzyme.
getNMissedCleavages(DigestionParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the number of missed cleavages using the digestion preferences.
getnMissedCleavages(String) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Returns the number of allowed missed cleavages for the given enzyme.
getNoModPeptide(HashSet<String>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns a version of the peptide which does not contain the given list of modifications.
getNonDiagonalScore() - Method in class com.compomics.util.math.matrix.DoubleMatrix
Returns a score based on the non-diagonal values.
getNonEnzymatic(long, DigestionParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns a list of non-enzymatic peptides for a given protein match.
getNoOneHitWonders() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if one hit wonders are excluded.
getNoProlineRuleSeries() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the id numbers of ion series to apply no product ions at proline rule at.
getNormalDistribution(ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.distributions.NormalDistribution
Returns the normal distribution corresponding to a given list of double calibrated on mean and standard deviation.
getNormalIcon() - Method in class com.compomics.util.gui.VennDiagramDialog
 
getNormalIcon() - Method in class com.compomics.util.gui.XYPlottingDialog
 
getNormalizationFactors() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Returns the normalization factors.
getNormalize() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Indicates whether the spectrum counting index should be normalized.
getNormalizedSpectrumCounting(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the spectrum counting metric of the protein match of interest using the preference settings normalized to the injected protein amount using the spectrum counting preferences of the identification features generator.
getNormalizedSpectrumCounting(long, SpectrumCountingParameters, Metrics) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the spectrum counting metric of the protein match of interest using the preference settings normalized to the injected protein amount using the given spectrum counting preferences.
getNormalizedSpectrumCounting(long, UnitOfMeasurement, SpectrumCountingMethod) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the spectrum counting metric of the protein match of interest using the preference settings normalized to the injected protein amount.
getNormalizedSpectrumCounting(long, Metrics, UnitOfMeasurement, Double, SpectrumCountingMethod) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the spectrum counting metric of the protein match of interest using the preference settings normalized to the injected protein amount.
getNormalizePeaksAcrossAllWindows() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the normalize peaks across all windows.
getNote() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the note.
getNotSelectedRowHtmlTagFontColor() - Static method in class com.compomics.util.gui.TableProperties
Returns the color to use for the HTML tags for the rows that are not selected, in HTML color code.
getNoVariantPreferences() - Static method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns the preferences corresponding to no variants allowed.
getNovorPtmMap() - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
Returns the Novor to utilities PTM map.
getNPeaks() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Returns the number of peaks.
getnPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the number of most intense peaks to consider.
getNPeaksAboveThreshold(Spectrum, int, int, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
Returns the number of peaks between the start index (inclusive) and the end index (exclusive) above the intensity threshold (inclusive).
getnPeaksInDoubleChargeWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the number of peaks in doubly charged windows.
getnPeaksInSingleChargeWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the number of peaks in singly charged windows.
getnProcessingNode() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the number of processing nodes used.
getNProperties() - Static method in enum com.compomics.util.experiment.biology.aminoacids.AminoAcid.Property
Returns the number of implemented properties.
getNProteins() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns the number of proteins for this match.
getNSpectra(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Estimates the number of spectra for the given protein match.
getNSpectra() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the number of imported spectra.
getNTargetedAA(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the number of targeted amino acids at the given index.
getNtermAsString(boolean, String[]...) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the N-terminal annotation as string.
getNTerminal(boolean, ModificationParameters, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the N-terminal tag of this tag as a string for sequence display.
getNTerminalGap() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the N-terminal gap of the tag.
getnTermModification() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the N-term modification.
getNtermModification(boolean, char, String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns the N-term modification for the given amino acid.
getNTermTruncatedProtein(int) - Method in class com.compomics.util.protein.Protein
This method truncates the sequence for this protein on the N-terminus to the requested size.
getNTermTruncatedSequence(int) - Method in class com.compomics.util.protein.AASequenceImpl
This method will return an AASequenceImpl that represents an N-terminal truncation of the current sequence.
getnThreads() - Method in class com.compomics.util.parameters.tools.ProcessingParameters
Returns the number or threads to use.
getNumber(Class) - Method in class com.compomics.util.db.object.ObjectsDB
Returns the number of instances of a given class stored in the db.
getNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Returns the number of the fragment in the sequence.
getNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Returns the number of the fragment in the tag.
getNumber(Class) - Method in class com.compomics.util.experiment.identification.Identification
Returns the number of objects of a given class
getNumberOfBatches() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the number of batches per node to strive for when using the MPI-based parallelization features.
getNumberOfCandidates() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the number of candidates.
getNumberOfClusters() - Method in class com.compomics.util.math.clustering.KMeansClustering
Returns the number of clusters.
getNumberOfDataPointsInPlot() - Method in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Returns the current number of data points in the mass error plot.
getNumberOfDataPointsInPlot() - Method in class com.compomics.util.gui.spectrum.MassErrorPlot
Returns the current number of data points in the mass error plot.
getNumberOfModificationsPerPeptide() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Returns the maximum number of modifications per peptide.
getNumberOfPeaksToKeepPerWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Return the number of peaks to keep per window.
getNumberOfPeptides() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Returns the number of peptides to report per spectrum.
getNumberOfSpectrumMatches() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the maximum number of spectrum matches.
getNumberOfSpectrumMatches() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Returns the maximum number of spectrum matches.
getNumberOfSpectrumMatches() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the maximum number of spectrum matches.
getNumberOfSpectrumMatches() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the number of PSMs to report per spectrum.
getNumberOfTasks() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Returns the number of tasks, null if not set.
getNumberOfWindows() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the number of windows.
getNumberTolerableTermini() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Returns the number of tolerable termini.
getNumChargeStates() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the number of charge states.
getNumericParameter(String) - Method in class com.compomics.util.experiment.ProjectParameters
 
getNumIntensityClasses() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the number of intensity classes.
getNumIntensityClasses() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the number of intensity classes.
getNUnique() - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the number of amino acids excluding combinations.
getNUniquePeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of unique peptides for this protein match.
getNUniqueValidatedPeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of unique validated peptides for this protein match.
getNValidatedPeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of validated peptides for a given protein match.
getNValidatedProteinGroups(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether a peptide is found in a single protein match.
getNValidatedProteinGroups(long, WaitingHandler) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether a peptide is found in a single protein match.
getNValidatedProteins() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of validated proteins.
getnValidatedProteins() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the number of validated proteins.
getnValidatedPsms() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns the number of validated PSMs for the currently selected peptide.
getNValidatedPsms() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of validated PSMs for the last selected peptide /!\ This value is only available after getSortedPsmKeys has been called.
getNValidatedSpectra(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of validated spectra for a given protein match.
getNValidatedSpectraForPeptide(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the number of validated spectra for a given peptide match.
getNVariableModifications(double) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the number of variable modifications found with the given mass.
getNVariableModifications() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the number of modifications carried by this peptide.
getnVariants() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns the total number of variants allowed.
getnX() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the number of Xs already considered in this draft.
getObject(long) - Method in class com.compomics.util.db.object.ObjectsCache
Returns the objects if present in the cache.
getObject(IdentificationFeaturesCache.ObjectType, long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns an object if present in the cache.
getObject() - Method in class com.compomics.util.general.BoxedObject
Returns the boxed object.
getObjectsCache() - Method in class com.compomics.util.db.object.ObjectsDB
Returns the cache used by this database.
getObjectsDB() - Method in class com.compomics.util.experiment.identification.Identification
Returns the objects database used in this class.
getObservableAminoAcids(String, ArrayList<Enzyme>, double) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
Returns the observable amino acids in the sequence when using the given enzymes with the given maximal peptide length.
getObservableCoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the best protein coverage possible according to the given cleavage settings.
getObservableLength(String, ArrayList<Enzyme>, double) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
Returns the number of observable amino acids in the sequence.
getObservedFractionalMassesAll() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the observed molecular masses in kDa for each fraction.
getOccurrence(Atom, Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Returns the occurrence of a given atom in the chain.
getOccurrence() - Method in class com.compomics.util.general.IsotopicElement
Getter for the occurrence of this element
getOccurrence() - Method in class com.compomics.util.gui.atoms.AtomPanel
Returns the occurrence of the selected atom.
getOccurrence(String, char) - Static method in class com.compomics.util.Util
Returns the occurrence of a character in a string.
getOlsAccessionLink(String) - Method in class com.compomics.util.gui.enzymes.EnzymesDialog
Returns a web link to the given PSI-MS CV term at https://www.ebi.ac.uk/ols/ontologies/ms.
getOlsAccessionLink(String) - Method in class com.compomics.util.gui.modification.ModificationsDialog
Returns a web link to the given PSI-MOD CV term at https://www.ebi.ac.uk/ols/ontologies/mod.
getOMSSAIndexes(File) - Static method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Imports the OMSSA indexes from an XML file.
getOmssaOutputTypes() - Static method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the output types available.
getOneOverCombinationDouble(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the invert of the number of k-combinations in a set of n elements.
getOntology() - Method in class com.compomics.util.pride.CvTerm
Returns the ontology.
getOperatingSystem() - Static method in class com.compomics.util.io.file.FileSystemAccessor
Get the operating system.
getOptionIDs() - Static method in enum com.compomics.cli.paths.PathSettingsCLIParams
Returns the list of supported command line options.
getOptionParameter(String) - Method in class com.compomics.util.general.CommandLineParser
This method will report the option parameter for an option that can take a parameter itself.
getOptions() - Method in class com.compomics.util.general.CommandLineParser
This method will report on all options that have been found, or return an empty String[] if none were present.
getOptionsAsString() - Static method in enum com.compomics.cli.enzymes.EnzymesCLIParams
Returns the options as a string.
getOptionsAsString() - Static method in enum com.compomics.cli.fasta.FastaParametersCLIParams
Returns the options as a string.
getOptionsAsString() - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
Returns the options left to the user as a string.
getOptionsAsString() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersCLI
 
getOptionsAsString() - Static method in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Returns the options as a string.
getOptionsAsString() - Static method in enum com.compomics.cli.modifications.ModificationsCLIParams
Returns the options as a string.
getOptionsAsString() - Static method in enum com.compomics.cli.paths.PathSettingsCLIParams
Returns the options as a string.
getOrderedDSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns an ordered list of sites where the D-score was used.
getOrderedFileNamesWithoutExtensions() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getOrderedFileNamesWithoutExtensions() - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getOrderedFileNamesWithoutExtensions() - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the spectrum file names without file extensions.
getOrderedProbabilisticSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns an ordered list of sites where the probabilistic score was used.
getOrderedPtmLocations() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns sites of all localized PTMs ordered increasingly.
getOrganismIdentifier(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getOrganismIdentifier() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the organism identifier.
getOrganismIdentifier(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
Returns the organism identifier for the given protein.
getOrientation() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the orientation.
getOriginalAminoAcid() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
 
getOriginalAminoAcids(Character) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Returns the possible original amino acids for the given substituted amino acid as a list of their single letter code.
getOriginalAminoAcids() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Returns the amino acids where a substitution has been registered.
getOutputFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the last used output folder.
getOutputFolderName() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the name of the output folder.
getOutputFormat() - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
Returns the format to convert to.
getOutputFormat() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns the output format.
getOutputFormat() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the output format.
getOutputOptions() - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
Returns an array of the indexes of the different output options.
getOutputParameters(int) - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
Returns the output option of the given index.
getOutputParametersNames() - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
Returns an array of the names of the different options.
getOutputResults() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the output results filter.
getOutputSuffix() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the output tags suffix.
getP(char) - Method in class com.compomics.util.experiment.identification.protein_sequences.AaOccurrence
Returns the log10 of the share of the given amino acid in the database.
getP(char[], int, int, double) - Method in class com.compomics.util.experiment.identification.protein_sequences.AaOccurrence
Returns the sum of the log10 of the share of the given amino acids in the database.
getPackageName() - Method in enum com.compomics.util.enumeration.CompomicsTools
Return the package name of the tool.
getPanelIndex() - Method in class com.compomics.util.gui.atoms.AtomPanel
Returns the panel index.
getParameterKey() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
 
getParameterKey() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
 
getParameterKey() - Method in interface com.compomics.util.experiment.personalization.UrParameter
This method returns the key of the parameter.
getParameterKey() - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
 
getParameters() - Method in class com.compomics.util.general.CommandLineParser
This method will report on all parameters that have been found, or return an empty String[] if none were present.
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
 
getParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
 
getParameters() - Method in interface com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog
Returns the parameters as set by the user.
getParametersList() - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Returns an ordered list of the names of the implemented parameters.
getParametersOptionsAsString() - Static method in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Returns the options as a string.
getParentFolder() - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Returns the parent folder.
getParentFolder() - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFolder
Returns the parent folder where to write cms files.
getParentMonoisotopicMassIsotopeError() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns true if the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.
getPath(String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Returns the path at the given line.
getPath() - Method in class com.compomics.util.db.object.ObjectsDB
Returns the path to the database.
getPathID(String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Returns the path id line.
getPathOfClass(String) - Static method in class com.compomics.util.io.file.FileSystemAccessor
Returns the absolute path of the underlying file system of the given class.
getPathParameter(UtilitiesPathParameters.UtilitiesPathKey) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Returns the path according to the given key and path.
getPatientInformation(PatientInformation) - Method in class com.compomics.util.experiment.patient.Patient
Returns patient information,
getPattern() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the amino acid pattern targeted by this modification.
getPattern() - Method in class com.compomics.util.gui.AminoAcidPatternDialog
Returns the pattern as edited by the user.
getPdbAccession() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Returns the PDB accession.
getPdbAccession() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Returns the PDB accession.
getPdbaccession() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Returns the PDB accessions.
getPdbEnd() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Returns the PDB end.
getPdbGroup() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Returns the PDB groups.
getPdbs() - Method in class com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
Returns a vector of the PDB files mapped to the given protein accession number.
getPdbStart() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Returns the PDB start.
getPeakAnnotation() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the annotation to use for the ion match as a String.
getPeakAnnotation(Ion, int) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the annotation to use for a given ion and charge as a String.
getPeakAnnotation(boolean, Ion, int) - Static method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the annotation to use for a given ion and charge as a String.
getPeakAnnotation(boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the annotation to use for the given ion match as a String.
getPeakListAsString() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Returns the peak list as an array list formatted as text, e.g.
getPeaks(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
Returns the peaks of the spectrum with the given title.
getPeaks(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getPeaks(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getPeaks(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the spectrum peaks.
getPeaks() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Getter for the peaks
getPeaks() - Method in interface com.compomics.util.interfaces.SpectrumFile
This method reports on the peaks in the spectrum, with the Doubles for the masses as keys in the HashMap, and the intensities for each peak as Double value for that mass key.
getPeaksAboveIntensityThreshold(Spectrum, AnnotationParameters.IntensityThresholdType, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
Returns the peaks above intensity threshold as an array of double (mz, intensity).
getPeaksInBin(int) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the indexes of the peaks at the given bin indexed by m/z.
getPeaksMap() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the peaks map.
getPeakWaterMarkColor() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Get the peak water mark color.
getPeakWidth() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the current width of the peaks.
getPepNovoPtmMap() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Returns the PepNovo to utilities PTM map.
getPeptide() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Getter for the peptide.
getPeptide(double, double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns a peptide from the peptide draft.
getPeptide(double, double, BoxedObject<Boolean>) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns a peptide from the peptide draft.
getPeptide() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
Get the theoretic peptide.
getPeptideAssumptionFilter() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the filter used when importing PSMs.
getPeptideAssumptionsMap() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns the peptide assumptions map: advocate id > score > list of assumptions.
getPeptideCount() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns the number of peptides found.
getPeptideDetailList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
Convert from JSON to a list of ProteinDetails.
getPeptideEnd(String, int) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the 0 based end index of the peptide on the protein sequence.
getPeptideEvidenceKey(String, int, long) - Static method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Returns the peptide evidence key as string for the given peptide attributes.
getPeptideFilters() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Returns the list of peptide quality filters.
getPeptideFromProtein(char[], int, double, double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns a peptide from the given sequence.
getPeptideFromProtein(char[], String, int, Double, Double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns a peptide from the given sequence on the given protein.
getPeptideFromProtein(char[], String, int, double, double, BoxedObject<Boolean>) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Returns a peptide from the given sequence on the given protein.
getPeptideHideFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
Returns the peptide hide filters.
getPeptideIdentification() - Method in class com.compomics.util.experiment.identification.Identification
Returns a list of the keys of all encountered peptides.
getPeptideLengthDistribution() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the distribution of validated peptide lengths.
getPeptideList() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns the current peptide list.
getPeptideMatch(long) - Method in class com.compomics.util.experiment.identification.Identification
Returns the peptide match with the given key.
getPeptideMatchesIterator(long[], WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Returns a peptide matches iterator for a given key list.
getPeptideMatchesIterator(WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Returns a peptide matches iterator for all PeptideMatches.
getPeptideMatchesKeys() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Getter for the peptide keys.
getPeptideNormalisationFactor(String) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Returns the peptide normalization factor for the given sample, 1.0 if not set.
getPeptideProteinIndexesMap(ArrayList<PeptideProteinMapping>) - Static method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Returns a map made from the given mappings containing the indexes of the peptides in the protein sequences indexed by peptide sequence and protein accession.
getPeptideProteinMap(ArrayList<PeptideProteinMapping>) - Static method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Returns a map made from the given mappings containing protein accessions for every peptide sequence.
getPeptides(ArrayList<PeptideProteinMapping>, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Aggregates the given mapping into a list of peptides.
getPeptideSelected() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the color for a selected peptide.
getPeptideSequence() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Returns the peptide sequence.
getPeptideSequences() - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
Get the set of peptide sequences.
getPeptideShakerPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the path to the PeptideShaker installation.
getPeptideStarFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
Returns the peptide star filters.
getPeptideVariantMatches() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Returns eventual variants found.
getPeptideVariantsParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the peptide variant parameters.
getPeptideVariantsPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog
Returns the peptide variants settings as set by the user.
getPepXmlOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the pepxml output is to be created.
getPercentLength() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns the length of the reference area in percent.
getPercentualScreenDimension(JFrame, double) - Static method in class com.compomics.util.gui.MonitorDimension
This method returns a Dimension with a percentual width and height in relation to the JFrame.
getPercentualScreenDimension(JPanel, double) - Static method in class com.compomics.util.gui.MonitorDimension
This method returns a Dimension with a percentual width and height in realtion to the JPanel.
getPercMax() - Method in class com.compomics.util.general.IsotopicDistribution
Getter for result of the isotopic distributions calculation.
getPercTot() - Method in class com.compomics.util.general.IsotopicDistribution
Getter for result of the isotopic distributions calculation.
getPhase() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the phase.
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the pI.
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getPI() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getPinOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the Percolator output is to be created.
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the pK1.
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getPK1() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the pK2.
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getPK2() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the pKa.
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getPKa() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getPlus1() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Returns the isotopic correction factor at +1 Da.
getPlus2() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Returns the isotopic correction factor at +2 Da.
getPmid() - Method in class com.compomics.util.experiment.identification.Advocate
Returns the PubMed id of the reference of the advocate of interest.
getPmid() - Method in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
Returns the PubMed id of the database, null if not set.
getPmid() - Method in class com.compomics.util.pride.prideobjects.Reference
Returns the PubMed ID of the reference.
getPNovoParameters() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
Returns the pNovo parameters as set by the user.
getPNovoPtmMap() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Returns the pNovo to utilities PTM map.
getPNovoPtmResiduesMap() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Returns the pNovo to original amino acids residue map.
getPosition() - Method in class com.compomics.util.protein.Enzyme
Simple getter for the cleavage position of the Enzyme.
getPossibilities() - Method in interface com.compomics.util.experiment.filtering.FilterItem
In case the filter has predefined values, return the possible values, null otherwise.
getPossibilities() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
 
getPossibilities() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
 
getPossibilities() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
 
getPossibilities() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
 
getPossibleChargesAsString() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
Returns the possible charges as a string.
getPossibleConfidenceLevels() - Static method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Convenience method returning all confidence levels as string.
getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
 
getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns the filter items accepted by this filter.
getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.PeptideFilter
 
getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.ProteinFilter
 
getPossibleFilterItems() - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
 
getPossibleFilterItemsNames() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns the filter items accepted by this filter.
getPossibleModificationNames(Peptide, ModificationMatch, IdfileReader, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
Returns the possible modification names.
getPossibleModificationNamesAndromeda(Peptide, ModificationMatch, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
Returns the possible Andromeda modification names.
getPossibleModificationNamesByMass(Peptide, ModificationMatch, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
Returns the possible modifications names by mass.
getPossibleModificationNamesByName(Peptide, ModificationMatch, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
Returns the possible modifications by name.
getPossibleModificationNamesOmssa(Peptide, ModificationMatch, SearchParameters, SequenceMatchingParameters, SequenceProvider, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
Returns the possible OMSSA modification names.
getPossibleModificationSites(Peptide, Modification, SequenceProvider, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns an array of the possible modification sites for the given modification on the given peptide.
getPossibleModificationSites(AminoAcidSequence, boolean, boolean, Modification, SequenceMatchingParameters) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns an array of the possible modification sites for the given modification on the given peptide.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
Returns the possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.Glycan
Returns the possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Returns the possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Returns the possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
Returns the possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Returns the possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Returns the possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Returns the possible subtypes.
getPossibleSubtypes(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.ions.Ion
Returns an array of possible subtypes.
getPossibleSubtypesAsSet(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.ions.Ion
Returns a hashset of possible subtypes.
getPossibleTags(boolean, int, int, int) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
Computes the possible tag assumptions which can be obtained from this one by accounting for other charges and isotopes.
getPossibleValues() - Method in interface com.compomics.util.experiment.filtering.FilterItem
Returns the possible items of this kind.
getPossibleValues() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
 
getPossibleValues() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
 
getPossibleValues() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
 
getPossibleValues() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
 
getPotentialModificationSites(Modification, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the potential modification sites as an ordered list of string.
getPotentialModificationSitesNoCombination(Modification, String, int) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the potential modification sites as an ordered list of sites.
getPpm() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns whether the precursor mass tolerance is in ppm.
getPpmError(double, double) - Static method in class com.compomics.util.Util
Returns the ppm value of the given mass error relative to its theoretical m/z value.
getPpmTolerance(double, double) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the relative tolerance in ppm corresponding to the absolute tolerance in Dalton at the given reference mass.
getPrecurorCharge() - Method in class com.compomics.util.io.PklFile
 
getPrecursor(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
Returns the precursor of the spectrum with the given title.
getPrecursor(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getPrecursor(BufferedRandomAccessFile, long, String) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
Returns the next precursor starting from the given index.
getPrecursor(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getPrecursor() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Returns the precursor.
getPrecursor(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the precursor.
getPrecursorAccuracy() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the precursor tolerance.
getPrecursorAccuracyType() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the precursor accuracy type.
getPrecursorAdjustmentStep() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the precursor adjustment step.
getPrecursorCharge() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Returns the charge of the precursor.
getPrecursorIntensity() - Method in class com.compomics.util.io.PklFile
 
getPrecursorIntensityAveragePerFraction(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Get the average precursor intensity in the given fraction.
getPrecursorIntensityAveragePerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the fraction precursor intensity average map.
getPrecursorIntensityPerFraction(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Get the precursor intensity in the given fraction.
getPrecursorIntensityPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the precursor intensity per fraction map.
getPrecursorIntensitySummedPerFraction(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Get the summed precursor intensity in the given fraction.
getPrecursorIntensitySummedPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the fraction summed intensity map.
getPrecursorMatch(double, double) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the ion match.
getPrecursorMz(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
Returns the m/z of the precursor of the spectrum with the given title.
getPrecursorMz(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getPrecursorMz(int) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the precursor mz for the spectrum at the given index.
getPrecursorMz(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getPrecursorMz(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the measured precursor m/z.
getPrecursorMZ() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Getter for the precursor MZ
getPrecursorMZ() - Method in interface com.compomics.util.interfaces.SpectrumFile
This method reports on the precursor M/Z
getPrecursorMz() - Method in class com.compomics.util.io.PklFile
 
getPrecursorRt(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
Returns the RT of the precursor of the spectrum with the given title.
getPrecursorRt(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getPrecursorRt(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getPrecursorRt(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the precursor RT window.
getPrecursorsInBin(int) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
Returns the precursors at the given bin indexed by mass.
getPrecursorToleance() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the precursor tolerance.
getPreferredAccessionColumnWidth(JTable, int, int) - Method in class com.compomics.util.gui.genes.GeneDetailsDialog
Gets the preferred width of the column specified by colIndex.
getPreferredColumnWidth(JTable, int, int) - Method in class com.compomics.util.examples.UtilitiesDemo
Gets the preferred width of the column specified by vColIndex.
getPreferredWidthOfCell(JTable, int, int) - Static method in class com.compomics.util.gui.GuiUtilities
Returns the preferred width of a given cell in a table.
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
 
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
 
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
 
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
 
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
 
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
 
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
 
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
 
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the CV term adapted to the fragment ion.
getPrideFolder() - Static method in class com.compomics.util.pride.PrideObjectsFactory
Returns the folder where pride annotation information should be saved.
getPrimaryKeyColumns() - Method in class com.compomics.util.db.DBMetaData
This method reports on the primary key columns for the table.
getPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
getPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
getPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
getPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
getPrimaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
Returns the primary progress counter.
getPrintExpectScore() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns true if the export score is to be printed.
getPrintPeptides() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true of a list of the peptides should be printed to the output folder.
getPrintProgressIndicatorSize() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the progress indicator size.
getProbabilisticScore(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the probabilistic score at a given site.
getProbabilisticScoreThreshold() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Returns the probabilistic score threshold (inclusive).
getProbabilisticSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns a set of sites where a probabilistic score is available
getProbability() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the match probability.
getProbabilityAt(double) - Method in interface com.compomics.util.math.statistics.Distribution
Returns the density function value at a given position.
getProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
 
getProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
 
getProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
 
getProcessedProteinKeys(WaitingHandler, FilterParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the sorted list of protein keys.
getProcessingParameters() - Method in class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
Returns the processing parameters as set by the user.
getProcessingType() - Method in class com.compomics.util.parameters.tools.ProcessingParameters
Returns the processing type.
getProfile() - Method in class com.compomics.util.gui.protein.ModificationProfile
Returns the profile.
getProgress() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
This method reports on the current progress of the progressdialog.
getProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Returns the progress bar for updates from external processes.
getProgressInPercent() - Method in class com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator
Returns the progress reading the file in percent.
getProgressInPercent() - Method in class com.compomics.util.io.flat.readers.SimpleGzReader
 
getProgressInPercent() - Method in class com.compomics.util.io.flat.readers.SimpleTextReader
 
getProgressInPercent() - Method in interface com.compomics.util.io.flat.SimpleFileReader
Returns the progress reading the file in percent.
getProjectCount(String, PrideFilter...) - Static method in class com.compomics.util.pride.PrideWebService
Returns a project count for the given criteria and filters.
getProjectDetail(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
Convert from JSON to a list of ProjectDetails.
getProjectDetail(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns the project details for a given accession.
getProjectFileCount(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of file details for a given project.
getProjectFileDetails(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of file details for a given project.
getProjectSummaryList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
Convert from JSON to a list of ProjectDetails.
getProjectSummaryList(String, PrideFilter...) - Static method in class com.compomics.util.pride.PrideWebService
Returns a ProjectSummaryList for the given query and filters.
getProjectType(String) - Static method in enum com.compomics.util.parameters.peptide_shaker.ProjectType
Returns the project type corresponding to the given GUI option.
getProjectUniqueName() - Method in class com.compomics.util.experiment.ProjectParameters
 
getProjectUniqueName(String) - Method in class com.compomics.util.experiment.ProjectParameters
 
getProperties(CompomicsTools, String) - Method in class com.compomics.util.io.PropertiesManager
Get a Properties instance for the parameter properties filename.
getPropertiesFile(String) - Static method in class com.compomics.util.junit.TestCaseLM
This method will read a Properties file from the current ClassLoader and return a Properties instance with the Properties from the file.
getProperty(AminoAcid.Property) - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns a property of the amino acid.
getProperty(int) - Method in enum com.compomics.util.experiment.biology.aminoacids.AminoAcid.Property
Returns the property at index.
getProperty() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
Returns the feature property.
getProperty() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
Returns the feature property;
getPrositeFormat() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the pattern in the PROSITE format.
getProteinAccession() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Returns the accession of the protein.
getProteinAccessions(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Returns the protein accessions linked to a given GO term.
getProteinConfidenceMwPlots() - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
Returns the protein confidence for inclusion in MW plots.
getProteinDatabase(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getProteinDatabase(String) - Method in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
Returns the protein database with the given full name, null if not found.
getProteinDatabase(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
Returns the the protein database for the given protein.
getProteinDetailList(String) - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
Convert from JSON to a list of ProteinDetails.
getProteinEvidencAsString(Integer) - Static method in class com.compomics.util.experiment.io.biology.protein.Header
Return the UniProt protein evidence type as text.
getProteinEvidence(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getProteinEvidence() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the protein evidence level as indexed in UniProt.
getProteinEvidence(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
Returns an integer representing the protein evidence level as indexed by UniProt.
getProteinFilters() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Returns the list of protein quality filters.
getProteinHideFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
Returns the protein hide filters.
getProteinIdentification() - Method in class com.compomics.util.experiment.identification.Identification
Returns a list of the keys of all encountered proteins.
getProteinIdentificationByAssay(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of protein details for a given assay.
getProteinIdentificationByProject(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of protein details for a given project.
getProteinIdentificationCountByAssay(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of protein details for a given assay.
getProteinIdentificationCountByProject(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of protein details for a given project.
getProteinIdentificationsByProjectAndProtein(String, String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of protein details for a given project and a given protein accession.
getProteinIdentificationsCountByProjectAndProtein(String, String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of protein details for a given project and a given protein accession.
getProteinInferenceClassAsString() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the protein inference class as a string for the given integer-based class
getProteinInferenceClassAsString(int) - Static method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the protein inference class as a string for the given integer-based class.
getProteinInferenceGroupClass() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the protein inference class of the protein match.
getProteinInferenceParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the protein inference parameters.
getProteinInferencePreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog
Returns the protein inference preferences.
getProteinKey() - Method in class com.compomics.util.experiment.biology.proteins.Protein
Returns the key for protein indexing.
getProteinKeys(WaitingHandler, FilterParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the ordered protein keys to display when no filtering is applied.
getProteinKeys() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the list of ordered protein keys.
getProteinList() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns the protein list.
getProteinListAfterHiding() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns the protein list after all hiding filters have been used.
getProteinMap() - Method in class com.compomics.util.experiment.identification.Identification
Returns a map of all the protein matches which can be ascribed to a protein indexed by its accession.
getProteinMapping() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the protein mapping as a map of 0-based indexes for every protein accession.
getProteinMapping(String, SequenceMatchingParameters) - Method in interface com.compomics.util.experiment.identification.protein_inference.FastaMapper
Returns the protein mapping in the FASTA file loaded in the sequence factory for the given peptide sequence in a map: peptide sequence found in the FASTA file | protein accession | list of indexes of the peptide sequence on the protein sequence.
getProteinMapping(Tag, SequenceMatchingParameters) - Method in interface com.compomics.util.experiment.identification.protein_inference.FastaMapper
Returns the protein mappings for the given peptide sequence.
getProteinMapping(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getProteinMapping(Tag, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getProteinMappingWithoutVariants(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Exact mapping peptides against the proteome.
getProteinMappingWithoutVariants(Tag, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Mapping tags against proteome without variants.
getProteinMappingWithVariants(Tag, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Mapping tags against proteome with variants.
getProteinMappingWithVariantsFixed(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Variant tolerant mapping peptides against the proteome.
getProteinMappingWithVariantsGeneric(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Variant tolerant mapping peptides against the proteome.
getProteinMappingWithVariantsSpecific(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Variant tolerant mapping peptides against the proteome
getProteinMatch(long) - Method in class com.compomics.util.experiment.identification.Identification
Returns the protein match with the given key.
getProteinMatches(long) - Method in class com.compomics.util.experiment.identification.Identification
Returns the keys of the protein matches where a peptide can be found.
getProteinMatchesIterator(long[], WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Returns a protein matches iterator for a given key list.
getProteinMatchesIterator(WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Returns a protein matches iterator for all PeptideMatches.
getProteinMatchKey(Peptide) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Convenience method which returns the protein key from a peptide.
getProteinNormalisationFactor(String) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Returns the protein normalization factor for the given sample, 1.0 if not set.
getProteinPtmComplexity() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the proteinPtmComplexity.
getProteinsForGoTerm(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the protein accessions for a GO accession.
getProteinStarFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
Returns the protein star filters.
getProteinToGoMap() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Returns the protein to GO terms accession map.
getProteinToGoMap() - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Returns the protein to GO accession map.
getProteoWizardPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the path to ProteoWizard.
getProtocol() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Returns the protocol ID.
getProtocols() - Method in class com.compomics.util.pride.PrideObjectsFactory
Returns the protocols.
getProtonMassMultiple(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
Returns the mass of the proton multiplied by i.
getPsiModCvTerm() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the PSI-MOD CV term associated with this modification.
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
 
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
 
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
 
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
 
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
 
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
 
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
 
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
 
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the CV term adapted to the fragment ion.
getPsiMsCvTerm() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Returns the CV term for the neutral loss.
getPSMCountByAssay(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of PSM details for a given assay.
getPSMCountByAssayAndSequence(String, String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of PSM details for a given assay and a given peptide sequence.
getPSMCountByProject(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of PSM details for a given project.
getPSMCountByProjectAndSequence(String, String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a count of PSM details for a given project and a given peptide sequence.
getPsmFilters() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Returns the list of PSM quality filters.
getPsmHideFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
Returns the psm hide filters.
getPsmList() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns the PSM list.
getPsmNormalisationFactor(String) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Returns the PSM normalization factor for the given sample, 1.0 if not set.
getPSMsByAssay(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of PSM details for a given assay.
getPSMsByAssayAndSequence(String, String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of PSM details for a given assay and a given peptide sequence.
getPSMsByProject(String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of PSM details for a given project.
getPSMsByProjectAndSequence(String, String) - Static method in class com.compomics.util.pride.PrideWebService
Returns a list of PSM details for a given project and a given peptide sequence.
getPsmScoringParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the scoring parameters used when scoring PSMs.
getPsmScoringPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog
Returns the PSM scoring preferences as set by the user.
getPsmStarFilters() - Method in class com.compomics.util.gui.filtering.FilterParameters
Returns the psm star filters.
getPTM(PepnovoParameters, String) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
Get a PTM.
getPtmIndex(String) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the index of a given modification, null if not found.
getPtmIndex(String) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the index of a given modification
getPtmIndexes() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the PTM indexes as a map.
getPtmIndexes() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the PTM indexes as a map.
getPtmLocationAtAA() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the map of the localization.
getPtmLocations(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the PTM locations at a given confidence level (see static fields).
getPtmName() - Method in class com.compomics.util.gui.protein.ModificationProfile
Returns the PTM name.
getPtmResidue(Character) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Returns the original amino acids residue corresponding to the given pNovo PTM character.
getPtmScoringPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
Returns the PTM scoring preferences as set by the user.
getPtmToPrideMap() - Method in class com.compomics.util.pride.PrideObjectsFactory
Returns the utilities PTM to pride map.
getQcCriteria() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the list of QC checks made for this match.
getQcFilters() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the qc filters map.
getQuantile(int, Integer, int, double) - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Get the quantile.
getQueryTemplate(boolean) - Method in enum com.compomics.util.pride.prideobjects.webservice.PrideQuery
Returns the actual query template.
getQuoteType() - Static method in class com.compomics.software.cli.CommandLineUtils
Returns the quote type to use.
getRandomIndexes(int, int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns a list of n random indexes between min and max included.
getRandomInteger(int, int) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns an integer randomly chosen between min and max included.
getRandomThreshold(int, int) - Method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
Returns the threshold (inclusive) to use to consider an assignment random.
getRank(int, boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Returns the rank.
getRank(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Returns the number of occurrences of a given character until position index.
getRank() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Get the identification rank.
getRankOne(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Returns the rank of ones.
getRankRecursive(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Returns the number of occurrences of a given character until position index.
getRankScore() - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
Returns the PepNovo rank score.
getRankZero(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Returns the rank of zeros.
getRawBins() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the bins in the map as collection of keys from the map.
getRawHeader() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the entire header.
getRawScore() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the raw score as provided by the identification algorithm.
getReader(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
Returns the cms file reader for the given ms file.
getReader() - Method in class com.compomics.util.io.flat.readers.SimpleGzReader
 
getReader() - Method in class com.compomics.util.io.flat.readers.SimpleTextReader
 
getReader() - Method in interface com.compomics.util.io.flat.SimpleFileReader
Returns the underlying reader.
getReadTweets() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the list of read tweets.
getReagent(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns the reagent of the given name, null if not found.
getReagentNames() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns the reagents available in this method.
getReagentsSortedByMass() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns the list of reagents sorted by ascending mass.
getRecalibratedMz(TreeMap<Double, Double>, double[]) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.RecalibrationUtils
Returns a recalibrated peak list.
getRecalibratedPrecursor(Precursor, double, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.RecalibrationUtils
Returns a recalibrated precursor.
getRef() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Returns the value used as reference for the correction factors.
getReference() - Method in class com.compomics.util.pride.prideobjects.Reference
Returns the reference as a string.
getReferenceGroups() - Method in class com.compomics.util.pride.PrideObjectsFactory
Returns the reference groups.
getReferenceMass() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Returns the reference total mass to use for normalization.
getReferences() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
Returns the references.
getRefinementFixedModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Return the refinement fixed modifications used for the second pass search.
getRefinementVariableModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Return the refinement variable modifications used for the second pass search.
getRefMass() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the reference mass used to convert ppm to Da.
getRefMass() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
getRelatedIons(char) - Static method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Returns the list of related ions for the given amino acid.
getRelatedIons(AminoAcid) - Static method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Returns the list of related ions for the given amino acid.
getRelatedIons() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Indicates whether related ions should be annotated by default.
getRelationship() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
Returns the relationship between the features.
getRelativeError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the relative m/z matching error in ppm.
getRelativeError(int, int) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the relative m/z matching error in ppm after isotope removal.
getRelimsPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the path to the Relims installation.
getRemoveMethionine() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns true if n-term methionine is to be removed.
getRemovePrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns if the precursor is to be removed.
getRemovePrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true of the precursor peak is to be removed.
getRemovePrecursorTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the precursor removal tolerance.
getRemovePrecursorTolerance() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the tolerance with which to remove the precursor peak.
getRemoveTempFolders() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the output and index folders are to be removed when the search has completed.
getReport(boolean) - Method in interface com.compomics.util.experiment.filtering.Filter
Returns a filter report depending on whether the condition was met.
getReport(boolean) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
 
getReport(File) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Returns the report.
getReporterIndex(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
This method returns the reporter ion name associated to the given sample.
getReporterIon(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Returns the reporter ion indexed by the given index.
getReporterIon(String) - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Returns the reporter ion corresponding to the given name.
getReporterIon() - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Returns the reporter ion to look for in the spectrum.
getReporterIon(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns the reporter ion of the given name, null if not found.
getReporterIonNames() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns a list containing the names of the reporter ions.
getReporterIons(ModificationParameters) - Static method in class com.compomics.util.experiment.biology.ions.IonFactory
Returns the reporter ions to annotate with the given PTM settings.
getReporterIons() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the reporter ions possibly encountered with this modification.
getReporterIons() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Indicates whether reporter ions should be annotated by default.
getReporterMethod() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Returns the reporter method used.
getReporterMethod(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
Returns the reporter methods corresponding to the given name.
getReporterPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the path to the Reporter installation.
getRepresentativeSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns a list of all representative sites of ambiguously localized modifications.
getRequireVariableMods() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns true if at least one variable modification is required per peptide.
getResidues() - Method in interface com.compomics.util.interfaces.Modification
This method reports on all the residues that can be modified by this Modification.
getResidues() - Method in class com.compomics.util.protein.ModificationImplementation
This method reports on all the residues that can be modified by this Modification.
getResidues() - Method in class com.compomics.util.protein.ModificationTemplate
This method reports on all the residues that can be modified by this Modification.
getResolution() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Returns the resolution.
getResolution() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Returns the resolution.
getResponseString() - Method in class com.compomics.util.io.ftp.FTP
Returns all server response strings.
getResponseStringNoReset() - Method in class com.compomics.util.io.ftp.FTP
This method allows the caller to read the response strings from the server, without resetting the internal buffer (and thus not clearing the messages read by this messages).
getRest() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the rest of the header.
getRestrict() - Method in class com.compomics.util.protein.Enzyme
Simple getter for the restricting residues of the Enzyme.
getRestrictionAfter() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Getter for the amino acids restricting when following the cleavage.
getRestrictionBefore() - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Getter for the amino acids restricting when preceding the cleavage.
getReverseComplementary() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
This method returns the reverse complementary strand for the sequence.
getRewindIons() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the rewind ions searched as list of integers as indexed in the FragmentIon class.
getRewindStart(String) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).
getRobustCorrelation(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the population Pearson correlation r between series1 and series2.
getRobustLinearRegression(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.linear_regression.LinearRegression
Returns a robust linear regression based on the median.
getRobustNonSymmetricalNormalDistribution(ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
Returns the non-symmetrical distribution of the input list of double calibrated on the median, 15.9% and 84.1% percentiles.
getRobustNonSymmetricalNormalDistributionFromSortedArray(double[]) - Static method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
Returns the non-symmetrical distribution of the input array of double calibrated on the median, 15.9% and 84.1% percentiles.
getRobustNonSymmetricalNormalDistributionFromSortedList(ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
Returns the non-symmetrical distribution of the input list of double calibrated on the median, 15.9% and 84.1% percentiles.
getRobustNormalDistribution(ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.distributions.NormalDistribution
Returns the normal distribution corresponding to a given list of double calibrated on median and 34.1% percentile to median distance
getRoundedMass(int) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Getter for the rounded mass difference induced by this modification.
getRoundedMass() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Getter for the rounded mass difference induced by this modification.
getRowCount() - Method in class com.compomics.util.db.DBResultSet
This method reports on the number of rows in the resultset.
getRowCount() - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
 
getRowCount() - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
 
getRowCount() - Method in class com.compomics.util.sun.TableMap
 
getRowNumber(int) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Returns the row number of the given view index.
getRtInMinutes() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
Returns the retention time in minutes.
getSameMassNotFixedModifications(double, SearchParameters) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns a list containing all not fixed modifications with the same mass.
getSample(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
This method returns the sample associated to the given ion.
getSampleIndex(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Returns the sample index for the given sample.
getSampleIndexes() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Returns a set containing the indexes of every sample.
getSamples() - Method in class com.compomics.util.pride.PrideObjectsFactory
Returns the samples.
getScalingFactor() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the scaling factor.
getScientificName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
Returns the scientific name corresponding to the given NCBI taxon.
getScore(int) - Static method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
Returns the PTM score indexed by the given id.
getScore(String) - Static method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
Returns the PTM score of the given name.
getScore() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the score.
getScore(Peptide, String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, PeptideSpectrumAnnotator, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the hyperscore.
getScore(Peptide, int, Spectrum, ArrayList<IonMatch>) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Returns the hyperscore.
getScore(Peptide, int, Precursor, boolean, int, int) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.PrecursorAccuracy
Scores the match between the given peptide and spectrum using the precursor m/z accuracy.
getScore(Peptide, String, String, Spectrum, AnnotationParameters, SpecificAnnotationParameters, PeptideSpectrumAnnotator, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
Returns the score.
getScore(Peptide, Spectrum, ArrayList<IonMatch>) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
Returns the score.
getScore(Peptide, Spectrum, HashMap<Double, ArrayList<IonMatch>>) - Method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
Returns the score.
getScore(int) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
Returns the PSM score of the given index.
getScore(String) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
Returns the PSM score of the given name.
getScore(Peptide, int, String, String, Spectrum, IdentificationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, PeptideSpectrumAnnotator, int) - Method in class com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
Scores the match between the given peptide and spectrum using the given score.
getScore(Peptide, int, String, String, Spectrum, IdentificationParameters, SpecificAnnotationParameters, ModificationParameters, SequenceProvider, SequenceMatchingParameters, PeptideSpectrumAnnotator, PsmScore) - Method in class com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
Scores the match between the given peptide and spectrum using the given score.
getScore() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the score assigned by the advocate.
getScore() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method will attribute a score to the current header, based on the following scoring list: SwissProt : 4 IPI, SwissProt reference : 3 IPI, TrEMBL or REFSEQ_NP reference : 2 IPI, without SwissProt, TrEMBL or REFSEQ_NP reference : 1 NCBI, SwissProt reference : 2 NCBI, other reference : 1 Unknown header format : 0
getScore() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the score.
getScoreCutoff() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the score cut-off.
getScoredModifications() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Returns a list of scored modifications.
getScoredSites() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns a set of sites where a score is available.
getScoreForAlgorithm(int) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Returns the scores set for a given algorithm.
getSearchGuiOutputParameters() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the selected SearchGUI output option.
getSearchGuiPath() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the path to the SearchGUI installation.
getSearchParameters() - Method in class com.compomics.util.experiment.io.identification.MzIdentMLIdfileSearchParametersConverter
Updated the search parameters object and returns the search parameters as a string.
getSearchParameters() - Method in class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
Returns a SearchParameters instance based on the user input in the GUI.
getSearchParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the parameters used for the spectrum matching.
getSearchTarget() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if target sequences are to be searched.
getSearchType() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the search type.
getSecondaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Returns the secondary progress bar for updates from external processes.
getSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
getSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
getSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
getSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
getSecondaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
Returns the secondary progress counter.
getSecondaryPtmLocations() - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Returns the not found, randomly or doubtfully localized PTMs.
getSections() - Method in class com.compomics.util.io.export.ExportScheme
returns the list of sections to be included in the scheme.
getSelect(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Returns the position of the i-th one
getSelectedCharges() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Returns the charges selected for annotation.
getSelectedDate() - Method in class com.compomics.util.gui.utils.DateChooser
This method returns a Calendar set at the selected date, or 'null' if no date was selected.
getSelectedFastaFile() - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
Returns the selected FASTA file.
getSelectedFile() - Method in class com.compomics.util.gui.file_handling.FileSelectionDialog
Returns the file selected by the user.
getSelectedFiles() - Method in class com.compomics.util.gui.file_handling.FileDisplayDialog
Returns the list of selected files.
getSelectedItem() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
Returns the item selected by the user.
getSelectedItems() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
Returns the items selected by the user in a list.
getSelectedMethod() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Returns the current spectrum counting method.
getSelectedOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the selected output type, omx, csv or pepXML.
getSelectedOutputFormat() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the selected output format.
getSelectedPositions() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Returns the selected positions.
getSelectedProbabilisticScore() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Returns the selected probabilistic score.
getSelectedRowHtmlTagFontColor() - Static method in class com.compomics.util.gui.TableProperties
Returns the color to use for the HTML tags for the selected rows, in HTML color code.
getSelectedSpecies() - Method in class com.compomics.util.gui.genes.SpeciesDialog
Deprecated.
Returns the species selected in the species drop down menu.
getSelection() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Returns true if there is a selection.
getSeparationLines() - Method in class com.compomics.util.io.export.ExportScheme
Returns the number of lines to be used to separate the sections.
getSeparator() - Method in class com.compomics.util.io.export.ExportScheme
Returns the column separator.
getSequence() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns the sequence as String.
getSequence() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns for the sequence.
getSequence() - Method in class com.compomics.util.experiment.biology.proteins.Protein
Getter for the protein sequence.
getSequence(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getSequence() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the sequence.
getSequence(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
 
getSequence(String) - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
Returns the protein sequence for the given accession.
getSequence() - Method in interface com.compomics.util.interfaces.Sequence
This method will retrieve the sequence.
getSequence() - Method in class com.compomics.util.nucleotide.NucleotideSequence
This method reports on the nucleotide sequence.
getSequence() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
This method will retrieve the sequence.
getSequence() - Method in class com.compomics.util.protein.AASequenceImpl
Simple getter for the sequence.
getSequence() - Method in class com.compomics.util.protein.Protein
This method reports on the sequence for the current protein.
getSequenceCoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the sequence coverage of the protein of interest.
getSequenceIterator(String, DigestionParameters, double, double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
Returns a sequence iterator for the given protein sequence and digestion preferences.
getSequenceMatchingParameters() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Returns the sequence matching preferences to use when mapping modifications on amino acid sequences.
getSequenceMatchingParameters() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns the sequence matching parameters.
getSequenceMatchingPreferences() - Method in class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
Returns the sequence matching settings as set by the user.
getSequenceMatchingType() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns the sequence matching type.
getSequenceProbabilities(Peptide, ArrayList<Modification>, ModificationParameters, Spectrum, SequenceProvider, AnnotationParameters, SpecificAnnotationParameters, boolean, SequenceMatchingParameters, SequenceMatchingParameters, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.modification.scores.PhosphoRS
Returns the PhosphoRS sequence probabilities for the modification possible locations.
getSerializationFolder() - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Returns the folder where to save the factory.
getSerializationFolder() - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the folder where the factory is saved.
getShortDescription() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns a short description of the parameters.
getShortName() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Getter for the short modification name.
getSimpleDescription(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getSimpleDescription(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
Returns the simple description of the protein with the given accession.
getSimpleLinearRegression(ArrayList<Double>, ArrayList<Double>) - Static method in class com.compomics.util.math.statistics.linear_regression.LinearRegression
Returns a simple linear regression.
getSimpleLinearRegressionOutlierRemoval(ArrayList<Double>, ArrayList<Double>, Double) - Static method in class com.compomics.util.math.statistics.linear_regression.LinearRegression
Returns a simple linear regression performed after outlier removal.
getSimpleProteinDescription() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns a simplified protein description for a UniProt header.
getSimplifyGroups() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns a boolean indicating whether the protein groups should be simplified.
getSimplifyGroupsConfidence() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns a boolean indicating whether the protein groups should be simplified based on the peptide confidence.
getSimplifyGroupsEnzymaticity() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns a boolean indicating whether the protein groups should be simplified based on the peptide enzymaticity.
getSimplifyGroupsEvidence() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns a boolean indicating whether the protein groups should be simplified based on the Uniprot evidence level.
getSimplifyGroupsVariants() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns a boolean indicating whether the protein groups should be simplified based on the peptide variant matching.
getSingleAAModification(Modification) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns a clone of the given Modification targeting a single amino acid instead of a pattern.
getSingleAAModification(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns a clone of the given Modification targeting a single amino acid instead of a pattern.
getSingleChargeWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Returns the window size for singly charged ions.
getSingleLetterCodeAsChar() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the single letter code as character.
getSite() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Getter for the modification site.
getSite(int, int) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns the 1-based index on the peptide.
getSkylinePath() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns the skyline path.
getSmallestCumulativeProbabilityAt(double) - Method in interface com.compomics.util.math.statistics.Distribution
Returns the cumulative density function value at a given position, starting from the low values if before the median, from the high otherwise.
getSmallestCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
 
getSmallestCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
 
getSmallestCumulativeProbabilityAt(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
 
getSoftwareVersions() - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
Returns the names and versions of the software used to generate the identification file in a map, e.g., Mascot > (2.2 and 2.3) and X!Tandem > Sledgehammer (2013.09.01.1).
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
 
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
 
getSortedEnzymeNames() - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Get the sorted list of enzyme names.
getSortedFeaturesList() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
Returns a sorted list of features categories.
getSortedImplementedIons() - Static method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Returns an ordered list of possible subtypes.
getSortedPeptideKeys(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns a sorted list of peptide keys from the protein of interest.
getSortedPsmKeys(long, boolean, boolean) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the ordered list of spectrum keys for a given peptide.
getSortedTermNames() - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Returns a sorted list of all GO Terms names linked to proteins in the proteinToGoMap.
getSortPsmsOnRt() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns true if the PSMs are sorted on retention time, false sorts on PSM score.
getSource() - Method in class com.compomics.util.gui.events.RescalingEvent
Returns the JPanel source.
getSource() - Method in class com.compomics.util.pride.prideobjects.Instrument
Returns the instrument source.
getSourceFile() - Method in class com.compomics.util.io.ftp.FTP
This method reports on the sourcefile currently used in transfer.
getSpAccession() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Returns the SP accession.
getSpAccession() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Returns the SP accession.
getSparklineColor() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Getter for the sparkline color.
getSparklineColorDoubtful() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the color for a doubtful sparkline bar chart plots.
getSparklineColorFalsePositives() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the color for false positives in sparkline bar chart plots.
getSparklineColorNonValidated() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Getter for the non-validated sparkline color.
getSparklineColorNotFound() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the color for a not found sparkline bar chart plots.
getSparklineColorPossible() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the color for a possible sparkline bar chart plots.
getSpeciesDescription(TreeMap<String, Integer>) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns a listing of the species occurrence map provided.
getSpecificAnnotationParameters(String, String, SpectrumIdentificationAssumption, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpectrumAnnotator) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the annotation preferences specific to a spectrum and an identification assumption.
getSpecificity(String) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Returns the expected specificity of the given enzyme.
getSpecificity(int) - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
Returns the specificity of the given index.
getSpecificityAt(double) - Method in class com.compomics.util.math.roc.DataRoc
 
getSpecificityAt(double) - Method in class com.compomics.util.math.roc.DistributionRoc
 
getSpecificityAt(double) - Method in interface com.compomics.util.math.statistics.ROC
Returns the 1-specificity at a given sensitivity.
getSpectrum() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileIterator
 
getSpectrum(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
Returns the spectrum with the given title.
getSpectrum(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getSpectrum(BufferedRandomAccessFile, long, String) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
Returns the next spectrum starting from the given index.
getSpectrum() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileIterator
 
getSpectrum(BufferedRandomAccessFile, long) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the next spectrum starting from the given index.
getSpectrum(String, String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getSpectrum() - Method in interface com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
Returns the spectrum corresponding to the title returned by the last call to the next() method.
getSpectrum() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator
 
getSpectrum(String, String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the spectrum with the given title in the given file.
getSpectrumAnnotatedMirroredPeakColor() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the color to use for the annotated mirrored peaks.
getSpectrumAnnotatedPeakColor() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the color to use for the annotated peaks.
getSpectrumAnnotatedPeakWidth() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the width of the annotated peaks.
getSpectrumAnnotation(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the spectrum annotations of a spectrum in a list of IonMatches using the intensity filter.
getSpectrumAnnotation(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the spectrum annotations of a spectrum in a list of IonMatches.
getSpectrumAnnotation(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the spectrum annotations of a spectrum in an array of IonMatches.
getSpectrumAnnotation(AnnotationParameters, ModificationParameters, SequenceMatchingParameters, SpecificAnnotationParameters, String, String, Spectrum, Tag) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
getSpectrumAnnotation(AnnotationParameters, ModificationParameters, SequenceMatchingParameters, SpecificAnnotationParameters, String, String, Spectrum, Tag, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
Returns the spectrum annotations of a spectrum in a list of IonMatches.
getSpectrumAnnotation(IonMatch[]) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel.
getSpectrumAnnotationStream(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the spectrum annotations of a spectrum in a list of IonMatches using the intensity filter.
getSpectrumAnnotationStream(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the spectrum annotations of a spectrum in a list of IonMatches.
getSpectrumAnnotationStream(AnnotationParameters, SpecificAnnotationParameters, String, String, Spectrum, Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Returns the spectrum annotations of a spectrum in a stream of IonMatches.
getSpectrumBackgroundPeakColor() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the color to use for the background peaks.
getSpectrumBackgroundPeakWidth() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the width of the background peaks.
getSpectrumCharges() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the spectrum charges to search for.
getSpectrumCount() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Returns the number of spectra matched.
getSpectrumCounting(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the spectrum counting metric of the protein match of interest using the preference settings.
getSpectrumCounting(long, SpectrumCountingMethod) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the spectrum counting metric of the protein match of interest for the given method.
getSpectrumFile() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns the name of the file where this spectrum was found.
getSpectrumFileId() - Method in class com.compomics.util.io.PklFile
 
getSpectrumFolder() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the last used spectrum folder.
getSpectrumIdentification() - Method in class com.compomics.util.experiment.identification.Identification
Returns a map of the spectrum matches keys indexed by spectrum file name.
getSpectrumIdentificationKeys() - Method in class com.compomics.util.experiment.identification.Identification
Returns the keys of all the spectrum matches in the db.
getSpectrumIdentificationSize() - Method in class com.compomics.util.experiment.identification.Identification
Returns the number of spectrum identifications.
getSpectrumIndex(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the spectrum index corresponding to the desired spectrum, i.e., returns 0 for the first spectrum in the file, 1 for the second, etc.
getSpectrumMatch(long) - Method in class com.compomics.util.experiment.identification.Identification
Returns the spectrum match with the given key.
getSpectrumMatchesIterator(long[], WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Returns a spectrum matches iterator for a given key list.
getSpectrumMatchesIterator(WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Returns a spectrum matches iterator for all SpectrumMatches.
getSpectrumMatchesIterator(WaitingHandler, String) - Method in class com.compomics.util.experiment.identification.Identification
Returns a psm iterator for all SpectrumMatches.
getSpectrumMatchesKeys() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Returns the keys of all spectra matched.
getSpectrumTitle() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns the title of the spectrum.
getSpectrumTitle(int) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns the spectrum title corresponding to the given spectrum number.
getSpectrumTitles(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
 
getSpectrumTitles() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns an ordered list of all spectrum titles.
getSpectrumTitles(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
 
getSpectrumTitles(String) - Method in interface com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Returns the spectrum titles for the given mass spectrometry file name.
getSpEnd() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Returns the SP end.
getSpStart() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
Returns the SP start.
getSqtOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the sqt output is to be created.
getStandardGeneticCode() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the standard genetic triplets associated to this amino acid.
getStandardGeneticCode() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getStandardGeneticCodeForCombination() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the genetic code as combination of the sub amino acid genetic codes.
getStandardHeight() - Method in class com.compomics.util.io.export.styles.DefaultStyle
 
getStandardHeight() - Method in interface com.compomics.util.io.export.WorkbookStyle
Returns the height of a standard line.
getStandardSearchPattern() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Computes a pattern which can be searched by standard search engines, i.e., a pattern targeting a single amino acid and not a complex pattern.
getStandardStyle() - Method in class com.compomics.util.io.export.styles.DefaultStyle
 
getStandardStyle(int) - Method in class com.compomics.util.io.export.styles.DefaultStyle
 
getStandardStyle() - Method in interface com.compomics.util.io.export.WorkbookStyle
Returns the standard cell style.
getStandardStyle(int) - Method in interface com.compomics.util.io.export.WorkbookStyle
Returns the standard cell style for the given hierarchical depth.
getStandardUnit(String) - Static method in enum com.compomics.util.experiment.units.StandardUnit
Returns the standard unit having the given full name.
getStarred() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns whether a match is starred or not.
getStart() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Get the start value.
getStart() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the start.
getStartBlock() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Returns the block start.
getStartLocation() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method reports on the start index of the header.
getStartPosition() - Method in class com.compomics.util.pdbfinder.das.readers.StartEndPosition
Returns the start position.
getStartProtein() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Returns the protein start.
getStdDown() - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
Returns the standard deviation to the left of the distribution.
getStdUp() - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
Returns the standard deviation to the right of the distribution.
getStoreSpectraFileName() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the name of the file where the binary spectra are to be stored.
getStringMatching() - Static method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns preferences for simple string matching.
getStringParameter(String) - Method in class com.compomics.util.experiment.ProjectParameters
 
getStringValue(boolean, boolean, boolean, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Sets the string value from the stringValue attribute, sets it from the composition if not set.
getStyle(ExcelWriter) - Static method in class com.compomics.util.io.export.styles.DefaultStyle
Returns the style attached to that writer or create a new one if none found.
getSubAminoAcids() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
In case of a combination of amino acids, returns the comprised amino acids or amino acid groups represented by their single letter code including sub combinations.
getSubAminoAcids(boolean) - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
In case of a combination of amino acids, returns the comprised amino acids or amino acid groups represented by their single letter code.
getSubFolder() - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFolder
Returns the sub-folder where to write cms files.
getSubMatrix(int, int, int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getSubNumber() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Returns the number of the fragment in the current amino acid sequence.
getSubPattern(int, int, boolean) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns a sub pattern of the pattern.
getSubPattern(int, boolean) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns a sub pattern of the pattern.
getSubsequence(String, int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getSubsequence(String, int, int) - Method in class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
 
getSubsequence(String, int, int) - Method in interface com.compomics.util.experiment.io.biology.protein.SequenceProvider
Returns the subsequence of the sequence of a given protein.
getSubstitutedAminoAcid() - Method in class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
 
getSubstitutionAminoAcids(Character) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Returns the possible substituted amino acids for the given amino acid as a list of their single letter code.
getSubstitutionAminoAcids() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Returns the possible substituted amino acids.
getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
 
getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
 
getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
 
getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
 
getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
 
getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
 
getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
 
getSubType() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
 
getSubType() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the ion subtype.
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
 
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
 
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
 
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
 
getSubTypeAsString(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Returns the type of fragment ion as a letter.
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
 
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
 
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
 
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
 
getSubTypeAsString(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Returns the type of fragment ion as a letter.
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the subtype as string.
getSummary(String, FastaParameters, WaitingHandler) - Static method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Gathers summary data on the FASTA file content.
getSummary(String, FastaParameters, boolean, WaitingHandler) - Static method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Gathers summary data on the FASTA file content.
getSupportedExtensions() - Static method in interface com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
Returns the supported extensions.
getTable() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
Returns the JTable containing the items.
getTable() - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
Returns the JTable for which to hide/show the column for.
getTable() - Method in class com.compomics.util.gui.XYPlottingDialog
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.AlignedTableCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.ByteArrayRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.FragmentIonTableCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.TimestampRenderer
 
getTableName() - Method in class com.compomics.util.db.DBMetaData
This method reports on the tablename.
getTableTooltips() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
Returns the tooltips used for the column headers.
getTag() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
Returns the tag to annotate.
getTag() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
Returns the tag of this assumption.
getTagAssumptionsMap() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns the tag assumptions map: advocate id > score > list of assumptions.
getTaggedModifiedSequence(ModificationParameters, SequenceProvider, SequenceMatchingParameters, boolean, boolean, boolean, HashSet<String>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the modified sequence as an tagged string with potential modification sites color coded or with Modification tags, e.g, <mox>.
getTaggedModifiedSequence(ModificationParameters, boolean, boolean, boolean, boolean, SequenceMatchingParameters, HashSet<String>) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the modified sequence as an tagged string with potential modification sites color coded or with modification tags, e.g, <mox>.
getTaggedModifiedSequence(ModificationParameters, Tag, boolean, boolean, boolean, boolean, SequenceMatchingParameters, HashSet<String>) - Static method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the modified sequence as an tagged string with potential modification sites color coded or with modification tags, e.g, <mox>.
getTaggedModifiedSequence(ModificationParameters, String, String[], String[], String[], String[], boolean, boolean) - Static method in class com.compomics.util.experiment.identification.utils.ModificationUtils
Returns the modified sequence as a tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
getTaggedModifiedSequence(Peptide, ModificationParameters, String[], String[], String[], String[], String[], String[], boolean, boolean, boolean) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the modified sequence as an tagged string with potential modification sites color coded or with Modification tags, e.g, <mox>.
getTaggingTimeSeconds() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the tagging time in seconds as listed in the file.
getTagLength() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the tag length.
getTagModificationsAsString(Tag) - Static method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns the tag modifications as a string.
getTagParameter(String) - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the tagging parameter corresponding to a given parameter name.
getTagsGenerator() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the tags generator used to create the file.
getTagsGeneratorVersion() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the version of the tags generator used to create the file.
getTagsParametersNames() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the name of the different parameters names found.
getTarget() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the index of the amino acid of interest in the pattern.
getTargetDecoyFileNameSuffix() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Returns the target-decoy file name suffix.
getTargetedAA(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the targeted amino acids at a given index in the pattern.
getTaxonomy(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
getTaxonomy() - Method in class com.compomics.util.experiment.io.biology.protein.Header
Returns the taxonomy.
getTaxonomy(String) - Method in interface com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
Returns the taxonomy for the given protein.
getTaxons() - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
Returns the taxons in this map.
getTaxons() - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
Returns the taxons in this map.
getTermAccession(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Returns the accession of a GO term.
getTermDomain(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoDomains
Returns the description of a GO term.
getTermName(String) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Returns the name of a GO term.
GettersAndSetters - Class in com.compomics.util.db.components
This class will generate (and subsequently output upon request) all relevant getters and setters for a DBAccessor.
GettersAndSetters() - Constructor for class com.compomics.util.db.components.GettersAndSetters
Empty default constructor
GettersAndSetters(DBMetaData) - Constructor for class com.compomics.util.db.components.GettersAndSetters
The constructor takes care of generating all getters and setters, based on the speicifed metadata.
getTextOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the text output is to be created.
getTheoreticalFragmentIonsSumOnly() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns true if the theoretical fragment ions are calculated on the sum in the bin alone.
getTheoreticMass() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the theoretic mass, from the atomic composition if available, from the theoreticMass field otherwise.
getTheoreticMass() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
 
getTheoreticMass() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
 
getTheoreticMass(boolean, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
Returns the theoretic mass of the tag, eventually without terminal gaps.
getTheoreticMass() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the theoretic mass of the given assumption.
getTheoreticMz(Integer) - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the m/z expected for this ion at the given charge.
getTheoreticMz(boolean, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
Returns the theoretic mass of the tag, eventually without terminal gaps.
getTheoreticMz() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Returns the theoretic m/z.
getThermoRawFileParserParameters() - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui.ThermoRawFileParserParametersDialog
Returns the parameters as created by the user.
getTicCutoffPercentage() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the TIC cutoff in percent.
getTicCutoffPercentage() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns the TicCutoffPercentage.
getTiesResolution() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns the ties resolution method to use when multiple peaks can be assigned to an ion.
getTimeEnd() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the ending time of the tagging as given in the file.
getTimeStart() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
Returns the starting time of the tagging as given in the file.
getTip(String, String, ArrayList<String>) - Static method in class com.compomics.util.messages.FeedBack
Creates a tip object.
getTip(String, String) - Static method in class com.compomics.util.messages.FeedBack
Creates a general tip with no key word.
getTitle() - Method in interface com.compomics.util.interfaces.Modification
This method returns the title of the modification, eg.
getTitle() - Method in interface com.compomics.util.io.export.ExportFeature
Returns the column title of the feature.
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
 
getTitle() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
 
getTitle() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
 
getTitle() - Method in class com.compomics.util.messages.FeedBack
Returns the title.
getTitle() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Returns the title.
getTitle() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Returns the title.
getTitle() - Method in class com.compomics.util.protein.Enzyme
Simple getter for the title (name) of the Enzyme.
getTitle() - Method in class com.compomics.util.protein.ModificationImplementation
This method returns the title of the modification, eg.
getTitle() - Method in class com.compomics.util.protein.ModificationTemplate
This method returns the title of the modification, eg.
getTooltipMap() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns the default map of icons for the validation levels.
getTopPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the top peaks number.
getTopPeaksWindow() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns the top peaks window size.
getTotalIntensity() - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Returns the total intensity of the peaks above the intensity threshold.
getTotalIntensity() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Returns the total intensity of the spectrum.
getTotalIntensity() - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Method calculates the total intensity of the peaks
getTotalIntensity() - Method in interface com.compomics.util.interfaces.SpectrumFile
This method returns the total intensity contributed by all the ions in this spectrum.
getTotalPartitions() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns total partitions.
getTotalPeptidesPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the total number of peptides per fraction.
getTotalSpectrumCounting() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the total spectrum counting.
getTotalSpectrumCountingMass() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the total spectrum counting masses.
getTrace() - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
getTransformedScore() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the log transformed score.
getTrimMs1Peaks() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if Ms1 peaks are to be trimmed.
getTrimMsMsPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if MsMs peaks are to be trimmed.
getTruncatedSequence(int, int) - Method in class com.compomics.util.protein.AASequenceImpl
This method will return an AASequenceImpl that represents an internal truncation of the current sequence.
getTruncationPosition() - Method in class com.compomics.util.protein.Protein
This method reports on the position of the truncation.
getTrypsinExample() - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the trypsin example as amino acid pattern.
getType() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the ion type.
getType() - Method in class com.compomics.util.experiment.identification.Advocate
Returns the type of advocate.
getType() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Return the type of the filter.
getType() - Method in class com.compomics.util.experiment.identification.IdentificationMatch
Returns the type of match.
getType() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
 
getType() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
 
getType() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
 
getType() - Method in class com.compomics.util.experiment.io.parameters.DummyParameters
 
getType() - Method in interface com.compomics.util.experiment.io.parameters.MarshallableParameter
Returns the type of marshalled parameter from an unmarshalled object.
getType() - Method in class com.compomics.util.experiment.patient.PatientInformation
Returns the type of information.
getType() - Method in class com.compomics.util.messages.FeedBack
Returns the feedback type.
getType() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
 
getType() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
 
getType() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the type.
getType() - Method in class com.compomics.util.pride.prideobjects.webservice.query.PrideFilter
Returns the filter type.
getTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the type of ion as string.
getTypeAsString(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.ions.Ion
Returns the type of ion as string.
getTypeAsString() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Returns a string with the different database types found.
getTypeCategory() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the type category.
getTypeForGenomeDivision(EnsemblGenomesSpecies.EnsemblGenomeDivision) - Method in class com.compomics.util.gui.genes.SpeciesDialog
Deprecated.
Returns the display name of an Ensembl genome division.
getTypeId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the type ID.
getTypeReference() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the type reference.
getTypesAsString() - Static method in enum com.compomics.util.experiment.biology.modifications.ModificationType
Returns all of the modification type options as a string.
getTypeSubparts() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the type subparts.
getTypeSuperparts() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns the type super parts.
getUnevenRowColor() - Method in class com.compomics.util.AlternateRowColoursJTable
This method returns the Color used for the uneven numbered rows, or 'null' if the default JTable background color is maintained for these rows.
getUniModAccessionLink(String) - Method in class com.compomics.util.gui.modification.ModificationsDialog
Returns a web link to the given Unimod CV term at http://www.unimod.org.
getUnimodCvTerm() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns the Unimod CV term associated with this modification.
getUniprotTaxonomy() - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the UniProt taxonomy mapping.
getUniprotTaxonomyFile(String) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Returns the UniProt taxonomy file.
getUniqueAminoAcids() - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns a char array of the one letter code of amino acids without combinations of amino acids.
getUniqueIndex(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns an index for the amino acid excluding combinations.
getUnit() - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Returns the unit used for normalization.
getUpperClearMzRange() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Returns the upper mass value for the clear mz range.
getUpperPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Returns the upper precursor mass.
getUrlOfZippedVersion(URL, String, boolean) - Static method in class com.compomics.software.autoupdater.WebDAO
Gets the first zip file from a URL, in case of a Maven repo deploy this should be the only zip in the folder.
getUrParam(UrParameter) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Returns the refinement parameter of the same type than the one provided.
getUrParams() - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Returns the user parameters map.
getUseDeltaScore() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true of delta score is to be used.
getUseFlankingPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if flanking peaks are to be used.
getUseGeneMapping() - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Returns a boolean indicating whether gene mappings should be used.
getUseNeutralLossPeaks() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns true if the neutral loss peaks are to be used.
getUseProvidedPrecursorInfo() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true of the provided precursor info is to be used.
getUserAdvocates() - Static method in class com.compomics.util.experiment.identification.Advocate
Returns the map of user advocates imported.
getUserModifications() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the names of the user defined modifications.
getUserModificationsOrdered() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Returns the alphabetically (case insensitive) ordered names of the user defined modifications.
getUserParametersFile() - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the user preferences file to be used.
getUserParametersFolder() - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns the user preferences file to be used.
getUserSelectedFile(Component, String, String, String, String, String, boolean) - Static method in class com.compomics.util.gui.file_handling.FileChooserUtil
Returns the file selected by the user, or null if no file was selected.
getUserSelectedFile(Component, String[], String[], String, String, String, boolean, boolean, boolean, int) - Static method in class com.compomics.util.gui.file_handling.FileChooserUtil
Returns the file selected by the user, or null if no file was selected.
getUserSelectedFolder(Component, String, String, String, String, boolean) - Static method in class com.compomics.util.gui.file_handling.FileChooserUtil
Returns the folder selected by the user, or null if no folder was selected.
getUseSmartPlusThreeModel() - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Returns true if the UseSmartPlusThreeModel is to be used.
getUseSparseMatrix() - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Deprecated.
from Comet release 2015.02 all searches use this internal data representation by default
getUtilitiesEnzyme(String) - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Returns the enzyme associated to the given cvTerm.
getUtilitiesModificationName(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Tries to convert a modification name to a utilities modification name.
getUtilitiesModificationName(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns the name of the modification indexed by the given index.
getUtilitiesPtmName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
Returns the utilities PTM name corresponding to the given Novor PTM short name.
getUtilitiesPtmName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Returns the utilities PTM name corresponding to the given PepNovo PTM name.
getUtilitiesPtmName(Character) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Returns the utilities PTM name corresponding to the given pNovo PTM character.
getUtilitiesUserParameters() - Method in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent
Returns the utilities user preferences.
getValidatedPeptidesPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the number of validated peptides per fraction.
getValidatedProteinList() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Returns a list of validated proteins.
getValidatedProteins(FilterParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the list of validated protein keys.
getValidatedProteins(WaitingHandler, FilterParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the list of validated protein keys.
getValidatedSequenceCoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns the sequence coverage of the protein of interest.
getValidatedSpectraPerFraction() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns the number of validated spectra per fraction.
getValidatedTargetProteinKeys() - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Returns the keys of the validated target protein matches.
getValidationLevelIndexes() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns an array of the validation level indexes in ascending order of confidence.
getValidationLevels() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns the implemented validation levels.
getValidationLevelsNames() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns a list of the names of the implemented validation levels.
getValidationQCParameters() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Returns the validation QC preferences as set by the user.
getValidationQCParameters() - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Returns the validation QC preferences.
getValue(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Returns the value used for comparison for a given filtering item.
getValue(int) - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
Returns the value set for a given filter.
getValue() - Method in interface com.compomics.util.interfaces.TableValueWrapper
This method returns the Object that this instance wraps around.
getValue() - Method in class com.compomics.util.pride.CvTerm
Returns the value.
getValue() - Method in class com.compomics.util.pride.prideobjects.webservice.query.PrideFilter
Returns the filter value.
getValue() - Method in class com.compomics.util.sun.SwingWorker
Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValueAt(int, int) - Method in class com.compomics.util.db.DBResultSet
Returns the value for the cell at columnIndex and rowIndex.
getValueAt(int, int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
 
getValueAt(int, int) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
 
getValueAt(int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
Returns the value of the matrix at given indexes.
getValueAt(double) - Method in class com.compomics.util.math.roc.DataRoc
 
getValueAt(double) - Method in class com.compomics.util.math.roc.DistributionRoc
 
getValueAt(double) - Method in interface com.compomics.util.math.statistics.ROC
Returns the sensitivity at a given 1-specificity, i.e., 1-type 2 error, the number of true healthy for a given type 1 error, the number of false healthy.
getValueAt(int, int) - Method in class com.compomics.util.sun.TableMap
 
getValueAt(int, int) - Method in class com.compomics.util.sun.TableSorter
 
getValueAtCumulativeProbability(double) - Method in interface com.compomics.util.math.statistics.Distribution
The value after which the cumulative density function will be smaller than p.
getValueAtCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
 
getValueAtCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
 
getValueAtCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
 
getValueAtDescendingCumulativeProbability(double) - Method in interface com.compomics.util.math.statistics.Distribution
The value after which the cumulative density function will be smaller than p when starting from high values.
getValueAtDescendingCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
 
getValueAtDescendingCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
 
getValueAtDescendingCumulativeProbability(double) - Method in class com.compomics.util.math.statistics.distributions.NormalDistribution
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns the van der Waals volume in Ã…3.
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
getVanDerWaalsVolume() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
getVariableModifications() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Getter for the modifications carried by this sequence in a map: aa number > modification matches.
getVariableModifications() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the variable modifications.
getVariableModifications() - Method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Returns eventual modifications found.
getVariableModifications() - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Returns the expected variable modification names included in this profile.
getVariableModificationsAsString(ModificationMatch[]) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the peptide modifications as a string.
getVariableModificationsAsString(Peptide) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns the peptide modifications as a string.
getVariantMatches() - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns the sequence variant matches of this peptide indexed by protein accession and peptide start.
getVariantMatches() - Method in class com.compomics.util.experiment.identification.matches.PeptideVariantMatches
Returns the map of variants indexed by 0 based position on the peptide.
getVariantMatches(ArrayList<PeptideProteinMapping>) - Static method in class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Returns the variant matches summarized in a map indexed by protein accession and peptide index on the protein sequence.
getVariantType() - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Returns whether the specific variant count limitations should be used.
getVennDiagramPanel() - Method in class com.compomics.util.gui.VennDiagramDialog
Returns the Venn diagram panel.
getVerbosity() - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Returns the verbosity type of progress output.
getVersion() - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
Returns the version of the features used to create the map.
getVersion() - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Returns the database version.
getVersion() - Static method in class com.compomics.util.Util
Retrieves the version number set in the pom file.
getVersionNumber() - Method in class com.compomics.software.autoupdater.MavenJarFile
Returns the version number.
getViewIndex(int) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Returns the view index of the given row.
getVisibleColumns() - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
Returns the list of visible columns.
getVisibleColumns() - Method in class com.compomics.util.gui.XYPlottingDialog
 
getWaitingIcon() - Method in class com.compomics.util.gui.VennDiagramDialog
 
getWaitingIcon() - Method in class com.compomics.util.gui.XYPlottingDialog
 
getWarning(String, String) - Static method in class com.compomics.util.messages.FeedBack
Creates a warning object.
getWindowIndexes(Spectrum, double, double) - Static method in class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
Returns the start (inclusive) and end (exclusive) indexes of the peaks between mzMin (inclusive) and mzMax (exclusive).
getWindowWidthThomsons() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns the window width in Thomson.
getWorkbook() - Method in class com.compomics.util.io.export.writers.ExcelWriter
Return the workBook.
getWorkbookStyle() - Method in class com.compomics.util.io.export.writers.ExcelWriter
Returns the workbook style.
getWriteMzId() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if mzId output is to be created.
getWritePepXml() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if pepXML output is to be created.
getWriter() - Method in class com.compomics.util.io.flat.SimpleFileWriter
Returns the underlying buffered writer.
getX() - Method in class com.compomics.util.XYZDataPoint
Returns the x value.
getXAxisData() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the x-axis data.
getXAxisZoomRangeLowerValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the lower range for the current zoom range.
getXAxisZoomRangeUpperValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the upper range for the current zoom range.
getXTandemFormat() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Get the X!Tandem enzyme format.
getxYValues() - Method in class com.compomics.util.math.roc.DataRoc
 
getxYValues() - Method in class com.compomics.util.math.roc.DistributionRoc
 
getxYValues() - Method in interface com.compomics.util.math.statistics.ROC
Returns xy values to draw the curve.
getY() - Method in class com.compomics.util.XYZDataPoint
Returns the y value.
getYAxisData() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the y-axis data.
getZ() - Method in class com.compomics.util.XYZDataPoint
Returns the z value.
gif - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
GIF - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
GLUTAMIC_ACID - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Glutamic acid immonium ion.
GlutamicAcid - Class in com.compomics.util.experiment.biology.aminoacids.impl
Glutamic Acid.
GlutamicAcid() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
Constructor.
Glutamine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Glutamine.
Glutamine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
Constructor.
GLUTAMINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Glutamine immonium ion.
Glycan - Class in com.compomics.util.experiment.biology.ions.impl
This class represents a glycan.
Glycan() - Constructor for class com.compomics.util.experiment.biology.ions.impl.Glycan
Empty default constructor
Glycan(String, String) - Constructor for class com.compomics.util.experiment.biology.ions.impl.Glycan
Constructor for a glycan.
Glycine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Glycine.
Glycine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
Constructor.
GLYCINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Glycine immonium ion.
GO_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
The suffix to use for files containing GO mappings.
GoDomains - Class in com.compomics.util.experiment.biology.genes.go
Class parsing go domains and storing them in a map.
GoDomains() - Constructor for class com.compomics.util.experiment.biology.genes.go.GoDomains
Constructor.
GoMapping - Class in com.compomics.util.experiment.biology.genes.go
Class parsing BioMart protein go mappings and storing them in maps.
GoMapping() - Constructor for class com.compomics.util.experiment.biology.genes.go.GoMapping
Constructor.
GraphicsPanel - Class in com.compomics.util.gui.spectrum
This class presents a JPanel that will hold and display a mass spectrum or a chromatogram.
GraphicsPanel() - Constructor for class com.compomics.util.gui.spectrum.GraphicsPanel
Empty default constructor
GraphicsPanel.DrawingStyle - Enum in com.compomics.util.gui.spectrum
An enumerator of the possible GraphicsPanel types.
GraphicsPanel.GraphicsPanelType - Enum in com.compomics.util.gui.spectrum
An enumerator of the possible GraphicsPanel types.
GraphicsPanelTableCellRenderer - Class in com.compomics.util.gui.renderers
A table cell renderer for GraphicsPanels.
GraphicsPanelTableCellRenderer() - Constructor for class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer
Empty default constructor
GraphicsPanelTableCellRenderer(double, double) - Constructor for class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer
Create a new GraphicsPanelTableCellRenderer with a given x-axis range to ensure that all spectra in the column have the same range.
gson - Variable in class com.compomics.util.io.json.JsonMarshaller
GSON parser instance to convert JSON to Java objects and back.
guiDefaultOption - Static variable in enum com.compomics.util.io.export.ExportFormat
The default export format to use for GUI exports.
GUIFileDAO - Class in com.compomics.software.autoupdater
GUIFileDAO.
GUIFileDAO() - Constructor for class com.compomics.software.autoupdater.GUIFileDAO
 
GuiUtilities - Class in com.compomics.util.gui
A class containing simple GUI helper methods.
GuiUtilities() - Constructor for class com.compomics.util.gui.GuiUtilities
 
gunzipFile(File, boolean) - Static method in class com.compomics.util.io.compression.GzUtils
Uncompresses the given gz file to the given destination file.
gunzipFile(File, File, boolean) - Static method in class com.compomics.util.io.compression.GzUtils
Uncompresses the given gz file to the given destination file.
GZ_EXTENSION - Static variable in class com.compomics.util.io.compression.GzUtils
The extension to use for gz files.
gzFile(File, boolean) - Static method in class com.compomics.util.io.compression.GzUtils
Gzip a file.If the gz file already exists it will be silently overwritten.
gzFile(File, File, boolean) - Static method in class com.compomics.util.io.compression.GzUtils
Gzip a file.If the gz file already exists it will be silently overwritten.
gzipTemp - Variable in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
If true, temp files are gzipped.
GzUtils - Class in com.compomics.util.io.compression
Convenience methods to work with gzipped files.
GzUtils() - Constructor for class com.compomics.util.io.compression.GzUtils
 

H

H - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
H - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The hydrogen atom.
H2O - Static variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
H2O loss.
H3PO4 - Static variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
H3PO4 loss.
halfGbFree() - Static method in class com.compomics.util.memory.MemoryConsumptionStatus
Indicates whether a GB of memory is free.
handleError(String, String, Throwable) - Static method in class com.compomics.cli.peptide_mapper.PeptideMapperCLI
 
handleParameters(String[]) - Static method in class com.compomics.cli.peptide_mapper.PeptideMapperCLI
 
hasAddenda() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method reports on the presence of addenda for this header.
hasArgument - Variable in enum com.compomics.cli.enzymes.EnzymesCLIParams
Boolean indicating whether this command line option needs an argument.
hasArgument - Variable in enum com.compomics.cli.fasta.FastaParametersCLIParams
Boolean indicating whether this command line option needs an argument.
hasArgument - Variable in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Boolean indicating whether this command line option needs an argument.
hasArgument - Variable in enum com.compomics.cli.modifications.ModificationsCLIParams
Boolean indicating whether this command line option needs an argument.
hasArguments() - Method in class com.compomics.util.general.CommandLineParser
This method returns 'true' if any arguments are present, 'false' otherwise.
hasChannels() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
 
hasChannels() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
 
hasChannels() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
 
hasChannels() - Method in interface com.compomics.util.io.export.features.ReporterExportFeature
Indicates whether the feature is channel dependent.
hasCombination(String) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether the given sequence contains an amino acid which is in fact a combination of amino acids.
hasCombination(IntStream) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether the given sequence contains an amino acid which is in fact a combination of amino acids.
hasCombination(char[]) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether the given sequence contains an amino acid which is in fact a combination of amino acids.
hasDeNovoTags() - Method in interface com.compomics.util.experiment.io.identification.IdfileReader
Returns a boolean indicating whether the file contains de novo results as tags.
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
 
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
 
hasEnzymaticPeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Returns true if the leading protein of the given group has any enzymatic peptides.
hasEnzymes() - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Returns a boolean indicating whether enzyme settings were set.
hasFlag(String) - Method in class com.compomics.util.general.CommandLineParser
This method test whether the specified flag was set on the command line.
hasGoMappings() - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Indicates whether the GO maps are populated.
hashCode() - Method in class com.compomics.util.BinaryArrayImpl
 
hashCode() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
 
hashCode() - Method in class com.compomics.util.protein.ModificationImplementation
Returns a hash code value for the object.
hashCode() - Method in class com.compomics.util.protein.ModificationTemplate
Returns a hash code value for the object.
hasInput() - Method in class com.compomics.cli.paths.PathSettingsCLIInputBean
Indicates whether the user gave some path configuration input.
hasInput() - Method in class com.compomics.util.gui.filtering.FilterDialog
Indicates whether something was input for the filter.
hasModificationIndexes() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Indicates whether the modification profile has PTM indexes.
hasModificationIndexes() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether the modification profile has PTM indexes.
hasNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.Ion
Indicates whether the ion has a neutral loss.
hasNormalizationFactors() - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Indicates whether normalization factors are set.
hasPeptideAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Indicates whether the spectrum match contains a peptide assumption.
hasPeptideAssumption(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Indicates whether the spectrum match contains a peptide assumption for the given advocate (see the Advocate class).
hasPeptideNormalisationFactors() - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Indicates whether the peptide normalization factors are set.
hasProteinNormalisationFactors() - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Indicates whether the protein normalization factors are set.
hasPsmNormalisationFactors() - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Indicates whether the PSM normalization factors are set.
hasQcFilters() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Indicates whether QC filters were implemented for this match.
hasTagAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Indicates whether the spectrum match contains a tag assumption.
hasTagAssumption(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Indicates whether the spectrum match contains a tag assumption for the given advocate (see the Advocate class).
HCNO - Static variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
HCNO loss.
He - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The helium atom.
HEAD_SECTION - Static variable in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Key for the head section.
Header - Class in com.compomics.util.experiment.io.biology.protein
This class represents the header for a Protein instance.
HEADER_LENGTH - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileWriter
The length of the file header.
HeaderIterator - Class in com.compomics.util.experiment.io.biology.protein.iterators
Iterator for the headers of a FASTA file.
HeaderIterator(File) - Constructor for class com.compomics.util.experiment.io.biology.protein.iterators.HeaderIterator
Constructor without sanity check.
HeadlessFileDAO - Class in com.compomics.software.autoupdater
HeadlessFileDAO.
HeadlessFileDAO() - Constructor for class com.compomics.software.autoupdater.HeadlessFileDAO
 
Helium - Class in com.compomics.util.experiment.biology.atoms.impl
The helium atom.
Helium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Helium
Constructor.
HelpDialog - Class in com.compomics.util.gui.error_handlers
A dialog used to display help text in HTML format.
HelpDialog(Frame, URL, Image, Image, String) - Constructor for class com.compomics.util.gui.error_handlers.HelpDialog
Creates a new HelpDialog with a JFrame as a parent.
HelpDialog(Frame, URL, Image, Image, String, int, int) - Constructor for class com.compomics.util.gui.error_handlers.HelpDialog
Creates a new HelpDialog with a JFrame as a parent.
HelpDialog(Frame, URL, String, Image, Image, String) - Constructor for class com.compomics.util.gui.error_handlers.HelpDialog
Creates a new HelpDialog with a JFrame as a parent.
HelpDialog(Frame, URL, String, Image, Image, String, int, int) - Constructor for class com.compomics.util.gui.error_handlers.HelpDialog
Creates a new HelpDialog with a JFrame as a parent.
HelpDialog(JDialog, URL, Image, Image, String) - Constructor for class com.compomics.util.gui.error_handlers.HelpDialog
Creates a new HelpDialog object with a JDialog as a parent.
HelpDialog(JDialog, URL, Image, Image, String, int, int) - Constructor for class com.compomics.util.gui.error_handlers.HelpDialog
Creates a new HelpDialog object with a JDialog as a parent.
HelpDialog(JDialog, URL, String, Image, Image, String) - Constructor for class com.compomics.util.gui.error_handlers.HelpDialog
Creates a new HelpDialog with a JDialog as a parent.
HelpDialog(JDialog, URL, String, Image, Image, String, int, int) - Constructor for class com.compomics.util.gui.error_handlers.HelpDialog
Creates a new HelpDialog with a JDialog as a parent.
HelpWindow - Class in com.compomics.util.examples
A window used to display help text in HTML format.
HelpWindow() - Constructor for class com.compomics.util.examples.HelpWindow
Empty default constructor
HelpWindow(JFrame, URL) - Constructor for class com.compomics.util.examples.HelpWindow
Creates a new HelpWindow object with a Frame as a parent.
HelpWindow(JDialog, URL) - Constructor for class com.compomics.util.examples.HelpWindow
Creates a new HelpWindow-object with a JDialog as a parent.
highLight(int, int, Graphics, Color, String, int, boolean, int, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method will highlight the specified point in the specified color by drawing a floating triangle + x-value above it.
highlightClicked(int, int, Graphics, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method will draw a highlighting triangle + x-value on top of the clicked marked point.
highLightPeak(int, int, Graphics, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method will draw a highlighting triangle + x-value on top of the marked point.
Histidine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Histidine.
Histidine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
Constructor.
HISTIDINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Histidine immonium ion.
HistogramUtils - Class in com.compomics.util.math
Simple functions to manipulate histograms.
HistogramUtils() - Constructor for class com.compomics.util.math.HistogramUtils
Empty default constructor
HOST - Static variable in class com.compomics.util.io.file.FolderMonitor
 
HPO3 - Static variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
H3PO3 loss.
HuffmanNode(int, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree.HuffmanNode
 
HuffmanNode(WaveletTree.HuffmanNode, WaveletTree.HuffmanNode) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree.HuffmanNode
 
Hydrogen - Class in com.compomics.util.experiment.biology.atoms.impl
The hydrogen atom.
Hydrogen() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Hydrogen
Constructor.
HyperScore - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores
Hyperscore as variation of the score implemented in X!Tandem www.thegpm.org/tandem.
HyperScore(PeptideFragmentationModel) - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Constructor.
HyperScore() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
Constructor using a uniform fragmentation.

I

I - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
I - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The Iodine atom.
iAnnotations - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds a set of Annotation instances.
iAnnotationsMirroredSpectra - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds a set of Annotation instances for the mirrored spectra.
iAnnotationYAxisThreshold - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The percent non-inclusive, minimal y-axis value (compared to the highest point in the spectrum) a point should have before being eligible for annotation.
iAreaUnderCurveColor - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Colors in which the chromatogram polyline is rendered.
iAreaUnderCurveColorMirroredSpectra - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Colors in which the chromatogram polyline is rendered for the mirrored spectra.
iArtifact - Variable in class com.compomics.util.protein.ModificationTemplate
Boolean to indicate whether this modification is an artifact.
iBase64String - Variable in class com.compomics.util.BinaryArrayImpl
Represents the binary contents of the array as an array of bytes.
iCleavables - Variable in class com.compomics.util.protein.Enzyme
Lookup cache for the cleavable residues.
iCleavage - Variable in class com.compomics.util.protein.Enzyme
This char[] holds the residues after which cleavage will occur.
iClicked - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Boolean that indicates whether a point has been marked by clicking.
iClickedDataSetIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Int that indicates which dataset contains the clicked point.
iClickedDataSetIndexMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Int that indicates which dataset contains the clicked point in the mirrored spectra.
iClickedIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Int that indicates which point was clicked.
iClickedIndexMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Int that indicates which point was clicked in the mirrored spectra.
iClickedList - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds all points clicked up to now.
iClickedListDatasetIndices - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds the dataset indices of all points clicked up to now.
iClickedListDatasetIndicesMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds the dataset indices of all points clicked up to now in the mirrored spectra.
iClickedListMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds all points clicked up to now in the mirrored spectra.
iClickedMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Boolean that indicates whether a point has been marked by clicking in the mirrored spectra.
iCode - Variable in class com.compomics.util.protein.ModificationTemplate
The code for this modification (eg., Mox).
iCurrentDrawStyle - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This variable holds the current drawing style.
id - Variable in enum com.compomics.cli.enzymes.EnzymesCLIParams
Short Id for the CLI parameter.
id - Variable in enum com.compomics.cli.fasta.FastaParametersCLIParams
Short id for the CLI parameter.
id - Variable in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Short Id for the CLI parameter.
id - Variable in enum com.compomics.cli.modifications.ModificationsCLIParams
Short Id for the CLI parameter.
id - Variable in enum com.compomics.cli.paths.PathSettingsCLIParams
The id of the command line option.
id - Variable in enum com.compomics.util.parameters.searchgui.OutputParameters
The index of the option.
iDataEndian - Variable in class com.compomics.util.BinaryArrayImpl
Represents the endian value of the binary array (mzData element .../data/endian).
iDataLength - Variable in class com.compomics.util.BinaryArrayImpl
Represents the length of the binary array (mzData element .../data/length).
iDataPointAndLineColor - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Colors in which the data points and peaks are rendered.
iDataPointAndLineColorMirroredSpectra - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Colors in which the data points and peaks are rendered for the mirrored spectra.
iDataPrecision - Variable in class com.compomics.util.BinaryArrayImpl
Represents the precision of the binary array (mzData element .../data/precision).
Identification - Class in com.compomics.util.experiment.identification
This class interacts with the back-end database to manage identification objects.
Identification() - Constructor for class com.compomics.util.experiment.identification.Identification
Empty default constructor
Identification(ObjectsDB) - Constructor for class com.compomics.util.experiment.identification.Identification
Constructor.
IdentificationAlgorithmParameter - Interface in com.compomics.util.gui.parameters.identification
Interface for the algorithm specific parameters.
identificationCharge - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
The charge used for identification.
IdentificationFeaturesCache - Class in com.compomics.util.experiment.identification.features
This class caches the identification features calculated by the IdentificationFeaturesGenerator for later reuse.
IdentificationFeaturesCache() - Constructor for class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Constructor.
IdentificationFeaturesCache.ObjectType - Enum in com.compomics.util.experiment.identification.features
An enumerator of the supported object types.
IdentificationFeaturesGenerator - Class in com.compomics.util.experiment.identification.features
This class provides identification features and stores them in cache.
IdentificationFeaturesGenerator() - Constructor for class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Empty default constructor.
IdentificationFeaturesGenerator(Identification, IdentificationParameters, SequenceProvider, SpectrumProvider, Metrics, SpectrumCountingParameters) - Constructor for class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Constructor.
identificationFile - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
The identification file.
IdentificationKeys - Class in com.compomics.util.experiment.identification
Placeholder for the keys of the objects in the identification.
IdentificationKeys() - Constructor for class com.compomics.util.experiment.identification.IdentificationKeys
 
IdentificationMatch - Class in com.compomics.util.experiment.identification
This is an abstract class for an identification match.
IdentificationMatch() - Constructor for class com.compomics.util.experiment.identification.IdentificationMatch
Empty default constructor
IdentificationMatch.MatchType - Enum in com.compomics.util.experiment.identification
The type of match.
IdentificationMethod - Class in com.compomics.util.experiment.identification
This class will contain all methods used to obtain identifications.
IdentificationMethod() - Constructor for class com.compomics.util.experiment.identification.IdentificationMethod
Empty default constructor
IdentificationMethod(int) - Constructor for class com.compomics.util.experiment.identification.IdentificationMethod
Constructor for the identification method
IdentificationParameters - Class in com.compomics.util.parameters.identification
Generic class grouping the parameters used for protein identification.
IdentificationParameters() - Constructor for class com.compomics.util.parameters.identification.IdentificationParameters
Creates empty identification parameters.
IdentificationParameters(SearchParameters) - Constructor for class com.compomics.util.parameters.identification.IdentificationParameters
Creates default identification parameters from the given search parameters.
IdentificationParameters(String, String, SearchParameters, AnnotationParameters, SequenceMatchingParameters, PeptideVariantsParameters, GeneParameters, PsmScoringParameters, PeptideAssumptionFilter, ModificationLocalizationParameters, ProteinInferenceParameters, IdMatchValidationParameters, FractionParameters, FastaParameters) - Constructor for class com.compomics.util.parameters.identification.IdentificationParameters
Constructor.
IdentificationParametersCLI - Class in com.compomics.cli.identification_parameters
The IdentificationParametersCLI allows creating search parameters files using command line arguments.
IdentificationParametersCLI(String[]) - Constructor for class com.compomics.cli.identification_parameters.IdentificationParametersCLI
Construct a new IdentificationParametersCLI runnable from a list of arguments.
IdentificationParametersCLIParams - Enum in com.compomics.cli.identification_parameters
Enum class specifying the SearchParameter command line option parameters to create a SearchParameters object
IdentificationParametersEditionDialog - Class in com.compomics.util.gui.parameters.identification
IdentificationParametersEditionDialog.
IdentificationParametersEditionDialog() - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
Empty default constructor
IdentificationParametersEditionDialog(Frame, IdentificationParameters, Image, Image, LastSelectedFolder, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
Creates a new IdentificationParametersEditionDialog with a frame as owner.
IdentificationParametersEditionDialog(Dialog, Frame, IdentificationParameters, Image, Image, LastSelectedFolder, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
Creates a new IdentificationParametersEditionDialog with a dialog as owner.
IdentificationParametersFactory - Class in com.compomics.util.experiment.identification.identification_parameters
Factory for the identification parameters.
IdentificationParametersInputBean - Class in com.compomics.cli.identification_parameters
This class parses the parameters from a command line and stores them in a SearchParameters object.
IdentificationParametersInputBean(CommandLine) - Constructor for class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Takes all the arguments from a command line.
IdentificationParametersMarshaller - Class in com.compomics.util.io.json.marshallers
This class is a convenience class to have a DefaultJsonConverter with the identification parameters interfaces.
IdentificationParametersMarshaller() - Constructor for class com.compomics.util.io.json.marshallers.IdentificationParametersMarshaller
Constructor.
IdentificationParametersNameDialog - Class in com.compomics.util.gui.parameters.identification
 
IdentificationParametersNameDialog() - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
Empty default constructor
IdentificationParametersNameDialog(Frame, IdentificationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
Creates a new IdentificationParametersNameDialog with a frame as owner.
IdentificationParametersNameDialog(Dialog, Frame, IdentificationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
Creates a new IdentificationParametersNameDialog with a dialog as owner.
IdentificationParametersOverviewDialog - Class in com.compomics.util.gui.parameters.identification
IdentificationParametersOverviewDialog.
IdentificationParametersOverviewDialog() - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
Empty default constructor
IdentificationParametersOverviewDialog(Dialog) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
Constructor with a dialog as owner.
IdentificationParametersOverviewDialog(Frame) - Constructor for class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
Constructor with a frame as owner.
identiPy - Static variable in class com.compomics.util.experiment.identification.Advocate
The IdentiPy search engine.
IdfileReader - Interface in com.compomics.util.experiment.io.identification
Generic interface for the parser of a file containing PSMs.
IdfileReaderFactory - Class in com.compomics.util.experiment.io.identification
This factory will provide the appropriate identification file reader for each type of file.
IdMatchValidationParameters - Class in com.compomics.util.parameters.identification.advanced
Generic class grouping the identification matches validation preferences.
IdMatchValidationParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Constructor for default settings.
IdMatchValidationParameters(IdMatchValidationParameters) - Constructor for class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Creates a new IdMatchValidationPreferences based on the values of the given IdMatchValidationPreferences.
iDotRadius - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This variable holds the dot radius; only used when drawing style is DOTS style.
iDragged - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This boolean is set to 'true' when dragging is performed.
iDragXLoc - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The current dragging location.
iEndXLoc - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
When the mouse is dragged, this represents the X-coordinate of the ending location.
iFilename - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The spectrum or chromatogram filename.
iFilenameColor - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This is the color the filename should be presented in.
iFilenameMirrorredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The spectrum or chromatogram filename for the mirrored spectrum or chromatogram.
ignoreExceptions - Variable in class com.compomics.util.exceptions.ExceptionHandler
If true exceptions will be ignored.
iHighLight - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Boolean that will be 'true' when a point needs highlighting.
iHighLightDatasetIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Index of the dataset containing the point that needs to be highlighted.
iHighLightDatasetIndexMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Index of the dataset containing the point that needs to be highlighted in the mirrored spectra.
iHighLightIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Index of the point that needs to be highlighted.
iHighLightIndexMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Index of the point that needs to be highlighted in the mirrored spectra.
iHighLightMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Boolean that will be 'true' when a point needs highlighting in the mirrored spectra.
iKnownMassDeltas - Static variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This HashMap instance holds all the known mass deltas (if any).
iLocation - Variable in class com.compomics.util.protein.ModificationImplementation
The location for the modification in the parent sequence.
ImageType - Enum in com.compomics.util.enumeration
Enumerator for supported export plot file types.
iMassDeltas - Variable in class com.compomics.util.protein.ModificationTemplate
This HashMap will contain the following 'key-value' mappings: (key > value)
(residue > double[]{MONOISOTOPIC_DELTA, AVERAGE_DELTA})
iMinDrag - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Minimal dragging distance in pixels.
iMiscleavages - Variable in class com.compomics.util.protein.Enzyme
This variable holds the number of supported missed cleavages.
ImmoniumIon - Class in com.compomics.util.experiment.biology.ions.impl
Represents an immonium ion.
ImmoniumIon() - Constructor for class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Empty default constructor
ImmoniumIonAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
Annotator for immonium and related ions.
ImmoniumIonAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
Empty default constructor
ImmoniumIonAnnotator(char[]) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
Constructor.
ImmoniumIonAnnotator(char[], boolean, boolean) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
Constructor.
implementations - Static variable in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
Array of the implemented features.
implementedForwardIons - Static variable in class com.compomics.util.parameters.identification.search.SearchParameters
Convenience array for forward ion type selection.
implementedRewindIons - Static variable in class com.compomics.util.parameters.identification.search.SearchParameters
Convenience array for rewind ion type selection.
importFromFile(File, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
Reads go mappings from a BioMart file.
importMaps(GeneMapping) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Imports the gene maps from a gene Mapping.
importMethods(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
Imports the methods from an XML file.
iMSLevel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The ms level of the current spectrum.
inBackend(long) - Method in class com.compomics.util.db.object.ObjectsDB
Indicates whether an object is loaded in the backend.
inCache(long) - Method in class com.compomics.util.db.object.ObjectsCache
Check if key in cache.
inCache(long) - Method in class com.compomics.util.db.object.ObjectsDB
Indicates whether an object is loaded in cache.
include(RowFilter.Entry<? extends DefaultTableModel, ? extends Integer>) - Method in class com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
 
increaseDepth() - Method in class com.compomics.util.io.export.ExportWriter
Notifies the writer that data of a higher hierarchical depth will be written, e.g.
increaseDepth() - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
increaseDepth() - Method in class com.compomics.util.io.export.writers.TextWriter
 
increaseIndent() - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Increases the indent counter.
increaseMissedCleavages() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Increases the number of missed cleavages.
increaseNX() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Increases the number of Xs already considered in this draft.
increasePrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
increasePrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
increasePrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
increasePrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
increasePrimaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
Increase the primary progress counter by one "counter".
increasePrimaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
Increase the primary progress counter by the given increment.
increaseSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
increaseSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Increase the secondary progress bar value by one "counter".
increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
increaseSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
increaseSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
increaseSecondaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
Increase the secondary progress counter by one "counter".
increaseSecondaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
Increase the secondary progress counter by the given value.
increasing - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
Indicates whether the score increases with the quality of the match.
inDB - Variable in class com.compomics.util.db.object.ObjectsCache.ObjectsCacheElement
The database state.
inDB(long) - Method in class com.compomics.util.db.object.ObjectsDB
Indicates whether an object is in the cache or the database.
indentCounter - Variable in class com.compomics.util.io.export.xml.SimpleXmlWriter
Integer keeping track of the number of indents to include at the beginning of each line.
index - Variable in enum com.compomics.util.experiment.biology.ions.Ion.IonType
The index of the type.
index - Variable in enum com.compomics.util.experiment.biology.modifications.ModificationType
The index of the type, must be the index in the values array.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
The index of this ms2pip feature.
index - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature.Property
The index of the option.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
The index of this ms2pip feature.
index - Static variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
The index of this ms2pip feature.
index - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.PeptideFragmentationModel
The index of the option.
index - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
The index of the score of interest.
index - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
The index of the format.
index - Variable in enum com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
The index of the format.
index - Variable in enum com.compomics.util.io.export.ExportFormat
The index of the format.
index - Variable in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
The index of the type as integer.
index - Variable in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
The index.
index - Variable in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
The index.
index - Variable in enum com.compomics.util.parameters.peptide_shaker.ProjectType
The index of the option.
IndexedMgfReader - Class in com.compomics.util.experiment.io.mass_spectrometry.mgf
Reader for mgf files based on random access.
IndexedMgfReader() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
General constructor for an mgf reader.
indexes - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MassIndexMap
 
indexStringLengths - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Length of the indexed string (all concatenated protein sequences).
inDoubleRange(String, String, double, double) - Static method in class com.compomics.software.cli.CommandParameter
Returns true if the input is a double value inside the given range.
inferParameters(String, WaitingHandler) - Static method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Infers the parameters used to parse the file.
inIntegerRange(String, String, int, int) - Static method in class com.compomics.software.cli.CommandParameter
Returns true if the input is an integer value inside the given range.
init(String, String, String, String, String, String, String) - Method in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Initializes the writing of the file.
init() - Method in class com.compomics.util.io.json.JsonMarshaller
Initializes the marshaller with (custom) type adapters.
init() - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
 
initialize(String) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Initializes the factory.
initiate(String[]) - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
Initiates the IdentificationParametersCli.
initiate(String) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Initiates the factory using the files of the static fields.
initiateSorter() - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Initiates the sorter to the current order of the table.
insert(int, AminoAcidSequence) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Inserts another sequence in this sequence.
insert(int, String) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Inserts another sequence in this sequence.
Insertion - Class in com.compomics.util.experiment.biology.variants.amino_acids
Class representing an amino acid insertion.
Insertion() - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Insertion
Empty default constructor
Insertion(char) - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Insertion
Constructor.
insertObject(long, Object) - Method in class com.compomics.util.db.object.ObjectsDB
Stores an object in the desired table.
insertObjects(HashMap<Long, Object>, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsDB
Inserts a set of objects in the given table.
installEscapeCloseOperation(JDialog) - Static method in class com.compomics.util.gui.GuiUtilities
Close a dialog using the escape key.
InstanceVariables - Class in com.compomics.util.db.components
This class represents the instance variables for a generated DBAccessor.
InstanceVariables() - Constructor for class com.compomics.util.db.components.InstanceVariables
Empty default constructor
InstanceVariables(DBMetaData) - Constructor for class com.compomics.util.db.components.InstanceVariables
This constructor will create all the code for the instance variables from the given DBMetaData.
Instrument - Class in com.compomics.util.pride.prideobjects
An object for storing Instrument details.
Instrument() - Constructor for class com.compomics.util.pride.prideobjects.Instrument
Empty default constructor
Instrument(String, CvTerm, CvTerm, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Instrument
Create a new Instrument object.
IntDecoder - Class in com.compomics.util.experiment.io.mass_spectrometry.mzml
Decodes ints from the half bytes in bytes.
IntDecoder(byte[], int) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mzml.IntDecoder
Constructor.
intensity - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
The intensity of the peak.
intensity - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
The measured intensity of the precursor.
intensity - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
The array of the intensities of the peaks.
intensityArray - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
The mz array of the spectrum.
IntensityHistogram - Class in com.compomics.util.gui.spectrum
Creates an IntensityHistogram plot.
IntensityHistogram() - Constructor for class com.compomics.util.gui.spectrum.IntensityHistogram
Empty default constructor
IntensityHistogram(IonMatch[], Spectrum, double) - Constructor for class com.compomics.util.gui.spectrum.IntensityHistogram
Creates an IntensityHistogram plot
intensityLimit - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The intensity limit to use.
intensityLimit - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
The intensity limit used for the index.
INTERACTIVE_STATUS - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This status indicates that no annotation will be displayed, but the user will have a fully functional interface (point clicking, selecting, sequencing etc.)
InterfaceAdapter<T> - Class in com.compomics.util.io.json.adapter
A generic adapter to parse used interfaces in a class.
InterfaceAdapter() - Constructor for class com.compomics.util.io.json.adapter.InterfaceAdapter
Empty default constructor.
interrupt() - Method in class com.compomics.util.sun.SwingWorker
A new method that interrupts the worker thread.
Iodine - Class in com.compomics.util.experiment.biology.atoms.impl
Iodine.
Iodine() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Iodine
Constructor.
iodoTMT_126 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 126.
iodoTMT_126_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 126 with ETD fragmentation.
iodoTMT_127 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 127.
iodoTMT_127_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 127 with ETD fragmentation.
iodoTMT_128 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 128.
iodoTMT_128_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 128 with ETD fragmentation.
iodoTMT_129 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 128.
iodoTMT_129_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 128 with ETD fragmentation.
iodoTMT_130 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 130.
iodoTMT_130_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 130 with ETD fragmentation.
iodoTMT_131 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 131.
iodoTMT_131_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT 131 with ETD fragmentation.
iodoTMT_zero - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT zero.
iodoTMT_zero_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iodoTMT zero with ETD fragmentation.
Ion - Class in com.compomics.util.experiment.biology.ions
This class models an ion.
Ion() - Constructor for class com.compomics.util.experiment.biology.ions.Ion
Empty default constructor
ion - Variable in class com.compomics.util.experiment.identification.matches.IonMatch
The matching ion.
Ion.IonType - Enum in com.compomics.util.experiment.biology.ions
An enumerator of the supported ion types.
IonFactory - Class in com.compomics.util.experiment.biology.ions
This factory generates the expected ions from a peptide.
IonFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
Feature based on a property of an ion.
IonFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
Empty default constructor
IonFeature.Property - Enum in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
Enum for the possible features.
IonLabelColorTableModel - Class in com.compomics.util.gui.spectrum
A table model to use for the ion label annotation colors.
IonLabelColorTableModel(HashMap<Ion.IonType, HashSet<Integer>>, HashSet<String>) - Constructor for class com.compomics.util.gui.spectrum.IonLabelColorTableModel
Constructor which sets a new table.
IonLabelColorTableModel() - Constructor for class com.compomics.util.gui.spectrum.IonLabelColorTableModel
Constructor which sets a new empty table.
IonMatch - Class in com.compomics.util.experiment.identification.matches
This class represents the assignment of a peak to a theoretical ion.
IonMatch() - Constructor for class com.compomics.util.experiment.identification.matches.IonMatch
Empty default constructor
IonMatch(double, double, Ion, int) - Constructor for class com.compomics.util.experiment.identification.matches.IonMatch
Constructor for an ion match.
IonMatch.MzErrorType - Enum in com.compomics.util.experiment.identification.matches
Enum of the supported error types.
IonMatchKeysCache - Class in com.compomics.util.experiment.identification.spectrum_annotation
Cache for the keys of the ions.
IonMatchKeysCache() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.IonMatchKeysCache
Constructor.
ionMatchKeysCache - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The cache to use for the ion match keys.
IoUtil - Class in com.compomics.util.io
Utils for I/O and file handling.
IoUtil() - Constructor for class com.compomics.util.io.IoUtil
 
iPointDetectionTolerance - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The deviation (both left and right) allowed for point highlighting detection.
iPointSize - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Size for the point on a polygon.
iPosition - Variable in class com.compomics.util.protein.Enzyme
This integer holds the position marker for the cleavage direction for this Enzyme.
iPrecursorCharge - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This String holds the charge for the precursor.
iPrecursorChargeMirorredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This String holds the charge for the precursor for the mirrored spectrum.
iPrecursorMZ - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This variable holds the precursor M/Z.
iPrecursorMZMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This variable holds the precursor M/Z for the mirrored spectrum.
iReport - Variable in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
The report to append.
iRestrict - Variable in class com.compomics.util.protein.Enzyme
This char[] holds the residues that will restrict cleavage when present after a cleavable residue.
iRestrictors - Variable in class com.compomics.util.protein.Enzyme
Lookup cache for the restricting residues.
Iron - Class in com.compomics.util.experiment.biology.atoms.impl
The iron atom.
Iron() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Iron
Constructor.
is64BitJava() - Static method in class com.compomics.software.CompomicsWrapper
Returns if the Java version used is 64 bit.
isAa(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns a boolean indicating whether the given character is a supported amino acid.
isAa(int) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns a boolean indicating whether the given character is a supported amino acid.
isAboveXAxis() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns true if the reference area is added above the x-axis, false adds the reference are below the x-axis
isAccounted(NeutralLossesMap, NeutralLoss, Ion) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns a boolean indicating whether the neutral loss should be accounted for.
isActive() - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Indicates whether the filter is active.
isAdditionalOutput() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Returns if additional output is to be included.
isAdjustPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Returns if the precursor mass is to be adjusted.
isAdvanced() - Method in interface com.compomics.util.io.export.ExportFeature
Indicates whether a feature is for advanced user only.
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
 
isAdvanced() - Method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
 
isAnnotateHighestPeak() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true if the most intense of possible peaks to annotate is to be selected, false if the most accurate is to be selected.
isArtifact() - Method in interface com.compomics.util.interfaces.Modification
This method indicates whether this modification is considered an artifact.
isArtifact() - Method in class com.compomics.util.protein.ModificationImplementation
This method indicates whether this modification is considered an artifact.
isArtifact() - Method in class com.compomics.util.protein.ModificationTemplate
This method indicates whether this modification is considered an artifact.
isAutomaticAnnotation() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns whether the annotation settings should be automatically inferred.
isAutoUpdate() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Indicates whether the tools should use the auto update function.
isBooleanInput(String, String) - Static method in class com.compomics.software.cli.CommandParameter
Returns true of the input is 0 or 1.
isCacheEmpty() - Method in class com.compomics.util.math.statistics.distributions.BinomialDistribution
Indicates whether all caches are empty.
isCanceled() - Method in class com.compomics.software.settings.gui.PathParametersDialog
Indicates whether the action was canceled by the user.
isCanceled() - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui.ThermoRawFileParserParametersDialog
Indicates whether the editing was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.AminoAcidPatternDialog
indicates whether the changes have been canceled
isCanceled() - Method in class com.compomics.util.gui.atoms.AtomChainDialog
Indicates whether the edition has been canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.enzymes.NewEnzymeDialog
Indicates whether the dialog was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.ExportFormatSelectionDialog
Returns true of the user canceled the dialog.
isCanceled() - Method in class com.compomics.util.gui.file_handling.FileSelectionDialog
Indicates whether the user canceled the dialog.
isCanceled() - Method in class com.compomics.util.gui.filtering.FilterDialog
Indicates whether the editing was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.genes.SpeciesDialog
Deprecated.
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.modification.ModificationDialog
Indicates whether the edition was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.FractionParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Indicates whether the preference edition was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
Indicates whether the cancel button was pressed by the user.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
Returns a boolean indicating whether the database selection was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.parameters.proteowizard.MsConvertParametersDialog
Indicates whether the editing was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.protein.FastaParametersDialog
Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
Returns a boolean indicating whether the selection was canceled by the user.
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
 
isCancelled() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
 
isCancelled() - Method in interface com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog
Indicates whether the user canceled the editing.
isCellEditable(int, int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
 
isCellEditable(int, int) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
 
isCellEditable(int, int) - Method in class com.compomics.util.sun.TableMap
 
isChanged() - Method in interface com.compomics.util.db.interfaces.DBElement
This method signals whether the DBElement has changes that should be persisted.
isCheckSpectrumCharges() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns whether the spectra are to be checked for missing charges.
isCleavageSite(String, String) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Returns a boolean indicating whether the given amino acids represent a cleavage site.
isCleavageSite(char, char) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Returns a boolean indicating whether the given amino acids represent a cleavage site.
isCleavageSiteNoCombination(Character, Character) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Returns a boolean indicating whether the given amino acids represent a cleavage site.
isCleaveNterMethionine() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether N-terminal methionines should be cleaved.
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Indicates whether the amino acid object refers to a combination of amino acids like B, J, Z or X.
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Alanine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Arginine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.B
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Glycine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Histidine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.J
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Proline
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Serine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Valine
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.X
 
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.impl.Z
 
isConfidentModificationSite(int, String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Indicates whether a site is already registered as confident modification site.
isConnectionActive() - Static method in class com.compomics.util.db.object.ObjectsDB
Indicates whether the connection to the DB is active.
isConnectionActive() - Method in class com.compomics.util.experiment.identification.Identification
Indicates whether the connection to the DB is active.
isCorrectPrecursorMass() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).
isCTerm() - Method in enum com.compomics.util.experiment.biology.modifications.ModificationType
Returns a boolean indicating whether the modification type targets the C-terminus of a protein or of a peptide.
isCterm(Peptide, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Indicates whether a peptide is at the C-terminus of a protein.
isCterm(Peptide, String, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Indicates whether a peptide is at the C-terminus of a given protein.
isDbSize() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Indicates whether the database size should be checked.
isDecoy() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns a boolean indicating whether the given match is decoy.
isDecoy(Peptide, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns a boolean indicating whether the peptide matches a decoy sequence.
isDecoy(String, FastaParameters) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given FASTA parameters.
isDecoy(String, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.ProteinUtils
Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given sequence provider.
isDecoySuffix() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Returns a boolean indicating whether the decoy flag is a suffix or a prefix.
isDeleted() - Method in interface com.compomics.util.db.interfaces.DBElement
This method signals whether the DBElement has been deleted in the persistent store.
isDependentLosses() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns whether neutral losses should be sequence dependent.
isDetermineChargePlusOneAlgorithmically() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether charge plus one should be determined algorithmically.
isDialogCanceled() - Method in class com.compomics.software.dialogs.PeptideShakerSetupDialog
Returns true of the dialog was canceled by the user.
isDialogCanceled() - Method in class com.compomics.software.dialogs.ProteoWizardSetupDialog
Returns true of the dialog was canceled by the user.
isDialogCanceled() - Method in class com.compomics.software.dialogs.ReporterSetupDialog
Returns true of the dialog was canceled by the user.
isDialogCanceled() - Method in class com.compomics.software.dialogs.SearchGuiSetupDialog
Returns true of the dialog was canceled by the user.
isDouble(String, String) - Static method in class com.compomics.software.cli.CommandParameter
Returns true if the argument can be parsed as a double value.
isDuplicateSpectra() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Indicates whether to use duplicate spectra option.
isEditable() - Method in class com.compomics.util.io.export.ExportScheme
Indicates whether the scheme is editable.
isElement(String) - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
Method that checks if a given string is an element we can calculate an isotopic distribution for
isElement(String) - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
Method that checks if a given string is an element we can calculate an isotopic distribution for
isEmpiricalCorrection() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Indicates whether empirical correction should be used.
isEmpty() - Method in class com.compomics.util.db.object.ObjectsCache
Indicates whether the cache is empty.
isEmpty() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Returns a boolean indicating if the mapping is empty.
isEnding(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the given amino acid sequence ends with the pattern.
isEnding(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the given amino acid sequence ends with the pattern.
isEnzymatic(Peptide, String, String, ArrayList<Enzyme>) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns a boolean indicating whether the peptide is enzymatic using one of the given enzymes.
isEnzymatic(Peptide, SequenceProvider, ArrayList<Enzyme>) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns a boolean indicating whether the peptide is enzymatic in at least one protein using one of the given enzymes.
isEnzymaticProduct(String, int, int) - Method in class com.compomics.util.protein.DualEnzyme
This method reports on the possibility that the presented subsequence (represented by the start and end location in the parent) is the result of enzymatic activity.
isEnzymaticProduct(String, String) - Method in class com.compomics.util.protein.Enzyme
This method reports on the possibility that the presented subsequence is the result of enzymatic activity.
isEnzymaticProduct(String, int, int) - Method in class com.compomics.util.protein.Enzyme
This method reports on the possibility that the presented subsequence (represented by the start and end location in the parent) is the result of enzymatic activity.
isEnzymaticProduct(String, String) - Method in class com.compomics.util.protein.RegExEnzyme
 
isEnzymaticProduct(String, int, int) - Method in class com.compomics.util.protein.RegExEnzyme
 
isEnzymaticTagsOnly() - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Returns true if tags should only be mapped to enzymatic peptides.
isEqualIL() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Indicates whether I and L should be considered indistinguishable.
isEstimateCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether the precursor charge shall be estimated for OMSSA.
isEstimateCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Indicates whether the precursor charge shall be estimated for PepNovo.
isFiltered() - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Indicates whether the protein list is filtered.
isFirstDecoy() - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Indicates whether the number of hits before the first decoy should be checked.
isFixed() - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Returns a boolean indicating whether the neutral loss is fixed or not.
isForward(int) - Static method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Indicates whether the given subtype refers to a forward or a rewind ion.
isFragmentAll() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Indicates whether the fragment all option should be used.
isFragmentIonPpm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Indicates whether the fragment ion accuracy is in ppm.
isFragmentIonPpm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Indicates whether the fragment ion accuracy is in ppm.
isGzip() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Indicates whether identification files should be gzipped.
isHeader() - Method in class com.compomics.util.io.export.ExportScheme
Indicates whether column header shall be used.
isHigherCharge() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Indicates whether higher charge should be considered.
isIncludeAmmonia() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns a boolean indicating whether ammonia losses should be accounted for.
isIncludeDateInOutputName() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Indicates whether the date should be included in the SearchGUI output name.
isIncludeDecoy() - Method in class com.compomics.util.io.export.ExportScheme
Indicates whether decoy hits should be included.
isIncludeSectionTitles() - Method in class com.compomics.util.io.export.ExportScheme
Indicates whether section titles shall be used.
isIncludeWater() - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Returns a boolean indicating whether water losses should be accounted for.
isIndeterminate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
This method signals whether the progressdialog is currently in indeterminate ('true') or determinate ('false') mode.
isIndexes() - Method in class com.compomics.util.io.export.ExportScheme
Indicates whether lines shall be indexed.
isInList(String, String, String[]) - Static method in class com.compomics.software.cli.CommandParameter
Returns true of the input is in the provided list.
isInList(String, String, List<String>) - Static method in class com.compomics.software.cli.CommandParameter
Returns true of the input is in the provided list.
isInteger(String, String) - Static method in class com.compomics.software.cli.CommandParameter
Returns true if the argument can be parsed as an integer value.
isIsPpm() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Indicates whether the mass tolerance is in ppm (true) or Dalton (false).
isList() - Method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
Returns a boolean indicating whether the list of implemented enzymes should be printed.
isList() - Method in class com.compomics.cli.modifications.ModificationsCLIInputBean
Returns a boolean indicating whether the list of implemented enzymes should be printed.
isListEnzymes() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Indicates whether the enzymes should be printed.
isListMods() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Indicates whether the modifications should be printed.
isLowMemoryMode() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Deprecated.
use getMaxLoadedProteins and getMaxLoadedSpectra instead
isMemoryMappedSequenceLibraries() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether sequence libraries should be mapped in memory.
isMiniature() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true if the graphics panel is to be drawn in a miniature form.
isModificationRefinement() - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Returns whether the protein mapping should be refined based on terminal and pattern modifications.
isMonoIsotopic() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns whether monoisotopic mass values shall be used (in contrast to average mass values).
isNeutralLossesAuto() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Indicates whether neutral losses should be automatically selected.
isNTerm() - Method in enum com.compomics.util.experiment.biology.modifications.ModificationType
Returns a boolean indicating whether the modification type targets the N-terminus of a protein or of a peptide.
isNterm(Peptide, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Indicates whether a peptide is at the N-terminus of a protein.
isNterm(Peptide, String, SequenceProvider) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Indicates whether a peptide is at the N-terminus of a given protein.
isNumber() - Method in interface com.compomics.util.experiment.filtering.FilterItem
Indicates whether the item expects a number as threshold.
isNumber() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
 
isNumber() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
 
isNumber() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
 
isNumber() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
 
Isoleucine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Isoleucine.
Isoleucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
Constructor.
ISOLEUCINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Isoleucine immonium ion.
isOne(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Returns true if the value is equal to one.
isOneInt(int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Returns true if the value is equal to one.
IsotopeDistributionGui - Class in com.compomics.util.gui.isotopic_calculator
This class is a GUI that visualizes the isotopic calculator.
IsotopeDistributionGui(boolean) - Constructor for class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
The constructor
isotopeMap - Variable in class com.compomics.util.experiment.biology.atoms.Atom
Map of the isotope masses relative to the monoisotopic peak (+1 for carbon 13).
IsotopicDistribution - Class in com.compomics.util.general
This class calculates the isotopic distribution based on a molecular formula.
IsotopicDistribution(MolecularFormula) - Constructor for class com.compomics.util.general.IsotopicDistribution
Constructor
IsotopicDistribution(MolecularFormula, int) - Constructor for class com.compomics.util.general.IsotopicDistribution
Constructor
IsotopicDistribution(int, int, int, int, int) - Constructor for class com.compomics.util.general.IsotopicDistribution
This will calculate the isotopic distribution pattern for the given elements.
IsotopicDistributionPanel - Class in com.compomics.util.gui.spectrum
This class provides a JPanel that can display a peptide isotopic distribution.
IsotopicDistributionPanel() - Constructor for class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
Empty default constructor
IsotopicDistributionPanel(String, Integer, boolean, int) - Constructor for class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
This constructor creates an IsotopicDistributionPanel based on the passed parameters.
IsotopicDistributionSpectrum - Class in com.compomics.util.general
This class is an implementation of the SpectrumFile specific for the isotopic distribution Created by IntelliJ IDEA.
IsotopicDistributionSpectrum() - Constructor for class com.compomics.util.general.IsotopicDistributionSpectrum
 
IsotopicElement - Class in com.compomics.util.general
This class represents the isotopically different element with the occurrence and the dalton difference between this and the natural variant.
isOutputHistograms() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicates whether histograms should be written in the result file.
isOutputProteins() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicates whether the protein bloc should be included in the export.
isOutputSequences() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns whether the protein sequences should be included in the protein block of the export.
isOutputSpectra() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicate whether the spectra should be exported in the result file.
isPeackPicking() - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
Returns true if peak picking is to be performed.
isPeakPicked() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns true if the indexed file seems to contain only peak picked spectra.
iSpecPanelListeners - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The list of SpectrumPanelListeners.
isPerformDeisotoping() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns whether deisotoping is to be performed.
isPerFraction() - Method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
Returns true if the feature is to be exported per fraction.
isPositiveDouble(String, String, boolean) - Static method in class com.compomics.software.cli.CommandParameter
Returns true if the argument can be parsed as a positive double value.
isPositiveInteger(String, String, boolean) - Static method in class com.compomics.software.cli.CommandParameter
Returns true if the argument can be parsed as a positive integer value.
isPotentialModificationsForFullRefinment() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicates whether the refinement modifications should be used for the full refinement.
isPpm - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Boolean indicating whether the tolerance is in ppm (true) or in Dalton (false).
isPrecursorAccuracyTypePpm() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns true if the current precursor accuracy type is ppm.
isPrecursorChargesMissing() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Returns true if the at least one spectrum is missing the precursor charge.
isProbabilisticScoreCalculation() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Indicates whether a probabilistic modification score is required.
isProbabilisticScoreNeutralLosses() - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Indicates whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score.
isProgressBarValid() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
This method reports on whether this instance can be controlled in a multithreaded environment.
isProteinQuickAcetyl() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicates whether the protein quick acetylation option should be triggered.
isQcPassed(String) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Indicates whether the given QC check was passed.
isQuickPyrolidone() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns whether the quick pyrolidone option should be triggered.
isRefine() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns whether the second pass search should be triggered.
isRefinePointMutations() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicates whether point mutations should be looked for during the refinement process.
isRefineSemi() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicates whether the semi enzymatic option of the second pass search should be triggered.
isRefineSnaps() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether snAPs should be used during the refinement process.
isRefineSpectrumSynthesis() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicates whether the spectrum synthesis option should be used during the refinement process.
isRefineUnanticipatedCleavages() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns whether the unanticipated cleavages option should be used during the refinement process.
isRemovePrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether the precursor shall be removed for OMSSA.
isReport() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
isReport() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
isReport() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
isReport() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
isReport() - Method in interface com.compomics.util.waiting.WaitingHandler
Indicates whether this waiting handler supports reports.
isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
isRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
isRunCanceled() - Method in interface com.compomics.util.waiting.WaitingHandler
Returns true if the run is canceled.
isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
isRunFinished() - Method in interface com.compomics.util.waiting.WaitingHandler
Returns true if the process is finished.
isRunning() - Method in class com.compomics.util.io.file.FolderMonitor
This method can be consulted to find out whether the monitor is running.
isSameAs(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether another AminoAcidPattern targets the same pattern.
isSameAs(AminoAcidSequence, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether another sequence has a matching sequence.
isSameAs(TagComponent, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
 
isSameAs(AtomImpl) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
Indicates whether another atom is the same as this one.
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
 
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.Glycan
 
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
 
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
 
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
 
isSameAs(RelatedIon) - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Compares the current related ion with another one based on their composition.
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
 
isSameAs(ReporterIon) - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Compares the current reporter ion with another one based on their masses.
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
 
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
 
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns a boolean indicating whether the ion is the same as another ion.
isSameAs(NeutralLoss) - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Method indicating whether another neutral loss is the same as the one considered.
isSameAs(Modification) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns true if the modification is the same as another one.
isSameAs(AaSubstitutionMatrix) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Indicates whether the given AaSubstitutionMatrix is the same as this one.
isSameAs(Filter) - Method in interface com.compomics.util.experiment.filtering.Filter
Indicates whether another filter is the same as the current filter.
isSameAs(TagComponent, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
 
isSameAs(Tag, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Indicates whether this tag is the same as another tag.
isSameAs(TagComponent, SequenceMatchingParameters) - Method in interface com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
Indicates whether another component is the same as the component of interest.
isSameAs(Filter) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
 
isSameAs(PeptideAssumptionFilter) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Indicates whether this filter is the same as another one.
isSameAs(ModificationMatch) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Indicates whether this modification match is the same of another one.
isSameAs(AnnotationParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns a boolean indicating whether the given annotation settings are the same as these ones.
isSameAs(FastaParameters) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Returns a boolean indicating whether the parsing parameters are the same as the given parameters.
isSameAs(Peak) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
Returns true if the peak has the same mz and intensity.
isSameAs(Precursor) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
Returns a boolean indicating whether the precursor is identical to the other precursor.
isSameAs(Spectrum) - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Returns a boolean indicating whether the spectrum is identical to the other spectrum.
isSameAs(UnitOfMeasurement) - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
Indicates whether the given unit of measurement is the same as another.
isSameAs(FractionParameters) - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
Returns a boolean indicating whether other given settings are the same as these.
isSameAs(PeptideVariantsParameters) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Indicates whether another peptide variant preferences is the same as this one.
isSameAs(SequenceMatchingParameters) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Indicates whether another sequence matching preferences is the same as this one.
isSameAs(ValidationQcParameters) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Returns true if the two ValidationQCPreferences are the same.
isSameAs(DigestionParameters) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Returns a boolean indicating whether these digestion parameters are the same as the given other parameters.
isSameAs(SpectrumCountingParameters) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Compares two spectrum counting preferences.
isSameAtomicComposition(Modification) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns true if the atomic composition of the modification is the same as another one.
isSameCompositionAs(AtomChain) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Indicates whether two atom chains are of the same composition by comparing their string and type.
isSameModificationStatus(Peptide) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Indicates whether another peptide has the same variable modifications as this peptide.
isSamePattern(Modification) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Returns true if the targeted pattern of the modification is the same as another one.
isSameSequence(Peptide, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Returns a boolean indicating whether another peptide has the same sequence as the given peptide
isSameSequenceAndModificationStatus(Peptide, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Indicates whether another peptide has the same sequence and modification status without accounting for modification localization.
isSameSequenceAndModificationStatusAs(AminoAcidSequence, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether another sequence targets the same sequence without accounting for PTM localization.
isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
 
isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
 
isSameSequenceAndModificationStatusAs(Tag, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Indicates whether this tag is the same as another tag without accounting for modification localization.
isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingParameters) - Method in interface com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
Indicates whether another component is the same as the component of interest.
isScalePrecursor() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether the precursor shall be scaled for OMSSA.
isScoringNeeded(int) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Indicates whether a score computation is needed for the given advocate.
isScoringNeeded(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Indicates whether a score computation is needed for the given advocates.
isScrolling - Variable in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
When true this indicates that the user is currently scrolling in the table and that the table should not update.
isScrolling() - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Indicates whether the table is currently being scrolled.
isSearchForwardFragmentFirst() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether forward ions (b1) should be searched first.
isSearchPositiveIons() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether positive ions are searched.
isSearchRewindFragments() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether C-terminal fragments should be searched.
isSelfUpdating() - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Indicates whether the table is in self update mode.
isSequenceMatchingType(String, String) - Static method in class com.compomics.software.cli.CommandParameter
Returns true of the input is in the provided list.
isSquare() - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
isStandAlone() - Method in class com.compomics.util.gui.FlamableJFrame
Returns true if frame is stand alone.
isStandardSearch() - Method in class com.compomics.util.experiment.biology.modifications.Modification
Indicates whether a modification can be searched with standard search engines, i.e., true if it targets a single amino acid position, false if it targets a complex pattern.
isStarting(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the given amino acid sequence starts with the pattern.
isStarting(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the given amino acid sequence starts with the pattern.
isStpBias() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Returns whether the stP bias should be triggered.
isSubscriptAnnotationNumbers() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true if the numbers in the peak annotations are to be subscripted.
issueCommand(String) - Method in class com.compomics.util.io.ftp.FTP
This method allows the caller to issue a command to the server.
issueCommandCheck(String) - Method in class com.compomics.util.io.ftp.FTP
This method will issue the specified command and throw an exception whenever the reply is not equal to success! It basically converts an FTP error code into an FtpProtocolException.
isTargetDecoy() - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Returns a boolean indicating whether the FASTA file should be processed as target-decoy or only target.
isTargetDecoyNeededForPsmScoring(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Indicates whether target decoy databases are needed for PSM scoring.
isTargeted(Character, int, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the given amino acid at the given index of the pattern is targeted without accounting for mutations.
iStartXLoc - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
When the mouse is dragged, this represents the X-coordinate of the starting location.
iStartYLoc - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
When the mouse is dragged, this represents the Y-coordinate of the starting location.
isToBeDeleted() - Method in interface com.compomics.util.db.interfaces.DBElement
This method signals whether the DBElement is marked for deletion.
iStoredSequence - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds a set of stored points from a previously established list.
iStoredSequenceDatasetIndices - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds the dataset indices of stored points from a previously established list.
iStoredSequenceDatasetIndicesMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds the dataset indices of stored points from a previously established list in the mirrored spectra.
iStoredSequenceMirrored - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds a set of stored points from a previously established list in the mirrored spectra.
isTruncated() - Method in class com.compomics.util.protein.Protein
This method reports on the 'truncatedness' of the protein.
isUniqueAa(char) - Static method in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Returns a boolean indicating whether the given character is a supported amino acid excluding combinations.
isUseChargeStateFromMS() - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Indicates whether the charge state from the spectrum should be used.
isUseCorrelationCorrectionScore() - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Indicates whether the correlation correction score should be used.
isUseNoiseSuppression() - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Indicates whether noise suppression should be used when importing spectra.
isUserDefined(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Convenience method returning a boolean indicating whether a Modification is user defined or default.
isValid() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
Returns true if valid.
isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
 
isValidated(long, String, String, PeptideAssumption, Identification, SequenceProvider, SpectrumProvider, IdentificationFeaturesGenerator, IdentificationParameters) - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
Tests whether a match is validated by this filter.
isValidated(String, FilterItemComparator, Object, long, String, String, PeptideAssumption, Identification, SequenceProvider, SpectrumProvider, IdentificationFeaturesGenerator, IdentificationParameters) - Method in class com.compomics.util.experiment.identification.filtering.AssumptionFilter
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.
isValidated(long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Tests whether a match is validated by this filter.
isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.
isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.PeptideFilter
 
isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.ProteinFilter
 
isValidated(String, FilterItemComparator, Object, long, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider) - Method in class com.compomics.util.experiment.identification.filtering.PsmFilter
 
isValidated() - Method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Indicates whether this level is considered as validated.
isValidatedOnly() - Method in class com.compomics.util.io.export.ExportScheme
Indicates whether only validated results should be exported.
isValidModifications(CommandLine) - Static method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Verifies that modifications are correctly recognized.
isValidStartup(CommandLine) - Static method in class com.compomics.cli.enzymes.EnzymesCLIInputBean
Verifies the command line start parameters.
isValidStartup(CommandLine) - Static method in class com.compomics.cli.fasta.FastaParametersInputBean
Verifies the command line start parameters.
isValidStartup(CommandLine, boolean) - Static method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Verifies the command line start parameters.
isValidStartup(CommandLine) - Static method in class com.compomics.cli.modifications.ModificationsCLIInputBean
Verifies the command line start parameters.
isVariant(Peptide, String) - Static method in class com.compomics.util.experiment.identification.utils.PeptideUtils
Returns a boolean indicating whether the peptide needs variants to be mapped to the given protein.
iTemplate - Variable in class com.compomics.util.protein.ModificationImplementation
The ModificationTemplate which holds all the shared information for a modification.
items - Variable in class com.compomics.util.gui.utils.user_choice.ListChooser
The list of items the user will choose from.
IteratorFactory - Class in com.compomics.util.experiment.identification.protein_sequences.digestion
The iterator goes through a sequence and lists possible peptides with their fixed modifications.
IteratorFactory() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
Empty default constructor
IteratorFactory(ArrayList<String>, Integer) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
Constructor.
IteratorFactory(ArrayList<String>) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
Constructor with 2 Xs allowed.
iTitle - Variable in class com.compomics.util.protein.Enzyme
This String holds the title (or name) for the enzyme.
iTitle - Variable in class com.compomics.util.protein.ModificationTemplate
The title for this modification (eg., Oxidation Met).
iTopPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Effective distance from the panel top border to 5 pixels above the top of the highest point (or y-tick mark).
iTRAQ4Plex_114 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 4Plex 114.
iTRAQ4Plex_115 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 4Plex 115.
iTRAQ4Plex_116 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 4Plex 116.
iTRAQ4Plex_117 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 4Plex 117.
iTRAQ8Plex_113 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 8Plex 113.
iTRAQ8Plex_114 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 8Plex 114.
iTRAQ8Plex_115 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 8Plex 115.
iTRAQ8Plex_116 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 8Plex 116.
iTRAQ8Plex_117 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 8Plex 117.
iTRAQ8Plex_118 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 8Plex 118.
iTRAQ8Plex_119 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 8Plex 119.
iTRAQ8Plex_121 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ 8Plex 121.
iTRAQ_145 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ (reporter + balancer).
iTRAQ_305 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion iTRAQ (reporter + balancer).
iXAxisData - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
All the x-axis data points.
iXAxisDataInPixels - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This array will hold the x-coordinates in pixels for all the x-axis values.
iXAxisDataInPixelsMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This array will hold the x-coordinates in pixels for all the x-axis values of the mirrored spectrum.
iXAxisDataMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
All the x-axis data points for the mirrored spectrum.
iXAxisLabel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The label (and unit between brackets, if available) for the x-axis.
iXAxisMax - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The maximum x-axis value to display.
iXAxisMin - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The minimum x-axis value to display.
iXAxisStartAtZero - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This boolean is set to 'true' if the x-axis should start at zero.
iXPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Effective distance from the x-axis to the panel border.
iXScaleUnit - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Scale unit for the X axis.
iXUnit - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Graphical unit for the X axis.
iYAxisData - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
All the y-axis values.
iYAxisDataInPixels - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This array will hold the y-coordinates in pixels for all the y-axis values.
iYAxisDataInPixelsMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This array will hold the y-coordinates in pixels for all the y-axis values of the mirrored spectrum.
iYAxisDataMirroredSpectrum - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
All the y-axis values for the mirrored spectra.
iYAxisLabel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The label (and unit between brackets, if available) for the y-axis.
iYAxisMax - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The maximum y-axis value to display.
iYAxisMin - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The minimum y-axis value to display.
iYScaleUnit - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Scale unit for the Y axis.
iYUnit - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Graphical unit for the Y axis.

J

J - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
J - Class in com.compomics.util.experiment.biology.aminoacids.impl
Isoleucine or Leucine.
J() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.J
Constructor.
JarFileFilter - Class in com.compomics.software.autoupdater
JarFileFilter.
JarFileFilter() - Constructor for class com.compomics.software.autoupdater.JarFileFilter
 
JavaHomeDialog - Class in com.compomics.software.dialogs
A dialog for changing the Java Home.
JavaHomeDialog(JFrame, JavaHomeOrMemoryDialogParent, JDialog, String) - Constructor for class com.compomics.software.dialogs.JavaHomeDialog
Creates a new JavaHomeDialog.
JavaHomeOrMemoryDialogParent - Interface in com.compomics.software.dialogs
Interface for parents of JavaMemoryDialog and JavaHomeDialog.
JavaMemoryDialog - Class in com.compomics.software.dialogs
A dialog for changing the Java memory setting.
JavaMemoryDialog(JFrame, JavaHomeOrMemoryDialogParent, JDialog, String) - Constructor for class com.compomics.software.dialogs.JavaMemoryDialog
Creates a new JavaMemoryDialog.
JavaParametersDialog - Class in com.compomics.software.dialogs
A dialog for showing Java memory settings.
JavaParametersDialog(JFrame, JavaHomeOrMemoryDialogParent, JDialog, String, boolean) - Constructor for class com.compomics.software.dialogs.JavaParametersDialog
Creates a new JavaSettingsDialog.
JExceptionDialog - Class in com.compomics.util.gui
This class implements a JDialog for the specific purpose of showing unrecoverable errors or exceptions.
JExceptionDialog(Frame, String, String[], Throwable) - Constructor for class com.compomics.util.gui.JExceptionDialog
This constructor takes all required parameters for the construction, initialization and execution of a JExceptionDialog.
JFrameForBytes - Class in com.compomics.util.gui
This class implements a JFrame, made specifically for the display of binary data.
JFrameForBytes(String, byte[]) - Constructor for class com.compomics.util.gui.JFrameForBytes
This constructor creates a JFrame for display of the binary data (specified as well).
JLabelAndComponentPanel - Class in com.compomics.util.gui
This class implements a JPanel that lays out a set of JLabel and a JComponent next to each other.
JLabelAndComponentPanel(JLabel[], JComponent[]) - Constructor for class com.compomics.util.gui.JLabelAndComponentPanel
Constructor which allows the specification of the labels and components to lay out.
JOptionEditorPane - Class in com.compomics.util.gui
A dialog to show HTML content with clickable links inside a JOptionsPane.
JOptionEditorPane() - Constructor for class com.compomics.util.gui.JOptionEditorPane
 
jpeg - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
JPEG - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
JpegFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.jpeg files.
JpegFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.JpegFileFilter
Empty default constructor
jpg - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
JPG - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
JsonMarshaller - Class in com.compomics.util.io.json
This class converts non-specific objects to the JSON format and vice versa.
JsonMarshaller() - Constructor for class com.compomics.util.io.json.JsonMarshaller
Default constructor.
JsonMarshaller(Class...) - Constructor for class com.compomics.util.io.json.JsonMarshaller
Constructor.
JTableForDB - Class in com.compomics.util.gui
This class extends a JTable with specific cellrenderers for fields, retrieved from DB.
JTableForDB() - Constructor for class com.compomics.util.gui.JTableForDB
Constructs a default JTable that is initialized with a default data model, a default column model, and a default selection model.
JTableForDB(int, int) - Constructor for class com.compomics.util.gui.JTableForDB
Constructs a JTable with numRows and numColumns of empty cells using DefaultTableModel.
JTableForDB(TableModel, TableColumnModel) - Constructor for class com.compomics.util.gui.JTableForDB
Constructs a JTable that is initialized with dm as the data model, cm as the column model, and a default selection model.
JTableForDB(TableModel) - Constructor for class com.compomics.util.gui.JTableForDB
Constructs a JTable that is initialized with dm as the data model, a default column model, and a default selection model.
JTableForDB(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class com.compomics.util.gui.JTableForDB
Constructs a JTable that is initialized with dm as the data model, cm as the column model, and sm as the selection model.
JTableForDB(Vector, Vector) - Constructor for class com.compomics.util.gui.JTableForDB
Constructs a JTable to display the values in the Vector of Vectors, rowData, with column names, columnNames.
JTableForDB(Object[][], Object[]) - Constructor for class com.compomics.util.gui.JTableForDB
Constructs a JTable to display the values in the two dimensional array, rowData, with column names, columnNames.

K

K - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
K - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The Potassium atom.
KEY - Static variable in class com.compomics.util.experiment.identification.IdentificationKeys
Key to use in the database.
key - Static variable in class com.compomics.util.experiment.ProjectParameters
 
keyValueToString(String, String) - Static method in class com.compomics.util.Util
Returns a string in the form key(value).
kMeanCluster(WaitingHandler) - Method in class com.compomics.util.math.clustering.KMeansClustering
Run the k-means clustering.
KMeansClustering - Class in com.compomics.util.math.clustering
K-means clustering.
KMeansClustering() - Constructor for class com.compomics.util.math.clustering.KMeansClustering
Empty default constructor
KMeansClustering(double[][], String[], int) - Constructor for class com.compomics.util.math.clustering.KMeansClustering
Constructor.
KMeansClustering(File, int) - Constructor for class com.compomics.util.math.clustering.KMeansClustering
Constructor.
KMeansClusteringSettings - Class in com.compomics.util.math.clustering.settings
Settings for k-means clustering.
KMeansClusteringSettings() - Constructor for class com.compomics.util.math.clustering.settings.KMeansClusteringSettings
Constructor.
kryo - Variable in class com.compomics.util.db.object.ObjectsDB
Configuration for fast serialization.

L

L - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
laodMappingFromFile(File, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.go.GoDomains
Reads go mappings from a file.
large - Variable in enum com.compomics.util.experiment.identification.features.IdentificationFeaturesCache.ObjectType
Boolean indicating whether this category contains large objects.
LAST_FOLDER_KEY - Static variable in class com.compomics.util.io.export.ExportWriter
Key to store the last export folder.
LAST_SELECTED_FOLDER_KEY - Static variable in class com.compomics.util.gui.error_handlers.BugReport
The specific key for bug reports.
lastFolderKey - Static variable in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
The key to use to store FASTA files paths.
lastModified - Variable in class com.compomics.util.experiment.io.biology.protein.FastaSummary
The last time the file was modified.
LastSelectedFolder - Class in com.compomics.util.io.file
Convenience class keeping class of the last selected folders.
LastSelectedFolder(String) - Constructor for class com.compomics.util.io.file.LastSelectedFolder
Constructs a new last selected folder class.
LastSelectedFolder() - Constructor for class com.compomics.util.io.file.LastSelectedFolder
Constructs a new last selected folder class.
launchTool(String, File, String, String) - Method in class com.compomics.software.CompomicsWrapper
Starts the launcher by calling the launch method.
launchTool(String, File, String, String, String[]) - Method in class com.compomics.software.CompomicsWrapper
Starts the launcher by calling the launch method.
left - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Left index.
length() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns the length of the pattern in amino acids.
length() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns the length of the sequence in amino acids.
length - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Current peptide sequence length.
length - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
The length.
length() - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Returns the length of the sequence.
length - Variable in class com.compomics.util.TempByteArray
The length used.
lessTablesPrimary - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Less table for doing an update step according to the LF step.
lessTablesReversed - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Less table for doing an update step according to the LF step reversed.
letter - Variable in class com.compomics.util.experiment.biology.atoms.Atom
The symbol for the atom.
Leucine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Leucine.
Leucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Leucine
Constructor.
LEUCINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Leucine immonium ion.
Li - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The phosphorus atom.
LIGHT_AQUA - Static variable in class com.compomics.util.AlternateRowColoursJTable
A soft-tone AQUA colour (r=219, g=238, b=244).
LIMIT - Static variable in class com.compomics.util.io.file.FolderMonitor
 
LINE_SEPARATOR - Static variable in class com.compomics.util.Util
The line separator.
LinearRegression - Class in com.compomics.util.math.statistics.linear_regression
Enum of the different implementations for a regression.
LinearRegression() - Constructor for class com.compomics.util.math.statistics.linear_regression.LinearRegression
Empty default constructor
linePermutation(int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
list() - Method in class com.compomics.util.io.ftp.FTP
LIST files on a remote FTP server.
ListChooser - Class in com.compomics.util.gui.utils.user_choice
Dialog for choosing an item in a list.
ListChooser() - Constructor for class com.compomics.util.gui.utils.user_choice.ListChooser
Empty default constructor
ListChooser(Frame, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.ListChooser
Constructor.
ListChooser(JDialog, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.ListChooser
Constructor.
Lithium - Class in com.compomics.util.experiment.biology.atoms.impl
The Lithium atom.
Lithium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Lithium
Constructor.
LITTLE_ENDIAN_LABEL - Static variable in class com.compomics.util.BinaryArrayImpl
Defines the valid String indicating little endian byte order.
ln(BigDecimal, MathContext) - Static method in class com.compomics.util.math.BigFunctions
Returns the natural logarithm of a big decimal.
lnBD(BigDecimal, MathContext) - Static method in class com.compomics.util.math.BigFunctions
Returns the log of a big decimal.
load(Connection, HashMap) - Method in interface com.compomics.util.db.interfaces.DBElement
This method should be called to fill the DBElement with current data as present in the database.
loadBackedUpModifications(SearchParameters, boolean) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Verifies that the modifications backed-up in the search parameters are loaded and alerts the user in case conflicts are found.
loadDataForRows(ArrayList<Integer>, WaitingHandler) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Loads the data needed for objects at rows of the given view indexes.
loadEnsemblSpeciesVersions(File) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Loads the given Ensembl species file.
loadFromFile(File) - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Loads an enzyme factory from a file.
loadFromFile(File) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Loads an enzyme factory from a file.
loadMapping(File, File) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
Loads the species mapping from a file.
loadMapping(File) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
Loads the species mapping from a file.
loadMapping(File) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
Loads the species mapping from a file.
loadMapping(File) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
Loads the species mapping from a file.
loadMappingsFromFile(File, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.go.GoMapping
Reads go mappings from a BioMart file.
loadObjectMutex - Static variable in class com.compomics.util.db.object.DbMutex
The cache load objects mutex.
loadObjects(Collection<Long>, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsDB
Loads objects from a table in the cache.
loadObjects(Class, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsDB
Loads all objects from a given class.
loadObjects(Class, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification
Loads all objects of the class in cache.
loadObjects(ArrayList<Long>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification
Loads all objects of given keys in cache.
loadPathParameterFromLine(String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Loads a path to be set from a line.
loadPathParametersFromFile(File) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Loads the path preferences from a text file.
loadPtmToPrideMap(SearchParameters) - Static method in class com.compomics.util.pride.PtmToPrideMap
Deprecated.
the CV term is now part of the PTM object
loadUserParameters() - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
Loads the user parameters.
lock(WaitingHandler) - Method in class com.compomics.util.db.object.ObjectsDB
Locking the db for storing.
log(double, double) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the log of the input in the desired base.
log(BigDecimal, double, MathContext) - Static method in class com.compomics.util.math.BigFunctions
Returns the log of the input in the desired base.
logError(String) - Method in class com.compomics.software.log.CliLogger
Logs an error.
logExceptionalEvent(String) - Method in class com.compomics.util.general.DefaultOutputLoggerImplementation
This method allows the logging of an exceptional event.
logExceptionalEvent(String) - Method in class com.compomics.util.general.FileLoggerImplementation
This method allows the logging of an exceptional event.
logExceptionalEvent(String) - Method in interface com.compomics.util.interfaces.Logger
This method allows the logging of an exceptional event.
Logger - Interface in com.compomics.util.interfaces
This interface describes the behaviour for a class that can log messages.
login(String, String) - Method in class com.compomics.util.io.ftp.FTP
Login user to a host with username user and password password.
login(String) - Method in class com.compomics.util.io.ftp.FTP
Login user to a host with username user and no password such as HP server which uses the form "<username>/<password>,user.<group>.
logMessage(String) - Method in class com.compomics.software.log.CliLogger
Logs a message.
logNormalEvent(String) - Method in class com.compomics.util.general.DefaultOutputLoggerImplementation
This method allows the logging of a 'normal' event.
logNormalEvent(String) - Method in class com.compomics.util.general.FileLoggerImplementation
This method allows the logging of a 'normal' event.
logNormalEvent(String) - Method in interface com.compomics.util.interfaces.Logger
This method allows the logging of a 'normal' event.
logTime(String) - Method in class com.compomics.util.general.DefaultOutputLoggerImplementation
This method allows the caller to have the logger record a timestamp (implementation specific format and content, although 'date - time' is a good rule of thumb) along with the specified message.
logTime(String) - Method in class com.compomics.util.general.FileLoggerImplementation
This method allows the caller to have the logger record a timestamp (implementation specific format and content, although 'date - time' is a good rule of thumb) along with the specified message.
logTime(String) - Method in interface com.compomics.util.interfaces.Logger
This method allows the caller to have the logger record a timestamp (implementation specific format and content, although 'date - time' is a good rule of thumb) along with the specified message.
lossesValidated(NeutralLossesMap, Ion) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns a boolean indicating whether the neutral losses of the given fragment ion fit the requirement of the given neutral losses map.
ls() - Method in class com.compomics.util.io.ftp.FTP
Folder-list files on a remote FTP server.
Lysine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Lysine.
Lysine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Lysine
Constructor.
LYSINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Lysine immonium ion.

M

M - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
m_strDestination - Variable in class com.compomics.util.io.ftp.FTP
 
m_strSource - Variable in class com.compomics.util.io.ftp.FTP
 
mad(double[]) - Static method in class com.compomics.util.math.BasicMathFunctions
Method estimating the median absolute deviation.
mad(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Method estimating the median absolute deviation.
MAGIC_NUMBER - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileUtils
The magic number of currently supported CMS files.
Magnesium - Class in com.compomics.util.experiment.biology.atoms.impl
The magnesium atom.
Magnesium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Magnesium
Constructor.
main(String[]) - Static method in class com.compomics.cli.enzymes.EnzymesCLI
Main method for the EnzymeCLI.
main(String[]) - Static method in class com.compomics.cli.identification_parameters.IdentificationParametersCLI
Starts the launcher by calling the launch method.
main(String[]) - Static method in class com.compomics.cli.modifications.ModificationsCLI
Main method for the ModificationsCLI.
main(String[]) - Static method in class com.compomics.cli.paths.PathSettingsCLI
Starts the launcher by calling the launch method.
main(String[]) - Static method in class com.compomics.cli.peptide_mapper.PeptideMapperCLI
Main class.
main(String[]) - Static method in class com.compomics.scripts_marc.MsFilePerformance
Main method.
main(String[]) - Static method in class com.compomics.software.SplashScreen
The main method.
main(String[]) - Static method in class com.compomics.util.db.DBAccessorGenerator
The main method allows to run this tool from the command-line.
main(String[]) - Static method in class com.compomics.util.examples.MirroredSpectraTestDialog
 
main(String[]) - Static method in class com.compomics.util.examples.UtilitiesDemo
Starts the UtilitiesDemo.
main(String[]) - Static method in class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
Main method for testing purposes only.
main(String[]) - Static method in class com.compomics.util.general.MassCalc
The main method can be used for command-line usage of this class.
main(String[]) - Static method in class com.compomics.util.general.Translate
Translate a DNA sequence into 6 reading frames.
main(String[]) - Static method in class com.compomics.util.gui.AaMass
 
main(String[]) - Static method in class com.compomics.util.gui.atoms.AtomChainDialog
Main method for testing purposes.
main(String[]) - Static method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
Main method
main(String[]) - Static method in class com.compomics.util.gui.JExceptionDialog
This main method is for testing purposes only.
main(String[]) - Static method in class com.compomics.util.gui.utils.DateChooser
Creates and opens a new DateChooser dialog.
main(String[]) - Static method in class com.compomics.util.gui.VennDiagramDialog
Main method.
main(String[]) - Static method in class com.compomics.util.io.file.FolderMonitor
Main method starting the foldermonitor that looks for changes to a monitored folder.
main(String[]) - Static method in class com.compomics.util.io.PropertiesManager
DO NOT RUN.
main(String[]) - Static method in class com.compomics.util.math.clustering.KMeansClustering
Main method for testing purposes.
main(String[]) - Static method in class com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
Main method.
main(String[]) - Static method in class com.compomics.util.protein.DualEnzyme
Tests the DualEnzyme by digesting a hardcoded protein.
makeSequenceIndependant() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Makes the neutral losses sequence independent.
makeUnique(char[]) - Static method in class com.compomics.util.ArrayUtil
Returns an array containing the unique characters of the given array.
mandatory - Variable in enum com.compomics.cli.enzymes.EnzymesCLIParams
Boolean indicating whether the parameter is mandatory.
mandatory - Variable in enum com.compomics.cli.fasta.FastaParametersCLIParams
Boolean indicating whether the parameter is mandatory.
mandatory - Variable in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Boolean indicating whether the parameter is mandatory.
mandatory - Variable in enum com.compomics.cli.modifications.ModificationsCLIParams
Boolean indicating whether the parameter is mandatory.
MANUAL_SELECTION - Static variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
Name of the manual selection filter.
manualValidation - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
The key of the manually validated matches.
MappingWorker - Class in com.compomics.cli.peptide_mapper
 
MappingWorker(WaitingHandlerCLIImpl, FastaMapper, IdentificationParameters, BufferedReader, PrintWriter, boolean) - Constructor for class com.compomics.cli.peptide_mapper.MappingWorker
 
mapTagToProteinTermini(MatrixContent, double, boolean, LinkedList<MatrixContent>[], int, int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
 
MarshallableParameter - Interface in com.compomics.util.experiment.io.parameters
Interface for a parameter which can be marshalled as .par file.
MarshallableParameter.Type - Enum in com.compomics.util.experiment.io.parameters
Enum of the type of parameter which can be encountered in a .par file.
mascot - Static variable in class com.compomics.util.experiment.identification.Advocate
The Mascot search engine.
MascotEnzymeReader - Class in com.compomics.util.io
This class will load Enzyme properties from a Mascot (www.matrixscience.com) formatted text file.
MascotEnzymeReader() - Constructor for class com.compomics.util.io.MascotEnzymeReader
Empty default constructor
MascotEnzymeReader(String) - Constructor for class com.compomics.util.io.MascotEnzymeReader
The constructor requires that you specify the file from which to load the enzyme information.
MascotEnzymeReader(InputStream) - Constructor for class com.compomics.util.io.MascotEnzymeReader
The constructor allows you specify to specify an inputstream from which to load the enzyme information.
MascotIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This IdfileReader reads identifications from a Mascot results file.
MascotIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
Default constructor for the purpose of instantiation.
MascotIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
Constructor for an Mascot dat result file reader.
MascotIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader
Constructor for an Mascot dat csv result file reader.
mass - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MassIndexMap
 
mass - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Current mass.
mass - Variable in enum com.compomics.util.experiment.mass_spectrometry.utils.StandardMasses
The mass.
MASS_PER_AA - Static variable in class com.compomics.util.experiment.identification.modification.mapping.ModificationLocalizationMapper
The mass added per amino acid as part of the reference mass when converting Dalton tolerances to ppm.
MASS_PER_AA - Static variable in class com.compomics.util.Util
The mass added per amino acid as part of the reference mass when converting a tolerance in Dalton to ppm.
MassCalc - Class in com.compomics.util.general
This class takes care of mass calculation, based on a sequence in IUPAC format.
MassCalc() - Constructor for class com.compomics.util.general.MassCalc
Default constructor.
MassCalc(int) - Constructor for class com.compomics.util.general.MassCalc
This constructor allows you to specify an identifier to select a element list to use for calculating a mass.
MassCalc(String) - Constructor for class com.compomics.util.general.MassCalc
This constructor allows the caller to use an elementlist of its own making.
MassCalc(HashMap) - Constructor for class com.compomics.util.general.MassCalc
This constructor allows the caller to initialize the elementlist with a HashMap of its own design.
MassCalc(int, HashMap) - Constructor for class com.compomics.util.general.MassCalc
This constructor allows the caller to supplement (or to replace elements in) a built-in elementlist with a HashMap of its own design.
MassCalcServlet - Class in com.compomics.util.general.servlet
This class implements the MassCalc class as a servlet.
MassCalcServlet() - Constructor for class com.compomics.util.general.servlet.MassCalcServlet
 
MassErrorBubblePlot - Class in com.compomics.util.gui.spectrum
Creates a MassErrorBubblePlot displaying the mz values vs the mass error with the intensity as the size of the bubbles.
MassErrorBubblePlot() - Constructor for class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Empty default constructor
MassErrorBubblePlot(ArrayList<String>, ArrayList<IonMatch[]>, ArrayList<Spectrum>, double, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(ArrayList<String>, ArrayList<IonMatch[]>, ArrayList<Spectrum>, double, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(ArrayList<String>, ArrayList<IonMatch[]>, ArrayList<Spectrum>, double, double, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Creates a new MassErrorBubblePlot.
MassErrorPlot - Class in com.compomics.util.gui.spectrum
Creates a MassErrorPlot displaying the mz values vs the mass error.
MassErrorPlot() - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot
Empty default constructor
MassErrorPlot(IonMatch[], Spectrum, double) - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot
Creates a new MassErrorPlot.
MassErrorPlot(IonMatch[], Spectrum, double, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot
Creates a new MassErrorPlot.
MassGap - Class in com.compomics.util.experiment.identification.amino_acid_tags
An undefined mass gap.
MassGap() - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
Empty default constructor.
MassGap(double) - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
Constructor.
MassIndexMap - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
The mass index map.
MassIndexMap() - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MassIndexMap
Empty default constructor
MassIndexMap(double, int[]) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MassIndexMap
 
massShift - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
m/z shift applied to all theoretic peaks.
massShiftCTerm - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
C-terminal m/z shift applied to all reverse ions.
massShiftNTerm - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
N-terminal m/z shift applied to all forward ions.
matches(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the pattern matches the given amino acid sequence.
matches(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the pattern matches the given amino acid sequence
matches(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
matches(AminoAcidSequence, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
matchesAt(String, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the pattern is found in the given amino acid sequence at the given index, where 0 is the first amino acid.
MatchesImportParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
The PeptideShaker import settings dialog.
MatchesImportParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog
Empty default constructor
MatchesImportParametersDialog(Frame, PeptideAssumptionFilter, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog
Creates a new ImportSettingsDialog with a frame as owner.
MatchesImportParametersDialog(Dialog, Frame, PeptideAssumptionFilter, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog
Creates a new ImportSettingsDialog with a dialog as owner.
matchesIn(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the pattern is found in the given amino acid sequence.
matchesIn(AminoAcidPattern, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Indicates whether the pattern is found in the given amino acid sequence.
matchesIn(String, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether the sequence is found in the given amino acid sequence.
matchesIn(AminoAcidSequence, SequenceMatchingParameters) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Indicates whether the sequence is found in the given amino acid sequence.
MatchesIterator - Class in com.compomics.util.experiment.identification.matches_iterators
An abstract iterator class to iterate identification matches.
MatchesIterator() - Constructor for class com.compomics.util.experiment.identification.matches_iterators.MatchesIterator
Empty default constructor
MatchesIterator(Class, Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.MatchesIterator
Constructor.
MatchesIterator(long[], Class, Identification, WaitingHandler, boolean, String) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.MatchesIterator
Constructor.
MatchFilter - Class in com.compomics.util.experiment.identification.filtering
Abstract representing a filter.
MatchFilter() - Constructor for class com.compomics.util.experiment.identification.filtering.MatchFilter
Empty default constructor
MatchFilter.FilterType - Enum in com.compomics.util.experiment.identification.filtering
Enum for the type of possible filter.
matchInSpectrum(double[], double[], Ion, Integer) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Matches a theoretic ion in the spectrum.
matchPeak(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpecificAnnotationParameters, double, double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
This method matches the potential fragment ions of a given peptide with a given peak according to the annotation settings.
matchPeak(SpecificAnnotationParameters, double, double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
This method matches the potential fragment ions of a given peptide with a given peak.
matchReporterIon(Ion, int, Spectrum, double) - Static method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Convenience method to match a reporter ion in a spectrum.
MatchValidationLevel - Enum in com.compomics.util.experiment.identification.validation
Enum listing the different levels of match validation.
MatrixContent - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
Element for the matrix necessary in pattern search of the FMIndex.
MatrixContent() - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Empty default constructor.
MatrixContent(int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor almost empty.
MatrixContent(int, int, int, MatrixContent, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor for simple sequence mapping.
MatrixContent(int, int, int, MatrixContent, int, double, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor for simple tag mapping.
MatrixContent(int, int, int, MatrixContent, int, double, int, String) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor for simple tag mapping with peptide sequence.
MatrixContent(int, int, int, MatrixContent, int, int, int, int, char) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor for sequence with variants.
MatrixContent(int, int, int, MatrixContent, int, int, int[], char) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor for sequence with variants.
MatrixContent(int, int, int, MatrixContent, double, int, int, int, int, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor.
MatrixContent(int, int, int, MatrixContent, double, String, String, int, int, ModificationMatch, ArrayList<ModificationMatch>, int, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor.
MatrixContent(int, int, int, MatrixContent, double, String, String, int, int, int, ModificationMatch, ArrayList<ModificationMatch>, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor.
MatrixContent(int, int, int, MatrixContent, double, int, int, int, int, char, String) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor.
MatrixContent(int, int, int, MatrixContent, double, int, int, int, int[], char, String) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor.
MatrixContent(int, int, int, MatrixContent, double, String, int, int, ModificationMatch, ArrayList<ModificationMatch>, int, int, char, String) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor.
MatrixContent(int, int, int, MatrixContent, double, String, int, int, ModificationMatch, ArrayList<ModificationMatch>, int, int[], char, String) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Constructor.
MatrixContent(MatrixContent) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Copy constructor.
MavenJarFile - Class in com.compomics.software.autoupdater
MavenJarFile.
MavenJarFile(URI) - Constructor for class com.compomics.software.autoupdater.MavenJarFile
Create a new MavenJarFile object.
MavenJarFile(File) - Constructor for class com.compomics.software.autoupdater.MavenJarFile
Create a new MavenJarFile object.
MAX_DEPTH - Static variable in class com.compomics.util.experiment.identification.modification.scores.PhosphoRS
The maximal depth to use per window.
MAX_ISOTOPIC_CORRRECTION - Static variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The maximal isotope correction.
MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH - Static variable in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
The maximum allowed length of the FASTA file name.
MAX_NEUTRAL_LOSSES - Static variable in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
The maximum number of neutral losses a fragment ion can have in order to be annotated.
maxDouble - Static variable in class com.compomics.util.math.BigMathUtils
Big decimal value of the maximal value of a double.
maxPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The maximum padding (distance between the axes and the border of the panel).
maxPTMsPerPeptide - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Maximal number of PTMs per peptide.
MDScore - Class in com.compomics.util.experiment.identification.modification.scores
This class estimates the MD score as described in https://www.ncbi.nlm.nih.gov/pubmed/21057138 Note: this implementation of the MD score is not restricted to phosphorylation.
MDScore() - Constructor for class com.compomics.util.experiment.identification.modification.scores.MDScore
Empty default constructor
mean(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Convenience method returning the mean of a list of doubles.
meanDistance - Variable in class com.compomics.util.math.statistics.linear_regression.RegressionStatistics
The mean of the squared distance of the points to the regression line.
median(double[]) - Static method in class com.compomics.util.math.BasicMathFunctions
Method to estimate the median for an unsorted list.
median(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Method to estimate the median of an unsorted list.
medianDistance - Variable in class com.compomics.util.math.statistics.linear_regression.RegressionStatistics
The median of the squared distance of the points to the regression line.
MedianRegression - Class in com.compomics.util.math.statistics.linear_regression.regressions
Performs a robust linear regression.
MedianRegression() - Constructor for class com.compomics.util.math.statistics.linear_regression.regressions.MedianRegression
Empty default constructor
medianSorted(double[]) - Static method in class com.compomics.util.math.BasicMathFunctions
Method to estimate the median for a sorted list.
medianSorted(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Method to estimate the median of a sorted list.
MemoryConsumptionStatus - Class in com.compomics.util.memory
This class provides information on the memory consumption status.
MemoryConsumptionStatus() - Constructor for class com.compomics.util.memory.MemoryConsumptionStatus
Empty default constructor
memoryUsed() - Static method in class com.compomics.util.memory.MemoryConsumptionStatus
Returns the share of memory being used.
merge(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Simple merger for two patterns.
merge(AminoAcidPattern, AminoAcidPattern) - Static method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Convenience method merging two different patterns (see public void merge(AminoAcidPattern otherPattern) for detailed information of the merging procedure).
mergeHistograms(Collection<HashMap<Double, Integer>>) - Static method in class com.compomics.util.math.HistogramUtils
Merges histograms in a single histogram by adding the values in each bin.
MetaDataXMLParser - Class in com.compomics.software.autoupdater
MetaDataXMLParser.
MetaDataXMLParser(XMLEventReader) - Constructor for class com.compomics.software.autoupdater.MetaDataXMLParser
Create a new MetaDataXMLParser.
metaMorpheus - Static variable in class com.compomics.util.experiment.identification.Advocate
The MetaMorpheus search engine.
MetaMorpheusParameters - Class in com.compomics.util.parameters.identification.tool_specific
The MetaMorpheus specific parameters.
MetaMorpheusParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Constructor.
MetaMorpheusParameters.MetaMorpheusDecoyType - Enum in com.compomics.util.parameters.identification.tool_specific
The available decoy types.
MetaMorpheusParameters.MetaMorpheusDissociationType - Enum in com.compomics.util.parameters.identification.tool_specific
The available dissociation types.
MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType - Enum in com.compomics.util.parameters.identification.tool_specific
The available fragmentation terminus types.
MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType - Enum in com.compomics.util.parameters.identification.tool_specific
The available initiator methionine behavior types.
MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType - Enum in com.compomics.util.parameters.identification.tool_specific
The available mass difference acceptor types.
MetaMorpheusParameters.MetaMorpheusSearchType - Enum in com.compomics.util.parameters.identification.tool_specific
The available search types.
MetaMorpheusParameters.MetaMorpheusToleranceType - Enum in com.compomics.util.parameters.identification.tool_specific
The available decoy types.
MetaMorpheusParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the MetaMorpheus specific parameters.
MetaMorpheusParametersDialog(Frame, MetaMorpheusParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
Creates new form MetaMorpheusDialog with a frame as owner.
MetaMorpheusParametersDialog(Dialog, Frame, MetaMorpheusParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
Creates new form MetaMorpheusDialog with a dialog as owner.
Methionine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Methionine.
Methionine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Methionine
Constructor.
METHIONINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Methionine immonium ion.
methodUsed - Variable in class com.compomics.util.experiment.quantification.Quantification
The quantification method used
METHYL_R_112 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for methylation of R (PMID: 16335983).
METHYL_R_115 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for methylation of R (PMID: 16335983).
METHYL_R_143 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for methylation of R (PMID: 16335983).
METHYL_R_70 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for methylation of R (PMID: 16335983).
METHYL_R_87 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for methylation of R.
Metrics - Class in com.compomics.util.experiment.identification.peptide_shaker
This class contains metrics gathered during the creation of a PeptideShaker project.
Metrics() - Constructor for class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Constructor.
MetricsPrefix - Enum in com.compomics.util.experiment.units
Enumeration of the metrics prefixes.
Mg - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The Magnesium atom.
mgf - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MGF - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MgfFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.mgf files.
MgfFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.MgfFileFilter
Empty default constructor
MgfFileIterator - Class in com.compomics.util.experiment.io.mass_spectrometry.mgf
An iterator of the spectra in an mgf file.
MgfFileIterator(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileIterator
Constructor.
MgfFileUtils - Class in com.compomics.util.experiment.io.mass_spectrometry.mgf
Utilities for the handling of mgf files.
MgfFileUtils() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
 
MgfFileWriter - Class in com.compomics.util.experiment.io.mass_spectrometry.mgf
This class writes spectrum files in Mascot Generic File (mgf) format.
MgfFileWriter() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileWriter
Empty default constructor
MgfFileWriter(File) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileWriter
Constructor.
MgfIndex - Class in com.compomics.util.experiment.io.mass_spectrometry.mgf
This class contains the indexes of an mgf file after indexing mapped with the title of the spectrum.
MgfIndex() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Empty default constructor
MgfIndex(ArrayList<String>, HashMap<String, Long>, HashMap<String, Integer>, HashMap<Integer, Double>, String, double, double, double, double, int, int, boolean, boolean, long) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Constructor.
MgfIndex(ArrayList<String>, HashMap<String, Integer>, HashMap<String, Long>, HashMap<String, Integer>, HashMap<Integer, Double>, String, double, double, double, double, int, int, boolean, boolean, long, int) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Constructor.
MIN_DEPTH - Static variable in class com.compomics.util.experiment.identification.modification.scores.PhosphoRS
The minimal depth to use per window.
MIN_ISOTOPIC_CORRRECTION - Static variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The minimum isotope correction.
miniature - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If set to true, the y-axis is removed, the y- and x-axis tags are removed, and any annotations are hidden.
minNormalDouble - Static variable in class com.compomics.util.math.BigMathUtils
Big decimal value of the minimal normal value of a double.
MirroredSpectraTestDialog - Class in com.compomics.util.examples
Mirrored spectra test class.
MirroredSpectraTestDialog() - Constructor for class com.compomics.util.examples.MirroredSpectraTestDialog
Empty default constructor
MirroredSpectraTestDialog(Frame, boolean) - Constructor for class com.compomics.util.examples.MirroredSpectraTestDialog
Creates a new MirroredSpectraTestDialog
mkdir(String) - Method in class com.compomics.util.io.ftp.FTP
Create a directory on the remote system
MOD_MASS_TOLERANCE - Static variable in class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
The mass tolerance to be used to match modifications from search engines and expected modifications.
model - Variable in class com.compomics.util.sun.TableMap
 
Modification - Class in com.compomics.util.experiment.biology.modifications
This class models a peptide or protein modification.
Modification() - Constructor for class com.compomics.util.experiment.biology.modifications.Modification
Constructor for the modification.
Modification(ModificationType, String, String, AtomChain, AtomChain, AminoAcidPattern, ModificationCategory) - Constructor for class com.compomics.util.experiment.biology.modifications.Modification
Constructor for a reference modification.
Modification(ModificationType, String, String, AtomChain, AtomChain, AminoAcidPattern, CvTerm, CvTerm, ModificationCategory) - Constructor for class com.compomics.util.experiment.biology.modifications.Modification
Constructor for a reference modification.
Modification(ModificationType, String, Double, ArrayList<String>, ModificationCategory) - Constructor for class com.compomics.util.experiment.biology.modifications.Modification
Simple constructor for a modification.
modification - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Index to the modifications list.
Modification - Interface in com.compomics.util.interfaces
This interface describes the behaviour for a modification on a peptide or aminoacid sequence.
MODIFICATION_LOCALIZATION_SEPARATOR - Static variable in class com.compomics.util.experiment.biology.proteins.Peptide
Separator preceding confident localization of the confident localization of a modification.
MODIFICATION_SEPARATOR - Static variable in class com.compomics.util.experiment.biology.proteins.Peptide
Separator used to separate modifications in peptide keys as string.
ModificationCategory - Enum in com.compomics.util.experiment.biology.modifications
Enum for the different modification categories supported.
ModificationChooser - Class in com.compomics.util.gui.utils.user_choice.list_choosers
Dialog for choosing an item in a list of modifications.
ModificationChooser() - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.ModificationChooser
Empty default constructor
ModificationChooser(Frame, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.ModificationChooser
Constructor.
ModificationChooser(JDialog, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.ModificationChooser
Constructor.
ModificationChooser(Frame, ArrayList<String>, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.ModificationChooser
Constructor with default values.
ModificationChooser(JDialog, ArrayList<String>, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.ModificationChooser
Constructor with default values.
modificationConversionToString() - Static method in class com.compomics.util.protein.ModificationFactory
Returns a String representation of the modification title to code mappings.
ModificationDialog - Class in com.compomics.util.gui.modification
This dialog allows the user to create/edit Modifications.
ModificationDialog(JDialog, Modification, boolean) - Constructor for class com.compomics.util.gui.modification.ModificationDialog
Creates a new Modification dialog.
ModificationDialog(JFrame, PtmToPrideMap, Modification, boolean) - Constructor for class com.compomics.util.gui.modification.ModificationDialog
Creates a new Modification dialog.
ModificationFactory - Class in com.compomics.util.experiment.biology.modifications
This factory will load Modification from an XML file and provide them on demand as standard class.
ModificationFactory - Class in com.compomics.util.protein
This class can be used to generate a Modification instance from a code or title.
ModificationFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Feature based on the modification status of an amino acid.
ModificationFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
Empty default constructor
ModificationFeature(ModificationFeature.Property) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
Constructor.
ModificationFeature.Property - Enum in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Enum for the possible features.
ModificationImplementation - Class in com.compomics.util.protein
This class implements a specific Modification.
ModificationImplementation() - Constructor for class com.compomics.util.protein.ModificationImplementation
Empty default constructor
ModificationImplementation(ModificationTemplate, int) - Constructor for class com.compomics.util.protein.ModificationImplementation
This constructor allows initialization of all the properties for the modification.
ModificationImplementation(String, String, HashMap, int) - Constructor for class com.compomics.util.protein.ModificationImplementation
This constructor allows initialization of all the properties for the modification.
ModificationImplementation(String, String, HashMap, boolean, int) - Constructor for class com.compomics.util.protein.ModificationImplementation
This constructor allows initialization of all the properties for the modification.
modificationLocalization(Peptide, HashMap<Integer, ArrayList<String>>, HashMap<ModificationMatch, ArrayList<String>>, IdentificationParameters, IdfileReader, ModificationProvider) - Static method in class com.compomics.util.experiment.identification.modification.mapping.ModificationLocalizationMapper
Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.
ModificationLocalizationMapper - Class in com.compomics.util.experiment.identification.modification.mapping
Function attempting to map modification localization based on their type.
ModificationLocalizationMapper() - Constructor for class com.compomics.util.experiment.identification.modification.mapping.ModificationLocalizationMapper
 
ModificationLocalizationParameters - Class in com.compomics.util.parameters.identification.advanced
This class contains the modification localization preferences.
ModificationLocalizationParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Constructor.
ModificationLocalizationParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
PTMLocalizationParametersDialog.
ModificationLocalizationParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
Empty default constructor
ModificationLocalizationParametersDialog(Frame, ModificationLocalizationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
Creates a new PTMLocalizationParametersDialog with a frame as owner.
ModificationLocalizationParametersDialog(Dialog, Frame, ModificationLocalizationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
Creates a new PTMLocalizationParametersDialog with a dialog as owner.
ModificationLocalizationScore - Enum in com.compomics.util.experiment.identification.modification
An enum of the modification localization scores.
ModificationMassMapper - Class in com.compomics.util.experiment.identification.modification.mapping
Function inferring the mass of a modification based on the search engine used.
ModificationMassMapper() - Constructor for class com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
 
ModificationMatch - Class in com.compomics.util.experiment.identification.matches
This class models the match between theoretic PTM and identification results.
ModificationMatch(String, int) - Constructor for class com.compomics.util.experiment.identification.matches.ModificationMatch
Constructor for a modification match.
ModificationMatch() - Constructor for class com.compomics.util.experiment.identification.matches.ModificationMatch
Default constructor for a modification match.
ModificationNameMapper - Class in com.compomics.util.experiment.identification.modification.mapping
Functions mapping search engine modifications to utilities by name.
ModificationNameMapper() - Constructor for class com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
 
ModificationParameters - Class in com.compomics.util.parameters.identification.search
This class stores the information about the modification parameters (usage, colors, names).
ModificationParameters() - Constructor for class com.compomics.util.parameters.identification.search.ModificationParameters
Constructor.
ModificationParameters(ModificationParameters) - Constructor for class com.compomics.util.parameters.identification.search.ModificationParameters
Constructor creating a new Modification profile based on the given one.
modificationPos - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
List of all modifications.
ModificationProfile - Class in com.compomics.util.gui.protein
A simple modification profile object.
ModificationProfile() - Constructor for class com.compomics.util.gui.protein.ModificationProfile
Empty default constructor
ModificationProfile(String, double[][], Color) - Constructor for class com.compomics.util.gui.protein.ModificationProfile
Modification profile constructor.
ModificationProvider - Interface in com.compomics.util.experiment.biology.modifications
Interface for a modification provider.
modifications - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
List of all modifications.
ModificationsCLI - Class in com.compomics.cli.modifications
Command line to manage the modifications.
ModificationsCLI(ModificationsCLIInputBean) - Constructor for class com.compomics.cli.modifications.ModificationsCLI
Constructor.
ModificationsCLIInputBean - Class in com.compomics.cli.modifications
This class parses the parameters from an ModificationsCLI.
ModificationsCLIInputBean(CommandLine) - Constructor for class com.compomics.cli.modifications.ModificationsCLIInputBean
Parses all the arguments from a command line.
ModificationsCLIParams - Enum in com.compomics.cli.modifications
Enum class specifying the ModificationsCLI parameters.
ModificationScoring - Class in com.compomics.util.experiment.identification.peptide_shaker
This class contains stores the modification localization scores.
ModificationScoring() - Constructor for class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Default constructor Constructor.
ModificationScoring(String) - Constructor for class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Constructor.
ModificationsDialog - Class in com.compomics.util.gui.modification
A dialog where the modification details can be modified.
ModificationsDialog(Frame, boolean) - Constructor for class com.compomics.util.gui.modification.ModificationsDialog
Creates a new ModificationsDialog.
ModificationSiteMapping - Class in com.compomics.util.experiment.identification.modification
This class contains convenience methods to map modifications on potential sites.
ModificationSiteMapping() - Constructor for class com.compomics.util.experiment.identification.modification.ModificationSiteMapping
Empty default constructor
modificationsToString() - Static method in class com.compomics.util.protein.ModificationFactory
Returns a String representation of the modifications.
ModificationTable - Class in com.compomics.util.gui.modification
Table containing information about the peak annotation of a modified peptide.
ModificationTable(Identification, AnnotationParameters, PeptideMatch, Modification, boolean, ModificationParameters, SequenceProvider, SpectrumProvider, SequenceMatchingParameters) - Constructor for class com.compomics.util.gui.modification.ModificationTable
Constructor.
ModificationtableContent - Class in com.compomics.util.experiment.identification.modification
Convenience class for the content of a PTM table.
ModificationtableContent() - Constructor for class com.compomics.util.experiment.identification.modification.ModificationtableContent
Constructor.
ModificationTemplate - Class in com.compomics.util.protein
This class holds a template for a Modification, meaning that it contains all shared characteristics of a Modification, but not the instance-specific one.
ModificationTemplate() - Constructor for class com.compomics.util.protein.ModificationTemplate
Empty default constructor
ModificationTemplate(String, String, HashMap) - Constructor for class com.compomics.util.protein.ModificationTemplate
This constructor allows initialization of all the properties for the modification template.
ModificationTemplate(String, String, HashMap, boolean) - Constructor for class com.compomics.util.protein.ModificationTemplate
This constructor allows initialization of all the properties for the modification template.
ModificationType - Enum in com.compomics.util.experiment.biology.modifications
Enum for the different types of modifications supported.
ModificationUtils - Class in com.compomics.util.experiment.identification.utils
This class groups functions that can be used to work with modifications.
ModificationUtils() - Constructor for class com.compomics.util.experiment.identification.utils.ModificationUtils
Empty default constructor.
modProfileEdited() - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
Returns true if the user edited the modification profile.
MolecularElement - Enum in com.compomics.util.enumeration
This ENUM types the distinct molecular elements.
MolecularFormula - Class in com.compomics.util.protein
This class represents the molecular formula.
MolecularFormula() - Constructor for class com.compomics.util.protein.MolecularFormula
Default constructor
MolecularFormula(Sequence) - Constructor for class com.compomics.util.protein.MolecularFormula
Constructor.
Monitorable - Interface in com.compomics.util.interfaces
This interface describes the behaviour for any Object whose progressing state can be monitored.
MonitorableFileInputStream - Class in com.compomics.util.io.file
This class implements an InputStream that reports on the progress of reading a file in integer quantities, even though the underlying file may have a binary size that is outside of integer range.
MonitorableFileInputStream(File) - Constructor for class com.compomics.util.io.file.MonitorableFileInputStream
This constructor takes a file to load the FileInputStream from.
MonitorableFileInputStream(String) - Constructor for class com.compomics.util.io.file.MonitorableFileInputStream
This constructor takes a file to load the FileInputStream from.
MonitorableInputStream - Class in com.compomics.util.io.file
This class provides a specific FilterInputStream that can be monitored for progress.
MonitorableInputStream(InputStream) - Constructor for class com.compomics.util.io.file.MonitorableInputStream
A MonitorableInputStream can only be constructed around an existing InputStream.
MonitorableInputStream(InputStream, int) - Constructor for class com.compomics.util.io.file.MonitorableInputStream
A MonitorableInputStream can only be constructed around an existing InputStream.
MonitorableInputStream(InputStream, boolean) - Constructor for class com.compomics.util.io.file.MonitorableInputStream
A MonitorableInputStream can only be constructed around an existing InputStream.
MonitorDimension - Class in com.compomics.util.gui
This class makes it possible to set the dimensions of a JFrame of JPanel to a certain percentage of the screen size.
MonitorDimension() - Constructor for class com.compomics.util.gui.MonitorDimension
 
monitorProgress() - Method in interface com.compomics.util.interfaces.Monitorable
This method returns the progress of the task.
monitorProgress() - Method in class com.compomics.util.io.file.MonitorableFileInputStream
This method returns the progress (as measured by taking the value of iMaximum, minus the current progress as reported by the cache).
monitorProgress() - Method in class com.compomics.util.io.file.MonitorableInputStream
This method returns the progress (as measured by taking the value of iMaximum, minus the current available bytes as reported by the underlying InputStream - variable iRemainder).
MONOAA - Static variable in class com.compomics.util.general.MassCalc
Index for the monoisotopic aminoacid masses.
MONOELEMENTS - Static variable in class com.compomics.util.general.MassCalc
Index for the monoisotopic masses of the biochemically relevant elements.
MONOISOTOPIC - Static variable in interface com.compomics.util.interfaces.Modification
Constant to indicate the position of the monoisotopic mass in the mass array.
monoisotopicAtomChain - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
The monoisotopic atom chain.
monoisotopicMass - Variable in class com.compomics.util.experiment.biology.atoms.Atom
The monoisotopic mass.
MONONUCLEOTIDES - Static variable in class com.compomics.util.general.MassCalc
Index for the monoisotopic nucleotide masses.
morpheus - Static variable in class com.compomics.util.experiment.identification.Advocate
The Morpheus search engine.
mouseWheelMoved(MouseWheelEvent) - Method in class com.compomics.util.gui.TableMouseWheelListener
 
ms2 - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MS2 - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MS2_IDENTIFICATION - Static variable in class com.compomics.util.experiment.identification.IdentificationMethod
index for identification method based on MS2 fragment ion matching
Ms2Exporter - Class in com.compomics.util.experiment.io.mass_spectrometry.ms2
This class writes spectrum files in MS2 format.
Ms2Exporter() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2Exporter
Empty default constructor.
Ms2Exporter(File) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2Exporter
Constructor.
Ms2FileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.ms2 files.
Ms2FileFilter() - Constructor for class com.compomics.util.io.file.filefilters.Ms2FileFilter
Empty default constructor
Ms2FileWriter - Class in com.compomics.util.experiment.io.mass_spectrometry.ms2
This class writes spectrum files in MS2 format.
Ms2FileWriter() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2FileWriter
Empty default constructor
Ms2FileWriter(File) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2FileWriter
Constructor.
Ms2pipFeature - Interface in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
Interface for an ms2pip feature.
msAmanda - Static variable in class com.compomics.util.experiment.identification.Advocate
The MS Amanda search engine.
MsAmandaIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This IdfileReader reads identifications from an MS Amanda csv result file.
MsAmandaIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
Default constructor for the purpose of instantiation.
MsAmandaIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
Constructor for an MS Amanda csv result file reader.
MsAmandaIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader
Constructor for an MS Amanda csv result file reader.
MsAmandaParameters - Class in com.compomics.util.parameters.identification.tool_specific
The MS Amanda specific parameters.
MsAmandaParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Constructor.
MsAmandaParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the MS Amanda specific settings.
MsAmandaParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
Empty default constructor
MsAmandaParametersDialog(Frame, MsAmandaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
Creates new form MsAmandaSettingsDialog with a frame as owner.
MsAmandaParametersDialog(Dialog, Frame, MsAmandaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
Creates new form MsAmandaSettingsDialog with a dialog as owner.
MsConvertParameters - Class in com.compomics.util.experiment.mass_spectrometry.proteowizard
The parameters to use when running msconvert.
MsConvertParameters() - Constructor for class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
Constructor.
MsConvertParametersDialog - Class in com.compomics.util.gui.parameters.proteowizard
Dialog for the creation and edition of msconvert parameters.
MsConvertParametersDialog(Frame, MsConvertParameters) - Constructor for class com.compomics.util.gui.parameters.proteowizard.MsConvertParametersDialog
Constructor.
MsFileExporter - Class in com.compomics.util.experiment.io.mass_spectrometry
This class writes ms files in various formats.
MsFileExporter() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter
 
MsFileExporter.Format - Enum in com.compomics.util.experiment.io.mass_spectrometry
Enum of the supported export formats.
MsFileHandler - Class in com.compomics.util.experiment.io.mass_spectrometry
A spectrum provider for mass spectrometry files based on Compomics Mass Spectrometry (cms) files.
MsFileHandler() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
Constructor.
MsFileIterator - Interface in com.compomics.util.experiment.io.mass_spectrometry
Interface for mass spectrometry file readers.
MsFilePerformance - Class in com.compomics.scripts_marc
This script test the speed of the ms file access.
MsFilePerformance() - Constructor for class com.compomics.scripts_marc.MsFilePerformance
 
msFit - Static variable in class com.compomics.util.experiment.identification.Advocate
The MS-Fit search engine, old school peptide mass fingerprinting.
msgf - Static variable in class com.compomics.util.experiment.identification.Advocate
The MS-GF+ search engine.
MsgfParameters - Class in com.compomics.util.parameters.identification.tool_specific
The MS-GF+ specific parameters.
MsgfParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Constructor.
MsgfParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the MS-GF+ specific settings.
MsgfParametersDialog(Frame, MsgfParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
Creates new form MsgfSettingsDialog with a frame as owner.
MsgfParametersDialog(Dialog, Frame, MsgfParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
Creates new form MsgfSettingsDialog with a dialog as owner.
MSNumpress - Class in com.compomics.util.experiment.io.mass_spectrometry.mzml
MSNumpress.
MSNumpress() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
 
MultipleAAPropertyFeature - Interface in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
Interface for the ms2pip features having multiple amino acid properties.
MutexMap - Class in com.compomics.util.experiment.identification.features
Mutex map for the features cache.
MutexMap() - Constructor for class com.compomics.util.experiment.identification.features.MutexMap
Empty default constructor
myriMatch - Static variable in class com.compomics.util.experiment.identification.Advocate
The MyriMatch search engine, old school peptide mass fingerprinting.
MyriMatchParameters - Class in com.compomics.util.parameters.identification.tool_specific
The MyriMatch specific parameters.
MyriMatchParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Constructor.
MyriMatchParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the MyriMatch specific settings.
MyriMatchParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
Empty default constructor
MyriMatchParametersDialog(Frame, MyriMatchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
Creates new form MyriMatchSettingsDialog with a frame as owner.
MyriMatchParametersDialog(Dialog, Frame, MyriMatchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
Creates new form MyriMatchSettingsDialog with a dialog as owner.
mz - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
The mass over charge ratio of the peak.
mz - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
The measured m/z of the precursor.
mz - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
The array of the m/z of the peaks.
mzArray - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
The mz array of the spectrum.
mzdata - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
mzData - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
mzDATA - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MZDATA - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MzDataFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.mzData files.
MzDataFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.MzDataFileFilter
Empty default constructor
MZIDENTML_VERSION - Static variable in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
The version of the mzIdentML format.
MzIdentMLIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This IdfileReader reads identifications from an mzIdentML result file.
MzIdentMLIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
Default constructor for the purpose of instantiation.
MzIdentMLIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
Constructor for an mzIdentML result file reader.
MzIdentMLIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader
Constructor for an mzIdentML result file reader.
MzIdentMLIdfileReader.RawValueConversionType - Enum in com.compomics.util.experiment.io.identification.idfilereaders
Enum for the raw value to e-value conversion.
MzIdentMLIdfileSearchParametersConverter - Class in com.compomics.util.experiment.io.identification
Reads basic search parameters from mzIdentML result files.
MzIdentMLIdfileSearchParametersConverter(File, SearchParameters, String, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identification.MzIdentMLIdfileSearchParametersConverter
Constructor.
MzIdentMLVersion - Enum in com.compomics.util.experiment.io.identification
Enum of the versions of the mzIdentML format supported.
mzML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
mzml - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MZML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MzMlFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.mzML files.
MzMlFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.MzMlFileFilter
Empty default constructor
MzmlFileIterator - Class in com.compomics.util.experiment.io.mass_spectrometry.mzml
An iterator of the spectra in an mzml file.
MzmlFileIterator(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator
Constructor.
MzmlFileIterator.Precision - Enum in com.compomics.util.experiment.io.mass_spectrometry.mzml
The supported precision types for the binary data as defined in the mzML specifications and the PSI-MS ontology.
MzmlFileUtils - Class in com.compomics.util.experiment.io.mass_spectrometry.mzml
Utilities for the handling of mzml files.
MzmlFileUtils() - Constructor for class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileUtils
 
mzTolerance - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The m/z tolerance for peak matching.
mzXML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
mzxml - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MZXML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
MzXmlFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.mzXML files.
MzXmlFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.MzXmlFileFilter
Empty default constructor

N

N - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
N - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The nitrogen atom.
n2sort() - Method in class com.compomics.util.sun.TableSorter
 
N_AA - Static variable in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
The number of amino acids to export before and after the peptide
N_TERM_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
 
Na - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The sodium atom.
name - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Name of the amino acid.
name - Variable in enum com.compomics.util.experiment.biology.aminoacids.AminoAcid.Property
The name of the property.
name - Variable in class com.compomics.util.experiment.biology.atoms.Atom
The name of the atom.
name - Variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
The name of the neutral loss.
name - Variable in enum com.compomics.util.experiment.filtering.FilterItemComparator
The symbol to use.
name - Variable in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
The name of the filtering item.
name - Variable in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
The name of the filtering item.
name - Variable in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
The name of the filtering item.
name - Variable in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
The name of the filtering item.
name - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
Name of the filter.
name - Variable in enum com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
The name of the error type.
name - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature.Property
The name of the option.
name - Variable in enum com.compomics.util.experiment.identification.peptide_fragmentation.PeptideFragmentationModel
The name of the option.
name - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
The name of the score.
name - Variable in enum com.compomics.util.experiment.io.identification.MzIdentMLVersion
The name of the option.
name - Variable in enum com.compomics.util.experiment.mass_spectrometry.FragmentationMethod
The name of the fragmentation method.
name - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
The name of the filter.
name - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
The name of the format.
name - Variable in enum com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
The name of the format.
name - Variable in enum com.compomics.util.io.export.ExportFormat
The name of the format.
name - Variable in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
The name.
name - Variable in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
The name.
name - Variable in enum com.compomics.util.parameters.peptide_shaker.ProjectType
The name of the option.
name - Variable in enum com.compomics.util.parameters.searchgui.OutputParameters
Name of the option.
needsModifications() - Method in interface com.compomics.util.experiment.filtering.FilterItem
Indicates whether the item expects a list of modifications to filter on.
needsModifications() - Method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
 
needsModifications() - Method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
 
needsModifications() - Method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
 
needsModifications() - Method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
 
needsUncompressing(String) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator
Reads true if the binary data is compressed.
needsUpdate(int, String) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Indicates whether the given column needs an update, i.e.
NeutralLoss - Class in com.compomics.util.experiment.biology.ions
This class represents a neutral loss.
NeutralLoss(String, AtomChain, boolean, char[]) - Constructor for class com.compomics.util.experiment.biology.ions.NeutralLoss
Constructor for a user defined neutral loss.
NeutralLoss() - Constructor for class com.compomics.util.experiment.biology.ions.NeutralLoss
Default construtor
NeutralLoss(String, AtomChain, boolean) - Constructor for class com.compomics.util.experiment.biology.ions.NeutralLoss
Constructor for a user defined neutral loss.
NeutralLoss(String, AtomChain, boolean, char[], boolean) - Constructor for class com.compomics.util.experiment.biology.ions.NeutralLoss
Constructor for a user defined neutral loss.
NeutralLossCombination - Class in com.compomics.util.experiment.biology.ions
This class represents a combination of multiple neutral losses.
NeutralLossCombination() - Constructor for class com.compomics.util.experiment.biology.ions.NeutralLossCombination
Empty default constructor
NeutralLossCombination(NeutralLoss[]) - Constructor for class com.compomics.util.experiment.biology.ions.NeutralLossCombination
Constructor.
NeutralLossesMap - Class in com.compomics.util.experiment.identification.spectrum_annotation
This class contains the informations relative to the accounting of neutral losses
NeutralLossesMap() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
Constructor.
neutron - Static variable in class com.compomics.util.experiment.biology.atoms.ElementaryElement
A neutron.
neutronMassMultiples - Static variable in class com.compomics.util.experiment.biology.atoms.ElementaryElement
Cache for the multiples of the neutron mass.
NewEnzymeDialog - Class in com.compomics.util.gui.enzymes
This dialog allows the user to create a new enzyme.
NewEnzymeDialog(EnzymesDialog) - Constructor for class com.compomics.util.gui.enzymes.NewEnzymeDialog
Creates a NewEnzymeDialog.
newLine(String) - Method in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
Appends a new line to the given section.
newLine() - Method in class com.compomics.util.io.export.ExportWriter
Adds a separator.
newLine() - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
newLine() - Method in class com.compomics.util.io.export.writers.TextWriter
 
newLine() - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Adds an end of line character.
newLine() - Method in class com.compomics.util.io.flat.SimpleFileWriter
Appends a new line to the output.
newVersionExists(Integer) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Returns true if a newer version of the species mapping exists in Ensembl.
newVersionReleased(MavenJarFile, URL) - Static method in class com.compomics.software.autoupdater.WebDAO
Returns true if a new version is available.
next() - Method in class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator
Returns the next match and updates the buffer.
next() - Method in class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator
Returns the next match and updates the buffer.
next() - Method in class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
Returns the next match and updates the buffer.
next() - Method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileIterator
 
next() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileIterator
 
next() - Method in interface com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
Returns the title of the next spectrum, null if none.
next() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.IntDecoder
Returns the next value.
next() - Method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator
 
nextObject() - Method in class com.compomics.util.experiment.identification.matches_iterators.MatchesIterator
Returns the next match and updates the buffer.
NH3 - Static variable in class com.compomics.util.experiment.biology.ions.NeutralLoss
NH3 loss.
Nitrogen - Class in com.compomics.util.experiment.biology.atoms.impl
The nitrogen atom.
Nitrogen() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Nitrogen
Constructor.
nlist() - Method in class com.compomics.util.io.ftp.FTP
NLIST files on a remote FTP server
NO_KEY - Static variable in class com.compomics.util.experiment.personalization.ExperimentObject
Value for a key not set.
NO_SPECIES_TAG - Static variable in class com.compomics.util.gui.genes.SpeciesDialog
Deprecated.
The text to use for no species selected.
NoDigestionCombinationIterator - Class in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
Iterator for no digestion of a sequence containing amino acid combinations.
NoDigestionCombinationIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionCombinationIterator
Empty default constructor
NoDigestionCombinationIterator(ProteinIteratorUtils, String, Double, Double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionCombinationIterator
Constructor.
NoDigestionIterator - Class in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
Iterator for no digestion.
NoDigestionIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionIterator
Empty default constructor
NoDigestionIterator(ProteinIteratorUtils, String, double, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionIterator
Constructor.
noErrors() - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Returns true of there were no errors.
NonSymmetricalNormalDistribution - Class in com.compomics.util.math.statistics.distributions
This class represents a non symmetrical normal distribution.
NonSymmetricalNormalDistribution() - Constructor for class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
Empty default constructor
NonSymmetricalNormalDistribution(double, double, double) - Constructor for class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution
Constructor.
NormalDistribution - Class in com.compomics.util.math.statistics.distributions
This class represents a normal distribution.
NormalDistribution() - Constructor for class com.compomics.util.math.statistics.distributions.NormalDistribution
Empty default constructor
NormalDistribution(double, double) - Constructor for class com.compomics.util.math.statistics.distributions.NormalDistribution
Constructor.
NormalizationFactors - Class in com.compomics.util.experiment.normalization
Class grouping the normalization factors used to normalize quantification results.
NormalizationFactors() - Constructor for class com.compomics.util.experiment.normalization.NormalizationFactors
Constructor.
normalize() - Method in class com.compomics.util.experiment.identification.modification.ModificationtableContent
Normalize intensities.
NormalKernelDensityEstimator - Class in com.compomics.util.math.statistics.distributions
This class makes use of "SSJ: Stochastic Simulation in Java" library from iro.umontreal.ca to estimate probability density function of an array of double.
NormalKernelDensityEstimator() - Constructor for class com.compomics.util.math.statistics.distributions.NormalKernelDensityEstimator
Empty default constructor
noSubstitution - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Empty substitution matrix.
NOT_FOUND - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Index indicating that the modification was not found.
NOT_GROUP - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Static index for a protein inference group: 0 - not a protein group or unique peptide of single protein group.
NotesDialog - Class in com.compomics.util.gui.error_handlers.notification
A simple dialog for displaying notes.
NotesDialog(Frame, boolean, ArrayList<String>) - Constructor for class com.compomics.util.gui.error_handlers.notification.NotesDialog
Creates a new NotesDialog.
notificationClicked(String) - Method in interface com.compomics.util.gui.error_handlers.notification.NotificationDialogParent
 
NotificationDialog - Class in com.compomics.util.gui.error_handlers.notification
An undecorated dialog for displaying notifications.
NotificationDialog(Frame, NotificationDialogParent, boolean, int, String) - Constructor for class com.compomics.util.gui.error_handlers.notification.NotificationDialog
Creates a new NotificationDialog.
NotificationDialogParent - Interface in com.compomics.util.gui.error_handlers.notification
A NotificationDialog parent interface.
notifyUser(Exception) - Method in class com.compomics.util.exceptions.exception_handlers.CommandLineExceptionHandler
 
notifyUser(Exception) - Method in class com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler
 
notifyUser(Exception) - Method in class com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler
 
notifyUser(Exception) - Method in class com.compomics.util.exceptions.ExceptionHandler
Notifies the user that an exception was caught.
novor - Static variable in class com.compomics.util.experiment.identification.Advocate
The Novor de novo sequencing algorithm.
NovorIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This IdfileReader reads identifications from a Novor csv result file.
NovorIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
Default constructor for the purpose of instantiation.
NovorIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
Constructor for an Novor csv result file reader.
NovorIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader
Constructor for an Novor csv result file reader.
NovorParameters - Class in com.compomics.util.parameters.identification.tool_specific
Novor specific parameters.
NovorParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.NovorParameters
Constructor.
NovorParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for editing Novor advanced settings.
NovorParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
Empty default constructor
NovorParametersDialog(Frame, NovorParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
Creates a new NovorSettingsDialog with a frame as owner.
NovorParametersDialog(Dialog, Frame, NovorParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
Creates a new NovorSettingsDialog with a dialog as owner.
nSequences - Variable in class com.compomics.util.experiment.io.biology.protein.FastaSummary
The number of sequences.
nSpectraInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether the number of spectra for a given protein match is in cache.
nTarget - Variable in class com.compomics.util.experiment.io.biology.protein.FastaSummary
The number of target sequences.
NTERM - Static variable in class com.compomics.util.protein.Enzyme
 
nTermCorrection - Variable in class com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
The mass to add to the N-terminal gap so that is corresponds to a peptide fragment.
nTermCorrection - Variable in class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
The mass to add to the N-terminal gap so that is corresponds to a peptide fragment.
NTERMINAL - Static variable in class com.compomics.util.protein.DualEnzyme
The code for N-terminal position in the resultant peptide.
NTERMINUS - Static variable in interface com.compomics.util.interfaces.Modification
The residue code for the N-terminus.
NTERMTRUNC - Static variable in class com.compomics.util.protein.Protein
The code for an N-terminal truncation.
NucleotideSequence - Class in com.compomics.util.nucleotide
This class combines a protein Header with a nucleotide sequence.
NucleotideSequence() - Constructor for class com.compomics.util.nucleotide.NucleotideSequence
Empty default constructor
NucleotideSequence(NucleotideSequenceImpl) - Constructor for class com.compomics.util.nucleotide.NucleotideSequence
This constructor requires a NucleotideSequenceImpl as argument.
NucleotideSequence(Header, NucleotideSequenceImpl) - Constructor for class com.compomics.util.nucleotide.NucleotideSequence
This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein.
NucleotideSequence(String) - Constructor for class com.compomics.util.nucleotide.NucleotideSequence
This constructor allows for the construction of a NucleotideSequence instance by passing a FASTA entry.
NucleotideSequence(String, String) - Constructor for class com.compomics.util.nucleotide.NucleotideSequence
This constructor allows for the construction of a NucleotideSequence instance through the passing of a NucleotideSequence String and a Sequence String.
NucleotideSequenceImpl - Class in com.compomics.util.nucleotide
This class represents a nucleotide sequence (RNA or DNA).
NucleotideSequenceImpl() - Constructor for class com.compomics.util.nucleotide.NucleotideSequenceImpl
Empty default constructor
NucleotideSequenceImpl(String) - Constructor for class com.compomics.util.nucleotide.NucleotideSequenceImpl
This constructor allows the construction of an Object, wrapping a nucleotidesequence.
NucleotideSequenceImpl(String, Properties) - Constructor for class com.compomics.util.nucleotide.NucleotideSequenceImpl
This constructor allows the construction of an Object, wrapping a nucleotidesequence.
NucleotideSequenceImpl(String, String) - Constructor for class com.compomics.util.nucleotide.NucleotideSequenceImpl
This constructor allows the construction of an Object, wrapping a nucleotidesequence.
number - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
The index of the filter.
numPTMs - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
The number of PTMs.
numSpecificVariants - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
The specific variants.
numVariants - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
List of all modifications.
numX - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Current number of contained X's.
nValidatedPeptidesInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether the number of validated peptides is in cache for a given protein match.
nValidatedSpectraForPeptideInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether the number of validated spectra for a peptide match is in cache.
nValidatedSpectraInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether the number of validated spectra is in cache for the given protein match.

O

O - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
O - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The oxygen atom.
object - Variable in class com.compomics.util.db.object.ObjectsCache.ObjectsCacheElement
The object.
ObjectMutex - Class in com.compomics.util.threading
This mutex can be used to manage threads editing experiment objects using their key.
ObjectMutex() - Constructor for class com.compomics.util.threading.ObjectMutex
Constructor.
ObjectsCache - Class in com.compomics.util.db.object
An object cache can be combined to an ObjectDB to improve its performance.
ObjectsCache(ObjectsDB) - Constructor for class com.compomics.util.db.object.ObjectsCache
Constructor.
ObjectsCache.ObjectsCacheElement - Class in com.compomics.util.db.object
Objects cache element.
ObjectsCacheElement(Object) - Constructor for class com.compomics.util.db.object.ObjectsCache.ObjectsCacheElement
Constructor.
ObjectsCacheElement(Object, boolean, boolean) - Constructor for class com.compomics.util.db.object.ObjectsCache.ObjectsCacheElement
Constructor.
ObjectsDB - Class in com.compomics.util.db.object
A database which can easily be used to store objects.
ObjectsDB() - Constructor for class com.compomics.util.db.object.ObjectsDB
Empty default constructor.
ObjectsDB(String, String) - Constructor for class com.compomics.util.db.object.ObjectsDB
Constructor.
ObjectsDB(String, String, boolean) - Constructor for class com.compomics.util.db.object.ObjectsDB
Constructor.
observableCoverageInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether the observable coverage of a protein match is in cache.
occurrenceTablesPrimary - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Wavelet tree for storing the burrows wheeler transform.
occurrenceTablesReversed - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Wavelet tree for storing the burrows wheeler transform reversed.
oldCleave(Protein) - Method in class com.compomics.util.protein.DualEnzyme
This cleave method will process sequence XDYRZ solely into YR peptides.
omssa - Static variable in class com.compomics.util.experiment.identification.Advocate
The OMSSA search engine.
OmssaParameters - Class in com.compomics.util.parameters.identification.tool_specific
The OMSSA specific parameters.
OmssaParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Constructor.
OmssaParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the OMSSA specific parameters.
OmssaParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
Empty default constructor
OmssaParametersDialog(Frame, OmssaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
Creates new form OmssaParametersDialog with a frame as owner.
OmssaParametersDialog(Dialog, Frame, OmssaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
Creates new form OmssaParametersDialog with a dialog as owner.
omx - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
OMX - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
OmxFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.omx files.
OmxFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.OmxFileFilter
Empty default constructor
onlyTrypticPeptides - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Flag for only considering tryptic digested peptides.
onyaseEngine - Static variable in class com.compomics.util.experiment.identification.Advocate
The Onyase engine script.
OnyaseIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
Id file reader for the scripts in Onyase.
OnyaseIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
Default constructor instantiation purposes.
OnyaseIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
Constructor for an onyase file reader.
openDataConnection(String) - Method in class com.compomics.util.io.ftp.FTP
This method will set up the networking for client-server data transfer and it will send the specified command to the server.
openServer(String) - Method in class com.compomics.util.io.ftp.FTP
open a FTP connection to host host.
openServer(String, int) - Method in class com.compomics.util.io.ftp.FTP
Open an FTP connection to host host on port port.
openURL(String) - Static method in class com.compomics.util.examples.BareBonesBrowserLaunch
Tries to opens the given URL in the default browser.
OperatingSystemEnum - Enum in com.compomics.util.enumeration
This ENUM types the distinct OS systems.
optimalLinearFixedPoint(double[], int) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Optimal linear fixed point.
optimalSlofFixedPoint(double[], int) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
Optimal slof fixed point.
originalAminoAcid - Variable in class com.compomics.util.experiment.biology.variants.AminoAcidSubstitution
The original amino acid represented by its single letter code.
out - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
OUT - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
OutFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.out files.
OutFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.OutFileFilter
Empty default constructor
OUTPUT_FOLDER_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for an output folder.
outputData() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Indicates whether data should be copied along with the identification files in the SearchGUI output.
outputFormat - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
Boolean indicating if this in a format that can be used as output.
OutputParameters - Enum in com.compomics.util.parameters.searchgui
This enum lists the possible output options.
Oxygen - Class in com.compomics.util.experiment.biology.atoms.impl
The oxygen atom.
Oxygen() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Oxygen
Constructor.

P

P - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
P - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The phosphorus atom.
padding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The padding (distance between the axes and the border of the panel).
paint(Graphics) - Method in class com.compomics.util.gui.protein.SequenceModificationPanel
Paints the SequenceModificationPanel.
paint(Graphics) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Invoked by Swing to draw components.
paint(Graphics) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Paints the SequenceFragmentationPanel.
PARAMETERS_EXTENSION - Static variable in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
The extension for a parameters file.
PARAMETERS_FOLDER - Static variable in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
The identification parameters.
paramsTag - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
Tag for the parameters file path.
parseFromFASTA(String) - Static method in class com.compomics.util.experiment.io.biology.protein.Header
Factory method that constructs a Header instance based on a FASTA header line.
parsePeptideFromAnnotatedSequence(String) - Static method in class com.compomics.util.protein.AASequenceImpl
This method allows the construction of an AASequenceImpl object, complete with modifications from an annotated sequence String (eg., something like: 'NH2-YS<P>FVATER-COOH' or 'Ace-MATHM<Mox>PIR-COOH').
parseSequenceAndModificationsFromString(String) - Method in class com.compomics.util.protein.AASequenceImpl
This method is designed to load a sequence and it's set of modifications from a String which holds the sequence, annotated with all the modifications applied to it.
passConnection(Connection, String) - Method in interface com.compomics.util.interfaces.Connectable
This method will be called by the class actually making the connection.
passes(String, double) - Method in enum com.compomics.util.experiment.filtering.FilterItemComparator
Indicates whether a given value passes a threshold using this comparator.
passes(String, String) - Method in enum com.compomics.util.experiment.filtering.FilterItemComparator
Indicates whether a given value passes a threshold using this comparator.
passes(String, Collection<String>) - Method in enum com.compomics.util.experiment.filtering.FilterItemComparator
Indicates whether a set of values passes a threshold using this comparator.
passes(String, String[]) - Method in enum com.compomics.util.experiment.filtering.FilterItemComparator
Indicates whether a set of values passes a threshold using this comparator.
passes(String, Stream<String>) - Method in enum com.compomics.util.experiment.filtering.FilterItemComparator
Indicates whether a set of values passes a threshold using this comparator.
passHotPotato(Throwable) - Method in class com.compomics.util.gui.FlamableJFrame
This method will handle all errors thrown from child threads.
passHotPotato(Throwable, String) - Method in class com.compomics.util.gui.FlamableJFrame
This method takes care of any unrecoverable exception or error, thrown by a child thread.
passHotPotato(Throwable) - Method in interface com.compomics.util.interfaces.Flamable
This method takes care of any unrecoverable exception or error, thrown by a child thread.
passHotPotato(Throwable, String) - Method in interface com.compomics.util.interfaces.Flamable
This method takes care of any unrecoverable exception or error, thrown by a child thread.
PASSWORD - Static variable in class com.compomics.util.io.file.FolderMonitor
 
PathKey - Interface in com.compomics.software.settings
Interface for a path key.
PathParametersDialog - Class in com.compomics.software.settings.gui
Dialog used to set paths.
PathParametersDialog() - Constructor for class com.compomics.software.settings.gui.PathParametersDialog
Empty default constructor
PathParametersDialog(Frame, String, HashMap<PathKey, String>) - Constructor for class com.compomics.software.settings.gui.PathParametersDialog
Creates a new PathSettingsDialog.
PathSettingsCLI - Class in com.compomics.cli.paths
Allows the user to set the path settings in command line.
PathSettingsCLI(PathSettingsCLIInputBean) - Constructor for class com.compomics.cli.paths.PathSettingsCLI
Constructor.
PathSettingsCLIInputBean - Class in com.compomics.cli.paths
Parses the command line and retrieves the user input.
PathSettingsCLIInputBean(CommandLine) - Constructor for class com.compomics.cli.paths.PathSettingsCLIInputBean
Construct a FollowUpCLIInputBean from an Apache CLI instance.
PathSettingsCLIParams - Enum in com.compomics.cli.paths
Parameters for the path settings command line.
Patient - Class in com.compomics.util.experiment.patient
This class groups the information about the patient from whom the sample is taken
Patient() - Constructor for class com.compomics.util.experiment.patient.Patient
Empty default constructor
Patient(String) - Constructor for class com.compomics.util.experiment.patient.Patient
Constructor,
PatientInformation - Class in com.compomics.util.experiment.patient
Information about the patient.
PatientInformation() - Constructor for class com.compomics.util.experiment.patient.PatientInformation
Empty default constructor
PatientInformation(String, String) - Constructor for class com.compomics.util.experiment.patient.PatientInformation
Constructor.
PdbBlock - Class in com.compomics.util.pdbfinder.pdb
PdbBlock.
PdbBlock() - Constructor for class com.compomics.util.pdbfinder.pdb.PdbBlock
Empty default constructor
PdbBlock(String, int, int, int, int) - Constructor for class com.compomics.util.pdbfinder.pdb.PdbBlock
Constructor.
PdbParameter - Class in com.compomics.util.pdbfinder.pdb
PdbParameter.
PdbParameter() - Constructor for class com.compomics.util.pdbfinder.pdb.PdbParameter
Empty default constructor
PdbParameter(String, String, String, String) - Constructor for class com.compomics.util.pdbfinder.pdb.PdbParameter
Constructor.
pdf - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PDF - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PdfFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.pdf files.
PdfFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.PdfFileFilter
Empty default constructor
Peak - Class in com.compomics.util.experiment.mass_spectrometry.spectra
This class represents a peak.
Peak() - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
Empty default constructor
Peak(double, double) - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
Constructor for a peak.
peakIntensity - Variable in class com.compomics.util.experiment.identification.matches.IonMatch
The matched peak intensity.
peakMz - Variable in class com.compomics.util.experiment.identification.matches.IonMatch
The matched peak m/z.
peaks - Static variable in class com.compomics.util.experiment.identification.Advocate
The PEAKS sequencing algorithm.
PEFF - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
peff - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PeffFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.peff files.
PeffFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.PeffFileFilter
Empty default constructor
pep_xml - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PEP_XML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
pepMass(String) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Computing the mass of a peptide.
pepnovo - Static variable in class com.compomics.util.experiment.identification.Advocate
The PepNovo+ de novo sequencing algorithm.
PepnovoAssumptionDetails - Class in com.compomics.util.experiment.refinement_parameters
This class contains pepnovo assumption details which are not contained in the tag assumption class which will be saved as additional parameter.
PepnovoAssumptionDetails() - Constructor for class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
Constructor.
PepNovoIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This class can be used to parse PepNovo identification files.
PepNovoIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
Default constructor for the purpose of instantiation.
PepNovoIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader
Constructor, initiate the parser.
PepnovoParameters - Class in com.compomics.util.parameters.identification.tool_specific
PepNovo specific parameters.
PepnovoParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Constructor.
PepNovoParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for editing the PepNovo advanced settings.
PepNovoParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
Empty default constructor
PepNovoParametersDialog(Frame, PepnovoParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
Creates a new PepNovoSettingsDialog with a frame as owner.
PepNovoParametersDialog(Dialog, Frame, PepnovoParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
Creates a new PepNovoSettingsDialog with a dialog as owner.
Peptide - Class in com.compomics.util.experiment.biology.proteins
This class represents a peptide.
Peptide() - Constructor for class com.compomics.util.experiment.biology.proteins.Peptide
Constructor for the peptide.
Peptide(String, ModificationMatch[], HashMap<String, HashMap<Integer, PeptideVariantMatches>>, boolean, double) - Constructor for class com.compomics.util.experiment.biology.proteins.Peptide
Constructor.
Peptide(String, ModificationMatch[], boolean, double) - Constructor for class com.compomics.util.experiment.biology.proteins.Peptide
Constructor.
Peptide(String, ModificationMatch[], boolean) - Constructor for class com.compomics.util.experiment.biology.proteins.Peptide
Constructor.
Peptide(String) - Constructor for class com.compomics.util.experiment.biology.proteins.Peptide
Constructor.
Peptide(String, ModificationMatch[]) - Constructor for class com.compomics.util.experiment.biology.proteins.Peptide
Constructor.
Peptide(String, ModificationMatch[], HashMap<String, HashMap<Integer, PeptideVariantMatches>>, boolean) - Constructor for class com.compomics.util.experiment.biology.proteins.Peptide
Constructor for the peptide.
peptide - Variable in class com.compomics.util.experiment.identification.protein_sequences.digestion.ExtendedPeptide
The peptide.
PEPTIDE_EVIDENCE_SECTION - Static variable in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Key for the peptide evidence section.
PEPTIDE_FINGERPRINTING - Static variable in class com.compomics.util.experiment.identification.IdentificationMethod
index for identification method based on peptide mass fingerprinting
PEPTIDE_SECTION - Static variable in class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Key for the peptide section.
PEPTIDE_SHAKER_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for a psdb file for PeptideShaker.
PEPTIDE_SHAKER_PX_ACCESSION_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument to open a given PX accession in PRIDE Reshake.
PEPTIDE_SHAKER_PX_ACCESSION_PRIVATE_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument to indicate that the PX accession to open in PRIDE Reshake is private.
PEPTIDE_SHAKER_URL_DOWNLOAD_FOLDER_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for the download folder for the URL for PeptideShaker.
PEPTIDE_SHAKER_URL_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for a zipped psdb URL for PeptideShaker.
PeptideAminoAcidFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Feature based on the amino acid properties of a peptide.
PeptideAminoAcidFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
Empty default constructor
PeptideAminoAcidFeature(AminoAcid.Property, AASequenceFeature.Function) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
Constructor.
PeptideAndProteinBuilder - Class in com.compomics.util.experiment.identification.protein_inference
This class builds peptides and proteins based on PSMs.
PeptideAndProteinBuilder() - Constructor for class com.compomics.util.experiment.identification.protein_inference.PeptideAndProteinBuilder
Empty default constructor
PeptideAndProteinBuilder(Identification) - Constructor for class com.compomics.util.experiment.identification.protein_inference.PeptideAndProteinBuilder
Constructor.
PeptideAssumption - Class in com.compomics.util.experiment.identification.spectrum_assumptions
This object models the assumption made by an advocate.
PeptideAssumption() - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
Default constructor for the purpose of instantiation.
PeptideAssumption(Peptide, int, int, int, double, double, String) - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
Constructor for a peptide assumption.
PeptideAssumption(Peptide, int, int, int, double, double) - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
Constructor for a peptide assumption.
PeptideAssumption(Peptide, int) - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
Constructor for a simple peptide assumption containing only the information necessary for spectrum annotation.
PeptideAssumptionFilter - Class in com.compomics.util.experiment.identification.filtering
This class filters peptide assumptions based on various properties.
PeptideAssumptionFilter() - Constructor for class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Constructor with default settings.
PeptideAssumptionFilter(int, int, double, boolean, boolean, Integer, Integer, Integer, Integer) - Constructor for class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Constructor for an Identification filter.
PeptideDraft - Class in com.compomics.util.experiment.identification.protein_sequences.digestion
Draft of a peptide used during protein sequence digestion.
PeptideDraft() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Empty default constructor
PeptideDraft(char[]) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Constructor.
PeptideDraft(char[], String, HashMap<Integer, String>, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Constructor.
PeptideDraft(char[], String, HashMap<Integer, String>, double, int) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Constructor.
PeptideDraft(char[], String, String, HashMap<Integer, String>, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Constructor.
PeptideDraft(char[], String, String, HashMap<Integer, String>, double, int) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Constructor.
PeptideFeature - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Feature based on a peptide property.
PeptideFeature() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
Empty default constructor
PeptideFeature(PeptideFeature.Property) - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
Constructor.
PeptideFeature.Property - Enum in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
Enum for the possible features.
PeptideFilter - Class in com.compomics.util.experiment.identification.filtering
Peptide filter.
PeptideFilter() - Constructor for class com.compomics.util.experiment.identification.filtering.PeptideFilter
Constructor.
PeptideFilter(String) - Constructor for class com.compomics.util.experiment.identification.filtering.PeptideFilter
Constructor.
PeptideFilter(String, String) - Constructor for class com.compomics.util.experiment.identification.filtering.PeptideFilter
Constructor.
PeptideFilter(String, String, String, String, String) - Constructor for class com.compomics.util.experiment.identification.filtering.PeptideFilter
Constructor.
PeptideFilterItem - Enum in com.compomics.util.experiment.identification.filtering.items
Enum of the different items a peptide filter can filter on.
PeptideFragmentationModel - Enum in com.compomics.util.experiment.identification.peptide_fragmentation
Enum for the different peptide fragmentation models implemented.
PeptideFragmentIon - Class in com.compomics.util.experiment.biology.ions.impl
This class models a peptide fragment ion.
PeptideFragmentIon() - Constructor for class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Empty default constructor
PeptideFragmentIon(int, int, double, NeutralLoss[]) - Constructor for class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Constructor.
PeptideFragmentIon(int, NeutralLoss[]) - Constructor for class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Constructor for a generic ion.
PeptideFragmentIon(int) - Constructor for class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Constructor for a generic ion without neutral losses.
peptideIdentification - Variable in class com.compomics.util.experiment.identification.IdentificationKeys
List of the keys of all imported peptides.
PeptideInference - Class in com.compomics.util.experiment.identification.peptide_inference
Functions related to peptide inference.
PeptideInference() - Constructor for class com.compomics.util.experiment.identification.peptide_inference.PeptideInference
 
peptideInference(Identification, IdentificationParameters, SequenceProvider, ModificationProvider, WaitingHandler) - Method in class com.compomics.util.experiment.identification.peptide_inference.PeptideInference
Infers the PTM localization and its confidence for the best match of every spectrum.
PeptideMapperCLI - Class in com.compomics.cli.peptide_mapper
Command line peptide mapping.
PeptideMapperCLI() - Constructor for class com.compomics.cli.peptide_mapper.PeptideMapperCLI
 
PeptideMatch - Class in com.compomics.util.experiment.identification.matches
This class models a peptide match.
PeptideMatch() - Constructor for class com.compomics.util.experiment.identification.matches.PeptideMatch
Default Constructor for the peptide match.
PeptideMatch(Peptide, long, long) - Constructor for class com.compomics.util.experiment.identification.matches.PeptideMatch
Constructor for the peptide match.
PeptideMatchesIterator - Class in com.compomics.util.experiment.identification.matches_iterators
An iterator for peptide matches.
PeptideMatchesIterator() - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator
Empty default constructor
PeptideMatchesIterator(Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator
Constructor.
PeptideMatchesIterator(long[], Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator
Constructor.
PeptideProteinMapping - Class in com.compomics.util.experiment.identification.protein_inference
Class used to model the mapping of a peptide to a protein sequence.
PeptideProteinMapping() - Constructor for class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Empty default constructor.
PeptideProteinMapping(String, String, int, ModificationMatch[], PeptideVariantMatches) - Constructor for class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Constructor.
PeptideProteinMapping(String, String, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Constructor.
PeptideProteinMapping(String, String, int, ModificationMatch[]) - Constructor for class com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
Constructor.
peptideSequence - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Current peptide sequence.
peptideSequenceSearch - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Current peptide sequence needed for search.
peptideShaker - Static variable in class com.compomics.util.experiment.identification.Advocate
The PeptideShaker multiple algorithm software.
PeptideShakerSetupDialog - Class in com.compomics.software.dialogs
A dialog used to set up the connection to PeptideShaker.
PeptideShakerSetupDialog(JFrame, boolean) - Constructor for class com.compomics.software.dialogs.PeptideShakerSetupDialog
Creates a new PeptideShakerSetupDialog.
PeptideShakerSetupDialog(JDialog, boolean) - Constructor for class com.compomics.software.dialogs.PeptideShakerSetupDialog
Creates a new PeptideShakerSetupDialog.
PeptideSpectrumAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
Annotates a spectrum with peptide fragments.
PeptideSpectrumAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Constructor.
PeptideUtils - Class in com.compomics.util.experiment.identification.utils
This class groups functions that can be used to work with peptides.
PeptideUtils() - Constructor for class com.compomics.util.experiment.identification.utils.PeptideUtils
Empty default constructor.
PeptideVariantMatches - Class in com.compomics.util.experiment.identification.matches
This class represents a set of variants found on a peptide.
PeptideVariantMatches() - Constructor for class com.compomics.util.experiment.identification.matches.PeptideVariantMatches
Empty default constructor
PeptideVariantMatches(HashMap<Integer, Variant>, int) - Constructor for class com.compomics.util.experiment.identification.matches.PeptideVariantMatches
Constructor.
PeptideVariantsParameters - Class in com.compomics.util.parameters.identification.advanced
Preferences for the allowed variants in peptide sequences.
PeptideVariantsParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Constructor.
PeptideVariantsParameters.VariantType - Enum in com.compomics.util.parameters.identification.advanced
Enum indicating all three variant types
PeptideVariantsParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
FractionSettingsDialog.
PeptideVariantsParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog
Empty default constructor
PeptideVariantsParametersDialog(Frame, PeptideVariantsParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog
Creates a new FractionSettingsDialog with a frame as owner.
PeptideVariantsParametersDialog(Dialog, Frame, PeptideVariantsParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog
Creates a new FractionSettingsDialog with a dialog as owner.
pepxml - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PEPXML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PepXmlFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.pep.xml, *.pepxml and *.xml files.
PepXmlFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.PepXmlFileFilter
Empty default constructor
PepxmlIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
Simple IdfileReader for Pepxml files.
PepxmlIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
Blank constructor for instantiation purposes.
PepxmlIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader
Constructor.
PERACETYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.impl.Glycan
Final index for peracetylated masses.
percent - Static variable in class com.compomics.util.experiment.units.Units
percent.
percentile(double[], double) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the desired percentile in a given array of unsorted double values.
percentile(ArrayList<Double>, double) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the desired percentile in a list of unsorted double values.
percentileSorted(double[], double) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the desired percentile in an array of sorted double values.
percentileSorted(ArrayList<Double>, double) - Static method in class com.compomics.util.math.BasicMathFunctions
Returns the desired percentile in a list of sorted double values.
percolator - Static variable in class com.compomics.util.experiment.identification.Advocate
The Percolator rescoring algorithm.
perFraction - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
Indicates whether a feature is to be exported per fraction.
PERMETHYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.impl.Glycan
Final index for permethylated masses.
persist(Connection) - Method in interface com.compomics.util.db.interfaces.Persistable
This method can be called to store the implemnted objects state to a persistent store for the first time (equivalent to SQL 'INSERT').
Persistable - Interface in com.compomics.util.db.interfaces
This interface indicates that the implementing class can be persisted in permanent storage.
PersistableCode - Class in com.compomics.util.db.components
This class generates the code to make a DBAccessor an implementation of the Persistable interface.
PersistableCode() - Constructor for class com.compomics.util.db.components.PersistableCode
Empty default constructor
PersistableCode(DBMetaData) - Constructor for class com.compomics.util.db.components.PersistableCode
This constructor allows the generation of the code for the implementation of the Persistable interface for a DBAccessor class, based on the specified metadata.
Phenylalanine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Phenylalanine.
Phenylalanine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
Constructor.
PHENYLALANINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Phenylananine immonium ion.
phenyx - Static variable in class com.compomics.util.experiment.identification.Advocate
The Phenyx search engine.
PHOSPHO_Y - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401).
PhosphoRS - Class in com.compomics.util.experiment.identification.modification.scores
This class estimates the PhosphoRS score as described in https://www.ncbi.nlm.nih.gov/pubmed/22073976.
PhosphoRS() - Constructor for class com.compomics.util.experiment.identification.modification.scores.PhosphoRS
Empty default constructor
Phosphorus - Class in com.compomics.util.experiment.biology.atoms.impl
The phosphorus atom.
Phosphorus() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Phosphorus
Constructor.
PickUp - Interface in com.compomics.util.interfaces
This interface describes the behaviour for a class that can pick up results.
PICKUP - Static variable in class com.compomics.util.io.file.FolderMonitor
 
pkl - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PKL - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PklFile - Class in com.compomics.util.io
Contains information about the contents of one PKL file.
PklFile() - Constructor for class com.compomics.util.io.PklFile
Empty default constructor
PklFile(File) - Constructor for class com.compomics.util.io.PklFile
Parse a PKL file and store the details in the PKLFile object.
PklFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.pkl files.
PklFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.PklFileFilter
Empty default constructor
PklSpoFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.pkl.spo files.
PklSpoFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.PklSpoFileFilter
Empty default constructor
pkx - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PKX - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PkxFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.pkx files.
PkxFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.PkxFileFilter
Empty default constructor
pmid - Variable in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
The PubMed id of the database.
png - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PNG - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PngFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.png files.
PngFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.PngFileFilter
Empty default constructor
pNovo - Static variable in class com.compomics.util.experiment.identification.Advocate
The pNovo+ de novo sequencing algorithm.
PNovoIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This class can be used to parse pNovo identification files.
PNovoIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
Default constructor for the purpose of instantiation.
PNovoIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader
Constructor, initiate the parser.
PNovoParameters - Class in com.compomics.util.parameters.identification.tool_specific
pNovo specific parameters.
PNovoParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Constructor.
PNovoParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for editing pNovo advanced settings.
PNovoParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
Empty default constructor
PNovoParametersDialog(Frame, PNovoParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
Creates a new PNovoSettingsDialog with a frame as owner.
PNovoParametersDialog(Dialog, Frame, PNovoParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
Creates a new PNovoSettingsDialog with a dialog as owner.
position - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement
 
position - Variable in class com.compomics.util.experiment.identification.protein_sequences.digestion.ExtendedPeptide
The position of the peptide on the protein.
possibleCharges - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
The charge of the precursor.
Potassium - Class in com.compomics.util.experiment.biology.atoms.impl
The potassium atom.
Potassium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Potassium
Constructor.
pow(BigDecimal, BigDecimal, MathContext) - Static method in class com.compomics.util.math.BigFunctions
Returns the first big decimal power the second using the given math context.
POWER - Variable in enum com.compomics.util.experiment.units.MetricsPrefix
The power of 10 to use.
ppm - Static variable in class com.compomics.util.experiment.units.Units
ppm.
PRECURSOR - Static variable in class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
For now only one type of precursor implemented.
precursor - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap.PrecursorWithTitle
The precursor
Precursor - Class in com.compomics.util.experiment.mass_spectrometry.spectra
This class models a precursor.
Precursor() - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
Empty default constructor
Precursor(double, double, int[]) - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
Constructor for the precursor.
Precursor(double, double, double, int[]) - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
Constructor with retention time window.
Precursor(double, double, int[], double, double) - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
Constructor with retention time window and no reference retention time.
precursor - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
The precursor if any.
PrecursorAccuracy - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores
The precursor accuracy as a score.
PrecursorAccuracy() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.PrecursorAccuracy
Empty default constructor
PrecursorAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
Annotator for the precursor peaks.
PrecursorAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.PrecursorAnnotator
Empty default constructor
PrecursorAnnotator(Peptide, String[]) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.PrecursorAnnotator
Constructor.
precursorCharge - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The precursor charge as deduced by the search engine.
PrecursorIon - Class in com.compomics.util.experiment.biology.ions.impl
A precursor ion.
PrecursorIon(double, NeutralLoss[]) - Constructor for class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
Constructor.
PrecursorIon(NeutralLoss[]) - Constructor for class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
Constructor for a generic ion.
PrecursorIon() - Constructor for class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
Constructor for a generic ion without neutral losses.
PrecursorIon(double) - Constructor for class com.compomics.util.experiment.biology.ions.impl.PrecursorIon
Constructor for a generic ion without neutral losses.
PrecursorMap - Class in com.compomics.util.experiment.mass_spectrometry.indexes
This map stores the precursors indexed by mass.
PrecursorMap() - Constructor for class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
Empty default constructor
PrecursorMap(HashMap<String, Precursor>, double, boolean) - Constructor for class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
Builds a precursor map.
PrecursorMap.PrecursorWithTitle - Class in com.compomics.util.experiment.mass_spectrometry.indexes
Convenience class storing the precursor and corresponding spectrum title.
PrecursorWithTitle(Precursor, String) - Constructor for class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap.PrecursorWithTitle
Constructor.
preferredMaxVariableModifications - Static variable in class com.compomics.util.parameters.identification.search.SearchParameters
The preferred maximal number of variable modifications.
preferredMinSequences - Static variable in class com.compomics.util.parameters.identification.search.SearchParameters
The preferred minimal number of protein sequences.
PREFIX - Variable in enum com.compomics.util.experiment.units.MetricsPrefix
The prefix in full letters.
prefixCharacter(String, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Backward propagation of the BWT to get the previous character.
prepareRenderer(TableCellRenderer, int, int) - Method in class com.compomics.util.AlternateRowColoursJTable
Prepares the renderer by querying the data model for the value and selection state of the cell at row, column.
previousContent - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Index of the originating entry of a particular cell with the pattern searching matrix.
PrideFilter - Class in com.compomics.util.pride.prideobjects.webservice.query
An object to set up a filter for use in a query to the PRIDE webservice.
PrideFilter() - Constructor for class com.compomics.util.pride.prideobjects.webservice.query.PrideFilter
Empty default constructor
PrideFilter(PrideFilterType, String) - Constructor for class com.compomics.util.pride.prideobjects.webservice.query.PrideFilter
Creates a new PrideFilter instance.
PrideFilterType - Enum in com.compomics.util.pride.prideobjects.webservice.query
An enum of the possible filters for the PRIDE Filter options.
PrideMarshaller - Class in com.compomics.util.io.json.marshallers
A json marshaller for use with the PRIDE webservice.
PrideMarshaller() - Constructor for class com.compomics.util.io.json.marshallers.PrideMarshaller
Create a PRIDE marshaller.
PrideObject - Interface in com.compomics.util.pride
Interface for a PRIDE object.
PrideObjectsFactory - Class in com.compomics.util.pride
This factory manages the pride objects saved in the user folder.
PrideQuery - Enum in com.compomics.util.pride.prideobjects.webservice
An enum that constructs the template queries for the PRIDE webservice.
PrideWebService - Class in com.compomics.util.pride
A java representation of the PRIDE web service.
PrideWebService() - Constructor for class com.compomics.util.pride.PrideWebService
Empty default constructor
PrideXmlValidator - Class in com.compomics.util.pride.validation
PRIDE XML schema validation.
PrideXmlValidator() - Constructor for class com.compomics.util.pride.validation.PrideXmlValidator
Set up a PrideXmlValidator using the default schema.
PrideXmlValidator(URL) - Constructor for class com.compomics.util.pride.validation.PrideXmlValidator
Set up a PrideXmlValidator using the provided schema.
printCentroids() - Method in class com.compomics.util.math.clustering.KMeansClustering
Print the centroids.
printClusters() - Method in class com.compomics.util.math.clustering.KMeansClustering
Print the current clusters.
printEnzymes() - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
Prints the available enzymes.
printHelp() - Static method in class com.compomics.cli.peptide_mapper.PeptideMapperCLI
 
printModifications() - Method in class com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
Prints the available modifications.
PrivacyParametersDialog - Class in com.compomics.util.gui
The privacy settings dialog allows the user to set the privacy settings.
PrivacyParametersDialog(Frame, Image) - Constructor for class com.compomics.util.gui.PrivacyParametersDialog
Creates a new PrivacySettingsDialog.
ProbabilityFilter - Class in com.compomics.util.math.statistics.linear_regression.filters
Filter removing points with outlying slope.
ProbabilityFilter() - Constructor for class com.compomics.util.math.statistics.linear_regression.filters.ProbabilityFilter
Empty default constructor
ProcessingParameters - Class in com.compomics.util.parameters.tools
ProcessingPreferences.
ProcessingParameters() - Constructor for class com.compomics.util.parameters.tools.ProcessingParameters
Constructor.
ProcessingParameters.ProcessingType - Enum in com.compomics.util.parameters.tools
Class indicating the type of processing.
ProcessingParametersDialog - Class in com.compomics.util.gui.parameters.tools
Dialog to edit the processing parameters.
ProcessingParametersDialog() - Constructor for class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
Empty default constructor
ProcessingParametersDialog(Frame, ProcessingParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
Creates a new ProcessingPreferencesDialog with a frame as owner.
ProcessingParametersDialog(Dialog, Frame, ProcessingParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
Creates a new ProcessingPreferencesDialog with a dialog as owner.
processMirroredXAndYData(double[], double[], Color, Color) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method reads the x and y values from the specified arrays and stores these internally for drawing.
processXAndYData(double[], double[], Color, Color) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method reads the x and y values from the specified arrays and stores these internally for drawing.
proFound - Static variable in class com.compomics.util.experiment.identification.Advocate
The Profound search engine.
ProgressDialog - Class in com.compomics.util.gui.waiting.waitinghandlers
This class implements a modal dialog that is displayed during a longer-lasting task.
ProgressDialog() - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
Empty default constructor
ProgressDialog(JFrame, String, String) - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
Deprecated.
use ProgressDialogX instead
ProgressDialogX - Class in com.compomics.util.gui.waiting.waitinghandlers
A dialog for displaying information about progress.
ProgressDialogX(Frame, Image, Image, boolean) - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Opens a new ProgressDialogX with a Frame as a parent.
ProgressDialogX(JDialog, Frame, Image, Image, boolean) - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Opens a new ProgressDialog with a JDialog as a parent.
ProgressDialogX(boolean) - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Opens a new ProgressDialog.
PROJEC_NAME_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for the PeptideShaker project name.
ProjectParameters - Class in com.compomics.util.experiment
This class contains project specific parameters.
ProjectParameters() - Constructor for class com.compomics.util.experiment.ProjectParameters
 
ProjectParameters(String) - Constructor for class com.compomics.util.experiment.ProjectParameters
 
ProjectType - Enum in com.compomics.util.parameters.peptide_shaker
This enum lists the different types of projects that can be created using PeptideShaker.
Proline - Class in com.compomics.util.experiment.biology.aminoacids.impl
Proline.
Proline() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Proline
Constructor.
PROLINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Proline immonium ion.
properties - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PROPERTIES - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PropertiesManager - Class in com.compomics.util.io
This class holds all user properties for ms_lims.
property - Variable in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
The peptide feature.
prot_xml - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PROT_XML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
Protein - Class in com.compomics.util.experiment.biology.proteins
This class models a protein.
Protein() - Constructor for class com.compomics.util.experiment.biology.proteins.Protein
Constructor for a protein.
Protein(String) - Constructor for class com.compomics.util.experiment.biology.proteins.Protein
Simplistic constructor for a protein (typically used when loading identification files).
Protein(String, String) - Constructor for class com.compomics.util.experiment.biology.proteins.Protein
Constructor for a protein.
Protein(String, String, boolean) - Constructor for class com.compomics.util.experiment.biology.proteins.Protein
Constructor for a protein.
Protein - Class in com.compomics.util.protein
This class implements the behaviour for a Protein instance.
Protein() - Constructor for class com.compomics.util.protein.Protein
Empty default constructor
Protein(AASequenceImpl) - Constructor for class com.compomics.util.protein.Protein
This constructor requires an AASequenceImpl as argument.
Protein(Header, AASequenceImpl) - Constructor for class com.compomics.util.protein.Protein
This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein.
Protein(Header, AASequenceImpl, boolean, int) - Constructor for class com.compomics.util.protein.Protein
This constructor allows the passing of a Header, as well as an AASequenceImpl for this Protein.
Protein(String) - Constructor for class com.compomics.util.protein.Protein
This constructor allows for the construction of a Protein instance by passing a FASTA entry.
Protein(String, boolean, int) - Constructor for class com.compomics.util.protein.Protein
This constructor allows for the construction of a Protein instance by passing a FASTA entry and boolean flag for truncation.
Protein(String, String) - Constructor for class com.compomics.util.protein.Protein
This constructor allows for the construction of a Protein instance through the passing of a Header String and a Sequence String.
Protein(String, String, boolean, int) - Constructor for class com.compomics.util.protein.Protein
This constructor allows for the construction of a Protein instance through the passing of a Header String and a Sequence String.
ProteinDatabase - Enum in com.compomics.util.experiment.io.biology.protein
Enum of the supported protein databases.
ProteinDetailsProvider - Interface in com.compomics.util.experiment.io.biology.protein
Interface for a class able to provide metadata on proteins.
ProteinFilter - Class in com.compomics.util.experiment.identification.filtering
Protein filter.
ProteinFilter() - Constructor for class com.compomics.util.experiment.identification.filtering.ProteinFilter
Constructor.
ProteinFilter(String) - Constructor for class com.compomics.util.experiment.identification.filtering.ProteinFilter
Constructor.
ProteinFilter(String, String) - Constructor for class com.compomics.util.experiment.identification.filtering.ProteinFilter
Constructor.
ProteinFilter(String, String, String, String, String) - Constructor for class com.compomics.util.experiment.identification.filtering.ProteinFilter
Constructor.
ProteinFilterItem - Enum in com.compomics.util.experiment.identification.filtering.items
Enum of the different items a protein filter can filter on.
ProteinGeneDetailsProvider - Class in com.compomics.util.experiment.biology.genes
Class used to map proteins to gene information.
ProteinGeneDetailsProvider() - Constructor for class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Constructor.
proteinIdentification - Variable in class com.compomics.util.experiment.identification.IdentificationKeys
List of the keys of all imported proteins.
ProteinInferenceParameters - Class in com.compomics.util.parameters.identification.advanced
Generic class grouping the protein inference preferences.
ProteinInferenceParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Empty default constructor
ProteinInferenceParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
Dialog for the edition of the protein inference settings.
ProteinInferenceParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog
Empty default constructor
ProteinInferenceParametersDialog(Frame, ProteinInferenceParameters, Image, Image, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog
Creates a new ProteinInferenceSettingsDialog with a frame as owner.
ProteinInferenceParametersDialog(Dialog, Frame, ProteinInferenceParameters, Image, Image, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog
Creates a new ProteinInferenceSettingsDialog with a dialog as owner.
ProteinIterator - Interface in com.compomics.util.experiment.io.biology.protein
Interface for a protein iterator.
ProteinIteratorUtils - Class in com.compomics.util.experiment.identification.protein_sequences.digestion
This class contains utilities used during the iteration of protein sequences.
ProteinIteratorUtils() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Empty default constructor
ProteinIteratorUtils(ArrayList<String>, Integer) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
Constructor.
proteinLynx - Static variable in class com.compomics.util.experiment.identification.Advocate
The ProteinLynx search engine, waters instruments.
proteinMap - Variable in class com.compomics.util.experiment.identification.IdentificationKeys
A map linking protein accessions to all their protein matches keys.
ProteinMatch - Class in com.compomics.util.experiment.identification.matches
This class models a protein match.
ProteinMatch() - Constructor for class com.compomics.util.experiment.identification.matches.ProteinMatch
Constructor for the protein match.
ProteinMatch(String) - Constructor for class com.compomics.util.experiment.identification.matches.ProteinMatch
Constructor for the protein match.
ProteinMatch(Peptide, long) - Constructor for class com.compomics.util.experiment.identification.matches.ProteinMatch
Constructor for the protein match.
ProteinMatchesIterator - Class in com.compomics.util.experiment.identification.matches_iterators
An iterator of protein matches.
ProteinMatchesIterator() - Constructor for class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator
Empty default constructor
ProteinMatchesIterator(Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator
Constructor.
ProteinMatchesIterator(long[], Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator
Constructor.
proteinPilot - Static variable in class com.compomics.util.experiment.identification.Advocate
The ProteinPilot search engine.
proteinProspector - Static variable in class com.compomics.util.experiment.identification.Advocate
The search engine results of Protein Prospector.
proteinScape - Static variable in class com.compomics.util.experiment.identification.Advocate
The search engine integrated in Protein Scape, Bruker instruments.
ProteinSequencePane - Class in com.compomics.util.gui.protein
This class contains a method that formats a given protein sequence such that both the covered parts of the sequence and the peptide selected in the peptide table is highlighted.
ProteinSequencePane() - Constructor for class com.compomics.util.gui.protein.ProteinSequencePane
Empty default constructor
ProteinUtils - Class in com.compomics.util.experiment.identification.utils
Convenience functions for the handling of proteins.
ProteinUtils() - Constructor for class com.compomics.util.experiment.identification.utils.ProteinUtils
Empty default constructor.
ProteoWizardFilter - Enum in com.compomics.util.experiment.mass_spectrometry.proteowizard
Filters which can be applied to msconvert.
ProteoWizardMsFormat - Enum in com.compomics.util.experiment.mass_spectrometry.proteowizard
The mass spectrometry formats supported by ProteoWizard.
ProteoWizardSetupDialog - Class in com.compomics.software.dialogs
A dialog used to set up the connection to ProteoWizard.
ProteoWizardSetupDialog(JFrame, boolean) - Constructor for class com.compomics.software.dialogs.ProteoWizardSetupDialog
Creates a new ProteoWizardSetupDialog.
ProteoWizardSetupDialog(JDialog, boolean) - Constructor for class com.compomics.software.dialogs.ProteoWizardSetupDialog
Creates a new ProteoWizardSetupDialog.
Protocol - Class in com.compomics.util.pride.prideobjects
An object for storing Protocol details.
Protocol() - Constructor for class com.compomics.util.pride.prideobjects.Protocol
Empty default constructor
Protocol(String, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Protocol
Create a new Protocol object.
PROTON - Static variable in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
Subtype int for a proton.
proton - Static variable in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
A proton.
protonMassMultiples - Static variable in class com.compomics.util.experiment.biology.ions.impl.ElementaryIon
Cache for the multiples of the proton mass.
protxml - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
PROTXML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
ProtXmlFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.prot.xml, *.protxml and *.xml files.
ProtXmlFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.ProtXmlFileFilter
Empty default constructor
PsAnnotationFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists the annotation export features.
PsFragmentFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists the fragment identification features.
PsIdentificationAlgorithmMatchesFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists the Algorithm identification features.
PsInputFilterFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This enum lists the export features related to the import features.
PsmFilter - Class in com.compomics.util.experiment.identification.filtering
PSM filter.
PsmFilter(String) - Constructor for class com.compomics.util.experiment.identification.filtering.PsmFilter
Constructor.
PsmFilter() - Constructor for class com.compomics.util.experiment.identification.filtering.PsmFilter
Constructor.
PsmFilter(String, String, String, String, String) - Constructor for class com.compomics.util.experiment.identification.filtering.PsmFilter
Constructor.
PsmFilterItem - Enum in com.compomics.util.experiment.identification.filtering.items
Enum of the different items a PSM filter can filter on.
PSModificationScores - Class in com.compomics.util.experiment.identification.peptide_shaker
This class contains the scores for the locations of the possible modifications.
PSModificationScores() - Constructor for class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores
Constructor.
PsmScore - Enum in com.compomics.util.experiment.identification.psm_scoring
Enum listing the PSM scores implemented in compomics utilities.
PsmScoresEstimator - Class in com.compomics.util.experiment.identification.psm_scoring
This class can be used to estimate PSM scores.
PsmScoresEstimator(PeptideFragmentationModel) - Constructor for class com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
Constructor.
PsmScoresEstimator() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
Constructor using a uniform fragmentation.
PsmScoringParameters - Class in com.compomics.util.parameters.identification.advanced
Generic class for peptide spectrum match scoring.
PsmScoringParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Constructor.
PsmScoringParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
Dialog for the edition of the PSM scoring settings.
PsmScoringParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog
Empty default constructor
PsmScoringParametersDialog(Frame, PsmScoringParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog
Creates a new PsmScoringSettingsDialog with a frame as owner.
PsmScoringParametersDialog(Dialog, Frame, PsmScoringParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog
Creates a new PsmScoringSettingsDialog with a dialog as owner.
PSParameter - Class in com.compomics.util.experiment.identification.peptide_shaker
PeptideShaker compomics utilities experiment customizable parameter.
PSParameter() - Constructor for class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Constructor.
PsPeptideFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists the peptide identification features.
PsProjectFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists the PSM identification features.
PsProteinFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists the protein identification features.
PsPsmFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists the PSM identification features.
PsPtmScoringFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This enum groups the export features related to PTM scoring.
PsSearchFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists the export features linked to the spectrum identification.
PsSpectrumCountingFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This class lists all the export features related to the spectrum counting.
PsValidationFeature - Enum in com.compomics.util.io.export.features.peptideshaker
This enum lists the export features linked to the validation process.
PTMFactoryMarshaller - Class in com.compomics.util.io.json.marshallers
This class is a convenience class to have a DefaultJsonConverter with the search parameter interfaces.
PTMFactoryMarshaller() - Constructor for class com.compomics.util.io.json.marshallers.PTMFactoryMarshaller
Constructor.
PtmToPrideMap - Class in com.compomics.util.pride
Map linking user modification names to Unimod CV terms.
PtmToPrideMap() - Constructor for class com.compomics.util.pride.PtmToPrideMap
Constructor.
PushBackStringReader - Class in com.compomics.util.io
This class implements a PushBackReader for Strings which allows the reading of entire lines as well as the pushing back of entire lines.
PushBackStringReader() - Constructor for class com.compomics.util.io.PushBackStringReader
Empty default constructor
PushBackStringReader(String) - Constructor for class com.compomics.util.io.PushBackStringReader
This constructor requires the passing of a String from which to construct the PushBackStringReader.
putAscii(String) - Method in class com.compomics.util.io.ftp.FTP
PUT a file on the FTP server in Ascii mode.
putBinary(String) - Method in class com.compomics.util.io.ftp.FTP
PUT a file to the FTP server in Binary mode
putCVTerm(String, CvTerm) - Method in class com.compomics.util.pride.PtmToPrideMap
Puts a new mapping in the map.
pwd() - Method in class com.compomics.util.io.ftp.FTP
Get the name of the present working directory on the ftp server file system.
Pyrrolysine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Pyrrolysine.
Pyrrolysine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
Constructor.
PYRROLYSINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Pyrrolysine immonium ion.

Q

Q - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
QQ - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for SUMO-2/3 Q87R.
QQ_H2O - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for SUMO-2/3 Q87R.
QQT - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for SUMO-2/3 Q87R.
QQT_H2O - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for SUMO-2/3 Q87R.
QQTG - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for SUMO-2/3 Q87R.
QQTG_H2O - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for SUMO-2/3 Q87R.
QQTGG - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for SUMO-2/3 Q87R.
QQTGG_H2O - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion for SUMO-2/3 Q87R.
Quantification - Class in com.compomics.util.experiment.quantification
An abstract quantification class.
Quantification() - Constructor for class com.compomics.util.experiment.quantification.Quantification
Empty default constructor
Quantification.QuantificationMethod - Enum in com.compomics.util.experiment.quantification
The implemented quantification methods.
queryEnsembl(String, File, String) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Sends an XML query to Ensembl and writes the result in a text file.
queryEnsembl(String, File, String, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Sends an XML query to Ensembl and writes the result in a text file.
queryEnsembl(String, String, File, String, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Sends an XML query to Ensembl and writes the result in a text file.

R

R - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
RANDOM - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Index for a random location choice.
rangeQuery(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Returns a list of character and new left/right index for a given range.
rangeQuery(int, int, ArrayList<int[]>) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Fills a list of character and new left/right index for a given range.
rangeQueryOneValue(int, ArrayList<int[]>) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Fills a list of character and new left/right index for a given index.
Rank - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
Rank as used in the FM index.
Rank() - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Empty default constructor.
Rank(byte[], long[]) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Constructor.
Rank(long[], int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
Constructor.
rank - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
The rank of the peptide assumption for the concerned spectrum.
rawFormat - Variable in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
Boolean indicating if this in a format for raw data, false means that it is a peak list format.
rawScore - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
The raw score as provided by the identification algorithm.
read(byte[]) - Method in class com.compomics.util.io.file.MonitorableFileInputStream
Reads up to byte.length bytes of data from this input stream into an array of bytes.
read() - Method in class com.compomics.util.io.file.MonitorableFileInputStream
Reads the next byte of data from this input stream.
read(byte[], int, int) - Method in class com.compomics.util.io.file.MonitorableFileInputStream
Reads up to len bytes of data from this input stream into an array of bytes.
read(byte[]) - Method in class com.compomics.util.io.file.MonitorableInputStream
Reads up to byte.length bytes of data from this input stream into an array of bytes.
read() - Method in class com.compomics.util.io.file.MonitorableInputStream
Reads the next byte of data from this input stream.
read(byte[], int, int) - Method in class com.compomics.util.io.file.MonitorableInputStream
Reads up to len bytes of data from this input stream into an array of bytes.
read(char[]) - Method in class com.compomics.util.io.flat.readers.SimpleGzReader
 
read(char[], int, int) - Method in class com.compomics.util.io.flat.readers.SimpleGzReader
 
read(char[]) - Method in class com.compomics.util.io.flat.readers.SimpleTextReader
 
read(char[], int, int) - Method in class com.compomics.util.io.flat.readers.SimpleTextReader
 
read(char[]) - Method in interface com.compomics.util.io.flat.SimpleFileReader
Reads characters into an array.
read(char[], int, int) - Method in interface com.compomics.util.io.flat.SimpleFileReader
Reads characters into an array.
read(JsonReader) - Method in class com.compomics.util.io.json.adapter.ColorAdapter
 
read(JsonReader) - Method in class com.compomics.util.io.json.adapter.FileAdapter
 
readDoubleAsString(String) - Static method in class com.compomics.util.Util
Method for reading a double value as a string which uses either "," or "." as the decimal symbol.
readFasta(String, String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Read a FASTA.
readLine() - Method in class com.compomics.util.io.flat.readers.SimpleGzReader
 
readLine() - Method in class com.compomics.util.io.flat.readers.SimpleTextReader
 
readLine() - Method in interface com.compomics.util.io.flat.SimpleFileReader
Reads a line of the file.
readLine() - Method in class com.compomics.util.io.PushBackStringReader
This method reads a line of text from the buffer.
readObject(File) - Static method in class com.compomics.util.io.file.SerializationUtils
Reads an object from a serialized file.
readReply() - Method in class com.compomics.util.io.ftp.FTP
This method attempts to read a reply from the FTP server.
readServerResponse() - Method in class com.compomics.util.io.ftp.FTP
This method allows the caller to capture the server response.
readUrl(String, String) - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
Read a URL.
readUrl(String, String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Read a URL.
Reagent - Class in com.compomics.util.experiment.quantification.reporterion
A reporter ion labeling reagent.
Reagent() - Constructor for class com.compomics.util.experiment.quantification.reporterion.Reagent
Empty default constructor
reallocateIndexes() - Method in class com.compomics.util.sun.TableSorter
 
RecalibrationUtils - Class in com.compomics.util.experiment.mass_spectrometry.spectra
Utility functions for spectrum recalibration.
RecalibrationUtils() - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.RecalibrationUtils
 
reconstructFasta(File) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Reconstructs the FASTA file stored in the index
redirectErrorStream(File) - Static method in class com.compomics.cli.paths.PathSettingsCLI
Redirects the error stream to the SearchGUI.log of a given folder.
Reference - Class in com.compomics.util.pride.prideobjects
A simple publication reference object.
Reference() - Constructor for class com.compomics.util.pride.prideobjects.Reference
Empty default constructor
Reference(String, String, String) - Constructor for class com.compomics.util.pride.prideobjects.Reference
Create a new Reference object.
ReferenceArea - Class in com.compomics.util.gui.spectrum
A reference area to be added to a GraphicsPanel.
ReferenceArea() - Constructor for class com.compomics.util.gui.spectrum.ReferenceArea
Empty default constructor
ReferenceArea(String, String, double, double, Color, float, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.ReferenceArea
Creates a new ReferenceArea.
ReferenceArea(String, String, double, double, Color, float, boolean, boolean, Color, boolean, Color, float, double, boolean) - Constructor for class com.compomics.util.gui.spectrum.ReferenceArea
Creates a new ReferenceArea.
ReferenceGroup - Class in com.compomics.util.pride.prideobjects
An object for storing ReferenceGroup details.
ReferenceGroup() - Constructor for class com.compomics.util.pride.prideobjects.ReferenceGroup
Empty default constructor
ReferenceGroup(ArrayList<Reference>, String) - Constructor for class com.compomics.util.pride.prideobjects.ReferenceGroup
Create a new ReferenceGroup object.
RegExEnzyme - Class in com.compomics.util.protein
This class implements the functionality of an Enzyme by simulating digestion based on a regular expression.
RegExEnzyme() - Constructor for class com.compomics.util.protein.RegExEnzyme
Empty default constructor.
RegExEnzyme(String, String, String, String) - Constructor for class com.compomics.util.protein.RegExEnzyme
Create a new RegExEnzyme.
RegExEnzyme(String, String, String, String, int) - Constructor for class com.compomics.util.protein.RegExEnzyme
Create a new RegExEnzyme.
register(File, WaitingHandler) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
Registers a mass spectrometry file and enables querying its spectra.If the file is not a cms file, a cms file will be created along with the ms file.
register(File, File, WaitingHandler) - Method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
Registers a mass spectrometry file and enables querying its spectra.If the file is not a cms file, a cms file will be created in the cms folder if not null, along the ms file otherwise.
registerIdFileReader(Class, String) - Static method in class com.compomics.util.experiment.io.identification.IdfileReaderFactory
This method registers a new IdfileReader Class, and the file extension it can read from.
registerSection(String) - Method in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
Registers a new section.
registerTempFolder(File) - Static method in class com.compomics.util.experiment.io.temp.TempFilesManager
Adds a temp folder to the references temp folders.
RegressionStatistics - Class in com.compomics.util.math.statistics.linear_regression
Results of a linear regression of equation y = a.x + b and Pearson correlation r.
RegressionStatistics() - Constructor for class com.compomics.util.math.statistics.linear_regression.RegressionStatistics
Empty default constructor
RegressionStatistics(Double, Double, Double, Double, Double) - Constructor for class com.compomics.util.math.statistics.linear_regression.RegressionStatistics
Constructor.
RELATED - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Static index for a protein group: 1 - related proteins or peptide from related protein groups (not necessarily unique to the group).
RELATED_AND_UNRELATED - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Static index for a protein group: 2 - related and a unrelated proteins or peptide shared by related and unrelated proteins (not necessarily unique to the group).
RELATED_C_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for C.
RELATED_C_2 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for C.
RELATED_D_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for D.
RELATED_E_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for E.
RELATED_F_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for F.
RELATED_H_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for H (C4H5N2).
RELATED_H_2 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for H.
RELATED_K_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for K.
RELATED_K_2 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for K.
RELATED_K_3 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for K.
RELATED_M_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for M (C2H4S).
RELATED_N_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for N.
RELATED_Q_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for Q.
RELATED_Q_2 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for Q.
RELATED_R_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for R.
RELATED_R_2 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for R.
RELATED_R_3 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for R.
RELATED_R_4 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for R (C5H10N2O).
RELATED_W_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for W (C9H7N).
RELATED_Y_1 - Static variable in class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Related ion for Y (C7H7O).
RelatedIon - Class in com.compomics.util.experiment.biology.ions.impl
Represents a related ion, i.e., an ion that is related to a given amino acid, and is its own factory.
RelatedIon() - Constructor for class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Empty default constructor
RelatedIon(AminoAcid, AtomChain, int) - Constructor for class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Constructor for a related ion.
RelatedIon(AminoAcid, AtomChain, int, boolean) - Constructor for class com.compomics.util.experiment.biology.ions.impl.RelatedIon
Constructor for a related ion.
release(long) - Method in class com.compomics.util.threading.ObjectMutex
Release function for the given key.
release(String) - Method in class com.compomics.util.threading.ObjectMutex
Release function for the given key.
release() - Method in class com.compomics.util.threading.SimpleSemaphore
Releases.
reLoadAllData() - Static method in class com.compomics.util.protein.ModificationFactory
This method can be used to refresh all data from the data store indicated in the ModificationFactory.properties file.
reloadFactory() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Reloads the factory getInstance() needs to be called afterwards.
remove(Connection) - Method in interface com.compomics.util.db.interfaces.DBElement
This method provides a convenient short-cut to delete the DBElement from the persistent store.
remove(Atom, Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Removes all the occurrences of the given atom.
removeAA(int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Removes an amino acid index from the pattern.
removeAllReferenceAreasXAxis() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Removes all the x-axis reference areas.
removeAllReferenceAreasYAxis() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Removes all the y-axis reference areas.
removeCharacters(String, char) - Static method in class com.compomics.util.Util
Removes characters from a string.
removeCharacters(String, String[]) - Static method in class com.compomics.util.Util
Removes characters from a string.
removeDuplicateSpectrumTitles(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
Removes duplicate spectrum titles (the first occurrence is kept).
removeElementsPanel(int) - Method in class com.compomics.util.gui.atoms.AtomChainDialog
Remove the given elements panel.
removeEnzyme(String) - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Removes an enzyme from the mapping.
removeException(long) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Removes an exception.
removeExportScheme(String) - Method in interface com.compomics.util.io.export.ExportFactory
Removes a user scheme.
removeExtension(String) - Static method in class com.compomics.util.io.IoUtil
Removes the extension from a file name or path.
removeFilterItem(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Removes an item from the filter.
removeFixedModification(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Removes a modification from the list of fixed modifications.
removeForbiddenCharacters(String) - Static method in class com.compomics.util.Util
Removes the forbidden characters from a string.
removeIdentificationParameters(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Deletes the identification parameters of the given name.
removeManualValidation(long) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Removes a manually validated Match.
removeMouseListenerToHeaderInTable(JTable) - Method in class com.compomics.util.sun.TableSorter
 
removeNeutralLoss(String) - Static method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Removes the neutral loss associated to the given name in the static map of the class.
removeObject(long) - Method in class com.compomics.util.db.object.ObjectsCache
Removes an object from the cache.
removeObject(long) - Method in class com.compomics.util.db.object.ObjectsDB
Removing an object from the cache and database.
removeObject(long) - Method in class com.compomics.util.experiment.identification.Identification
Removes an object from the database.
removeObjects(Collection<Long>, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsDB
Removing an object from the cache and database.
removeObjects(IdentificationFeaturesCache.ObjectType) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Clears all objects of the given type.
removeObjects(ArrayList<Long>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification
Remove a list of objects from the database.
removePeptideAssumption(PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Removes an assumption from the mapping.
removeReferenceAreaXAxis(String) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Removes the x-axis reference area with the given identifier.
removeReferenceAreaYAxis(String) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Removes the y-axis reference area with the given identifier.
removeRefinementFixedModification(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Removes a fixed modification from the list of refinement modifications.
removeRefinementVariableModification(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Removes a variable modification from the list of refinement modifications.
removeSection(String) - Method in class com.compomics.util.io.export.ExportScheme
Removes an entire section from the mapping.
removeSubString(String, String) - Static method in class com.compomics.util.Util
Removes characters from a string.
removeTagAssumption(TagAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Removes an assumption from the mapping.
removeUnknownModifications() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Returns a boolean indicating whether unknown modifications shall be removed.
removeUrParam(long) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Removes a user parameter from the user parameters map.
removeUserPtm(String) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Removes a user Modification.
removeVariableModification(String) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Removes a modification from the list of variable modifications.
removeZeroes(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
Removes zero intensity peaks.
rename(String, String) - Method in class com.compomics.util.io.ftp.FTP
Rename a file on the remote server.
renameDuplicateSpectrumTitles(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
Renames duplicate spectrum titles.
renameFastaFileName(File) - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
Copies the content of the FASTA file to a new file and replaces any white space in the file name with '_' instead.
renameXTandemFile() - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Returns true if the X! Tandem file should be renamed.
replaceAll(String, char, char) - Static method in class com.compomics.util.Util
Replaces all characters equals to a by b in the given string.
reportBothBestHitsForTD() - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Returns true if target and decoy are ranked separately, false if shared rank.
ReportEditor - Class in com.compomics.util.gui.export.report
Dialog for editing reports.
ReportEditor(Frame, ExportFactory, String, boolean) - Constructor for class com.compomics.util.gui.export.report.ReportEditor
Constructor.
ReportEditor(Frame, ExportFactory) - Constructor for class com.compomics.util.gui.export.report.ReportEditor
Constructor.
ReporterExportFeature - Interface in com.compomics.util.io.export.features
Reporter extension of the utilities export features.
ReporterIon - Class in com.compomics.util.experiment.biology.ions.impl
This class models a reporter ion and is its own factory.
ReporterIon() - Constructor for class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Empty default constructor
ReporterIon(String, double) - Constructor for class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Constructor for a user-defined reporter ion.
ReporterIon(String, double, boolean) - Constructor for class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Constructor for a user-defined reporter ion.
ReporterIon(String, AtomChain) - Constructor for class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Constructor for a user-defined reporter ion.
ReporterIon(String, AtomChain, boolean) - Constructor for class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Constructor for a user-defined reporter ion.
ReporterIonAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
Annotator for reporter ions.
ReporterIonAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ReporterIonAnnotator
Empty default constructor
ReporterIonAnnotator(ReporterIon[]) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ReporterIonAnnotator
Constructor.
ReporterIonQuantification - Class in com.compomics.util.experiment.quantification.reporterion
This class contains quantification parameters.
ReporterIonQuantification() - Constructor for class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Empty default constructor
ReporterIonQuantification(Quantification.QuantificationMethod) - Constructor for class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Constructor for the reporter ion quantification.
ReporterMethod - Class in com.compomics.util.experiment.quantification.reporterion
This class contains information relative to a reporter quantification method.
ReporterMethod() - Constructor for class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Empty default constructor
ReporterMethod(String, ArrayList<Reagent>) - Constructor for class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Constructor for a reporter method.
ReporterMethodFactory - Class in com.compomics.util.experiment.quantification.reporterion
This factory imports reporter methods details from an XMl file.
ReporterPeptideFeature - Enum in com.compomics.util.io.export.features.reporter
This enum lists all the peptide export features available from reporter complementarily to the ones available in PeptideShaker.
ReporterProteinFeatures - Enum in com.compomics.util.io.export.features.reporter
This enum lists all the protein export features available from reporter complementarily to the ones available in PeptideShaker.
ReporterPsmFeatures - Enum in com.compomics.util.io.export.features.reporter
This enum lists all the PSM export features available from reporter complementarily to the ones available in PeptideShaker.
ReporterSetupDialog - Class in com.compomics.software.dialogs
A dialog used to set up the connection to Reporter.
ReporterSetupDialog(JFrame, boolean) - Constructor for class com.compomics.software.dialogs.ReporterSetupDialog
Creates a new ReporterSetupDialog.
reportFailed - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
Report when the filter is not passed.
reportPassed - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
Report when the filter is passed.
representativeComposition - Variable in class com.compomics.util.experiment.biology.atoms.Atom
Map of the isotope representative composition of the stable isotopes.
rescale(double, double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method rescales the x-axis while notifying the observers.
rescale(double, double, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method rescales the x-axis, allowing the caller to specify whether the observers need be notified.
rescaled(RescalingEvent) - Method in interface com.compomics.util.gui.interfaces.SpectrumPanelListener
This method will be called whenever the SpectrumPanel is rescaled.
RescalingEvent - Class in com.compomics.util.gui.events
This class implements a resizing event that occurred on a SpectrumPanel.
RescalingEvent(JPanel, double, double) - Constructor for class com.compomics.util.gui.events.RescalingEvent
The constructor takes the resizing event X coordinates in mass units.
reset() - Method in class com.compomics.util.io.file.MonitorableFileInputStream
Repositions this stream to the position at the time the mark method was last called on this input stream.
reset() - Method in class com.compomics.util.io.file.MonitorableInputStream
Repositions this stream to the position at the time the mark method was last called on this input stream.
resetPeptideNormalisationFactors() - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Resets the peptide normalization factors.
resetPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
resetPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
resetPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
resetPrimaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
resetPrimaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
Reset the primary progress counter to 0.
resetProteinNormalisationFactors() - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Resets the protein normalization factors.
resetPsmNormalisationFactors() - Method in class com.compomics.util.experiment.normalization.NormalizationFactors
Resets the PSM normalization factors.
resetQcResults() - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Resets the results of the QC filters.
resetSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
resetSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
resetSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
resetSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
resetSecondaryProgressCounter() - Method in interface com.compomics.util.waiting.WaitingHandler
Reset the secondary progress counter to 0.
resetSorting(ProgressDialogX) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Sorts the table according to a given column using the built in sorter.
resizePlot(int, int) - Method in class com.compomics.util.gui.VennDiagramPanel
 
restart() - Method in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent
Restart the given tool with the new Java options.
Retrievable - Interface in com.compomics.util.db.interfaces
This interface indicates that the implementing class can be retrieved from permanent storage.
RetrievableCode - Class in com.compomics.util.db.components
This class generates the code to make a DBAccessor an implementation of the Retrieveable interface.
RetrievableCode() - Constructor for class com.compomics.util.db.components.RetrievableCode
Empty default constructor
RetrievableCode(DBMetaData) - Constructor for class com.compomics.util.db.components.RetrievableCode
This constructor allows the generation of the code for the implementation of the Retrievable interface for a DBAccessor class, based on the specified metadata.
retrieve(Connection, HashMap) - Method in interface com.compomics.util.db.interfaces.Retrievable
This method allows the implemented object to retrieve its state from the persistent store.
retrieveObject(long) - Method in class com.compomics.util.db.object.ObjectsDB
Retrieves an object from the database or cache.
retrieveObject(long) - Method in class com.compomics.util.experiment.identification.Identification
Returns an array of all objects of a given list of keys
retrieveObjects(Collection<Long>, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsDB
Retrieves some objects from the database or cache.
retrieveObjects(Class, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsDB
Retrieves all objects from a given class.
retrieveObjects(Collection<Long>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification
Returns an array of all objects of a given list of keys
retrieveObjects(Class, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification
Returns an array of all objects of a given class
reverse() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Returns an amino acid pattern which is a reversed version of the current pattern.
reverse() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Returns an amino acid sequence which is a reversed version of the current pattern.
reverse(boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Returns a new tag instance which is a reversed version of the current tag.
reverse(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
Returns a new TagAssumption instance where the tag is a reversed version of this tag.
right - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Right index.
rmdir(String) - Method in class com.compomics.util.io.ftp.FTP
Delete the specified directory from the ftp server file system.
ROC - Interface in com.compomics.util.math.statistics
This class can be used to draw ROC curves.
roundDouble(double, int) - Static method in class com.compomics.util.Util
Rounds a double value to the wanted number of decimal places.
rSquared - Variable in class com.compomics.util.math.statistics.linear_regression.RegressionStatistics
The coefficient of determination.
rt - Variable in class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
The retention time when the precursor was isolated.
run() - Method in class com.compomics.cli.peptide_mapper.MappingWorker
 
run() - Method in class com.compomics.util.io.file.FolderMonitor
When an object implementing interface Runnable is used to create a thread, starting the thread causes the object's run method to be called in that separately executing thread.
run() - Method in class com.compomics.util.io.StreamGobbler
 
runGptm() - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Returns true if the G-PTM search is to be performed.
runMapping(File, WaitingHandlerCLIImpl, IdentificationParameters, String, String, int, boolean) - Static method in class com.compomics.cli.peptide_mapper.PeptideMapperCLI
 

S

S - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
S - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The sulfur atom.
sameLists(ArrayList<?>, ArrayList<?>) - Static method in class com.compomics.util.Util
Convenience methods indicating whether the content of two lists have the same content.
sameModificationsAs(Peptide, ArrayList<String>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Indicates whether another peptide has the same variable modifications at the same localization as this peptide.
sameModificationsAs(Peptide) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Indicates whether another peptide has the same modifications at the same localization as this peptide.
Sample - Class in com.compomics.util.pride.prideobjects
An object for storing Sample details.
Sample() - Constructor for class com.compomics.util.pride.prideobjects.Sample
Empty default constructor
Sample(String, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Sample
Create a new Sample object.
SAMPLE_BATCH_SIZE - Static variable in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
The batch size of proteins to sample.
SampleSelection - Class in com.compomics.util.gui
Class which allows the selection of the right identification.
SampleSelection(Frame, boolean, String[], String) - Constructor for class com.compomics.util.gui.SampleSelection
Constructor.
save(Connection) - Method in interface com.compomics.util.db.interfaces.DBElement
This method can be called when changes need to be persisted.
saveCache(WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsCache
Saves the cache content in the database.
saveFactory() - Method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Saves the factory in the user folder.
saveFactory() - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Saves the factory in the user folder.
saveFile(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
Save to file.
saveIdentificationParameters(IdentificationParameters, File) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
Saves the identification parameters to a file.
saveIdentificationParameters(SearchParameters, File) - Static method in class com.compomics.util.parameters.identification.search.SearchParameters
Saves the identification parameters to a serialized file.
saveIdentificationParametersAsTextFile(File) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Saves the identification parameters as a human readable text file.
saveMapping(File) - Method in class com.compomics.util.experiment.biology.genes.go.GoDomains
Saves the mapping to the given file.
saveObjects(int) - Method in class com.compomics.util.db.object.ObjectsCache
Saves an entry in the database if modified and clears it from the cache.
saveObjects(int, WaitingHandler, boolean) - Method in class com.compomics.util.db.object.ObjectsCache
Saves an entry in the database if modified.
saveObjectToJson(Object, File) - Method in class com.compomics.util.io.json.JsonMarshaller
Save an object to JSON.
saveSummary(String, FastaSummary) - Static method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Saves the summary in the user folder.
saveToFile(EnzymeFactory, File) - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Saves en enzyme factory to a file.
saveToFile(ModificationFactory, File) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Saves a Modification factory to a file.
saveUrl(File, String, int, String, String, WaitingHandler) - Static method in class com.compomics.util.io.IoUtil
Save a file from a URL.
saveUserParameters(UtilitiesUserParameters) - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
Convenience method saving the user parameters.
scaffold - Static variable in class com.compomics.util.experiment.identification.Advocate
The Scaffold multiple search engine data interpretation software.
scaleToMax(double[]) - Static method in class com.compomics.util.ArrayUtil
Scales the given values using the maximum value.
scaleValues(double[], double) - Static method in class com.compomics.util.ArrayUtil
Scales the values using the reference value.
ScalingFactorsEstimators - Class in com.compomics.util.experiment.quantification.spectrumcounting
This class estimates spectrum counting scaling factors.
ScalingFactorsEstimators() - Constructor for class com.compomics.util.experiment.quantification.spectrumcounting.ScalingFactorsEstimators
Empty default constructor
ScalingFactorsEstimators(SpectrumCountingParameters) - Constructor for class com.compomics.util.experiment.quantification.spectrumcounting.ScalingFactorsEstimators
Constructor.
score - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
The (advocate specific) score used to rank this assumption.
SCORE_1_ROW_INDEX - Static variable in class com.compomics.util.gui.protein.ModificationProfile
The score above the sequence row index.
SCORE_2_ROW_INDEX - Static variable in class com.compomics.util.gui.protein.ModificationProfile
The score under the sequence row index.
Se - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The selenium atom.
searchDecoyDatabase() - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Returns whether MS-GF+ is to create and search a decoy database.
SEARCHGUI_FASTA_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for FASTA file for SearchGUI.
SEARCHGUI_PARAMETERS_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for a parameters file for SearchGUI.
SEARCHGUI_RAW_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for raw files for SearchGUI.
SEARCHGUI_SPECTRUM_FILE_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for mgf files for SearchGUI.
SearchGuiSetupDialog - Class in com.compomics.software.dialogs
A dialog used to set up the connection between PeptideShaker and SearchGUI.
SearchGuiSetupDialog(JFrame, boolean) - Constructor for class com.compomics.software.dialogs.SearchGuiSetupDialog
Creates a new SearchGuiSetupDialog.
SearchGuiSetupDialog(JDialog, boolean) - Constructor for class com.compomics.software.dialogs.SearchGuiSetupDialog
Creates a new SearchGuiSetupDialog.
SearchParameters - Class in com.compomics.util.parameters.identification.search
This class groups the parameters used for identification.
SearchParameters() - Constructor for class com.compomics.util.parameters.identification.search.SearchParameters
Constructor.
SearchParameters(SearchParameters) - Constructor for class com.compomics.util.parameters.identification.search.SearchParameters
Constructor.
SearchParameters.MassAccuracyType - Enum in com.compomics.util.parameters.identification.search
Possible mass accuracy types.
SearchParametersDialog - Class in com.compomics.util.gui.parameters.identification.search
The search settings dialog.
SearchParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
Empty default constructor
SearchParametersDialog(Frame, SearchParameters, Image, Image, boolean, boolean, LastSelectedFolder, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
Creates a new SearchSettingsDialog with a frame as owner.
SearchParametersDialog(Dialog, Frame, SearchParameters, Image, Image, boolean, boolean, LastSelectedFolder, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
Creates a new SearchSettingsDialog with a dialog as owner.
sectionCompleted(String) - Method in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
Registers a section as completed and transfers its content to the main file.
select(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Inverse function to the rank function: given the i'th occurrence of a character in the tree, it provides its position
SELECT_SPECIES_TAG - Static variable in class com.compomics.util.gui.genes.SpeciesDialog
Deprecated.
The text to use to tell the user to please select a species in the list.
selectDB(boolean) - Method in class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
Allows the user to select a FASTA file, loads its information, and returns a boolean indicating whether the process loading was successful.
SelectedValuesTableFilter() - Constructor for class com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
 
Selenium - Class in com.compomics.util.experiment.biology.atoms.impl
Selenium.
Selenium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Selenium
Constructor.
Selenocysteine - Class in com.compomics.util.experiment.biology.aminoacids.impl
SeC (U) (Mascot)-
Selenocysteine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
Constructor.
SELENOCYSTEINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Selenocysteine immonium ion.
SELFDEFINED - Static variable in class com.compomics.util.general.MassCalc
Value for the self-defined masses.
SelfUpdatingTableModel - Class in com.compomics.util.gui.tablemodels
These table models include a self updating function.
SelfUpdatingTableModel() - Constructor for class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
 
sendBinaryFile(String) - Method in class com.compomics.util.io.ftp.FTPClient
This method sends a binary file to the default FTP location on the server.
sendFiles(String[], boolean[]) - Method in class com.compomics.util.io.ftp.FTPClient
This method sends a group of files to the default FTP location on the server.
sendFiles(String[], boolean) - Method in class com.compomics.util.io.ftp.FTPClient
This method sends a group of files to the default FTP location on the server.
sendGAUpdate(String, String, String) - Static method in class com.compomics.util.Util
Function for sending event requests to Google analytics.
sendIncoming(Object) - Method in interface com.compomics.util.interfaces.PickUp
This method should be called by the notifier when appropriate.
sendServer(String) - Method in class com.compomics.util.io.ftp.FTP
Sends command cmd to the server.
sendTextFile(String) - Method in class com.compomics.util.io.ftp.FTPClient
This method sends a text file to the default FTP location on the server.
SENTINEL - Static variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Sentinel character necessary for computation of the suffix array.
SEPARATOR - Static variable in class com.compomics.software.cli.CommandLineUtils
The command line argument separator.
separator - Static variable in class com.compomics.software.settings.UtilitiesPathParameters
The separator between a path ID and a path.
SEPARATOR - Static variable in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
The separator used to separate line contents.
SEPARATOR - Static variable in class com.compomics.util.experiment.biology.genes.go.GoDomains
The separator used to separate line contents.
SEPARATOR - Static variable in class com.compomics.util.experiment.biology.genes.go.GoMapping
The separator used to separate line contents.
SEPARATOR - Static variable in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
The separator used to separate line contents.
SEPARATOR - Static variable in class com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
The separator used to separate line contents.
SEPARATOR - Static variable in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
The separator used to separate line contents.
SEPARATOR - Static variable in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
The separator used to separate line contents.
SEPARATOR - Static variable in class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
The separator used to separate line contents.
SEPARATOR - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
The separator used to separate locations in the modification location key.
separator - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
The columns separator.
Sequence - Interface in com.compomics.util.interfaces
This interface defines the default behavior of any kind of sequence with a certain mass - be it DNA, protein or something else.
sequenceCoverageInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether the sequence coverage is in cache.
SequenceDbDetailsDialog - Class in com.compomics.util.gui.parameters.identification.search
This dialog displays information about a sequence database.
SequenceDbDetailsDialog(Dialog, Frame, String, FastaParameters, LastSelectedFolder, boolean, Image, Image) - Constructor for class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
Creates a new SequenceDbDetailsDialog with a dialog as owner.
SequenceDbDetailsDialog(Frame, String, FastaParameters, LastSelectedFolder, boolean, Image, Image) - Constructor for class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
Creates a new SequenceDbDetailsDialog.
SequenceFragmentationPanel - Class in com.compomics.util.gui.spectrum
This class was imported from the Peptizer and MascotDatfile parser, and was developed to display fragmentation information on the modified sequence as inspired by X!Tandem.
SequenceFragmentationPanel() - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Empty default constructor
SequenceFragmentationPanel(String, IonMatch[], boolean, boolean, ModificationParameters, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Creates a new SequenceFragmentationPanel working with B and Y ions.
SequenceFragmentationPanel(String, IonMatch[], boolean, ModificationParameters, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Creates a new SequenceFragmentationPanel working with B and Y ions.
SequenceIterator - Interface in com.compomics.util.experiment.identification.protein_sequences.digestion
Interface for an iterator returning peptides along a protein sequence.
SequenceMatchingParameters - Class in com.compomics.util.parameters.identification.advanced
The sequence matching options.
SequenceMatchingParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Constructor for empty preferences.
SequenceMatchingParameters.MatchingType - Enum in com.compomics.util.parameters.identification.advanced
The different types of amino acid matching.
SequenceMatchingParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
Dialog for the edition of the sequence matching settings.
SequenceMatchingParametersDialog(Frame, SequenceMatchingParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
Creates a new SequenceMatchingSettingsDialog with a frame as owner.
SequenceMatchingParametersDialog(Dialog, Frame, SequenceMatchingParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
Creates a new SequenceMatchingSettingsDialog with a dialog as owner.
SequenceModificationPanel - Class in com.compomics.util.gui.protein
A panel for displaying modification profiles.
SequenceModificationPanel() - Constructor for class com.compomics.util.gui.protein.SequenceModificationPanel
Empty default constructor
SequenceModificationPanel(String, ArrayList<ModificationProfile>, boolean, String, String) - Constructor for class com.compomics.util.gui.protein.SequenceModificationPanel
Creates a new SequenceFragmentationPanel.
SequenceProvider - Interface in com.compomics.util.experiment.io.biology.protein
Interface for a class able to retrieve the sequence of a given protein.
sequest - Static variable in class com.compomics.util.experiment.identification.Advocate
The Sequest search engine.
SequestFragmentationModel - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models
Fragmentation model originally described in the Sequest algorithm (https://www.ncbi.nlm.nih.gov/pubmed/24226387) adapted to utilities objects.
SequestFragmentationModel() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.SequestFragmentationModel
Empty default constructor
SequestParamsFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for sequest.params files.
SequestParamsFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.SequestParamsFileFilter
Empty default constructor
SerializationUtils - Class in com.compomics.util.io.file
This class implements convenience methods for serialization and deserialization.
SerializationUtils() - Constructor for class com.compomics.util.io.file.SerializationUtils
Empty default constructor
serialize(T, Type, JsonSerializationContext) - Method in class com.compomics.util.io.json.adapter.InterfaceAdapter
 
serialVersionUID - Static variable in interface com.compomics.util.io.export.ExportFeature
Serial number for backward compatibility.
Serine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Serine.
Serine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Serine
Constructor.
SERINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Serine immonium ion.
serverInput - Variable in class com.compomics.util.io.ftp.FTP
Buffered stream for reading replies from server.
serverIsOpen() - Method in class com.compomics.util.io.ftp.FTP
Return server connection status
serverOutput - Variable in class com.compomics.util.io.ftp.FTP
Stream for printing to the server.
serverResponse - Variable in class com.compomics.util.io.ftp.FTP
Array of strings (usually 1 entry) for the last reply from the server.
setAaAtIndex(int, char) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
replaces the amino acid at the given position by the given amino acid represented by its single letter code.
setAaIndex(int) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
Sets the index on the sequence.
setAaIndex(int) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
Sets the index on the sequence.
setAaSubstitutionMatrix(AaSubstitutionMatrix) - Method in class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
Sets the substitution matrix to display.
setAaSubstitutionMatrix(AaSubstitutionMatrix) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Sets the amino acid substitution matrix to use.
setAboveXAxis(boolean) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set if the reference area is to be added above the x-axis, false adds the reference are below the x-axis
setAccession(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the accession.
setAccession(String) - Method in class com.compomics.util.pride.CvTerm
Sets the accession.
setAccessions(String[]) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Sets the accessions of the proteins in this group.
setActicationType(String) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Sets the activation type.
setActive(boolean) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets whether the filter is active.
setAdditionalOutput(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set if additional output is to be included.
setAdjustPrecursorMass(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set if the precursor mass is to be adjusted.
setAdvocate(int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Sets the advocate id.
setAlgorithmDeltaPEP(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the difference in identification algorithm level PEP with the next best peptide assumption with sequence difference for the given search engine.
setAlignNonConfidentModifications(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Sets whether the non confidently localized modifications should be aligned on the confident sites.
setAllPathsIn(String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Sets all the paths inside a given folder.
setAlpha(float) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the alpha level (transparency).
setAlphaLevel(float) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Sets the alpha level
setAminoAcid(char) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature
Sets the amino acid targeted represented as single letter code.
setAminoAcidFeature1(AAPropertyFeature) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
Sets the first amino acid feature.
setAminoAcidFeature2(AAPropertyFeature) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
Sets the second amino acid feature.
setAminoAcidProperty(AminoAcid.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature
 
setAminoAcidProperty(AminoAcid.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
 
setAminoAcidProperty(AminoAcid.Property) - Method in interface com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.SingleAAPropertyFeature
Sets the amino acid property to consider.
setAminoAcidScores(ArrayList<double[]>) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Set the amino acid scores.
setAnnotateHighestPeak(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the most intense of possible peaks to annotate is to be selected, false if the most accurate is to be selected.
setAnnotationParameters(AnnotationParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the annotation parameters used for identification.
setAnnotations(List<SpectrumAnnotation>, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method sets all the annotations on this instance.
setAnnotations(List<SpectrumAnnotation>) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method sets all the annotations on this instance.
setAnnotationsMirrored(List<SpectrumAnnotation>, boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method sets all the annotations for the mirrored spectra.
setAnnotationsMirrored(List<SpectrumAnnotation>) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method sets all the annotations for the mirrored spectra.
setAnnotationYAxisThreshold(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method allows the caller to set the minimal non-inclusive y-axis value threshold in percent (compared to the highest point in the spectrum or chromatogram) a point must pass before being eligible for annotation.
setAreaColor(Color) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the area color.
setAreaUnderCurveColor(Color, int) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Sets the color of the area under the curve for profile chromatograms and spectra for the dataset with the given dataset index.
setAtomChainAdded(AtomChain) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Sets the atom chain added.
setAtomChainRemoved(AtomChain) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Sets the atom chain removed.
setAtomicComposition(AtomChain) - Method in class com.compomics.util.experiment.biology.ions.Ion
Returns the atomic composition.
setAtomSymbol(String) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
Sets the atom symbol as specified in the Atom class.
setAutomaticAnnotation(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets whether the annotation settings should be automatically inferred.
setAutoUpdate(Boolean) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Sets whether the gene mappings should be automatically updated.
setAutoUpdate(Boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets whether the tools should use the auto update function.
setBackgroundPeakWidth(float) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set the backgroundPeakWidth peak width.
setBackgroundSpecies(Integer) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Sets the taxon of the species selected as background species.
setBackgroundSpeciesFromFastaSummary(FastaSummary) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Set the background species to the most common species in the FASTA file.
setBatchSize(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the batch size.
setBestPeak(double[], double[], int[], IonMatch) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Returns the peak to retain of the matched peaks according to the ties resolution setting.
setBestPeptideAssumption(PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Setter for the best peptide assumption.
setBestTagAssumption(TagAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Setter for the best tag assumption.
setBinMax(Integer) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Sets the highest bin in index.
setBinMin(Integer) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Sets the lowest bin in index.
setBlob(byte[]) - Method in class com.compomics.util.db.object.objects.BlobObject
Sets the byte representation of the object.
setBlock(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Sets the block.
setBlocks(PdbBlock[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Set the blocks.
setBoldFont(boolean) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set if the label is to be in bold.
setBorderColor(Color) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the border color.
setBorderWidth(float) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the border width.
setCategory(ModificationCategory) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Set the modification category.
setCharge(int) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Setter for the charge
setCharge(int) - Method in interface com.compomics.util.interfaces.SpectrumFile
This method sets the charge of the precursor ion.
setCheckDuplicateTitles(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set if the spectra should be checked for duplicate titles or not.
setCheckMgfSize(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set if the mgf should be checked for size.
setCheckPeakPicking(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set if the spectra should be checked for peak picking or not.
setCheckSpectrumCharges(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set if the spectra are to be checked for missing charges.
setClassSizeMultiplier(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the intensity class size multiplier.
setCleavage(char[]) - Method in class com.compomics.util.protein.DualEnzyme
This method allows the caller to specify the cleavable residues.
setCleavage(String) - Method in class com.compomics.util.protein.DualEnzyme
This method allows the caller to specify the cleavable residues.
setCleavage(char[], int) - Method in class com.compomics.util.protein.DualEnzyme
This method allows the caller to specify the cleavable residues.
setCleavage(String, int) - Method in class com.compomics.util.protein.DualEnzyme
This method allows the caller to specify the cleavable residus.
setCleavage(char[]) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to specify the cleavable residues.
setCleavage(String) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to specify the cleavable residues.
setCleavage(String) - Method in class com.compomics.util.protein.RegExEnzyme
This method can be used to set the cleavage pattern for this RegExEnzyme.
setCleavage(char[]) - Method in class com.compomics.util.protein.RegExEnzyme
 
setCleavageParameter(DigestionParameters.CleavageParameter) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Sets the cleavage parameters.
setCleaveNterMethionine(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether N-terminal methionines should be cleaved.
setClipNtermMethionine(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the starting methionine peptides will be included both with and without the starting M.
setCloseDialogWhenImportCompletes(boolean, boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Set if the value for if the dialog is to be closed when completed and if the option is enabled or not.
setColor(String, int) - Method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Sets a new color for the given expected modification.
setColor(Color) - Method in class com.compomics.util.gui.protein.ModificationProfile
Sets the PTM color.
setColor(String, int) - Method in class com.compomics.util.parameters.identification.search.ModificationParameters
Sets a new color for the given expected modification.
setColumn(int, ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
setComparatorForItem(String, FilterItemComparator) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the comparator for a given item.
setComplementMzTolerance(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the complement m/z tolerance.
setComplementScoreWeight(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set the complement score weight.
setComposition(AtomChain) - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Sets the composition of the neutral loss.
setComputeExactPValues(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the exact p-values are to be computed.
setComputeSpScore(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the SP score is to be computed.
setComputeXCorr(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Sets if a Sequest-like cross correlation score will be calculated for the top ranking hits in each spectrum’s result set.
setConcatenatTargetDecoy(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the target and decoy results are to be concatenated.
setCondition(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the description of the condition to meet.
setConfidenceMargin(Double) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Sets the margin to the threshold to use as factor of the resolution.
setConfidenceThreshold(double) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Sets the confidence below which a peptide is considered absent.
setConfident(boolean) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Sets whether the modification is confidently localized on the sequence.
setConsecutiveIonProbability(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Set the consecutive ion probability.
setContacts(ArrayList<Contact>) - Method in class com.compomics.util.pride.prideobjects.ContactGroup
Set the contacts.
setContent(ArrayList<TagComponent>) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Sets the content for the given tag.
setContinueReading(boolean) - Method in class com.compomics.util.io.StreamGobbler
Set if the reading is to continue or not.
setControlSamples(ArrayList<String>) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Sets the indexes of the samples labeled as control.
setCorrectPrecursorMass(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Sets whether the precursor mass shall be corrected (TagDB setting).
setCreationTime(Date) - Method in class com.compomics.util.experiment.ProjectParameters
 
setcTermModification(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Sets the C-term modification.
setCurrentPeptideKey(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the current peptide key.
setCurrentProteinKey(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the current protein key.
setCvTerm(CvTerm) - Method in class com.compomics.util.experiment.biology.enzymes.Enzyme
Sets the CV term associated with this enzyme.
setCvTerms(ArrayList<CvTerm>) - Method in class com.compomics.util.pride.prideobjects.Instrument
Set the CV terms.
setCvTerms(ArrayList<CvTerm>) - Method in class com.compomics.util.pride.prideobjects.Protocol
Set the CV terms.
setCvTerms(ArrayList<CvTerm>) - Method in class com.compomics.util.pride.prideobjects.Sample
Set the CV terms.
setDatabaseType(ProteinDatabase) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the database type.
setDataFilters(HashMap<String, String>) - Method in class com.compomics.util.gui.XYPlottingDialog
Set the data filters.
setDataPointAndLineColor(Color, int) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Sets the color of data points and line for the dataset with the given dataset index.
setDateTimeFormat(String) - Method in class com.compomics.util.gui.JTableForDB
This method allows the setting of the date /time format.
setDbFolder(File) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets the last used database folder.
setDbSize(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Sets whether the database size should be checked.
setDebugInteractions(boolean) - Static method in class com.compomics.util.db.object.ObjectsDB
Turn the debugging of interactions on or off.
setDeconvolutionIntensityRatio(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the deconvolution intensity ratio.
setDeconvolutionMassTolerance(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the deconvolution mass tolerance.
setDeconvolutionMassToleranceType(MetaMorpheusParameters.MetaMorpheusToleranceType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the deconvolution mass tolerance type.
setDecoy(boolean) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Sets whether the given match is decoy
setDecoyFlag(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Sets the decoy flag.
setDecoyFormat(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the decoy format.
setDecoyMode(AndromedaParameters.AndromedaDecoyMode) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Set the decoy mode.
setDecoySeed(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the decoy seed.
setDecoysInFirstBin(Integer) - Method in class com.compomics.util.parameters.identification.advanced.PsmScoringParameters
Sets the minimal number of decoys to include in a bin to set the bin size of the score histogram.
setDecoySuffix(boolean) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Sets whether the decoy flag is a suffix or a prefix.
setDecoyType(MetaMorpheusParameters.MetaMorpheusDecoyType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the decoy type.
setDefaultAdvancedSettings() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Set the advanced settings to the default values.
setDefaultAdvancedSettings(SearchParameters) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Set the advanced settings to the values in the given search parameters object or to the default values of the advanced settings are not set for a given advocate.
setDefaultEnzymes() - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Sets the instance to only contain the default enzymes.
setDefaultPeptideFDR(double) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Sets the default peptide FDR.
setDefaultProteinFDR(double) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Sets the default protein FDR.
setDefaultPsmFDR(double) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Sets the default PSM FDR.
setDeisotopingMode(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the deisotoping flag value.
setDeltaMassWindow(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set the size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
setDeltaPEP(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the difference in identification algorithm level PEP with the next best peptide assumption with sequence difference across all search engines.
setDeltaScore(int, double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Sets the delta score at a given site.
setDeNovoCharge(int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Set the charge to use for the fragment ions in the de novo sequencing
setDeNovoGuiPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the path to the DeNovoGUI installation.
setDependentLosses(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets whether neutral losses should be sequence dependent.
setDescription(String) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Sets the description of this substitution matrix.
setDescription(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the description of the filter.
setDescription(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Sets the description for this database.
setDescription(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the description.
setDescription(String) - Method in class com.compomics.util.experiment.patient.PatientInformation
Sets the description of the information.
setDescription(String, boolean) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the description of the parameters.
setDescriptionProteinName(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the protein name.
setDescriptionShort(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the short description.
setDestinationFile(String) - Method in class com.compomics.util.io.ftp.FTP
This method allows the specification of the destinationfile.
setDetector(CvTerm) - Method in class com.compomics.util.pride.prideobjects.Instrument
Set the instrument detector.
setDeterminate(int, int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
This method sets the progressbar to determinate mode, with the specified minimum and maximum values.
setDetermineChargePlusOneAlgorithmically(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether charge plus one should be determined algorithmically.
setDigestionParameters(DigestionParameters) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the digestion preferences.
setDigestionType(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the enzyme digestion type.
setDiscardLowQualitySpectra(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Sets whether low quality spectra shall be discarded.
setDisplayedTips(ArrayList<String>) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the list of displayed tips.
setDisplayProgress(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setDisplayProgress(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setDisplayProgress(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setDisplayProgress(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setDisplayProgress(boolean) - Method in interface com.compomics.util.waiting.WaitingHandler
Set if the waiting handler is to show the progress for the current process or not.
setDissociationType(MetaMorpheusParameters.MetaMorpheusDissociationType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the dissociation type.
setDoi(String) - Method in class com.compomics.util.pride.prideobjects.Reference
Set the Digital Object Identifier (DOI) of the reference.
setDoPrecursorDeconvolution(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether precursor deconvolution is to be carried out.
setDoubleChargeWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the window size for doubly charged ions.
setDrawLabel(boolean) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set to true if the label is to be drawn, false otherwise.
setDrawOnTop(boolean) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set to true if the area is to be drawn in front of the data, false otherwise.
setDScoreThreshold(double) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Sets the D-score threshold.
setDuplicateSpectra(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets whether to use duplicate spectra option.
setDynamicRange(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets the dynamic range for spectrum filtering.
setEditable(boolean) - Method in class com.compomics.util.io.export.ExportScheme
Sets whether the scheme is editable.
setEMail(String) - Method in class com.compomics.util.pride.prideobjects.Contact
Set the contact e-mail.
setEmpiricalCorrection(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets whether empirical correction should be used.
setEnd(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the end value.
setEndBlock(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Set the block end.
setEndProtein(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Set the protein end.
setEnsemblVersionsMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Sets the Ensembl version map.
setEnzymaticTagsOnly(boolean) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Sets whether tags should only be mapped to enzymatic peptides.
setEnzymes(ArrayList<Enzyme>) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Sets the enzymes used for digestion.
setEnzymeType(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the enzyme type.
setEqualIL(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets whether I and L should be considered indistinguishable.
setEstimateCharge(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether the precursor charge shall be estimated for OMSSA.
setEstimateCharge(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Sets whether the precursor charge shall be estimated for PepNovo.
setEvenRowColor(Color) - Method in class com.compomics.util.AlternateRowColoursJTable
Sets the colour of the even numbered rows; by default, the LIGHT_AQUA background color will be used..
setExceptions(HashSet<Long>) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the excepted matches.
setExcluded(int, ArrayList<Character>) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Excludes the given amino acids from the targeted amino acids at the given index.
setExperiment_type(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Set the experiment type.
setExportFeatures(String, ArrayList<ExportFeature>) - Method in class com.compomics.util.io.export.ExportScheme
Sets the export features of a given section.
setFastaParameters(FastaParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the ASTA processing parameters.
setFastIndexFolderName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the name of the FASTA index folder.
setFeature(IonFeature.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature
Sets the peptide feature.
setFile(File) - Method in class com.compomics.util.gui.file_handling.FileAndFileFilter
Set the file.
setFileFilter(FileFilter) - Method in class com.compomics.util.gui.file_handling.FileAndFileFilter
Set the file filter.
SetFileMode(int) - Method in class com.compomics.util.io.ftp.FTP
This method sets the file transfer mode.
setFilename(String) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Setter for the filename
setFilename(String) - Method in interface com.compomics.util.interfaces.SpectrumFile
This method sets the filename for the file.
setFilename(String) - Method in class com.compomics.util.io.ftp.FTP
This method sets the name of the file to up- or download.
setFileName(String) - Method in class com.compomics.util.io.PklFile
 
setFilenameColor(Color) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method sets the display color for the filename on the panel.
setFilter() - Method in class com.compomics.util.gui.filtering.FilterDialog
/** Modifies the filter according to the user selection.
setFiltered(boolean) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets whether the protein list is filtered.
setFilterFromSearchParameters(SearchParameters) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Updates the filter based on the search parameters.
setFilterItem(String, FilterItemComparator, Object) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets an item to the filter.
setFirstDecoy(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Sets whether the number of hits before the first decoy should be checked.
setFixed(boolean) - Method in class com.compomics.util.experiment.biology.ions.NeutralLoss
Sets whether the loss is fixed or not.
setFixedAaModifications(HashMap<Integer, String>) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Sets the modifications at specific amino acids.
setFixedVariants(HashMap<String, ArrayList<SNPElement>>) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
sets the fixed variants
setFlanking(boolean) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Set whether the flanking amino acids of a mapped peptide are to be reported.
setFontColor(Color) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Set the color for the font of the peptide sequence.
setFontSize(int) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the font size.
setFontSizeLegend(int) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the font size of the legend.
setForeignAccession(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the foreign accession.
setForeignDescription(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the foreign description.
setForeignID(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the foreign ID.
setForwardIons(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the forward ions searched as list of integers as indexed in the FragmentIon class.
setFoundModifications(TreeSet<String>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the list of variable modifications found in the dataset.
setFractionMolecularWeightRanges(HashMap<String, XYDataPoint>) - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
Set the user provided molecular weight ranges for the fractions.
setFractionOfPeaksForChargeEstimation(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the fraction of peaks to be retained for charge >1 estimation.
setFractionParameters(FractionParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the fraction parameters.
setFractionPEP(String, Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the fraction confidence.
setFractionPEP(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
 
setFractionPsmMatches(HashMap<String, ArrayList<Long>>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the fraction PSM matches.
setFractions(ArrayList<String>) - Method in class com.compomics.util.experiment.identification.Identification
Sets the fractions.
setFractionScore(String, double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the fraction confidence.
setFractionScore(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the fraction score map.
setFragmentAccuracyType(SearchParameters.MassAccuracyType) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the fragment accuracy type.
setFragmentAll(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets whether the fragment all option should be used.
setFragmentationMethod(FragmentationMethod) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the fragmentation method used.
setFragmentationMethod(String) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
Set the fragmentation method.
setFragmentationModel(String) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Sets the name of the fragmentation model.
setFragmentationRule(String) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the fragmentation rule.
setFragmentationTerminus(MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the fragmentation terminus.
setFragmentationType(int) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set the fragmentation ID.
setFragmentBinOffset(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the fragment ion bin offset.
setFragmentIonAccuracy(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets the fragment ion accuracy.
setFragmentIonAccuracy(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Sets the fragment ion accuracy.
setFragmentIonAccuracy(double) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the fragment ion m/z tolerance.
setFragmentIonPpm(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets whether the fragment ion accuracy is in ppm.
setFragmentIonPpm(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Sets whether the fragment ion accuracy is in ppm.
setFunction(AASequenceFeature.Function) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature
Sets the function used to compare the amino acid properties.
setGeneMappingFolder(String) - Static method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Sets the folder where gene mappings are saved.
setGeneName(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Set the gene name.
setGeneNameToChromosomeMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Sets the gene name to chromosome map.
setGeneNameToEnsemblIdMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Sets the gene name to Ensembl ID map.
setGeneParameters(GeneParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the gene parameters.
setGenerateDecoyDatabase(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set whether a decoy database shall be created and searched against.
setGenerateQuery(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Sets a boolean indicating whether a blast query shall be generated.
setGoAccessionToProteinMap(HashMap<String, HashSet<String>>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Sets the GO to protein accession map.
setGoNamesMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Sets the GO accession to names map.
setGPtmCategories(ArrayList<ModificationCategory>) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the modification categories to include in the G-PTM search.
setGroupClass(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
 
setGzip(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets whether identification files should be gzipped.
setHeader(Header) - Method in class com.compomics.util.nucleotide.NucleotideSequence
This method sets the header.
setHeader(Header) - Method in class com.compomics.util.protein.Protein
Simple setter for the header.
setHidden(boolean) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Hide/Unhide a match.
setHigherCharge(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets whether higher charge should be considered.
setHighIntensityCutOff(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the high intensity cut-off as percentage of the most intense ion peak.
setHitListLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the length of the hit list for OMSSA.
setHitListLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Sets the length of the hit list.
setID(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the ID.
setId(long) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Sets the id of the object.
setIdentificationAlgorithmParameter(int, IdentificationAlgorithmParameter) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Adds identification algorithm specific parameters.
setIdentificationCharge(int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Sets the identification charge.
setIdentificationFeaturesCache(IdentificationFeaturesCache) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Sets the the identification features cache.
setIdentificationFile(String) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Sets the identification file.
setIdentificationKeys(IdentificationKeys) - Method in class com.compomics.util.experiment.identification.Identification
Sets the identification keys.
setIdentificationParameters(IdentificationParameters) - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Sets the identification parameters.
setIdentifier(String) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Sets the references identifier.
setIdValidationParameters(IdMatchValidationParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the identification matches validation parameters.
setIgnoreExceptions(boolean) - Method in class com.compomics.util.exceptions.ExceptionHandler
Sets whether exceptions should be ignored.
setIncludeAmmonia(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets whether ammonia losses should be accounted for.
setIncludeDateInOutputName(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets whether the date should be included in the SearchGUI output name.
setIncludeDecoy(Boolean) - Method in class com.compomics.util.io.export.ExportScheme
Sets whether decoy hits should be included.
setIncludeWater(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets whether water losses should be accounted for.
setIndentString(String) - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Sets the indent string to use, e.g.
setIndeterminate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
This method makes the progressbar indeterminate.
setIndexOnProtein(int) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Sets the peptide index on the protein.
setInferred(boolean) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Sets whether the modification is inferred from another peptide.
setInitiatorMethionineBehavior(MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the initiator methionine behavior.
setInstitution(String) - Method in class com.compomics.util.pride.prideobjects.Contact
Set the instituttion.
setInstrumentID(String) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the instrument ID.
setInstrumentID(int) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set the instrument ID.
setIntegerParameter(String, Integer) - Method in class com.compomics.util.experiment.ProjectParameters
 
setIntensity(double) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Setter for the intensity.
setIntensity(double) - Method in interface com.compomics.util.interfaces.SpectrumFile
This method sets the intensity of the precursor ion.
setIntensityCutOffIncrement(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the intensity cut-off increment.
setIntensityLimit(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets the intensity percentile to consider for annotation.
setIntensityScoreWeight(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set the intensity score weight.
setIntensityThresholdType(AnnotationParameters.IntensityThresholdType) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets the intensity threshold type.
setIntensityValues(double[]) - Method in class com.compomics.util.io.PklFile
 
setIntermediateScore(Integer, Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Adds an intermediate score.
setIntermediateScores(HashMap<Integer, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
 
setIonColor(Ion, Color) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Sets an annotation color for the given ion.
setIonMatches(IonMatch[]) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Set the ArrayList with FragmentIon matches.
setIsotope(Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
Sets the isotope, 0 for monoisotope.
setIsotopeCorrection(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the isotope correction setting.
setIsotopeMzTolerance(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the deisotoping m/z tolerance.
setIsPpm(boolean) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Sets whether the mass tolerance is in ppm (true) or Dalton (false).
setIsScrolling(boolean) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Set if the user is currently scrolling or not.
setIterativeReplaceEvalue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the e-value threshold to use to replace a hit for the iterative search.
setIterativeSequenceEvalue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the e-value threshold to use to consider a sequence for the iterative search.
setIterativeSpectrumEvalue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the e-value threshold to use consider a spectrum for the iterative search.
setiXAxisMax(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Sets the maximum value for the x-axis.
setiXAxisMin(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Sets the minimum value for the x-axis.
setiYAxisMax(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Sets the maximum value for the y-axis.
setiYAxisMin(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Sets the minimum value for the y-axis.
setJavaHome(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the Java Home folder.
setKeepTerminalAminoAcids(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the option for keeping the terminal amino acids when generating the decoys
setKey(long) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Sets the object key.
setKey(long) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Sets a new key for the match.
setKeyWords(ArrayList<String>) - Method in class com.compomics.util.messages.FeedBack
Sets the the key words for this report.
setKnownMassDeltas(HashMap<Double, String>) - Static method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set all the known mass deltas (if any).
setLabel(String) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Sets the label.
setLabelColor(Color) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the label color.
setLabelDifference(int) - Method in class com.compomics.util.general.IsotopicDistribution
This method set the label dalton difference
setLastSelectedFolder(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Sets the last selected folder.
setLastSelectedFolder(String, String) - Method in class com.compomics.util.io.file.LastSelectedFolder
Sets the last selected folder of the given use case.
setLastSelectedFolder(String) - Method in class com.compomics.util.io.file.LastSelectedFolder
Sets the last selected folder.
setLastSelectedFolder(LastSelectedFolder) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets the last selected folder.
setLeadingAccession(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Sets the leading accession for this match.
setLegendDatasetAFourWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the legend location of Dataset A in a four way Venn diagram.
setLegendDatasetAThreeWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the legend location of Dataset A in a three way Venn diagram.
setLegendDatasetBFourWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the legend location of Dataset B in a four way Venn diagram.
setLegendDatasetBThreeWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the legend location of Dataset B in a three way Venn diagram.
setLegendDatasetCFourWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the legend location of Dataset C in a four way Venn diagram.
setLegendDatasetCThreeWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the legend location of Dataset C in a three way Venn diagram.
setLegendDatasetDFourWay(XYDataPoint) - Method in class com.compomics.util.gui.VennDiagramPanel
Set the legend location of Dataset D in a four way Venn diagram.
setLimitX(double) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Sets the maximal share of X's a match can contain, range [0.0-1.0].
setLine(int, ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
setLocalPrideFolder(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the local PRIDE folder.
setLocation(int, int) - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method allows the caller to add information to the header about location of the sequence in a certain master sequence.
setLocation(int) - Method in interface com.compomics.util.interfaces.Modification
This method allows the setting of the location for this modification.
setLocation(int) - Method in class com.compomics.util.protein.ModificationImplementation
This method allows the setting of the location for this modification.
setLookAndFeel() - Static method in class com.compomics.util.gui.UtilitiesGUIDefaults
Sets the look and feel to the default utilities look and feel.
setLowerClearMzRange(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the lower mass value for the clear mz range.
setLowerPrecursorMass(int) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Set the lower precursor mass.
setLowIntensityCutOff(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the low intensity cut-off as percentage of the most intense ion peak.
setLowMemoryMode(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Deprecated.
use setMaxLoadedProteins and setMaxLoadedSpectra instead
setManualValidation(HashSet<Long>) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the list of manually validated keys.
setManualValidation(boolean) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets whether the match validation was manually inspected.
setMaps(GoMapping) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Imports the GO maps from a GO mapping.
setMass(double) - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Method to set the mass of the reporter ion.
setMass(double) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Sets the mass.
setMass(double) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.MassGap
Sets the mass of the gap.
setMass(double) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Sets the mass.
setMassAnalyzer(String) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
Set the mass analyzer.
setMassDiffAcceptorType(MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the mass difference acceptor type.
setMassErrorDistribution(String, double[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Sets a mass error distribution in the massErrorDistribution map.
setMassShift(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Sets an m/z shift on all ions.
setMassShifts(double, double, double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Sets the m/z shifts.
setMassTolerance(double, boolean, SpectrumAnnotator.TiesResolution) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Sets a new m/z tolerance for peak matching.
setMatchingKey(long) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Sets the key accounting for sequence matching preferences.
setMatchValidationLevel(MatchValidationLevel) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the validation level of the match.
setMatchValidationLevel(Integer) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Sets the lowest validation level to consider as an integer as indexed in the MatchValidationLevel enum.
setMaxCharge(Integer) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Sets the maximum charge in this file.
setMaxChargeSearched(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the maximal charge searched.
setMaxCombinations(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the maximal number of combinations.
setMaxDynamicMods(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the maximum number of dynamic mods.
setMaxDynamicMods(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the maximum number of variable modifications.
setMaxEValue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the maximal e-value searched for.
setMaxEValue(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets the maximal e-value searched for.
setMaxFragmentCharge(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the maximum fragment ion charge.
setMaxFragmentCharge(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the maximal fragment charge.
setMaxFragmentPerSeries(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the maximal number of fragments to retain per series.
setMaxFragmentSize(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the max fragmentation size.
setMaxHeterozygousVariants(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the max heterozygous variants.
setMaxHitsPerSpectrumPerCharge(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Set the maximal number of hits searched per spectrum and per charge.
setMaximumExpectationValueRefinement(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets the maximum expectation value to use for refinement.
setMaxIntensity(Double) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Sets the maximum precursor intensity in this file.
setMaxIsotopes(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Sets the maximal number of isotopes allowed (inclusive).
setMaxIsotopicCorrection(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the maximal isotopic correction.
setMaxIterations(int) - Method in class com.compomics.util.math.clustering.KMeansClustering
Set the maximum number of iterations.
setMaxLoadedProteins(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum number of proteins loaded into memory.
setMaxLoadedSpectra(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum number of spectra loaded into memory.
setMaxMissedCleavages(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Set the maximum number of missed cleavages.
setMaxModificationIsoforms(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the max modification isoforms.
setMaxModifications(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum number of modifications per peptide.
setMaxModificationSites(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum number of modifications sites per modification per peptide.
setMaxModsForPeptide(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the max mods for peptide.
setMaxMW(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the molecular weight of the fattest protein in the dataset.
setMaxMz(Double) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Sets the maximum m/z in this file.
setMaxMzDeviation(double) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Sets the maximal m/z deviation allowed.
setMaxMzLadders(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the maximal m/z ladder length.
setMaxNeutralLosses(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum number of water and ammonia losses per peptide.
setMaxNeutralLossesPerModification(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum number identical modification specific losses per peptide.
setMaxNPeptides(Integer) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the maximal number of peptides among the proteins of the dataset.
setMaxNPsms(Integer) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the the maximal amount of PSMs in the proteins of the dataset.
setMaxNumberOfModifications(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the maximal number of modifications.
setMaxPadding(int) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set the max padding (distance between the axes and the border of the panel).
setMaxPeakCount(Integer) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Sets the maximum peak count in this file.
setMaxPeakCount(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set the maximum peak count.
setMaxPeakCount(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the max peak count.
setMaxPepLength(int) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Sets the maximal peptide length allowed.
setMaxPeptideLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Sets the maximal peptide length allowed.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the maximum peptide length.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum peptide length.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Sets the maximal peptide length allowed.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Sets the maximal peptide length allowed.
setMaxPeptideLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the maximal peptide length allowed.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Sets the maximal peptide length allowed.
setMaxPeptideLengthNoEnzyme(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the maximal peptide length to use when searching with no enzyme.
setMaxPeptideMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the maximal peptide mass.
setMaxPeptidePrecursorErrorDa(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the max peptide precursor mass error in Dalton.
setMaxPeptidePrecursorErrorPpm(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the max peptide precursor mass error in ppm.
setMaxPrecursorAdjustment(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set the maximum precursor adjustment.
setMaxPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the maximum precursor mass.
setMaxPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Sets the maximum precursor mass.
setMaxPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Sets the maximum precursor mass.
setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setMaxPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setMaxPrimaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
Set the maximum value for the primary progress counter.
setMaxProteinAccessionLength(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the max protein accession length.
setMaxProteinAveragePrecursorIntensity(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the maximum protein average precursor intensity.
setMaxProteinSummedPrecursorIntensity(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the maximum summed protein precursor intensity.
setMaxPtmsPerTagPeptide(int) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Sets the maximum number of PTMs to consider when mapping tags to protein sequences.
setMaxRank(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum rank.
setMaxRT(Double) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Sets the maximal RT in this file.
setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setMaxSecondaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
Set the maximum value for the secondary progress counter.
setMaxSpectrumChargeRange(int) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the maximum charge added when the charge is missing for a given spectrum.
setMaxSpectrumCount(int) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the maximal amount of PSMs for the peptides in the current peptide list.
setMaxSpectrumCounting(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the maximal spectrum counting value of the proteins of the dataset.
setMaxSpectrumMz(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the max spectrum m/z to search for.
setMaxTagCount(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the maximum number of tags per spectrum to be generated.
setMaxTagPrecursorErrorDa(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the max tag precursor mass error in Dalton.
setMaxTagPrecursorErrorPpm(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the max tag precursor mass error in ppm.
setMaxValidatedPeptidesPerFraction(Integer) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the maximum validated peptides at the fraction level.
setMaxValidatedSpectraPerFraction(Integer) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the maximum validated spectra at the fraction level.
setMaxVariableModifications(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the maximum number of variable modifications per peptide.
setMaxVariableModificationsPerPeptide(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the maximum number of variable modifications of allowed on a single peptide.
setMaxVariableModificationsPerTypePerPeptide(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the maximum number of variable modifications of each modification type allowed on a single peptide.
setMaxVariableMods(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the maximum number of variable modifications per peptide.
setMemoryMappedSequenceLibraries(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether sequence libraries should be mapped in memory.
setMemoryParameter(int) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets the upper memory limit.
setMemoryShare(double) - Method in class com.compomics.util.db.object.ObjectsCache
Sets the share of heap size which can be used before emptying the cache.
setMessage(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
This method allows the caller to set a message on the progressbar.
setMessage(String) - Method in class com.compomics.util.messages.FeedBack
Sets the message.
setMethod(ReporterMethod) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Sets the reporter method used.
setMethodUsed(Quantification.QuantificationMethod) - Method in class com.compomics.util.experiment.quantification.Quantification
setter for the method used
setMgfMaxSize(double) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the max mgf file size before splitting.
setMgfNSpectra(int) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the max number of spectra in an mgf file.
setMH(double) - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
Sets the PepNovo provided mH.
setMinAllowedIntensityRatioToBasePeak(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the minimum allowed intensity ratio to base peak.
setMinAminoAcidScore(int) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Set the minimum amino acid score.
setMinAnnotatedPeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the minimal number of annotated peaks a peptide should have.
setMinChargeSearched(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the minimal charge searched.
setMinFragmentMz(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets the minimal fragment m/z.
setMiniature(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the graphics panel is to be drawn in a miniature form.
setMinimalChargeForMultipleChargedFragments(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.
setMinIsotopes(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Sets the minimal number of isotopes allowed (inclusive).
setMinIsotopicCorrection(int) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the minimal isotopic correction.
setMinMissedCleavages(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Set the minimum number of missed cleavages.
setMinPeakIntensity(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the minimum peak intensity.
setMinPeaks(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the minimum number of peaks.
setMinPeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the minimal number of peaks a spectrum should contain.
setMinPeaksPerSpectrum(int) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets the minimal number of peaks per spectrum.
setMinPepLength(int) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Sets the maximal peptide length allowed.
setMinPeptideLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Sets the minimal peptide length allowed.
setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the minimum peptide length.
setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the minimum peptide length.
setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Sets the minimal peptide length allowed.
setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Sets the minimal peptide length allowed.
setMinPeptideLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the minimal peptide length allowed.
setMinPeptideLength(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Sets the minimal peptide length allowed.
setMinPeptideLengthNoEnzyme(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the minimal peptide length to use when searching with no enzyme.
setMinPrecPerSpectrum(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the minimal number of precursors per spectrum.
setMinPrecursorAdjustment(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set the minimum precursor adjustment.
setMinPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the minimum precursor mass.
setMinPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Sets the minimum precursor mass.
setMinPrecursorMass(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Sets the minimum precursor mass.
setMinPrecursorMass(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets the minimal precursor mass.
setMinRT(Double) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Sets the minimum RT in this file.
setMinSpectrumChargeRange(int) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the minimum charge added when the charge is missing for a given spectrum.
setMinSpectrumMz(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the min spectrum m/z to search for.
setMinSpectrumPeaks(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the min number of peaks in a spectrum.
setMinTagLength(int) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Set the minimum tag length.
setMinTerminiCleavages(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the minimum number of termini cleavages.
setMinus1(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Sets the isotopic correction factor at -1 Da.
setMinus2(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Sets the isotopic correction factor at -2 Da.
setMinVariantDepth(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the min variant depth.
setMiscleavages(int) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to specify the number of allowed missed cleavages for this enzyme.
setModel(TableModel, boolean) - Method in class com.compomics.util.gui.JTableForDB
This method allows you to specify a tablemodel and a boolean which indicates whether or not the table should be sortable by clicking the column headers.
setModel(TableModel) - Method in class com.compomics.util.gui.JTableForDB
Sets a TableModel for the table and defaults it to being sortable.
setModel(TableModel) - Method in class com.compomics.util.sun.TableMap
 
setModel(TableModel) - Method in class com.compomics.util.sun.TableSorter
 
setModification(String) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Sets the theoretic PTM.
setModificationLocalizationParameters(ModificationLocalizationParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the modification localization parameters.
setModificationParameters(ModificationParameters) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the modification settings.
setModificationRefinement(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Sets whether the protein mapping should be refined based on terminal and pattern modifications.
setModifications(ArrayList<String>) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the variable modifications searched.
setModifications(Vector) - Method in class com.compomics.util.protein.AASequenceImpl
Simple setter for the modifications.
setModPeptidesAreDifferent(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether modified peptides are considered different.
setMonoIsotopic(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set whether monoisotopic mass values shall be used (in contrast to average mass values).
setMonoisotopicPrecursor(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the precursor mass is monoisotopic.
setMsFormat(ProteoWizardMsFormat) - Method in class com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
Sets the format to convert to.
setMsFormat(ThermoRawFileParserOutputFormat) - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
Sets the format to convert to.
setMzBinOffset(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the m/z bin offset.
setMzBinWidth(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the m/z bin width.
setMzFidelityScoreWeight(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set the mzFidelity score weight.
setMzidOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the mzid output is to be created.
setMzValues(double[]) - Method in class com.compomics.util.io.PklFile
 
setnAaDeletions(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Sets the number of amino acid deletions allowed.
setnAaInsertions(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Sets the number of amino acid insertions allowed.
setnAaSubstitutions(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Sets the number of amino acid substitutions allowed.
setnAaSwap(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Sets the number of amino acid swaps allowed.
setName(String) - Method in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Setter for the ion name.
setName(String) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Sets the modification name.
setName(String) - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Sets the name of this substitution matrix.
setName(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the name of the filter.
setName(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Sets a new name for the database.
setName(String) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Sets the name of the reagent.
setName(String) - Method in class com.compomics.util.io.export.ExportScheme
Sets the name of the scheme.
setName(String) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the name of the parameters.
setName(String) - Method in class com.compomics.util.pride.CvTerm
Sets the name.
setName(String) - Method in class com.compomics.util.pride.prideobjects.Contact
Set the contact name.
setName(String) - Method in class com.compomics.util.pride.prideobjects.ContactGroup
Set the contact group name.
setName(String) - Method in class com.compomics.util.pride.prideobjects.Instrument
Set the instrument name.
setName(String) - Method in class com.compomics.util.pride.prideobjects.Protocol
Set the protocol name.
setName(String) - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
Set the references group name.
setName(String) - Method in class com.compomics.util.pride.prideobjects.Sample
Set the name of the sample.
setnAnnotatedMostIntensePeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the minimal number of annotated most intense peaks.
setnClusters(int) - Method in class com.compomics.util.math.clustering.settings.KMeansClusteringSettings
Sets the number of clusters to use.
setnConfidentProteins(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the number of confident proteins.
setNeutralLosses(ArrayList<NeutralLoss>) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Sets the neutral losses possibly encountered with this modification.
setNeutralLossesAuto(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Sets whether neutral losses should be automatically selected.
setNeutralLossesMap(NeutralLossesMap) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Sets the map of neutral losses to annotate.
setNeutralLossesSequenceAuto(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets whether neutral losses are considered only for amino acids of interest or not.
setNeutronThreshold(double) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the mass after which exact neutron mass should be considered in the calculation.
setNewTitle(String) - Method in class com.compomics.util.gui.DummyFrame
Update the frame title and return the frame.
setnMissedCleavages(String, int) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Sets the number of allowed missed cleavages.
setNoOneHitWonders(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether one hit wonders are to be excluded.
setNoProlineRuleSeries(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the id numbers of ion series to apply no product ions at proline rule at.
setNormalizationFactors(NormalizationFactors) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Sets the normalization factors.
setNormalize(Boolean) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Sets whether the spectrum counting index should be normalized.
setNormalizePeaksAcrossAllWindows(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the normalize peaks across all windows.
setNovorPtmMap(HashMap<String, String>) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
Set the Novor to utilities PTM map.
setnPeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets the number of most intense peaks to consider.
setnPeaksInDoubleChargeWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the number of peaks in doubly charged windows.
setnPeaksInSingleChargeWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the number of peaks in singly charged windows.
setnTermModification(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Sets the N-term modification.
setnThreads(int) - Method in class com.compomics.util.parameters.tools.ProcessingParameters
Sets the number or threads to use.
setNumberOfBatches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the number of batches per node to strive for when using the MPI-based parallelization features.
setNumberOfCandidates(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the number of candidates.
setNumberOfModificationsPerPeptide(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set the maximum number of modifications per peptide.
setNumberOfPeaksToKeepPerWindow(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the number of peaks to keep per window.
setNumberOfPeptides(int) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Set the number of peptides to report per spectrum.
setNumberOfSpectrumMarches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set the maximum number of spectrum matches.
setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the maximum number of spectrum matches.
setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the maximum number of spectrum matches.
setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the number of PSMs to report per spectrum.
setNumberOfTasks(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set the number of tasks.
setNumberOfWindows(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the number of windows.
setNumberTolerableTermini(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set the number of tolerable termini.
setNumChargeStates(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the number of charge states.
setNumericParameter(String, Double) - Method in class com.compomics.util.experiment.ProjectParameters
 
setNumIntensityClasses(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the number of intensity classes.
setNumIntensityClasses(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the number of intensity classes.
setnValidatedProteins(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the number of validated proteins.
setnValidatedPsms(int) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the number of validated PSMs for the currently selected peptide.
setnVariants(int) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Sets the total number of variants allowed.
setObject(K) - Method in class com.compomics.util.general.BoxedObject
Sets the boxed object.
setObjectCache(ObjectsCache) - Method in class com.compomics.util.db.object.ObjectsDB
Sets the object cache to be used by this database.
setObservedFractionalMassesAll(HashMap<String, ArrayList<Double>>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the observed molecular masses for each fraction in kDa.
setOccurrence(Atom, Integer, Integer) - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Sets the occurrence of a given atom.
setOntology(String) - Method in class com.compomics.util.pride.CvTerm
Sets the ontology.
setOrganismIdentifier(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the organism identifier.
setOutputData(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets whether data should be copied along with the identification files in the SearchGUI output.
setOutputFolder(File) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets the last used output folder.
setOutputFolderName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the name of the output folder.
setOutputFormat(String) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set the output format.
setOutputFormat(String) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the output format.
setOutputHistograms(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether histograms should be written in the result file
setOutputProteins(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the protein bloc should be included in the export.
setOutputResults(String) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Set the output results filter.
setOutputSequences(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the protein sequences should be included in the protein block of the export.
setOutputSpectra(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the spectra should be exported in the result file.
setOutputSuffix(String) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the output tags suffix.
setParametersFromSearch(SearchParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets identification parameters based on given search parameters.
setParametersFromSearchParameters(SearchParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Updates the annotation parameters based on search parameters.
setParentFolder(String) - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Set the parent folder.
setParentFolder(String) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFolder
Sets the parent folder where to write cms files to.
setParentMonoisotopicMassIsotopeError(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.
setPassive(boolean) - Method in class com.compomics.util.io.ftp.FTP
Set Passive mode Transfers.
setPathParameter(UtilitiesPathParameters.UtilitiesPathKey, String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Sets the path according to the given key and path.
setPathSettings() - Method in class com.compomics.cli.paths.PathSettingsCLI
Sets the path settings according to the pathSettingsCLIInputBean.
setPattern(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Sets the amino acid pattern targeted by this modification.
setPdbaccession(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Set the PDB accession.
setPeackPicking(boolean) - Method in class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
Set if peak picking is to be performed.
setPeakPicked(Boolean) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Set if the indexed file seems to contain only peak picked spectra or not.
setPeaks(HashMap) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Setter for the peaks
setPeaks(HashMap) - Method in interface com.compomics.util.interfaces.SpectrumFile
This method sets the peaks on the spectrum.
setPeakWaterMarkColor(Color) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set the peak water mark color.
setPeakWidth(float) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set the peak width.
setPepNovoPtmMap(Map<String, String>) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
Set the PepNovo to utilities PTM map.
setPeptide(Peptide) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Setter for the peptide.
setPeptide(Peptide, int, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpecificAnnotationParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Sets a new peptide to annotate.
setPeptide(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>, int, SpecificAnnotationParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
Sets a new peptide to annotate.
setPeptide(Peptide) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
Returns the peptides.
setPeptideAssumptionFilter(PeptideAssumptionFilter) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the filter used when importing PSMs.
setPeptideAssumptionMap(HashMap<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>>) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Sets the peptide assumption map.
setPeptideFilters(ArrayList<Filter>) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Sets the list of peptide quality filters.
setPeptideHideFilters(HashMap<String, PeptideFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
Sets the peptide hide filters.
setPeptideLengthDistribution(NonSymmetricalNormalDistribution) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the distribution of validated peptide lengths.
setPeptideList(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the current peptide list.
setPeptideMatchesKeys(long[]) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Sets the peptide keys for this protein match.
setPeptideSequenceFont(Font) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Set the font to use for the peptide sequence.
setPeptideShakerPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the path to the PeptideShaker installation.
setPeptideStarFilters(HashMap<String, PeptideFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
Sets the peptide star filters.
setPeptideVariantsParameters(PeptideVariantsParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the peptide variant parameters.
setPepXmlOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the pepxml output is to be created.
setPercentLength(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the length of the reference area in percent.
setPerformDeisotoping(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Sets if deisotoping is to be performed.
setPinOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the Percolator output is to be created.
setPlus1(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Sets the isotopic correction factor at +1 Da.
setPlus2(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Sets the isotopic correction factor at +2 Da.
setPmid(String) - Method in class com.compomics.util.pride.prideobjects.Reference
Set the PubMed ID of the reference.
setPNovoPtmMap(HashMap<Character, String>) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Set the pNovo to utilities PTM map.
setPNovoPtmResiduesMap(HashMap<Character, Character>) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Set the pNovo to original amino acids residue map.
setPointSize(Integer) - Method in class com.compomics.util.gui.spectrum.ChromatogramPanel
This method allows the caller to set the point size for the profileChromatogram.
setPosition(int) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to set the cleavage position for the Enzyme.
setPotentialModificationsForFullRefinment(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the refinement modifications should be used for the full refinement
setPpm(boolean) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Sets whether the precursor mass tolerance is in ppm.
setPrecurorCharge(int) - Method in class com.compomics.util.io.PklFile
 
setPrecursorAccuracy(double) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the precursor tolerance.
setPrecursorAccuracyType(SearchParameters.MassAccuracyType) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the precursor accuracy type.
setPrecursorAdjustmentStep(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set the precursor adjustment step.
setPrecursorCharge(int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Sets the precursor charge.
setPrecursorChargesMissing(Boolean) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex
Set if at least one spectrum is missing the precursor charge.
setPrecursorIntensity(double) - Method in class com.compomics.util.io.PklFile
 
setPrecursorIntensityAveragePerFraction(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the precursor intensity per fraction map.
setPrecursorIntensityPerFraction(HashMap<String, ArrayList<Double>>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Get the precursor intensity in the given fraction.
setPrecursorIntensitySummedPerFraction(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the summed precursor intensity per fraction map.
setPrecursorMZ(double) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Setter for the precursor MZ
setPrecursorMZ(double) - Method in interface com.compomics.util.interfaces.SpectrumFile
This method sets the precursor M/Z on the file.
setPrecursorMz(double) - Method in class com.compomics.util.io.PklFile
 
setPrideFolder(String) - Static method in class com.compomics.util.pride.PrideObjectsFactory
Sets the folder where pride annotation information should be saved.
setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setPrimaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
Sets the primary progress counter to the given value.
setPrimaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setPrimaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setPrimaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setPrimaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setPrimaryProgressCounterIndeterminate(boolean) - Method in interface com.compomics.util.waiting.WaitingHandler
Sets whether the primary progress counter is indeterminate or not.
setPrintExpectScore(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set if the export score is to be printed.
setPrintPeptides(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if a list of the peptides should be printed to the output folder.
setPrintProgressIndicatorSize(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the progress indicator size.
setProbabilisticScore(int, double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Sets the probabilistic score at a given site.
setProbabilisticScoreCalculation(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Sets whether a probabilistic modification score is required.
setProbabilisticScoreNeutralLosses(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Sets whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score.
setProbabilisticScoreThreshold(double) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Sets the probabilistic score threshold (inclusive).
setProbability(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Set the probability.
setProcessingType(ProcessingParameters.ProcessingType) - Method in class com.compomics.util.parameters.tools.ProcessingParameters
Sets the processing type.
setProfile(double[][]) - Method in class com.compomics.util.gui.protein.ModificationProfile
Sets the profile.
setProfileMode(boolean) - Method in class com.compomics.util.gui.spectrum.ChromatogramPanel
Set the drawing style to profile or centroid mode.
setProfileMode(boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Change the drawing type of the spectrum.
setProgress(int, String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
This method allows the caller to set the progress on the progressbar to the specified value, along with the specified message.
setProgress(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
This method sets the progress to the specified value.
setProperty(ModificationFeature.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature
Sets the feature property.
setProperty(PeptideFeature.Property) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature
Sets the feature property.
setProteinConfidenceMwPlots(Double) - Method in class com.compomics.util.parameters.identification.advanced.FractionParameters
Sets the protein confidence for inclusion in MW plots.
setProteinEvidence(Integer) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the protein evidence level.
setProteinFilters(ArrayList<Filter>) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Sets the list of protein quality filters.
setProteinHideFilters(HashMap<String, ProteinFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
Sets the protein hide filters.
setProteinInferenceClass(int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the protein group class.
setProteinInferenceParameters(ProteinInferenceParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the protein inference parameters.
setProteinKeys(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Sets the ordered protein list.
setProteinKeys(long[]) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the list of ordered protein keys.
setProteinList(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the protein list.
setProteinListAfterHiding(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the protein list after all hiding filters have been used.
setProteinMapping(TreeMap<String, int[]>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Sets the protein mapping as a map of 0-based indexes for every protein accession.
setProteinPtmComplexity(double) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Set the proteinPtmComplexity.
setProteinQuickAcetyl(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the protein quick acetylation option should be triggered.
setProteinStarFilters(HashMap<String, ProteinFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
Sets the protein star filters.
setProteinToGoMap(HashMap<String, HashSet<String>>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps
Sets the protein to GO terms accession map.
setProteoWizardPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the path to ProteoWizard.
setProtocol(int) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set the protocol ID.
setPsiModCvTerm(CvTerm) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Set the PSI-MOD CV term associated with this modification.
setPsmFilters(ArrayList<Filter>) - Method in class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Sets the list of PSM quality filters.
setPsmHideFilters(HashMap<String, PsmFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
Sets the psm hide filters.
setPsmList(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the PSM list.
setPsmScoringParameters(PsmScoringParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the scoring preferences used when scoring PSMs.
setPsmStarFilters(HashMap<String, PsmFilter>) - Method in class com.compomics.util.gui.filtering.FilterParameters
Sets the psm star filters.
setPtmIndex(String, int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the index for a given modification.
setPtmIndex(String, int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the index for a given modification.
setPtmIndexes(ModificationParameters) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Set the PTM indexes of the modifications searched.
setPtmName(String) - Method in class com.compomics.util.gui.protein.ModificationProfile
Sets the PTM name.
setPtmToPrideMap(PtmToPrideMap) - Method in class com.compomics.util.pride.PrideObjectsFactory
Sets a new PTM to PRIDE map.
setQcFilters(HashMap<String, Boolean>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets the qc filters.
setQcResult(String, boolean) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Sets whether the match passed a quality control check.
setQuickPyrolidone(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the quick pyrolidone option should be triggered.
setRank(int) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Set the rank of the PeptideAssumption.
setRankScore(double) - Method in class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails
Sets the PepNovo rank score.
setRawHeader(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the entire header.
setRawScore(double) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Sets the raw score as provided by the identification algorithm.
setReadOnly(boolean) - Method in class com.compomics.util.db.object.ObjectsCache
Sets the cache in read only.
setReadOnly(boolean) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the cache in read only.
setReadTweets(ArrayList<String>) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the list of read tweets.
setRef(double) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Sets the value used as reference for the correction factors.
setReference(String) - Method in class com.compomics.util.pride.prideobjects.Reference
Set the reference.
setReferenceMass(Double) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Sets the reference total mass to use for normalization.
setReferences(ArrayList<Reference>) - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
Set the references.
setRefine(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the second pass search should be triggered.
setRefinePointMutations(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether point mutations should be looked for during the refinement process.
setRefineSemi(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the semi enzymatic option of the second pass search should be triggered.
setRefineSnaps(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether snAPs should be used during the refinement process.
setRefineSpectrumSynthesis(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the spectrum synthesis option should be used during the refinement process.
setRefineUnanticipatedCleavages(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the unanticipated cleavages option should be used during the refinement process.
setRefMass(double) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the reference mass used to convert ppm to Da.
setRefMass(double) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
setRelatedIons(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets whether related ions should be annotated by default.
setRelationship(AAPropertyRelationshipFeature.Relationship) - Method in class com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature
Sets the relationship between the features.
setRelimsPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the path to the Relims installation.
setRemoveMethionine(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Sets if n-term methionine is to be removed.
setRemovePrecursor(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set if the precursor is to be removed.
setRemovePrecursor(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether the precursor shall be removed for OMSSA.
setRemovePrecursor(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the precursor peak is to be removed.
setRemovePrecursorTolerance(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the precursor removal tolerance.
setRemovePrecursorTolerance(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the tolerance with which to remove the precursor peak.
setRemoveTempFolders(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the output and index folders are to be removed when the search has completed.
setRemoveUnknownModifications(boolean) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Set whether unknown modifications shall be removed.
setRenameXTandemFile(boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set if the X! Tandem file should be renamed.
setReportBothBestHitsForTD(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
Set if target and decoy are ranked separately or shared.
setReporterIon(ReporterIon) - Method in class com.compomics.util.experiment.quantification.reporterion.Reagent
Sets the reporter ion to look for in the spectrum.
setReporterIons(ArrayList<ReporterIon>) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Sets the reporter ions possibly encountered with this modification.
setReporterIons(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets whether reporter ions should be annotated by default.
setReporterPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the path to the PeptideShaker installation.
setReportFailed(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the report when the filter is not passed.
setReportPassed(String) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the report when the filter is passed.
setRequireVariableMods(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set if at least one variable modification is required per peptide.
setResolution(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Set the resolution.
setRest(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the rest of the header.
setRestrict(char[]) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to specify the residues that restrict cleavage.
setRestrict(String) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to specify the residues which restrict cleavage.
setRewindIons(ArrayList<Integer>) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Sets the rewind ions searched as list of integers as indexed in the FragmentIon class.
setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setRunCanceled() - Method in interface com.compomics.util.waiting.WaitingHandler
Set the process as canceled.
setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setRunFinished() - Method in interface com.compomics.util.waiting.WaitingHandler
Set the process as finished.
setRunGptm(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether the G-PTM search is to be performed.
setRunNotFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Set the run to not finished.
setSampleIndex(String, Integer) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Set the sample index for the given sample.
setScalePrecursor(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether the precursor shall be scaled for OMSSA.
setScalingFactor(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Sets the scaling factor.
setSchema(URL) - Method in class com.compomics.util.pride.validation.PrideXmlValidator
Set the schema.
setScientificXAxis(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the x-axis tags are to be drawn using scientific annotation.
setScientificXAxis(String) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the x-axis tags are to be drawn using scientific annotation.
setScientificYAxis(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the y-axis tags are to be drawn using scientific annotation.
setScientificYAxis(String) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the y-axis tags are to be drawn using scientific annotation.
setScore(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Set the peptide score.
setScore(double) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Sets the score.
setScoreCutoff(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the score cut-off.
setSearchDecoyDatabase(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
Set whether MS-GF+ is to create and search a decoy database.
setSearchForwardFragmentFirst(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether forward ions (b1) should be searched first.
setSearchGuiOutputParameters(OutputParameters) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets how SearchGUI output files should be organized.
setSearchGuiPath(String) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the path to the SearchGUI installation.
setSearchParameters(SearchParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the parameters used for the spectrum matching.
setSearchPositiveIons(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether positive ions are searched.
setSearchRewindFragments(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether C-terminal fragments should be searched.
setSearchTarget(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether target sequences are to be searched.
setSearchType(MetaMorpheusParameters.MetaMorpheusSearchType) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the search type.
setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setSecondaryProgressCounter(int) - Method in interface com.compomics.util.waiting.WaitingHandler
Sets the secondary progress counter to the given value.
setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setSecondaryProgressCounterIndeterminate(boolean) - Method in interface com.compomics.util.waiting.WaitingHandler
Sets the secondary progress counter to indeterminate or not.
setSecondaryProgressText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setSecondaryProgressText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setSecondaryProgressText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setSecondaryProgressText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setSecondaryProgressText(String) - Method in interface com.compomics.util.waiting.WaitingHandler
Set the secondary progress counter text.
setSelectedCharges(HashSet<Integer>) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Sets the charges selected for annotation.
setSelectedExportFolder(LastSelectedFolder) - Method in class com.compomics.util.gui.VennDiagramDialog
 
setSelectedExportFolder(LastSelectedFolder) - Method in class com.compomics.util.gui.XYPlottingDialog
 
setSelectedIonsMap(HashMap<Ion.IonType, HashSet<Integer>>) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Sets the map of ions to annotate.
setSelectedMethod(SpectrumCountingMethod) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Set the current spectrum counting method.
setSelectedOutput(String) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the output type, omx, csv or pepXML.
setSelectedOutputFormat(CometParameters.CometOutputFormat) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Sets the output format.
setSelectedPositions(Integer[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Set the selected positions.
setSelectedProbabilisticScore(ModificationLocalizationScore) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Sets the selected probabilistic score.
setSelfUpdating(boolean) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Sets whether the table is in self update mode.
setSequence(String) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Sets the sequence.
setSequence(String) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Sets for the sequence.
setSequence(char[]) - Method in class com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
Sets the sequence.
setSequence(String, boolean) - Method in class com.compomics.util.gui.protein.SequenceModificationPanel
Set the Sequence for the SequenceFragmentationPanel.
setSequence(String, boolean) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Set the Sequence for the SequenceFragmentationPanel.
setSequence(String) - Method in interface com.compomics.util.interfaces.Sequence
This method will set the sequence.
setSequence(NucleotideSequenceImpl) - Method in class com.compomics.util.nucleotide.NucleotideSequence
This method allows the setting of a sequence.
setSequence(String) - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
This method will set the sequence.
setSequence(String) - Method in class com.compomics.util.protein.AASequenceImpl
Simple setter for the sequence.
setSequence(AASequenceImpl) - Method in class com.compomics.util.protein.Protein
Simple setter for the sequence.
setSequenceMatchingParameters(SequenceMatchingParameters) - Method in class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
Sets the sequence matching preferences to use when mapping modifications on amino acid sequences.
setSequenceMatchingParameters(SequenceMatchingParameters) - Method in class com.compomics.util.parameters.identification.IdentificationParameters
Sets the sequence matching preferences.
setSequenceMatchingType(SequenceMatchingParameters.MatchingType) - Method in class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
Sets the sequence matching type.
setSerializationFolder(String) - Static method in class com.compomics.util.experiment.biology.enzymes.EnzymeFactory
Sets the folder where to save the factory.
setSerializationFolder(String) - Static method in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Sets the folder where the factory is saved.
setShortName(String) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Sets the short modification name.
setShowAllPeaks(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Set if all peaks or just the annotated ones are to be shown.
setShowForwardIonDeNovoTags(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Set if the automatic forward ion de novo tags are to be shown.
setShowLegend(boolean) - Method in class com.compomics.util.gui.VennDiagramPanel
Set if the legend is to be shown.
setShowPrecursorDetails(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set whether the precursor details are to be shown.
setShowResolution(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set whether the resolution is to be shown.
setShowRewindIonDeNovoTags(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Set if the automatic rewind ion de novo tags are to be shown.
setSimplifyGroups(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Sets whether the protein groups should be simplified based on the PeptideShaker confidence.
setSimplifyGroupsConfidence(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Sets whether the protein groups should be simplified based on the peptide confidence level.
setSimplifyGroupsEnzymaticity(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Sets whether the protein groups should be simplified based on the peptide enzymaticity.
setSimplifyGroupsEvidence(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Sets whether the protein groups should be simplified based on the Uniprot evidence level.
setSimplifyGroupsVariants(boolean) - Method in class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
Sets whether the protein groups should be simplified based on the peptide variant matching.
setSingleChargeWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets the window size for singly charged ions.
setSite(int) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Setter for the modification site, 1 is the first amino acid.
setSiteConfidence(int, int) - Method in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Sets the confidence level of a modification site.
setSkylinePath(String) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets the skyline path.
setSortPsmsOnRt(Boolean) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set if the PSMs are sorted on retention time, false sorts on PSM score.
setSource(CvTerm) - Method in class com.compomics.util.pride.prideobjects.Instrument
Set the instrument source.
setSourceFile(String) - Method in class com.compomics.util.io.ftp.FTP
This method allows to set the source for the file that is to be transferred.
setSparklineColor(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Setter for the sparkline color.
setSparklineColorDoubtful(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Setter for the doubtful sparkline color.
setSparklineColorFalsePositives(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Setter for the false positives sparkline color.
setSparklineColorNonValidated(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Setter for the non-validated sparkline color.
setSparklineColorNotFound(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Setter for the not found sparkline color.
setSparklineColorPossible(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Setter for the possible sparkline color.
setSpecificity(String, DigestionParameters.Specificity) - Method in class com.compomics.util.parameters.identification.search.DigestionParameters
Sets the expected specificity of the enzyme.
setSpectrum(String, String, Spectrum, double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Sets a new spectrum to annotate.
setSpectrumAnnotatedMirroredPeakColor(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the color to use for the annotated mirrored peaks.
setSpectrumAnnotatedPeakColor(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the color to use for the annotated peaks.
setSpectrumAnnotatedPeakWidth(float) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the width of the annotated peaks.
setSpectrumBackgroundPeakColor(Color) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the color to use for the background peaks.
setSpectrumBackgroundPeakWidth(float) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Set the width of the background peaks.
setSpectrumCharges(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the spectrum charges to search for.
setSpectrumCountingPreferences(SpectrumCountingParameters) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Sets the spectrum counting preferences.
setSpectrumFile(String) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Sets the spectrum file name.
setSpectrumFile(SpectrumFile) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
This method initializes a SpectrumPanel based on the spectrum information in the specified SpectrumFile.
setSpectrumFileId(String) - Method in class com.compomics.util.io.PklFile
 
setSpectrumFolder(File) - Method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets the last used spectrum folder.
setSpectrumMatchesKeys(long[]) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Sets the spectrum matches keys.
setSpectrumPeakColor(Color) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Set the default spectrum peak color.
setSpectrumProfileModeLineColor(Color) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
Set the default spectrum profile mode color.
setSpectrumTitle(String) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Sets the spectrum title.
setSqtOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the sqt output is to be created.
setStarred(boolean) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Star/Unstar a match.
setStart(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the start value.
setStartBlock(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Set the block start.
setStartProtein(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
Set the protein start.
setStoreSpectraFileName(String) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the name of the file where the binary spectra are to be stored.
setStpBias(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether the stP bias should be triggered
setString(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Sets the string to display in the progress bar.
setStringParameter(String, String) - Method in class com.compomics.util.experiment.ProjectParameters
 
setSubscriptAnnotationNumbers(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the numbers in the peak annotations are to be subscripted.
setTag(Tag, ModificationParameters, SequenceMatchingParameters, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
Sets a new tag to match.
setTag(Tag) - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
 
setTagAssumptionMap(HashMap<Integer, TreeMap<Double, ArrayList<TagAssumption>>>) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Sets the tag assumption map.
setTagLength(int) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets the tag length.
setTarget(Integer) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Sets the index of the amino acid of interest in the pattern.
setTargetDecoy(boolean) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Sets whether the FASTA file should be processed as target-decoy or only target.
setTargetDecoyFileNameSuffix(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaParameters
Set the target-decoy file name suffix.
setTargeted(int, ArrayList<Character>) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Sets the amino acids targeted at a given index.
setTaxonomy(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
Sets the taxonomy.
setTerminalMassShifts(double, double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Sets the terminal m/z shifts.
setTextOutput(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the text output is to be created.
setTheoreticalFragmentIonsSumOnly(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set if the theoretical fragment ions are calculated on the sum in the bin alone.
setTheoreticMass(double) - Method in class com.compomics.util.experiment.biology.ions.Ion
Sets a new theoretic mass.
setTicCutoffPercentage(double) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Set the TIC cutoff in percent.
setTicCutoffPercentage(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Set the TicCutoffPercentage.
setTiesResolution(SpectrumAnnotator.TiesResolution) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Sets the ties resolution method to use when multiple peaks can be assigned to an ion.
setTitle(String) - Method in class com.compomics.util.messages.FeedBack
Sets the title.
setTitle(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
Set the title.
setTitle(String) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to change the title (name) of the Enzyme.
setToolTips(Vector) - Method in class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
Set the tooltips.
setTopPeaks(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the top peaks number.
setTopPeaksWindow(int) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
Sets the top peaks window size.
setTotalIntensity(double) - Method in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Set the total intensity.
setTotalPartitions(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the total partitions.
setTotalPeptidesPerFraction(HashMap<String, Integer>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Set the total number of peptides per fraction.
setTotalSpectrumCounting(Double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the total spectrum counting.
setTotalSpectrumCountingMass(double) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the total spectrum counting value.
setTrimMs1Peaks(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether Ms1 peaks are to be trimmed.
setTrimMsMsPeaks(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether MsMs peaks are to be trimmed.
setType(MatchFilter.FilterType) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the type of the filter.
setType() - Method in class com.compomics.util.experiment.io.parameters.DummyParameters
 
setType() - Method in interface com.compomics.util.experiment.io.parameters.MarshallableParameter
Sets the parameters type.
setType(String) - Method in class com.compomics.util.experiment.patient.PatientInformation
Sets the type of information.
setType(FeedBack.FeedBackType) - Method in class com.compomics.util.messages.FeedBack
Sets the feedback type.
setType() - Method in class com.compomics.util.parameters.identification.IdentificationParameters
 
setType() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
 
setUnevenRowColor(Color) - Method in class com.compomics.util.AlternateRowColoursJTable
Sets the colour of the uneven numbered rows; by default, the default JTable background color will be used..
setUnimodCvTerm(CvTerm) - Method in class com.compomics.util.experiment.biology.modifications.Modification
Set the Unimod CV term associated with this modification.
setUnit(UnitOfMeasurement) - Method in class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Sets the unit used for normalization.
setUnstoppable(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Set this to true of the process the progress bar is used for is not possible to stop, or not possible to stop nicely.
setUpGUI(Frame, String) - Method in class com.compomics.software.settings.gui.PathParametersDialog
Sets up the GUI components.
setUpGUI() - Method in class com.compomics.util.gui.filtering.FilterDialog
Sets up the GUI components.
setUpperClearMzRange(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Set the upper mass value for the clear mz range.
setUpperPrecursorMass(int) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
Set the upper precursor mass.
setUpTable() - Method in class com.compomics.util.gui.filtering.FilterDialog
Updates the table content according to the selected filter.
setUpTable() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser
Updates the table content.
setUrParams(HashMap<Long, UrParameter>) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Sets the user parameters map.
setUseChargeStateFromMS(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
Sets whether the charge state from the spectrum should be used.
setUseCorrelationCorrectionScore(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
Sets whether the correlation correction score should be used.
setUseDeltaScore(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether delta score is to be used.
setUseFlankingPeaks(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if flanking peaks are to be used.
setUseGeneMapping(Boolean) - Method in class com.compomics.util.parameters.identification.advanced.GeneParameters
Sets whether gene mappings should be used.
setUseMassDeltaCombinations(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
If true, pairs of delta mass annotations are used when doing de novo sequencing.
setUseNeutralLossPeaks(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set if the neutral loss peaks are to be used.
setUseNoiseSuppression(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Sets whether noise suppression should be used when importing spectra.
setUseProvidedPrecursorInfo(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether the provided precursor info is to be used.
setUserAdvocates(HashMap<Integer, Advocate>) - Static method in class com.compomics.util.experiment.identification.Advocate
Returns the map of user advocates imported.
setUserParametersFolder(String) - Static method in class com.compomics.util.parameters.UtilitiesUserParameters
Sets the user preferences file to be used.
setUseSmartPlusThreeModel(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
Sets if the UseSmartPlusThreeModel is to be used.
setUseSparseMatrix(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
Deprecated.
from Comet release 2015.02 all searches use this internal data representation by default
setValidatedOnly(Boolean) - Method in class com.compomics.util.io.export.ExportScheme
Sets whether only validated results should be exported.
setValidatedPeptidesPerFraction(HashMap<String, Integer>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Get the number of validated peptides in the given fraction.
setValidatedProteinList(long[]) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
Sets the list of validated proteins.
setValidatedSpectraPepFraction(HashMap<String, Integer>) - Method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Get the number of validated spectra in the given fraction.
setValidatedTargetProteinKeys(long[]) - Method in class com.compomics.util.experiment.identification.peptide_shaker.Metrics
Sets the keys of the validated target protein matches.
setValidationQCParameters(ValidationQcParameters) - Method in class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
Sets the validation QC preferences.
setValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Sets the progress bar value.
setValue(String) - Method in class com.compomics.util.pride.CvTerm
Sets the value.
setValueAt(int, int, Double) - Method in class com.compomics.util.math.matrix.DoubleMatrix
 
setValueAt(Object, int, int) - Method in class com.compomics.util.sun.TableMap
 
setValueAt(Object, int, int) - Method in class com.compomics.util.sun.TableSorter
 
setValueForItem(String, Object) - Method in class com.compomics.util.experiment.identification.filtering.MatchFilter
Sets the value for a given item.
setVariableModifications(ModificationMatch[]) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
Sets the variable modifications.
setVariableModifications(ModificationMatch[]) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Sets the variable modifications.
setVariantMatches(HashMap<String, HashMap<Integer, PeptideVariantMatches>>) - Method in class com.compomics.util.experiment.biology.proteins.Peptide
Sets the sequence variant matches of this peptide.
setVatiantType(PeptideVariantsParameters.VariantType) - Method in class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
Sets whether the specific variant count limitations should be used.
setVerbosity(Integer) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
Set the verbosity type of progress output.
setVersion(String) - Method in class com.compomics.util.experiment.io.biology.protein.FastaSummary
Sets the database version.
setVisible(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setVisibleColumns(HashMap<Integer, Boolean>) - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
Sets the list of visible columns.
setVisibleColumns(HashMap<Integer, Boolean>) - Method in class com.compomics.util.gui.XYPlottingDialog
 
setWaitingText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setWaitingText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setWaitingText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setWaitingText(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
 
setWaitingText(String) - Method in interface com.compomics.util.waiting.WaitingHandler
Sets the text describing what is currently being waited for.
setWindowWidthThomsons(Double) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set the window width in Thomson.
setWorkbookStyle(WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter
Sets the workbook style.
setWriteMzId(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether mzId output is to be created.
setWritePepXml(Boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
Set whether pepXML output is to be created.
setX(double) - Method in class com.compomics.util.XYZDataPoint
Sets the x value.
setXAxisStartAtZero(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method sets the start value of the x-axis to zero.
setY(double) - Method in class com.compomics.util.XYZDataPoint
Sets the y value.
setYAxisZoomExcludesBackgroundPeaks(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Set if the automatic y-axis zoom only considers the annotated peaks.
setYAxisZoomExcludesBackgroundPeaks(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the automatic y-axis zoom only considers the annotated peaks.
setYDataIsPositive(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set to true of all y data values can be assumed to be positive.
setZ(double) - Method in class com.compomics.util.XYZDataPoint
Sets the z value.
shortName - Variable in enum com.compomics.util.experiment.biology.modifications.ModificationType
The short name of the type.
showAllPeaks() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
If true, all peaks are shown, false displays the annotated peaks, and the non-annotated in the background.
showAllPeaks - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If false, only the annotated peaks will be shown.
showAnnotatedPeaksOnly(boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
If true only the annotated peaks will be drawn.
showFileName - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The boolean is set to 'true' if the file name is to be shown in the panel.
showForwardIonDeNovoTags() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns true if the automatic forward ion de novo tags are to be shown.
showLegend() - Method in class com.compomics.util.gui.VennDiagramPanel
Show the legend or not.
showPrecursorDetails - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The boolean is set to 'true' if the precursor details is to be shown in the panel.
showPrecursorDetails() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true of the precursor details are to be shown.
showResolution - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The boolean is set to 'true' if the resolution is to be shown in the panel.
showResolution() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true if the resolution is to be shown.
showRewindIonDeNovoTags() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns true if the automatic rewind ion de novo tags are to be shown.
shuttlesort(int[], int[], int, int) - Method in class com.compomics.util.sun.TableSorter
 
signalStop() - Method in class com.compomics.util.io.file.FolderMonitor
This method can be used to signal the monitor to halt its monitoring.
SIMPLE_DATA_FORMAT - Static variable in interface com.compomics.util.waiting.WaitingHandler
Convenience date format.
SimpleFileReader - Interface in com.compomics.util.io.flat
Interface for file readers.
SimpleFileWriter - Class in com.compomics.util.io.flat
Simple gz file writer that is thread safe and throws exceptions as runtime exceptions.
SimpleFileWriter(File, boolean) - Constructor for class com.compomics.util.io.flat.SimpleFileWriter
Constructor.
SimpleGzReader - Class in com.compomics.util.io.flat.readers
Simple wrapper for a gz file reader.
SimpleGzReader(File) - Constructor for class com.compomics.util.io.flat.readers.SimpleGzReader
Constructor.
SimpleLinearRegression - Class in com.compomics.util.math.statistics.linear_regression.regressions
Performs a simple linear regression.
SimpleLinearRegression() - Constructor for class com.compomics.util.math.statistics.linear_regression.regressions.SimpleLinearRegression
Empty default constructor
SimpleMzIdentMLExporter - Class in com.compomics.util.experiment.io.identification.writers
Simple mzIdentML exporter for PSM-level results.
SimpleMzIdentMLExporter(String, String, String, File, File, ArrayList<File>, File, HashMap<String, ArrayList<String>>, File, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, ModificationProvider, FastaSummary, String, String, String, String, String, String, String, boolean) - Constructor for class com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter
Constructor.
SimpleNoiseDistribution - Class in com.compomics.util.experiment.mass_spectrometry
This class makes a simple modeling of the noise using a normal distribution on the log of the peak intensities and returns the associated binned cumulative probability for a given intensity.
SimpleNoiseDistribution() - Constructor for class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
Empty default constructor
SimpleNoiseDistribution(double[]) - Constructor for class com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
Constructor.
SimplePeptideAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
A simple annotator for peptides.
SimplePeptideAnnotator(Peptide, String[], int, AnnotationParameters) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
Constructor.
SimplePeptideAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
Empty default constructor
SimplePeptideAnnotator(Peptide, String[], int, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, ReporterIon[]) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
Constructor.
SimplePeptideAnnotator.IonSeries - Enum in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
The type of ion series to annotate.
SimpleSemaphore - Class in com.compomics.util.threading
A simple semaphore where thread interrupted exception are thrown as runtime exception.
SimpleSemaphore(int, boolean) - Constructor for class com.compomics.util.threading.SimpleSemaphore
Constructor.
SimpleSemaphore(int) - Constructor for class com.compomics.util.threading.SimpleSemaphore
Constructor.
SimpleTextReader - Class in com.compomics.util.io.flat.readers
Simple wrapper for a flat file reader.
SimpleTextReader(File) - Constructor for class com.compomics.util.io.flat.readers.SimpleTextReader
Constructor.
SimpleXmlWriter - Class in com.compomics.util.io.export.xml
Simple writer for xml files.
SimpleXmlWriter() - Constructor for class com.compomics.util.io.export.xml.SimpleXmlWriter
Empty default constructor
SimpleXmlWriter(BufferedWriter) - Constructor for class com.compomics.util.io.export.xml.SimpleXmlWriter
Constructor.
SINGLE_AA_SUFFIX - Static variable in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Suffix for the modification clone targeting a single amino acid instead of a pattern.
SingleAAPropertyFeature - Interface in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
Interface for the ms2pip features having a single amino acid property.
singleBaseSubstitution - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Substitution matrix allowing for a single base substitution.
singleLetterCode - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Single letter code of the amino acid.
SingleProteinSequenceProvider - Class in com.compomics.util.experiment.identification.protein_sequences
Sequence provider for a single protein.
SingleProteinSequenceProvider() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
Empty default constructor.
SingleProteinSequenceProvider(Protein) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider
Constructor.
singleRangeQuery(int, int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Returns a new left/right index range for a given character recursively.
site(String) - Method in class com.compomics.util.io.ftp.FTP
Site Command
size() - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
Returns the number of atoms in this atom chain.
skip(long) - Method in class com.compomics.util.io.file.MonitorableFileInputStream
Skips over and discards n bytes of data from the input stream.
skip(long) - Method in class com.compomics.util.io.file.MonitorableInputStream
Skips over and discards n bytes of data from the input stream.
SNPElement - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
 
SNPElement(int, char, char) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement
 
SnrScore - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores
This score uses the intensity distribution of the peaks to evaluate an SNR score.
SnrScore() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
Constructor.
Sodium - Class in com.compomics.util.experiment.biology.atoms.impl
The sodium atom.
Sodium() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Sodium
Constructor.
sonar - Static variable in class com.compomics.util.experiment.identification.Advocate
The Sonar search engine, integrated in radars.
sort(int, ProgressDialogX) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
Sorts the table according to a given column using the built in sorter.
sort(Object) - Method in class com.compomics.util.sun.TableSorter
 
sortByColumn(int) - Method in class com.compomics.util.sun.TableSorter
 
sortByColumn(int, boolean) - Method in class com.compomics.util.sun.TableSorter
 
sourceAA - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement
 
SparklineColorsDialog - Class in com.compomics.util.gui.parameters
Dialog for user selection of the colors used by the sparklines.
SparklineColorsDialog(JFrame, UtilitiesUserParameters) - Constructor for class com.compomics.util.gui.parameters.SparklineColorsDialog
Creates a new SparklineColorsDialog.
SparklineColorsDialog(JDialog, UtilitiesUserParameters) - Constructor for class com.compomics.util.gui.parameters.SparklineColorsDialog
Creates a new SparklineColorsDialog.
SPECIES_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for the species.
SPECIES_TYPE_OPTION - Static variable in class com.compomics.software.ToolFactory
The command line argument for the species type.
SpeciesDialog - Class in com.compomics.util.gui.genes
Deprecated.
use the GenePreferencesDialog instead
SpeciesDialog(Frame, boolean, Image, Image, Integer) - Constructor for class com.compomics.util.gui.genes.SpeciesDialog
Deprecated.
Creates a new SpeciesDialog.
SpeciesDialog(JDialog, JFrame, boolean, Image, Image, Integer) - Constructor for class com.compomics.util.gui.genes.SpeciesDialog
Deprecated.
Creates a new SpeciesDialog.
SpeciesFactory - Class in com.compomics.util.experiment.biology.taxonomy
Class related to the handling of species.
speciesOccurrence - Variable in class com.compomics.util.experiment.io.biology.protein.FastaSummary
The species occurrence in the FASTA file.
SpecificAnnotationParameters - Class in com.compomics.util.experiment.identification.spectrum_annotation
The spectrum annotation preferences specific to a spectrum and an identification assumption.
SpecificAnnotationParameters() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
Empty default constructor
specificAnnotationSettings - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
If provided, the annotator will only look for the ions included in the specific annotation settings.
SpecificSingleEnzymeCombinationIterator - Class in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
Iterator for enzymatic digestion.
SpecificSingleEnzymeCombinationIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeCombinationIterator
Empty default constructor
SpecificSingleEnzymeCombinationIterator(ProteinIteratorUtils, String, Enzyme, int, double, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeCombinationIterator
Constructor.
SpecificSingleEnzymeIterator - Class in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
Iterator for enzymatic digestion.
SpecificSingleEnzymeIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeIterator
Empty default constructor
SpecificSingleEnzymeIterator(ProteinIteratorUtils, String, Enzyme, int, double, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeIterator
Constructor.
spectraST - Static variable in class com.compomics.util.experiment.identification.Advocate
The SpectraST spectral library search engine (TPP).
spectraTag - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
Tag for the spectrum file.
Spectrum - Class in com.compomics.util.experiment.mass_spectrometry.spectra
This class models a spectrum.
Spectrum() - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Empty default constructor.
Spectrum(Precursor, double[], double[]) - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
Constructor.
SpectrumAnnotation - Interface in com.compomics.util.gui.interfaces
This interface describes the behaviour for a spectrum annotation.
SpectrumAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation
The spectrum annotator annotates peaks in a spectrum.
SpectrumAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Empty default constructor
SpectrumAnnotator.TiesResolution - Enum in com.compomics.util.experiment.identification.spectrum_annotation
Enum of the possibilities for ties resolution when multiple peaks can be annotated.
spectrumCountingInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether the default spectrum counting value is in cache for a protein match.
SpectrumCountingMethod - Enum in com.compomics.util.experiment.quantification.spectrumcounting
Enum of the implemented spectrum counting methods.
SpectrumCountingParameters - Class in com.compomics.util.parameters.quantification.spectrum_counting
This class contains the spectrum counting parameters.
SpectrumCountingParameters() - Constructor for class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Default constructor.
SpectrumCountingParameters(SpectrumCountingParameters) - Constructor for class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Creates new preferences based on other spectrum counting preferences.
spectrumFile - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The file of the currently loaded spectrum.
SpectrumFile - Interface in com.compomics.util.interfaces
This interface describes the behaviour for a spectrum file (ie., PKL file, Mascot Generic file, dat file, ...).
spectrumIdentification - Variable in class com.compomics.util.experiment.identification.IdentificationKeys
Map mapping spectra per file.
SpectrumIdentificationAssumption - Class in com.compomics.util.experiment.identification
Spectrum identification assumption made by an identification algorithm.
SpectrumIdentificationAssumption() - Constructor for class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
Empty default constructor.
SpectrumIndex - Class in com.compomics.util.experiment.mass_spectrometry.indexes
This map stores the fragment ions indexed by mass.
SpectrumIndex() - Constructor for class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Constructor for an empty index.
SpectrumIndex(double[], double[], double, double, boolean) - Constructor for class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
Builds a new index.
SpectrumMatch - Class in com.compomics.util.experiment.identification.matches
This class models a spectrum match.
SpectrumMatch() - Constructor for class com.compomics.util.experiment.identification.matches.SpectrumMatch
Constructor for the spectrum match.
SpectrumMatch(String, String) - Constructor for class com.compomics.util.experiment.identification.matches.SpectrumMatch
Constructor for the spectrum match.
SpectrumMatchesIterator - Class in com.compomics.util.experiment.identification.matches_iterators
An iterator for spectrum matches.
SpectrumMatchesIterator() - Constructor for class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
Empty default constructor
SpectrumMatchesIterator(Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
Constructor.
SpectrumMatchesIterator(long[], Identification, WaitingHandler, boolean) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
Constructor.
SpectrumMatchesIterator(long[], Identification, WaitingHandler, boolean, String) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
Constructor.
spectrumMill - Static variable in class com.compomics.util.experiment.identification.Advocate
The Spectrum Mill search engine, Agilent.
SpectrumPanel - Class in com.compomics.util.gui.spectrum
This class presents a JPanel that will hold and display a mass spectrum in centroid or profile mode.
SpectrumPanel(SpectrumFile) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile as an interactive lines plot.
SpectrumPanel(SpectrumFile, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile as a line plot.
SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
SpectrumPanel() - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
Empty default constructor
SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color, int, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color, int, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color, int, boolean, boolean, boolean, int) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
SpectrumPanel(SpectrumFile, GraphicsPanel.DrawingStyle, boolean, Color, int, boolean, boolean, boolean, int, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
SpectrumPanel(double[], double[], double, String, String) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the passed parameters.
SpectrumPanel(double[], double[], double, String, String, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the passed parameters.
SpectrumPanel(double[], double[], double, String, String, int, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the passed parameters.
SpectrumPanel(double[], double[], double, String, String, int, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the passed parameters.
SpectrumPanel(double[], double[], double, String, String, int, boolean, boolean, boolean, int) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the passed parameters.
SpectrumPanel(double[], double[], double, String, String, int, boolean, boolean, boolean, int, boolean) - Constructor for class com.compomics.util.gui.spectrum.SpectrumPanel
This constructor creates a SpectrumPanel based on the passed parameters.
SpectrumPanelListener - Interface in com.compomics.util.gui.interfaces
This interface describes the behaviour for a listener that wants to receive information about events that occurred on a SpectrumPanel.
SpectrumProvider - Interface in com.compomics.util.experiment.mass_spectrometry
Interface for objects providing spectra.
spectrumTitle - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The title of the currently loaded spectrum.
spectrumTitle - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap.PrecursorWithTitle
The spectrum title
SpectrumUtil - Class in com.compomics.util.experiment.mass_spectrometry.spectra
Utilities functions to handle spectra.
SpectrumUtil() - Constructor for class com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
 
SplashScreen - Class in com.compomics.software
Class that takes care of converting an svg file to a png file using the command line version of apache batik.
SplashScreen(String[]) - Constructor for class com.compomics.software.SplashScreen
Constructor.
splitFile(File, int, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
Splits an mgf file into smaller ones and returns the indexes of the generated files.
splitInput(String) - Static method in class com.compomics.software.cli.CommandLineUtils
Splits the input of comma separated command line input and returns the results as an arraylist.
spo - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
SPO - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
sqid - Static variable in class com.compomics.util.experiment.identification.Advocate
The SeQuence IDentfication (SQID) search engine.
standardGeneticCode - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
The standard genetic code.
StandardMasses - Enum in com.compomics.util.experiment.mass_spectrometry.utils
Enum of standard masses.
StandardUnit - Enum in com.compomics.util.experiment.units
The standard units implemented.
start(String) - Static method in class com.compomics.util.io.StartBrowser
Opens the given URL in the default browser.
start() - Method in class com.compomics.util.sun.SwingWorker
Start the worker thread.
start() - Method in class com.compomics.util.waiting.Duration
Sets the start time to the system current time in milliseconds.
StartBrowser - Class in com.compomics.util.io
This class starts a browser for the given URL.
StartBrowser() - Constructor for class com.compomics.util.io.StartBrowser
Empty constructor.
StartEndPosition - Class in com.compomics.util.pdbfinder.das.readers
StartEndPosition.
StartEndPosition() - Constructor for class com.compomics.util.pdbfinder.das.readers.StartEndPosition
Empty default constructor
StartEndPosition(int, int) - Constructor for class com.compomics.util.pdbfinder.das.readers.StartEndPosition
Constructor.
startGenerator(String, String, String, String) - Method in class com.compomics.util.db.DBAccessorGenerator
This method starts the generator for the specified parameters.
startGenerator(String, String, String, String, String, String, boolean) - Method in class com.compomics.util.db.DBAccessorGenerator
This method starts the generator for the specified parameters.
startNewSection() - Method in class com.compomics.util.io.export.ExportWriter
Starts a new section.
startNewSection(String) - Method in class com.compomics.util.io.export.ExportWriter
Starts a new section.
startNewSection(String, WorkbookStyle) - Method in class com.compomics.util.io.export.ExportWriter
Starts a new section.
startNewSection(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
startNewSection(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.TextWriter
 
startPeptideShaker(JFrame) - Static method in class com.compomics.software.ToolFactory
Starts PeptideShaker from the location of utilities preferences.
startPeptideShaker(JFrame, File) - Static method in class com.compomics.software.ToolFactory
Starts PeptideShaker from the location of utilities preferences and opens the file given as argument.
startPeptideShakerFromURL(JFrame, String, String) - Static method in class com.compomics.software.ToolFactory
Starts PeptideShaker from the location of utilities preferences and opens the file given as argument.
startReporter(JFrame) - Static method in class com.compomics.software.ToolFactory
Starts Reporter from the location of utilities preferences.
startReshake(JFrame, String) - Static method in class com.compomics.software.ToolFactory
Starts PeptideShaker from the location of utilities preferences in the Reshake mode and attempts at selecting the given project.
startSearchGUI(JFrame) - Static method in class com.compomics.software.ToolFactory
Starts SearchGUI from the location of utilities preferences.
startSearchGUI(JFrame, ArrayList<File>, ArrayList<File>, File, File, File, String, String, String) - Static method in class com.compomics.software.ToolFactory
Starts SearchGUI from the location of utilities preferences.
startShake() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Make the dialog shake when the process has completed.
std(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Convenience method returning the standard deviation of a list of doubles.
StreamGobbler - Class in com.compomics.util.io
A stream gobbler.
StreamGobbler() - Constructor for class com.compomics.util.io.StreamGobbler
Empty default constructor
StreamGobbler(InputStream) - Constructor for class com.compomics.util.io.StreamGobbler
Constructor.
StreamUtil - Class in com.compomics.util
Convenience methods to work with lambdas.
StreamUtil() - Constructor for class com.compomics.util.StreamUtil
 
strFileNameAndPath - Variable in class com.compomics.util.io.ftp.FTP
String to hold the file we are up/downloading
StringListChooser - Class in com.compomics.util.gui.utils.user_choice.list_choosers
Dialog for choosing an item in a list of String.
StringListChooser() - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
Empty default constructor
StringListChooser(Frame, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
Constructor.
StringListChooser(JDialog, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
Constructor.
subAminoAcidsWithCombination - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
The sub amino acids with combination.
subAminoAcidsWithoutCombination - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
The sub amino acids without combination.
Substitution - Class in com.compomics.util.experiment.biology.variants.amino_acids
Class representing an amino acid substitution.
Substitution() - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
Empty default constructor
Substitution(char, char) - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Substitution
Constructor.
SUBTRACT_ISOTOPE - Static variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Minimal isotopic correction when matching an ion.
suffixCharacter(String, int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Forward propagation of the BWT to get the n'th consecutive character
Sulfur - Class in com.compomics.util.experiment.biology.atoms.impl
The sulfur atom.
Sulfur() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Sulfur
Constructor.
sum(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Convenience method returning the sum of a list of doubles.
supportedVersion(File) - Static method in class com.compomics.util.parameters.identification.IdentificationParameters
Returns a boolean indicating whether the version of the parameters file is supported.
svg - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
SVG - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
SvgFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.svg files.
SvgFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.SvgFileFilter
Empty default constructor
Swap - Class in com.compomics.util.experiment.biology.variants.amino_acids
Class representing an amino acid swap.
Swap() - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Swap
Empty default constructor
Swap(char, char) - Constructor for class com.compomics.util.experiment.biology.variants.amino_acids.Swap
Constructor.
swap(int, int) - Method in class com.compomics.util.sun.TableSorter
 
swapRows(int, int) - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
Swap two rows in the pattern.
SwingUtils - Class in com.compomics.util.gui.utils
Swing utilities methods.
SwingUtils() - Constructor for class com.compomics.util.gui.utils.SwingUtils
Empty default constructor
SwingWorker - Class in com.compomics.util.sun
This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class com.compomics.util.sun.SwingWorker
Start a thread that will call the construct method and then exit.
SYMBOL - Variable in enum com.compomics.util.experiment.units.MetricsPrefix
The prefix symbol.
synonymousVariant - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Substitution matrix grouping synonymous amino acids.
syst() - Method in class com.compomics.util.io.ftp.FTP
Retrieve the system type from the remote server.

T

T - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
TAB_HTML - Static variable in interface com.compomics.util.waiting.WaitingHandler
The tab space to add when using HTML.
TAB_NON_HTML - Static variable in interface com.compomics.util.waiting.WaitingHandler
The tab space to add when not using HTML.
tableChanged(TableModelEvent) - Method in class com.compomics.util.sun.TableMap
 
tableChanged(TableModelEvent) - Method in class com.compomics.util.sun.TableSorter
 
TableMap - Class in com.compomics.util.sun
In a chain of data manipulators some behaviour is common.
TableMap() - Constructor for class com.compomics.util.sun.TableMap
Empty default constructor
TableMouseWheelListener - Class in com.compomics.util.gui
MouseWheelListener for SelfUpdatingTableModels that supports scrolling in a more efficient way.
TableMouseWheelListener(JTable) - Constructor for class com.compomics.util.gui.TableMouseWheelListener
Constructor.
TableProperties - Class in com.compomics.util.gui
This class groups properties for the tables
TableProperties() - Constructor for class com.compomics.util.gui.TableProperties
 
TableScrollBarListener - Class in com.compomics.util.gui
AdjustmentListener for SelfUpdatingTableModels supporting scrolling in a more efficient way.
TableScrollBarListener(JTable) - Constructor for class com.compomics.util.gui.TableScrollBarListener
Constructor.
TableSorter - Class in com.compomics.util.sun
A sorter for TableModels.
TableSorter() - Constructor for class com.compomics.util.sun.TableSorter
 
TableSorter(TableModel) - Constructor for class com.compomics.util.sun.TableSorter
 
tableToFile(JTable, String, ProgressDialogX, boolean, BufferedWriter) - Static method in class com.compomics.util.Util
Writes the table to a file as separated text.
tableToText(JTable, String, ProgressDialogX, boolean) - Static method in class com.compomics.util.Util
Returns the table as a separated text file.
TableValueWrapper - Interface in com.compomics.util.interfaces
This interface describes the behaviour for a class that wraps a table element.
Tag - Class in com.compomics.util.experiment.identification.amino_acid_tags
This class represents a sequence mass tag.
Tag() - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Constructor for an empty tag.
Tag(Tag) - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Creates a new tag instance based on the given one.
Tag(double, AminoAcidSequence, double) - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.Tag
Constructor for a tag consisting of a sequence tag between two mass tags.
TagAssumption - Class in com.compomics.util.experiment.identification.spectrum_assumptions
This class represent a tag assumption made by an identification algorithm based on a sequence tag.
TagAssumption() - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
Constructor for en empty assumption.
TagAssumption(int, int, Tag, int, double, double) - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
Constructor.Note: if PsmScores.scoreRoundingDecimal is not null the scored will be floored accordingly.
TagComponent - Interface in com.compomics.util.experiment.identification.amino_acid_tags
Interface for a sequence tag component.
tagComponent - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Information about the component where the X belongs to.
TagElement - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
The tag element.
TagFactory - Class in com.compomics.util.experiment.identification
Convenience class for sequence tag generation.
TagFactory() - Constructor for class com.compomics.util.experiment.identification.TagFactory
Empty default constructor
TagFragmentIon - Class in com.compomics.util.experiment.biology.ions.impl
A fragment ion obtained from a tag.
TagFragmentIon() - Constructor for class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Empty default constructor
TagFragmentIon(int, int, int, double, NeutralLoss[], double) - Constructor for class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Constructor.
TagFragmentIon(int, NeutralLoss[]) - Constructor for class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Constructor for a generic ion.
TagFragmentIon(int) - Constructor for class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Constructor for a generic ion without neutral losses.
TagSpectrumAnnotator - Class in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
Annotates a spectrum with information from a tag.
TagSpectrumAnnotator() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
Empty default constructor
tagToString(Tag) - Static method in class com.compomics.cli.peptide_mapper.PeptideMapperCLI
 
TagUtils - Class in com.compomics.util.experiment.identification.utils
This class groups functions that can be used to work with peptides.
TagUtils() - Constructor for class com.compomics.util.experiment.identification.utils.TagUtils
Empty default constructor
tarFolder(File, File, WaitingHandler) - Static method in class com.compomics.util.io.compression.TarUtils
Tar a given folder to a file.
tarFolderContent(File, File, HashSet<String>, WaitingHandler) - Static method in class com.compomics.util.io.compression.TarUtils
Tar the content of a given folder to a file.
targetAA - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement
 
TarUtils - Class in com.compomics.util.io.compression
This class contains convenience methods for taring files.
TarUtils() - Constructor for class com.compomics.util.io.compression.TarUtils
Empty default constructor
TempByteArray - Class in com.compomics.util
Convenience class for storing an array buffer and a length.
TempByteArray(byte[], int) - Constructor for class com.compomics.util.TempByteArray
Constructor.
TempFilesManager - Class in com.compomics.util.experiment.io.temp
This class can be used to reference temp files and manage them.
TempFilesManager() - Constructor for class com.compomics.util.experiment.io.temp.TempFilesManager
 
TestCaseLM - Class in com.compomics.util.junit
This TestCase extension contains some useful methods for loading Properties files from the classpath and getting general files' full name or an InputStream from the classpath.
testFTPConnection() - Method in class com.compomics.util.io.ftp.FTPClient
This method can be used to test the connection with the FTP server.
testPath(String) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Tests whether it is possible to write in a destination folder.
TEXTMODE - Static variable in class com.compomics.util.io.file.FolderMonitor
 
TextWriter - Class in com.compomics.util.io.export.writers
ExportWriter for the export to text files.
TextWriter() - Constructor for class com.compomics.util.io.export.writers.TextWriter
Empty default constructor
TextWriter(File, String, int, boolean) - Constructor for class com.compomics.util.io.export.writers.TextWriter
Constructor.
theoreticalFragmentIons - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The theoretic fragment ions.
theoreticMass - Variable in class com.compomics.util.experiment.biology.ions.Ion
Deprecated.
use the double value instead.
theoreticMass1 - Variable in class com.compomics.util.experiment.biology.ions.Ion
The theoretic mass.
ThermoRawFileParserOutputFormat - Enum in com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser
The mass spectrometry output formats supported by ThermoRawFileParser.
ThermoRawFileParserParameters - Class in com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser
The parameters to use when running ThermoRawFileParser.
ThermoRawFileParserParameters() - Constructor for class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
Constructor.
ThermoRawFileParserParametersDialog - Class in com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui
Dialog for the creation and edition of ThermoRawFileParser parameters.
ThermoRawFileParserParametersDialog(Frame, ThermoRawFileParserParameters) - Constructor for class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui.ThermoRawFileParserParametersDialog
Constructor.
ThermoRawFileParserParametersDialog(Dialog, ThermoRawFileParserParameters) - Constructor for class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui.ThermoRawFileParserParametersDialog
Constructor.
thousand - Static variable in class com.compomics.util.math.BigMathUtils
Big decimal value of 1000.
threeLetterCode - Variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
Three letter code of the amino acid.
Threonine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Threonine.
Threonine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Threonine
Constructor.
THREONINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Threonine immonium ion.
tide - Static variable in class com.compomics.util.experiment.identification.Advocate
The Tide search engine.
TideIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This IdfileReader reads identifications from an Tide tsv results file.
TideIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
Default constructor for the purpose of instantiation.
TideIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
Constructor for a Tide tsv results file reader.
TideIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader
Constructor for an Tide tsv result file reader.
TideParameters - Class in com.compomics.util.parameters.identification.tool_specific
The Tide specific parameters.
TideParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.TideParameters
Constructor.
TideParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the Tide specific settings.
TideParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
Empty default constructor
TideParametersDialog(Frame, TideParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
Creates a new TideSettingsDialog with a frame as owner.
TideParametersDialog(Dialog, Frame, TideParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
Creates a new TideSettingsDialog with a dialog as owner.
tiesResolution - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
The methods to use to select the best peak when multiple are possible.
tiff - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
TIFF - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
TiffFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.tiff files.
TiffFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.TiffFileFilter
Empty default constructor
TIMEOUT_DAYS - Static variable in class com.compomics.cli.peptide_mapper.PeptideMapperCLI
 
TimestampRenderer - Class in com.compomics.util.gui.renderers
TimestampRenderer.
TimestampRenderer() - Constructor for class com.compomics.util.gui.renderers.TimestampRenderer
Empty default constructor
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
The title of the feature which will be used for column heading.
title - Variable in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
The title of the feature which will be used for column heading.
TITLE_SEPARATOR - Static variable in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileUtils
The separator to use when concatenating spectrum titles in a string.
TITLED_BORDER_HORIZONTAL_PADDING - Static variable in class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
The horizontal padding used before and after the text in the titled borders.
titles - Variable in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
The titles of the spectra.
TMT_126 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 126.
TMT_126_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 126 with ETD fragmentation.
TMT_127C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 127C.
TMT_127C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 127C with ETD fragmentation.
TMT_127N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 127N.
TMT_127N_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 127N with ETD fragmentation.
TMT_128C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 128C.
TMT_128C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 128C with ETD fragmentation.
TMT_128N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 128N.
TMT_128N_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 128N with ETD fragmentation.
TMT_129C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 129C.
TMT_129C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 129C with ETD fragmentation.
TMT_129N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 129N.
TMT_129N_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 129N with ETD fragmentation.
TMT_130C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 130C.
TMT_130C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 130C with ETD fragmentation.
TMT_130N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 130N.
TMT_130N_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 130N with ETD fragmentation.
TMT_131 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 131.
TMT_131_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 131 with ETD fragmentation.
TMT_131C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 131C.
TMT_131C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT 131C with ETD fragmentation.
TMT_226 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT (reporter + balancer).
TMT_230 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMT (reporter + balancer).
TMTpro_126 - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-126.
TMTpro_127C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-127C.
TMTpro_127N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-127N.
TMTpro_128C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-128C.
TMTpro_128N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-128N.
TMTpro_129C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-129C.
TMTpro_129N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-129N.
TMTpro_130C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-130C.
TMTpro_130N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-130N.
TMTpro_131C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-131C.
TMTpro_131N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-131N.
TMTpro_132C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-132C.
TMTpro_132N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-132N.
TMTpro_133C - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-133C.
TMTpro_133N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-133N.
TMTpro_134N - Static variable in class com.compomics.util.experiment.biology.ions.impl.ReporterIon
Standard reporter ion TMTpro-134N.
toJson(Object) - Method in class com.compomics.util.io.json.JsonMarshaller
Convert an object to JSON.
tolerance - Variable in class com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
The mass tolerance.
ToolFactory - Class in com.compomics.software
This class can be used to start compomics tools.
ToolFactory() - Constructor for class com.compomics.software.ToolFactory
 
ToolTipComboBoxRenderer - Class in com.compomics.util.gui.renderers
A combo box renderer that allows tooltip for each element in the combo box list.
ToolTipComboBoxRenderer() - Constructor for class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
Empty default constructor
ToolTipComboBoxRenderer(Vector, int) - Constructor for class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
Creates a new instance of the MyComboBoxRenderer.
ToolTipComboBoxRenderer(Vector, int, Color) - Constructor for class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
Creates a new instance of the MyComboBoxRenderer.
toString() - Method in class com.compomics.cli.enzymes.EnzymesCLI
 
toString() - Method in class com.compomics.cli.modifications.ModificationsCLI
 
toString() - Method in class com.compomics.cli.paths.PathSettingsCLI
 
toString() - Method in class com.compomics.util.BinaryArrayImpl
Returns a useful String representation of this Imlplementation instance that includes details of all fields.
toString() - Method in class com.compomics.util.db.components.Constructors
This method outputs the generated code in String format.
toString() - Method in class com.compomics.util.db.components.DeleteableCode
This method will report on the generated code.
toString() - Method in class com.compomics.util.db.components.GettersAndSetters
This method generates the code for the getters and setters.
toString() - Method in class com.compomics.util.db.components.InstanceVariables
This method generates the code for the instance variables.
toString() - Method in class com.compomics.util.db.components.PersistableCode
This method will report on the generated code.
toString() - Method in class com.compomics.util.db.components.RetrievableCode
This method will report on the generated code.
toString() - Method in class com.compomics.util.db.components.UpdateableCode
This method will report on the generated code.
toString() - Method in class com.compomics.util.db.DBAccessor
This method returns the generated code as a String.
toString() - Method in class com.compomics.util.db.DBMetaData
This method presents a String representation for this object.
toString() - Method in exception com.compomics.util.db.GeneratorException
This method returns a String with the description for this exception.
toString() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
 
toString() - Method in class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence
 
toString() - Method in class com.compomics.util.experiment.biology.atoms.Atom
 
toString() - Method in class com.compomics.util.experiment.biology.atoms.AtomChain
 
toString() - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
 
toString(boolean) - Method in class com.compomics.util.experiment.biology.atoms.AtomImpl
Returns the atom as a string.
toString(int) - Static method in class com.compomics.util.experiment.biology.ions.Charge
Returns a string representing the charge.
toString() - Method in class com.compomics.util.experiment.biology.modifications.Modification
 
toString() - Method in enum com.compomics.util.experiment.biology.modifications.ModificationCategory
 
toString() - Method in enum com.compomics.util.experiment.biology.modifications.ModificationType
 
toString() - Method in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
 
toString() - Method in enum com.compomics.util.experiment.filtering.FilterItemComparator
 
toString() - Method in class com.compomics.util.experiment.identification.Advocate
 
toString() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag
 
toString() - Method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
 
toString() - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.TagElement
Creating String output.
toString() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
 
toString() - Method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
 
toString() - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method reports on the entire processed(!) header.
toString(String) - Method in class com.compomics.util.experiment.io.biology.protein.Header
This method reports on the entire processed(!) header, with the given decoy tag added.
toString() - Method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
 
toString() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Peak
 
toString() - Method in class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
 
toString() - Method in enum com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
 
toString() - Method in enum com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCountingMethod
 
toString() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
 
toString() - Method in class com.compomics.util.general.IsotopicElement
To string method
toString(boolean) - Method in interface com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter
Returns the parameters as a string.
toString() - Method in interface com.compomics.util.interfaces.Modification
This method returns a String representation of the Modification.
toString() - Method in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
 
toString() - Method in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
 
toString() - Method in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
 
toString() - Method in enum com.compomics.util.parameters.identification.search.SearchParameters.MassAccuracyType
 
toString() - Method in class com.compomics.util.parameters.identification.search.SearchParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.search.SearchParameters
Returns the search parameters as a string.
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.CometParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MsgfParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.NovorParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.OmssaParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.PNovoParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.TideParameters
 
toString(boolean) - Method in class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
 
toString() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
toString() - Method in class com.compomics.util.protein.DualEnzyme
This method generates a String representation of the DualEnzyme, which is useful for displaying as useful information for the user or during testing/debugging.
toString(String) - Method in class com.compomics.util.protein.DualEnzyme
This method generates a String representation of the DualEnzyme, which is useful for displaying as useful information for the user or during testing/debugging.
toString() - Method in class com.compomics.util.protein.Enzyme
This method generates a String representation of the Enzyme, which is useful for displaying as useful information for the user or during testing/debugging.
toString(String) - Method in class com.compomics.util.protein.Enzyme
This method generates a String representation of the Enzyme, which is useful for displaying as useful information for the user or during testing/debugging.
toString() - Method in class com.compomics.util.protein.ModificationImplementation
This method returns a String representation of the Modification.
toString() - Method in class com.compomics.util.protein.ModificationTemplate
This method returns a String representation of the Modification.
toString() - Method in class com.compomics.util.protein.MolecularFormula
To string method
toString() - Method in class com.compomics.util.protein.RegExEnzyme
 
toString(String) - Method in class com.compomics.util.protein.RegExEnzyme
 
toString() - Method in class com.compomics.util.waiting.Duration
 
transformScore(double) - Static method in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Returns a score from a raw score where the score = -10*log(rawScore).
transitionsSingleBaseSubstitution - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Substitution matrix allowing for a single base transition variant.
Translate - Class in com.compomics.util.general
This class allows the user to translate a DNA sequence into 6 reading frames.
Translate() - Constructor for class com.compomics.util.general.Translate
 
translate() - Method in class com.compomics.util.nucleotide.NucleotideSequence
This method translates the nucleotide sequence in six reading frames.
translate() - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
This method translates the specified nucleotidesequence into the six reading frames.
translateToStopCodonSeparatedEntries(String, String) - Method in class com.compomics.util.nucleotide.NucleotideSequenceImpl
This method translates the specified nucleotidesequence into the six reading frames.
transpose(DoubleMatrix) - Static method in class com.compomics.util.math.matrix.DoubleMatrix
 
transversalSingleBaseSubstitution - Static variable in class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Substitution matrix allowing for a single base transversion variant.
trueFalse - Static variable in enum com.compomics.util.experiment.filtering.FilterItemComparator
Array of possibilities used for a boolean value.
Tryptophan - Class in com.compomics.util.experiment.biology.aminoacids.impl
Tryptophan.
Tryptophan() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
Constructor.
TRYPTOPHAN - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Tryptophan immonium ion.
two - Static variable in class com.compomics.util.math.BigMathUtils
Big decimal value of 2.
txt - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
TXT - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
type - Variable in class com.compomics.util.experiment.biology.ions.Ion
Type of ion.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
The type of export feature.
type - Static variable in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
The type of export feature.
Tyrosine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Tyrosine.
Tyrosine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
Constructor.
TYROSINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Tyrosine immonium ion.

U

U - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
unBlob() - Method in class com.compomics.util.db.object.objects.BlobObject
Returns the object represented by this blob.
uncompress(byte[], int) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
Uncompresses the given byte array.
UNDERIVATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.impl.Glycan
Final index for underivated masses.
unGzipAndUntarFile(GZIPInputStream, File, WaitingHandler) - Method in class com.compomics.software.autoupdater.FileDAO
Untars and ungzips a .tar.gz file.
UniformFragmentation - Class in com.compomics.util.experiment.identification.peptide_fragmentation.models
Dummy intensity predictor that returns 1.0 for every ion.
UniformFragmentation() - Constructor for class com.compomics.util.experiment.identification.peptide_fragmentation.models.UniformFragmentation
Empty default constructor
UNIPROT_TAXONOMY_FILENAME - Static variable in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
The name of the UniProt taxonomy file.
UniprotTaxonomy - Class in com.compomics.util.experiment.biology.taxonomy.mappings
Mapping of the UniProt taxonomy.
UniprotTaxonomy() - Constructor for class com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
Constructor.
unit - Variable in enum com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
The unit to use
UnitOfMeasurement - Class in com.compomics.util.experiment.units
The unit to use for a measure.
UnitOfMeasurement() - Constructor for class com.compomics.util.experiment.units.UnitOfMeasurement
Empty default constructor
UnitOfMeasurement(String, String, MetricsPrefix) - Constructor for class com.compomics.util.experiment.units.UnitOfMeasurement
Constructor.
UnitOfMeasurement(StandardUnit, MetricsPrefix) - Constructor for class com.compomics.util.experiment.units.UnitOfMeasurement
Constructor.
UnitOfMeasurement(StandardUnit) - Constructor for class com.compomics.util.experiment.units.UnitOfMeasurement
Constructor.
Units - Class in com.compomics.util.experiment.units
Convenience class providing units.
Units() - Constructor for class com.compomics.util.experiment.units.Units
Empty default constructor
UNKNOWN - Static variable in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
Tag for unknown species.
UnknownElementMassException - Exception in com.compomics.util.general
This class implements an Exception, thrown when a MassCalc instance is confronted with an element symbol it cannot retrieve in its element lists.
UnknownElementMassException(String) - Constructor for exception com.compomics.util.general.UnknownElementMassException
The constructor requires the caller to specify the element which was not recognized.
unlock() - Method in class com.compomics.util.db.object.ObjectsDB
Unlocking the db after storing.
unreadLine() - Method in class com.compomics.util.io.PushBackStringReader
This method 'unreads' a line of text from the Buffer.
UNRELATED - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.PSParameter
Static index for a protein group: 3 - unrelated proteins proteins or peptide shared by unrelated proteins.
UnspecificCombinationIterator - Class in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
Iterator for unspecific cleavage.
UnspecificCombinationIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificCombinationIterator
Empty default constructor
UnspecificCombinationIterator(ProteinIteratorUtils, String, double, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificCombinationIterator
Constructor.
UnspecificIterator - Class in com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
Iterator for unspecific cleavage.
UnspecificIterator() - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificIterator
Empty default constructor
UnspecificIterator(ProteinIteratorUtils, String, double, double) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificIterator
Constructor.
unzip(File, File, WaitingHandler) - Static method in class com.compomics.util.io.compression.ZipUtils
Unzips the content of an archive into a given folder.
unzipFile(ZipFile, File) - Method in class com.compomics.software.autoupdater.FileDAO
Unzips a zip archive.
update(Connection) - Method in interface com.compomics.util.db.interfaces.Updateable
This method allows the implemented object to store its altered state in the persistent store.
Updateable - Interface in com.compomics.util.db.interfaces
This interface indicates that the implementing class can be updated in permanent storage.
UpdateableCode - Class in com.compomics.util.db.components
This class generates the code to make a DBAccessor an implementation of the Updateable interface.
UpdateableCode() - Constructor for class com.compomics.util.db.components.UpdateableCode
Empty default constructor
UpdateableCode(DBMetaData) - Constructor for class com.compomics.util.db.components.UpdateableCode
This constructor allows the generation of the code for the implementation of the Updateable interface for a DBAccessor class, based on the specified metadata.
updateAtomComposition() - Method in class com.compomics.util.gui.atoms.AtomChainDialog
Updates the atom composition panel.
updateCoverableAA(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Updates the array of booleans indicating whether the amino acids of given peptides can generate peptides.
updateEnsemblVersion(String, String) - Method in class com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
Update the Ensembl version for the given species in the local map and in the Ensembl versions file.
updateEnzymesTable() - Method in class com.compomics.util.gui.enzymes.EnzymesDialog
Update the layout of the enzymes table.
updateGUI() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
Populates the GUI using the given identification parameters.
updateIdentificationParameters() - Method in class com.compomics.cli.identification_parameters.IdentificationParametersInputBean
Updates the identification parameters according to the command line.
updateIdentificationParameters(IdentificationParameters, IdentificationParameters) - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
Replaces old parameters by new.
updateLog4jConfiguration(Logger, CompomicsTools) - Method in class com.compomics.util.io.PropertiesManager
This method will delete the log4j log file in the folder of the package and will create a log file in the CompomicsTools specific .compomics folder
updateMassShifts() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Updates the mass shifts.
updateModifications() - Method in class com.compomics.util.gui.modification.ModificationsDialog
Updates the modification lists and tables.
updateModSelection() - Method in class com.compomics.util.gui.modification.ModificationsDialog
Updates the modification selection in the default table.
updateNConfidentPeptides(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Updates the number of confident peptides for a given protein match.
updateNConfidentSpectra(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Updates the number of confident spectra for a given protein match.
updateNConfidentSpectraForPeptide(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Updates the number of confident spectra for a given peptide match.
updateObject(long, Object) - Method in class com.compomics.util.db.object.ObjectsDB
Update the object with the given key.
updateObject(long, Object) - Method in class com.compomics.util.experiment.identification.Identification
Updates an object in the database.
updateObservableCoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Updates the best protein coverage possible according to the given cleavage settings.
updateParameters(IdentificationParameters) - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
Updates the given identification parameters attributes.
updatePlot() - Method in class com.compomics.util.gui.VennDiagramPanel
Update the plot.
updatePlot() - Method in class com.compomics.util.gui.XYPlottingDialog
Update the plot.
updateProperties(CompomicsTools, String, Properties) - Method in class com.compomics.util.io.PropertiesManager
Update the content of a user properties instance to the ms_lims properties directory.
updateSequenceCoverage(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Updates the sequence coverage of the protein of interest.
updateTable() - Method in class com.compomics.util.gui.filtering.FilterDialog
Updates the table.
updateTable() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
Updates the parameters table.
urlWasRead() - Method in class com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
Returns true if the PDB URL was read, false otherwise.
UrParameter - Interface in com.compomics.util.experiment.personalization
This interface is used to reference refinement parameters.
useBoldFont() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns true of the label should be in bold.
useLogFile() - Method in class com.compomics.cli.paths.PathSettingsCLIInputBean
Return true if a log file is to be used.
useMassDeltaCombinations() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
If true, pairs of delta mass annotations are used when doing de novo sequencing.
USER - Static variable in class com.compomics.util.io.file.FolderMonitor
 
usersModsSorted - Variable in class com.compomics.util.experiment.biology.modifications.ModificationFactory
Set to true if the users mods are sorted alphabetically.
Util - Class in com.compomics.util
Includes general help methods that are used by the other classes.
Util() - Constructor for class com.compomics.util.Util
Empty default constructor.
UtilitiesDemo - Class in com.compomics.util.examples
This class serves as a demo of how the compomics-utilities library can be used in other projects.
UtilitiesDemo() - Constructor for class com.compomics.util.examples.UtilitiesDemo
Creates a new UtilitiesDemo frame and makes it visible.
UtilitiesGUIDefaults - Class in com.compomics.util.gui
This class contains a list of GUI defaults to be used across the tools using the utilities library to make sure that the tools have the same look and feel.
UtilitiesGUIDefaults() - Constructor for class com.compomics.util.gui.UtilitiesGUIDefaults
 
UtilitiesPathParameters - Class in com.compomics.software.settings
This class sets the path preferences for the files to read/write.
UtilitiesPathParameters() - Constructor for class com.compomics.software.settings.UtilitiesPathParameters
Empty default constructor.
UtilitiesPathParameters.UtilitiesPathKey - Enum in com.compomics.software.settings
Enum of the paths which can be set in utilities.
UtilitiesUserParameters - Class in com.compomics.util.parameters
Utilities user parameters can be used to store user parameters.
UtilitiesUserParameters() - Constructor for class com.compomics.util.parameters.UtilitiesUserParameters
Constructor.

V

V - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
validate(File) - Method in class com.compomics.util.pride.validation.PrideXmlValidator
Returns true of the given PRIDE XML file is valid.
validateDoubleInput(Component, JLabel, JTextField, String, String, boolean, boolean, boolean) - Static method in class com.compomics.util.gui.GuiUtilities
Validate double input.
validatedSequenceCoverageInCache(long) - Method in class com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
Indicates whether the sequence coverage is in cache.
validateInput() - Method in class com.compomics.util.gui.filtering.FilterDialog
Validates the input.
validateInput() - Method in class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
Validates the user input.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
Validates the user input.
validateInput() - Method in class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
Validates the user input.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog
Inspects the parameter validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog
Inspects the parameter validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog
Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog
Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog
Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog
Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog
Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog
Inspects the parameter validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
Inspects the parameters validity.
validateInput() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
Validates the user input.
validateInput() - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
Validates the user input.
validateInput() - Method in class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
Validates the user input.
validateIntegerInput(Component, JLabel, JTextField, String, String, boolean, boolean, boolean) - Static method in class com.compomics.util.gui.GuiUtilities
Validate integer input.
validateModifications(Peptide, SequenceMatchingParameters, SequenceMatchingParameters, ModificationParameters) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Verifies that the definition of every modification name is available.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog
Inspects the parameters validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog
Inspects the parameters validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog
Inspects the parameters validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog
Inspects the parameters validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
Inspects the search parameter validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
Inspects the parameters validity.
validatePeptide(Peptide, SequenceMatchingParameters, DigestionParameters) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.
validatePrecursor(PeptideAssumption, String, String, SpectrumProvider, SearchParameters) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Validates the mass deviation of a peptide assumption.
validateProteins(Peptide, SequenceMatchingParameters, SequenceProvider) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
Validates a peptide depending on its protein inference status.
ValidationParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
Dialog for the edition of the sequence matching settings
ValidationParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
Empty default constructor
ValidationParametersDialog(Frame, IdMatchValidationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
Creates a new ValidationSettingsDialog with a frame as owner.
ValidationParametersDialog(Dialog, Frame, IdMatchValidationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
Creates a new ValidationSettingsDialog with a dialog as owner.
ValidationQcParameters - Class in com.compomics.util.parameters.identification.advanced
This class lists the criteria used for quality control of the validated matches.
ValidationQcParameters() - Constructor for class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Creates a validation quality control preferences object with default settings.
ValidationQcParameters(ValidationQcParameters) - Constructor for class com.compomics.util.parameters.identification.advanced.ValidationQcParameters
Creates a validation quality control preferences object based on an other ValidationQCPreferences.
ValidationQCParametersDialog - Class in com.compomics.util.gui.parameters.identification.advanced
Dialog for the edition of validation QC filters.
ValidationQCParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Empty default constructor
ValidationQCParametersDialog(Frame, ValidationQcParameters, ArrayList<String>, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Creates a new ValidationQCPreferencesDialog with a frame as owner.
ValidationQCParametersDialog(Dialog, Frame, ValidationQcParameters, ArrayList<String>, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
Creates a new ValidationQCPreferencesDialog with a dialog as owner.
Valine - Class in com.compomics.util.experiment.biology.aminoacids.impl
Valine.
Valine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Valine
Constructor.
VALINE - Static variable in class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
Valine immonium ion.
valueOf(String) - Static method in enum com.compomics.cli.enzymes.EnzymesCLIParams
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.cli.fasta.FastaParametersCLIParams
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.cli.modifications.ModificationsCLIParams
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.cli.paths.PathSettingsCLIParams
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.enumeration.CompomicsTools
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.enumeration.ImageType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.enumeration.MolecularElement
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.enumeration.OperatingSystemEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.biology.aminoacids.AminoAcid.Property
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.biology.ions.Ion.IonType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.biology.modifications.ModificationCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.biology.modifications.ModificationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies.EnsemblGenomeDivision
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.filtering.FilterItemComparator
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.Advocate.AdvocateType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.features.IdentificationFeaturesCache.ObjectType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.filtering.MatchFilter.FilterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.IdentificationMatch.MatchType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature.Relationship
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature.Function
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature.Property
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature.Property
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature.Property
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.PeptideFragmentationModel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters.IntensityThresholdType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator.IonSeries
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator.TiesResolution
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader.RawValueConversionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.io.identification.MzIdentMLVersion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter.Format
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator.Precision
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.io.parameters.MarshallableParameter.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.mass_spectrometry.FragmentationMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.mass_spectrometry.utils.StandardMasses
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.quantification.Quantification.QuantificationMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCountingMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.units.MetricsPrefix
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.units.StandardUnit
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.gui.spectrum.GraphicsPanel.DrawingStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.gui.spectrum.GraphicsPanel.GraphicsPanelType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.gui.VennDiagramPanel.VennDiagramType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.gui.XYPlottingDialog.PlottingDialogPlotType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.ExportFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.math.roc.DataRoc.RocInterpolation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.messages.FeedBack.FeedBackType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters.VariantType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.search.SearchParameters.MassAccuracyType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.AndromedaParameters.AndromedaDecoyMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.CometParameters.CometOutputFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusDecoyType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusDissociationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusSearchType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusToleranceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.peptide_shaker.ProjectType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.parameters.tools.ProcessingParameters.ProcessingType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.pride.prideobjects.webservice.file.FileType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.pride.prideobjects.webservice.PrideQuery
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.pride.prideobjects.webservice.query.PrideFilterType
Returns the enum constant of this type with the specified name.
values() - Static method in enum com.compomics.cli.enzymes.EnzymesCLIParams
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.cli.fasta.FastaParametersCLIParams
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.cli.modifications.ModificationsCLIParams
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.cli.paths.PathSettingsCLIParams
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.enumeration.CompomicsTools
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.enumeration.ImageType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.enumeration.MolecularElement
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.enumeration.OperatingSystemEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.biology.aminoacids.AminoAcid.Property
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.biology.ions.Ion.IonType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.biology.modifications.ModificationCategory
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.biology.modifications.ModificationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies.EnsemblGenomeDivision
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.filtering.FilterItemComparator
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.Advocate.AdvocateType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in class com.compomics.util.experiment.identification.Advocate
Returns the implemented advocates in an array.
values() - Static method in enum com.compomics.util.experiment.identification.features.IdentificationFeaturesCache.ObjectType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.filtering.items.PsmFilterItem
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.filtering.MatchFilter.FilterType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.IdentificationMatch.MatchType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature.Relationship
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature.Function
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature.Property
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature.Property
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature.Property
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.peptide_fragmentation.PeptideFragmentationModel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScore
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters.IntensityThresholdType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator.IonSeries
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator.TiesResolution
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.identification.validation.MatchValidationLevel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.io.biology.protein.ProteinDatabase
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader.RawValueConversionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.io.identification.MzIdentMLVersion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter.Format
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator.Precision
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.io.parameters.MarshallableParameter.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.mass_spectrometry.FragmentationMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.mass_spectrometry.utils.StandardMasses
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.quantification.Quantification.QuantificationMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCountingMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.units.MetricsPrefix
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.experiment.units.StandardUnit
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.gui.spectrum.GraphicsPanel.DrawingStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.gui.spectrum.GraphicsPanel.GraphicsPanelType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.gui.VennDiagramPanel.VennDiagramType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.gui.XYPlottingDialog.PlottingDialogPlotType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.ExportFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsAnnotationFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsFragmentFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsIdentificationAlgorithmMatchesFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsInputFilterFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsProjectFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsPsmFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsPtmScoringFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsSearchFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsSpectrumCountingFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.peptideshaker.PsValidationFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.reporter.ReporterPeptideFeature
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.reporter.ReporterProteinFeatures
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.io.export.features.reporter.ReporterPsmFeatures
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.math.roc.DataRoc.RocInterpolation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.messages.FeedBack.FeedBackType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters.VariantType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.search.SearchParameters.MassAccuracyType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.AndromedaParameters.AndromedaDecoyMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.CometParameters.CometOutputFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusDecoyType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusDissociationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusSearchType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusToleranceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.peptide_shaker.ProjectType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.searchgui.OutputParameters
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.parameters.tools.ProcessingParameters.ProcessingType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.pride.prideobjects.webservice.file.FileType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.pride.prideobjects.webservice.PrideQuery
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.pride.prideobjects.webservice.query.PrideFilterType
Returns an array containing the constants of this enum type, in the order they are declared.
valuesMap - Variable in class com.compomics.util.experiment.identification.filtering.MatchFilter
Map of the values to filter on.
Variant - Interface in com.compomics.util.experiment.biology.variants
Interface for a variant.
variant - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
Type of edit operation, either deletion 'd', substitution 's' or insertion 'i'.
variantAminoAcid - Variable in class com.compomics.util.experiment.biology.variants.AminoAcidSubstitution
The variant amino acid represented by its single letter code.
VennDiagram - Class in com.compomics.util.math
Class for calculating the groups for Venn diagrams.
VennDiagram() - Constructor for class com.compomics.util.math.VennDiagram
Empty default constructor
VennDiagramDialog - Class in com.compomics.util.gui
A dialog for creating and displaying Venn diagrams.
VennDiagramDialog(Frame, Image, Image, boolean) - Constructor for class com.compomics.util.gui.VennDiagramDialog
Creates a new XYPlottingDialog.
VennDiagramLegendLocationDialog - Class in com.compomics.util.gui
Dialog for setting the location of the legend items in a Venn diagram.
VennDiagramLegendLocationDialog(VennDiagramDialog, boolean) - Constructor for class com.compomics.util.gui.VennDiagramLegendLocationDialog
Creates a new VennDiagramLegendLocationDialog.
vennDiagramMaker(ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Static method in class com.compomics.util.math.VennDiagram
Create the Venn diagram groupings based on the provided data.
VennDiagramPanel - Class in com.compomics.util.gui
A panel displaying a Venn diagram based on the provided data.
VennDiagramPanel(ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>, String, String, String, String, Color, Color, Color, Color) - Constructor for class com.compomics.util.gui.VennDiagramPanel
Creates a new VennDiagramPanel.
VennDiagramPanel.VennDiagramType - Enum in com.compomics.util.gui
The supported Venn diagram types.
VERIFIER_FACTORY - Static variable in class com.compomics.util.pride.validation.PrideXmlValidator
The verifier factory.
version - Variable in class com.compomics.util.experiment.io.parameters.DummyParameters
Version number.
version - Variable in class com.compomics.util.parameters.identification.IdentificationParameters
Version number.
version - Variable in class com.compomics.util.parameters.identification.search.SearchParameters
Version number.
versionTag - Static variable in class com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader
Tag for the version.
VERY_CONFIDENT - Static variable in class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
Index for a very confident assignment.
VisibleTableColumnsDialog - Class in com.compomics.util.gui
A dialog that lets the user decide which columns to show/hide in a JTable.
VisibleTableColumnsDialog(JDialog, VisibleTableColumnsDialogParent, boolean) - Constructor for class com.compomics.util.gui.VisibleTableColumnsDialog
Creates a new VisibleTableColumnsDialog.
VisibleTableColumnsDialog(JFrame, VisibleTableColumnsDialogParent, boolean) - Constructor for class com.compomics.util.gui.VisibleTableColumnsDialog
Creates a new VisibleTableColumnsDialog.
VisibleTableColumnsDialogParent - Interface in com.compomics.util.gui
Interface for parents of VisibleTableColumnsDialog.

W

W - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
WaitingActionListener - Interface in com.compomics.util.waiting
This class is used to pass actions like cancel while waiting.
WaitingDialog - Class in com.compomics.util.gui.waiting.waitinghandlers
A dialog displaying progress details.
WaitingDialog() - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Empty default constructor
WaitingDialog(Frame, Image, Image, boolean, String, String, String, boolean) - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Creates a new WaitingDialog.
WaitingDialog(Frame, Image, Image, boolean, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Creates a new WaitingDialog.
WaitingDialogExceptionHandler - Class in com.compomics.util.exceptions.exception_handlers
Exception handler for processes making use of a waiting dialog.
WaitingDialogExceptionHandler() - Constructor for class com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler
Empty default constructor
WaitingDialogExceptionHandler(WaitingDialog, String) - Constructor for class com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler
Constructor.
WaitingDialogExceptionHandler(WaitingDialog) - Constructor for class com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler
Constructor.
WaitingHandler - Interface in com.compomics.util.waiting
An interface for code dealing with how to handle information that is displayed to the user during loading or processing.
WaitingHandlerCLIImpl - Class in com.compomics.util.gui.waiting.waitinghandlers
This class is an implementation of the WaitingHandler interface to be used when operating through the Command Line Interface.
WaitingHandlerCLIImpl() - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
Empty default constructor
WaitingHandlerDummy - Class in com.compomics.util.gui.waiting.waitinghandlers
This class is an implementation of the WaitingHandler interface to be used when a process can be canceled, but no monitoring is needed.
WaitingHandlerDummy() - Constructor for class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy
Empty default constructor
warning(SAXParseException) - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Receive notification of a warning.
WATER_MASS - Static variable in class com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
The mass of water (H2O).
WaveletTree - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
Wavelet tree.
WaveletTree() - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Empty default constructor.
WaveletTree(byte[], long[], WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Constructor.
WaveletTree(byte[], WaitingHandler, WaveletTree.HuffmanNode) - Constructor for class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree
Constructor.
WaveletTree.HuffmanNode - Class in com.compomics.util.experiment.identification.protein_inference.fm_index
Class for huffman nodes.
WebDAO - Class in com.compomics.software.autoupdater
WebDAO.
WebDAO() - Constructor for class com.compomics.software.autoupdater.WebDAO
 
welcomeMsg - Variable in class com.compomics.util.io.ftp.FTP
Welcome message from the server, if any.
WINDOW_SIZE - Static variable in class com.compomics.util.experiment.identification.modification.scores.PhosphoRS
The window size in m/z.
withinMassTolerance(double, int) - Method in class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex
Lookup, if mass can be described a combination of numX different amino acids
WorkbookStyle - Interface in com.compomics.util.io.export
This interface sets the style of a workbook export.
write(String, String) - Method in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
Writes content to the given section.
write(String, char[], int, int) - Method in class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
Writes content to the given section.
write(String) - Method in class com.compomics.util.io.export.ExportWriter
Writes text to the export.
write(String, WorkbookStyle) - Method in class com.compomics.util.io.export.ExportWriter
Writes text to the export.
write(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
write(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.TextWriter
 
write(String) - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Writes the content to the file.
write(char[], int, int) - Method in class com.compomics.util.io.flat.SimpleFileWriter
Writes a a buffer of characters to the file.
write(String) - Method in class com.compomics.util.io.flat.SimpleFileWriter
Writes text.
write(String, boolean) - Method in class com.compomics.util.io.flat.SimpleFileWriter
Writes text.
write(JsonWriter, Color) - Method in class com.compomics.util.io.json.adapter.ColorAdapter
 
write(JsonWriter, Object) - Method in class com.compomics.util.io.json.adapter.FileAdapter
 
writeAplFile(SpectrumProvider, String, File, SearchParameters, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter
Writes the spectra of a file in the Andromeda peak list (apl) format.
writeComment(String, String) - Method in class com.compomics.software.log.CliLogger
Write a comment line as '# key: value'.
writeConfigurationToFile(File) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Writes all path configurations to the given file.
writeConfigurationToFile(BufferedWriter) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Writes the configuration file using the provided buffered writer.
writeHeader() - Method in class com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2Exporter
Writes the header of the file.
writeHeader() - Method in class com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2FileWriter
Writes the header of the file.
writeHeaders() - Method in class com.compomics.software.log.CliLogger
Writes the headers to the files.
writeHeaderText(String) - Method in class com.compomics.util.io.export.ExportWriter
Writes header text to the export.
writeHeaderText(String, WorkbookStyle) - Method in class com.compomics.util.io.export.ExportWriter
Writes header text to the export.
writeHeaderText(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
writeHeaderText(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.TextWriter
 
writeIndent() - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Writes the current indent.
writeLine(String) - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Writes the given line.
writeLine(String...) - Method in class com.compomics.util.io.flat.SimpleFileWriter
Writes a new line using the give elements.
writeLine(String) - Method in class com.compomics.util.io.flat.SimpleFileWriter
Writes a new line.
writeLineDecreasedIndent(String) - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Writes the given line with a decreased indent.
writeLineIncreasedIndent(String) - Method in class com.compomics.util.io.export.xml.SimpleXmlWriter
Writes the given line with an increased indent.
writeMainTitle(String) - Method in class com.compomics.util.io.export.ExportWriter
Writes the main title.
writeMainTitle(String, WorkbookStyle) - Method in class com.compomics.util.io.export.ExportWriter
Writes the main title.
writeMainTitle(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter
 
writeMainTitle(String, WorkbookStyle) - Method in class com.compomics.util.io.export.writers.TextWriter
 
writeMgfFile(SpectrumProvider, String, File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter
Writes the spectra of a file in the Mascot Generic File (mgf) format.
writeMs2File(SpectrumProvider, String, File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter
Writes the spectra of a file in the ms2 format.
writeMsFile(SpectrumProvider, String, File, MsFileExporter.Format, SearchParameters, WaitingHandler) - Static method in class com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter
Writes the spectra of a file in the given format.
writeObject(Object, File) - Static method in class com.compomics.util.io.file.SerializationUtils
Writes an object to the destination file.
writePathToFile(BufferedWriter, UtilitiesPathParameters.UtilitiesPathKey) - Static method in class com.compomics.software.settings.UtilitiesPathParameters
Writes the path of interest using the provided buffered writer.
WriterBySection - Class in com.compomics.util.io.compression.SectionGzWriter
This writer writes the different sections of a file in temp files and bundles them together upon completion.
WriterBySection(File, File, boolean, boolean, boolean) - Constructor for class com.compomics.util.io.compression.SectionGzWriter.WriterBySection
Constructor.
writeSpectrum(String, Spectrum, FragmentationMethod, int) - Method in class com.compomics.util.experiment.io.mass_spectrometry.apl.AplFileWriter
Writes the given spectrum to the file.
writeSpectrum(String, Spectrum) - Method in class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileWriter
Writes the given spectrum to the file.
writeSpectrum(Spectrum, int) - Method in class com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2Exporter
Writes the given spectrum in ms2 format.
writeSpectrum(Spectrum, int) - Method in class com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2FileWriter
Writes the given spectrum in ms2 format.
writeStreamToDisk(InputStream, String, File) - Method in class com.compomics.software.autoupdater.FileDAO
Writes a stream to disk.
writeToCSVFile(Writer, String) - Method in class com.compomics.util.db.DBResultSet
This method allows the caller to write the current dataset to the specified Writer.
writeToFASTAFile(PrintWriter) - Method in class com.compomics.util.nucleotide.NucleotideSequence
This method can be used to append this nucleotide sequence to the FASTA DB flatfile the PrintWriter points to.
writeToFASTAFile(PrintWriter) - Method in class com.compomics.util.protein.Protein
This method can be used to append this protein to the FASTA DB flatfile the PrintWriter points to.
writeToFile(File) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Method to write to a given file
writeToFile(File) - Method in interface com.compomics.util.interfaces.SpectrumFile
This method allows the caller to write the spectrum file to the specified folder using its current filename.
writeToHTMLTable(Writer, int) - Method in class com.compomics.util.db.DBResultSet
This method allows the caller to write the current dataset to the specified Writer.
writeToStream(OutputStream) - Method in class com.compomics.util.general.IsotopicDistributionSpectrum
Method to write to a givern stream
writeToStream(OutputStream) - Method in interface com.compomics.util.interfaces.SpectrumFile
This method allows to write the spectrum file to the specified OutputStream.

X

X - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
X - Class in com.compomics.util.experiment.biology.aminoacids.impl
Unknown amino acid (Mascot).
X() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.X
Constructor.
X_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Identifier for an x ion.
X_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Identifier for an x ion.
xAxisZoomRangeLowerValue - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The lower range for the current zoom range.
xAxisZoomRangeUpperValue - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The upper range for the current zoom range.
XMassDiff - Variable in class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
The X mass difference,
xml - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
XML - Static variable in class com.compomics.util.io.file.filefilters.FileFilterUtils
 
XmlFileFilter - Class in com.compomics.util.io.file.filefilters
File filter for *.xml files.
XmlFileFilter() - Constructor for class com.compomics.util.io.file.filefilters.XmlFileFilter
Empty default constructor
XMLValidationErrorHandler - Class in com.compomics.util.pride.validation
Edited using IntelliJ IDEA Date: 16-Sep-2005 Time: 15:26:12
XMLValidationErrorHandler() - Constructor for class com.compomics.util.pride.validation.XMLValidationErrorHandler
Constructor.
xTagCount - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The number of X-axis tags.
xtandem - Static variable in class com.compomics.util.experiment.identification.Advocate
The X! Tandem search engine.
XTandemIdfileReader - Class in com.compomics.util.experiment.io.identification.idfilereaders
This IdfileReader reads identifications from an X! Tandem xml result file.
XTandemIdfileReader() - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
Default constructor for the purpose of instantiation.
XTandemIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
Constructor for an X!Tandem xml result file reader.
XTandemIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
Constructor for an X!Tandem xml result file reader.
XtandemParameters - Class in com.compomics.util.parameters.identification.tool_specific
The X!Tandem specific parameters.
XtandemParameters() - Constructor for class com.compomics.util.parameters.identification.tool_specific.XtandemParameters
Constructor.
XTandemParametersDialog - Class in com.compomics.util.gui.parameters.identification.algorithm
Dialog for the X!Tandem specific settings.
XTandemParametersDialog() - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
Empty default constructor
XTandemParametersDialog(Frame, XtandemParameters, ModificationParameters, double, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
Creates new form XtandemParametersDialog with a frame as owner.
XTandemParametersDialog(Dialog, Frame, XtandemParameters, ModificationParameters, double, boolean) - Constructor for class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
Creates new form XtandemParametersDialog with a dialog as owner.
XYPlotFiltersDialog - Class in com.compomics.util.gui
Dialog for editing the data filters for an XYPlottingDialog.
XYPlotFiltersDialog(XYPlottingDialog, boolean) - Constructor for class com.compomics.util.gui.XYPlotFiltersDialog
Creates a new XYPlotFiltersDialog.
XYPlottingDialog - Class in com.compomics.util.gui
A dialog that makes it straightforward to inspect compare the values of two columns in a table in a XY plot.
XYPlottingDialog(Frame, JTable, String, XYPlottingDialog.PlottingDialogPlotType, ArrayList<String>, Image, Image, boolean) - Constructor for class com.compomics.util.gui.XYPlottingDialog
Creates a new XYPlottingDialog.
XYPlottingDialog.PlottingDialogPlotType - Enum in com.compomics.util.gui
The plotting dialog types.
XYPlottingDialog.SelectedValuesTableFilter - Class in com.compomics.util.gui
A filter that filters the table based on if the data point is selected in the plot or not.
XYZDataPoint - Class in com.compomics.util
Object that stores data about one data point in an XYZ plot.
XYZDataPoint() - Constructor for class com.compomics.util.XYZDataPoint
Empty default constructor
XYZDataPoint(double, double, double) - Constructor for class com.compomics.util.XYZDataPoint
Create a new XYZDataPoint.

Y

Y - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
Y_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Identifier for a y ion.
Y_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Identifier for a y ion.
yAxisZoomExcludesBackgroundPeaks() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
Returns true if the automatic y-axis zoom excludes background peaks.
yAxisZoomExcludesBackgroundPeaks - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If true, the automatic y-axis zoom excludes the background peaks.
yAxisZoomOnlyExcludesBackgroundPeaks() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true if the automatic y-axis zoom excludes background peaks.
yDataIsPositive - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If set to true, all y data is assumed to be positive.
yDataIsPositive() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true of all the y-data is to be assumed as positive.
yTagCount - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The number of Y-axis tags.

Z

Z - Static variable in class com.compomics.util.experiment.biology.aminoacids.AminoAcid
 
Z - Class in com.compomics.util.experiment.biology.aminoacids.impl
Glu or Gln: Glx (Mascot).
Z() - Constructor for class com.compomics.util.experiment.biology.aminoacids.impl.Z
Constructor.
Z_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
Identifier for a z ion.
Z_ION - Static variable in class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
Identifier for a z ion.
zCore - Static variable in class com.compomics.util.experiment.identification.Advocate
The ZCore search engine, ETD search engine.
ZERO - Static variable in class com.compomics.util.experiment.identification.utils.ModificationUtils
Array for N-term.
Zinc - Class in com.compomics.util.experiment.biology.atoms.impl
The zinc atom.
Zinc() - Constructor for class com.compomics.util.experiment.biology.atoms.impl.Zinc
Constructor.
zip(File, File) - Static method in class com.compomics.util.io.compression.ZipUtils
Zips a file.
zip(File, File, WaitingHandler, long) - Static method in class com.compomics.util.io.compression.ZipUtils
Zips a file.
ZipUtils - Class in com.compomics.util.io.compression
Convenience class for the handling of zip files.
ZipUtils() - Constructor for class com.compomics.util.io.compression.ZipUtils
Empty default constructor
Zn - Static variable in class com.compomics.util.experiment.biology.atoms.Atom
The Zinc atom.
zstdCompress(byte[]) - Static method in class com.compomics.util.io.compression.ZstdUtils
Compresses the given byte array.
zstdCompress(ZstdCompressor, byte[]) - Static method in class com.compomics.util.io.compression.ZstdUtils
Compresses the given byte array.
zstdDecompress(byte[], int) - Static method in class com.compomics.util.io.compression.ZstdUtils
Decompresses the given byte array.
zstdDecompress(ZstdDecompressor, byte[], int) - Static method in class com.compomics.util.io.compression.ZstdUtils
Decompresses the given byte array.
ZstdUtils - Class in com.compomics.util.io.compression
Functions needed for compression and decompression.
ZstdUtils() - Constructor for class com.compomics.util.io.compression.ZstdUtils
 
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