Index (computational omics utilities 4.5.7 API)

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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.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.PeptideFragmentIon: Identifier for an a ion.
A_ION - Static variable in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Identifier for an a ion.
AAIntensityRankScore - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores: The intensity rank sub-score as adapted from the DirecTag paper where the minimal value per amino-scid is retained (http://www.ncbi.nlm.nih.gov/pubmed/18630943).
AAIntensityRankScore() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAIntensityRankScore
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.
AAMS2MzFidelityScore - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores: The m/z fidelity sub-score as adapted from the DirecTag paper where the minimal value per amino-scid is retained (http://www.ncbi.nlm.nih.gov/pubmed/18630943).
AAMS2MzFidelityScore() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAMS2MzFidelityScore
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.
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: Send Abort command.
AbstractIdentificationParametersCli - Class in com.compomics.util.experiment.identification.parameters_cli: This class serves as a base for the implementation of IdentificationParametersCLI in specific tools.
AbstractIdentificationParametersCli() - Constructor for class com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli
accept(File, String) - Method in class com.compomics.software.autoupdater.JarFileFilter
accept(File) - Method in class com.compomics.util.io.filefilters.DatFileFilter: Accept all directories, *.dat files.
accept(File) - Method in class com.compomics.util.io.filefilters.DtaFileFilter: Accept all directories, *.dta files.
accept(File) - Method in class com.compomics.util.io.filefilters.FastaFileFilter: Accept all directories, *.fasta files.
accept(File) - Method in class com.compomics.util.io.filefilters.JpegFileFilter: Accept all directories, *.jpeg files.
accept(File) - Method in class com.compomics.util.io.filefilters.MgfFileFilter: Accept all directories, *.mgf files.
accept(File) - Method in class com.compomics.util.io.filefilters.Ms2FileFilter: Accept all directories, *.ms2 files.
accept(File) - Method in class com.compomics.util.io.filefilters.MzDataFileFilter: Accept all directories, and *.mzData files.
accept(File) - Method in class com.compomics.util.io.filefilters.MzMlFileFilter: Accept all directories, and *.mzML files.
accept(File) - Method in class com.compomics.util.io.filefilters.MzXmlFileFilter: Accept all directories, and *.mzXML files.
accept(File) - Method in class com.compomics.util.io.filefilters.OmxFileFilter: Accept all directories, *.omx files.
accept(File) - Method in class com.compomics.util.io.filefilters.OutFileFilter: Accept all directories, *.out files.
accept(File) - Method in class com.compomics.util.io.filefilters.PdfFileFilter: Accept all directories, *.pdf files.
accept(File) - Method in class com.compomics.util.io.filefilters.PeffFileFilter: Accept all directories, *.peff files.
accept(File) - Method in class com.compomics.util.io.filefilters.PepXmlFileFilter: Accept all directories, *.pep.xml, *.pepxml and *.xml files.
accept(File) - Method in class com.compomics.util.io.filefilters.PklFileFilter: Accept all directories, *.pkl files.
accept(File) - Method in class com.compomics.util.io.filefilters.PklSpoFileFilter: Accept all directories, *.pkl.spo files.
accept(File) - Method in class com.compomics.util.io.filefilters.PkxFileFilter: Accept all directories, *.pkx files.
accept(File) - Method in class com.compomics.util.io.filefilters.PngFileFilter: Accept all directories, *.png files.
accept(File) - Method in class com.compomics.util.io.filefilters.ProtXmlFileFilter: Accept all directories, *.prot.xml, *.protxml and *.xml files.
accept(File) - Method in class com.compomics.util.io.filefilters.SequestParamsFileFilter: Accept all directories, sequest.params files.
accept(File) - Method in class com.compomics.util.io.filefilters.SvgFileFilter: Accept all directories, *.svg files.
accept(File) - Method in class com.compomics.util.io.filefilters.TiffFileFilter: Accept all directories, *.tiff files.
accept(File) - Method in class com.compomics.util.io.filefilters.XmlFileFilter: Accept all directories, *.xml files.
accept(File, String) - Method in class com.compomics.util.io.FilenameExtensionFilter: Tests if a specified file should be included in a file list.
accept(File) - Method in class com.compomics.util.io.FilenameExtensionFilter
ACE_K_126 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for lysine acetylation (PMID: 18338905).
ACE_K_143 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for lysine acetylation (PMID: 18338905).
add(MutationMatrix) - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Adds the content of a mutation matrix in this matrix.
addAccession(String, ArrayList<Integer>) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Adds an accession to the node.
addActiveConnection(String, String) - Static method in class com.compomics.util.db.DerbyUtil: Registers a new active connection.
addAddendum(String) - Method in class com.compomics.util.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(PtmtableContent) - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent: Add all.
addAminoAcidPattern(AminoAcidPattern) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag: Adds a sequence of amino acids to the tag.
addAminoAcidSequence(AminoAcidSequence) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag: Adds a sequence of amino acids to the tag.
addAnalysisSet(Sample, SampleAnalysisSet) - Method in class com.compomics.util.experiment.MsExperiment: Method to link an analysis set to an experiment.
addAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>, boolean, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Adds the assumptions corresponding to a spectrum to the database.
addAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Adds the assumptions corresponding to a spectrum.
addAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds assumptions for a given match to the database.
addAutomaticDeNovoSequencing(Peptide, ArrayList<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(Peptide, ArrayList<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(Peptide, ArrayList<IonMatch>, int, int, int, boolean, boolean, double, double, 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(Tag, ArrayList<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, ArrayList<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, ArrayList<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, ArrayList<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.
addAutomaticDeNovoSequencing(Peptide, ArrayList<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.
addAutomaticDeNovoSequencing(Tag, ArrayList<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
addContactGroup(ContactGroup) - Method in class com.compomics.util.pride.PrideObjectsFactory: Adds a contact group in the PRIDE objects.
addDb(ObjectsDB) - Method in class com.compomics.util.db.ObjectsCache: Adds a database in the list of the databases handled by the cache.
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.EnzymeFactory: Adds an enzyme in the factory.
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.
addFastaFile(File, SequenceInputType, WaitingHandler) - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Adds a FASTA file to the working folder.
addFavoriteDB(File) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets the last used databases.
addFileToZip(File, ZipOutputStream, WaitingHandler, long) - 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.massspectrometry.proteowizard.MsConvertParameters: Adds a filter.
addFixedModification(PTM) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: 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.
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.
addHit(int, SpectrumIdentificationAssumption, boolean) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Add a first hit.
addIdentificationParameters(IdentificationParameters) - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory: Adds the given identification parameters to the factory.
addIdentificationResults(int, Identification) - Method in class com.compomics.util.experiment.ProteomicAnalysis: Adds identification results obtained with an identification method.
addIdNameMapping(String, File) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Adds an id to spectrum name in the mapping.
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.ptm.PtmtableContent: Add intensity.
addIonType(Ion.IonType, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Adds a new ion type and subtype to annotate.
addIonType(Ion.IonType) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Adds a new ion type to annotate.
addIonType(Ion.IonType, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Adds a new ion type and subtype to annotate.
addIonType(Ion.IonType) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Adds a new ion type to annotate.
addLabel(String, boolean) - Method in class com.compomics.util.experiment.ShotgunProtocol: Adds a label.
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.
addMass(int, double) - Method in class com.compomics.util.experiment.biology.ions.Glycan: Add a mass for this glycan.
addMass(double) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Adds a mass to the segment.
addMassGap(double) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag: Adds a mass gap to the tag.
addMatch(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds an identification match to the database.
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.massspectrometry.MgfReader: Add missing precursor charges.
addMissingSpectrumTitles(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Adds missing spectrum titles.
addModification(Modification) - Method in class com.compomics.util.protein.AASequenceImpl: This method adds a modification to the list of modifications.
addModificationMatch(int, ModificationMatch) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Adds a modification to one of the amino acid pattern.
addModificationMatch(int, ModificationMatch) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Adds a modification to one of the amino acid sequence.
addModificationMatch(ModificationMatch) - Method in class com.compomics.util.experiment.biology.Peptide: Adds a modification match.
addModificationMatches(int, ArrayList<ModificationMatch>) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Adds a list of modifications to one of the amino acid pattern.
addModificationMatches(int, ArrayList<ModificationMatch>) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Adds a list of modifications to one of the amino acid sequence.
addModificationTerminus(String) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Adds a modification to the terminus of sequencing.
addModificationTerminus(String, double) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Adds a modification to the terminus of sequencing.
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
addMutation(Character, Character) - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Adds a possible mutation.
addMutation(Integer, Character) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Adds a mutation to the segment.
addNeutralLoss(NeutralLoss) - Static method in class com.compomics.util.experiment.biology.NeutralLoss: Adds a neutral loss to the class static map.
addNeutralLoss(NeutralLoss) - Method in class com.compomics.util.experiment.biology.PTM: Adds a neutral loss.
addNeutralLoss(NeutralLoss) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Adds a neutral loss.
addNeutralLoss(NeutralLoss, Integer, Integer) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap: Adds a new neutral loss to the map.
addNeutralLoss(String, Integer, Integer) - 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.SpecificAnnotationSettings: Adds a neutral loss.
addObject(String, String, String, Object, boolean) - Method in class com.compomics.util.db.ObjectsCache: Adds an object to the cache.
addPatientInformation(PatientInformation, Comparable) - Method in class com.compomics.util.experiment.patient.Patient: Adds patient information,
addPeak(Peak) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Adds a peak to the spectrum peak list.
addPeptideMatch(PeptideMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds a peptide match to the database.
addPeptideMatchKey(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Add a subordinated peptide key.
addPeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Adds a peptide match parameter to the database.
addPeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds a peptide match parameter to the database.
addPeptideNormalisationFactor(String, double) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors: Adds a peptide normalization factor.
addProteinMatch(ProteinMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds a protein match to the database.
addProteinMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Adds a protein match parameter to the database.
addProteinMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds a protein match parameter to the database.
addProteinNormalisationFactor(String, double) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors: Adds a protein normalization factor.
addProteinTreeImportTime(long, long) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Adds a protein tree import time.
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.
addQuantificationResults(Quantification.QuantificationMethod, Quantification) - Method in class com.compomics.util.experiment.ProteomicAnalysis: Adds quantification results to the current analysis.
addRawAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>) - Method in class com.compomics.util.experiment.identification.Identification: Adds the raw assumptions corresponding to a spectrum to the database.
addRawAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds raw assumptions for a given match to the database.
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(PTM) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Adds a fixed refinement modification.
addRefinementVariableModification(PTM) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Adds a variable refinement modification.
addReporterIon(ReporterIon) - Static method in class com.compomics.util.experiment.biology.ions.ReporterIon: Adds a reporter ion to the class static map.
addReporterIon(ReporterIon) - Method in class com.compomics.util.experiment.biology.PTM: Adds a reporter ion.
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.preferences.PsmScoringPreferences: 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.SpecificAnnotationSettings: 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
addSequenceSegmentsToCache(HashMap<Integer, ArrayList<SequenceSegment>>, String, AminoAcid, Integer, Integer, boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Adds the possible new sequence segments generated when appending the given amino acid to the given cache and returns the list of possible segments.
addSequenceSegmentsToCacheSynchronized(HashMap<Integer, ArrayList<SequenceSegment>>, String, AminoAcid, Integer, Integer, boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Adds the possible new sequence segments generated when appending the given amino acid to the given cache and returns the list of possible segments.
addSharedProteinNormalisationFactor(String, double) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors: Adds a unique protein normalization factor.
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.
addSpectra(File) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Add spectra to the factory.
addSpectra(File, WaitingHandler) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Add spectra to the factory.
addSpectrumMatch(SpectrumMatch) - Method in class com.compomics.util.experiment.identification.Identification: Adds a spectrum match to the identification.
addSpectrumMatch(SpectrumMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds a spectrum match to the database.
addSpectrumMatches(Iterable<SpectrumMatch>) - Method in class com.compomics.util.experiment.identification.Identification: Add a set of spectrumMatches to the model.
addSpectrumMatchKey(String) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch: Add a spectrum match key.
addSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Adds a spectrum match parameter to the database.
addSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Adds a spectrum match parameter to the database.
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.
addTable(String) - Method in class com.compomics.util.db.ObjectsDB: Adds the desired table in the database.
addTheoreticProtein(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Setter for the matching protein.
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, WaitingHandler, long) - Static method in class com.compomics.util.io.compression.ZipUtils: Adds a new file to the zip stream.
addUniqueProteinNormalisationFactor(String, double) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors: Adds a unique protein normalization factor.
addUrParam(UrParameter) - Method in class com.compomics.util.experiment.personalization.ExperimentObject: Method to add a user refinement parameter.
addUserAdvocate(String) - Static method in class com.compomics.util.experiment.identification.Advocate: Adds a user advocate and returns it.
addUserPTM(PTM) - Method in class com.compomics.util.experiment.biology.PTMFactory: Adds a new user modification.
addVariableModification(PTM) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Adds a variable modification.
addVariableModifications(HashMap<String, Double>, SequenceSegment, ArrayList<SequenceSegment>) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Adds the potential sequence segments obtained after adding the given variable modifications on a segment terminus to the given list of possible segments.
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
AdvancedProteinDatabaseDialog - Class in com.compomics.util.gui.protein: A dialog for advanced database settings.
AdvancedProteinDatabaseDialog(Frame) - Constructor for class com.compomics.util.gui.protein.AdvancedProteinDatabaseDialog: Creates a new AdvancedProteinDatabaseDialog.
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 - 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: Alanine.
Alanine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Alanine: Constructor.
ALANINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for an alanine immonium ion.
AlgorithmSettingsDialog - Interface in com.compomics.util.gui.parameters.identification_parameters: Interface for an algorithm settings dialog.
align(Collection<Integer>, Collection<Integer>) - Static method in class com.compomics.util.experiment.identification.ptm.PtmSiteMapping: 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.ptm.PtmSiteMapping: Aligns two series of integer, minimizing the distance between them.
alignAll(HashMap<Integer, ArrayList<Integer>>) - Static method in class com.compomics.util.experiment.identification.ptm.PtmSiteMapping: 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(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(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(int, int, int, int, String, String) - Constructor for class com.compomics.util.pdbfinder.das.readers.AlignmentBlock: Constructor.
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.
AminoAcid - Class in com.compomics.util.experiment.biology: Class representing amino acids.
AminoAcid() - Constructor for class com.compomics.util.experiment.biology.AminoAcid
aminoAcidCombinations - Variable in class com.compomics.util.experiment.biology.AminoAcid: The amino acid combinations.
AminoAcidPattern - Class in com.compomics.util.experiment.biology: An amino acid pattern is a sequence of amino acids.
AminoAcidPattern() - Constructor for class com.compomics.util.experiment.biology.AminoAcidPattern: Creates a blank pattern.
AminoAcidPattern(String) - Constructor for class com.compomics.util.experiment.biology.AminoAcidPattern: Constructor taking a sequence of targeted amino acids as input.
AminoAcidPattern(AminoAcidSequence) - Constructor for class com.compomics.util.experiment.biology.AminoAcidPattern: Creates an amino acid pattern based on the given amino acid sequence.
AminoAcidPattern(AminoAcidPattern) - Constructor for class com.compomics.util.experiment.biology.AminoAcidPattern: Creates a pattern from another pattern.
AminoAcidPattern(ArrayList<String>) - Constructor for class com.compomics.util.experiment.biology.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.
aminoAcidScores - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: The individual amino acid scores.
AminoAcidSequence - Class in com.compomics.util.experiment.biology: This class represents a series of amino acids with associated modifications.
AminoAcidSequence() - Constructor for class com.compomics.util.experiment.biology.AminoAcidSequence: Creates a blank sequence.
AminoAcidSequence(String) - Constructor for class com.compomics.util.experiment.biology.AminoAcidSequence: Constructor taking a sequence of amino acids as input.
AminoAcidSequence(String, HashMap<Integer, ArrayList<ModificationMatch>>) - Constructor for class com.compomics.util.experiment.biology.AminoAcidSequence: Constructor taking a sequence of amino acids as input.
AminoAcidSequence(AminoAcidSequence) - Constructor for class com.compomics.util.experiment.biology.AminoAcidSequence: Creates a sequence from another sequence.
aminoAcidStrings - Static variable in class com.compomics.util.experiment.biology.AminoAcid: The amino acid one letter codes as string array.
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.
andromeda - Static variable in class com.compomics.util.experiment.identification.Advocate: The Andromeda search engine.
AndromedaIdfileReader - Class in com.compomics.util.experiment.io.identifications.idfilereaders: This IdfileReader reads identifications from an Andromeda result file.
AndromedaIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader: Default constructor for the purpose of instantiation.
AndromedaIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader: Constructor for an Andromeda result file reader.
AndromedaParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: The Andromeda specific parameters.
AndromedaParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Constructor.
AndromedaSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for the Andromeda specific settings.
AndromedaSettingsDialog(Frame, AndromedaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.AndromedaSettingsDialog: Creates a new TideSettingsDialog with a frame as owner.
AndromedaSettingsDialog(Dialog, Frame, AndromedaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.AndromedaSettingsDialog: Creates a new TideSettingsDialog 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.
AnnotationSettings - Class in com.compomics.util.experiment.identification.spectrum_annotation: This class contains the spectrum annotation preferences.
AnnotationSettings() - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Constructor.
AnnotationSettings(SearchParameters) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Constructor setting preferences from search parameters.
AnnotationSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters: A simple dialog for setting the spectrum annotation preferences.
AnnotationSettingsDialog(Frame, AnnotationSettings, double, ArrayList<NeutralLoss>, ArrayList<Integer>, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.AnnotationSettingsDialog: Creates a new AnnotationPreferencesDialog with a frame as owner.
AnnotationSettingsDialog(Dialog, Frame, AnnotationSettings, double, ArrayList<NeutralLoss>, ArrayList<Integer>, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.AnnotationSettingsDialog: Creates a new AnnotationPreferencesDialog with a dialog as owner.
AplExporter - Class in com.compomics.util.experiment.io.massspectrometry.export: This converter writes spectrum files in APL format.
AplExporter() - Constructor for class com.compomics.util.experiment.io.massspectrometry.export.AplExporter
append(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Appends another pattern at the end of this pattern.
append(AtomImpl) - Method in class com.compomics.util.experiment.biology.AtomChain: Appends an atom to the chain of atoms.
append(AtomImpl, int) - Method in class com.compomics.util.experiment.biology.AtomChain: Appends an atom to the chain of atoms.
append(File, File) - Static method in class com.compomics.util.Util: Appends the content of a file to another.
appendAscii(String) - Method in class com.compomics.util.io.FTP: APPEND (with create) to a file to the FTP server in Ascii mode.
appendBinary(String) - Method in class com.compomics.util.io.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.AminoAcidSequence: Appends another sequence at the end of this sequence.
appendCTerm(String) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Appends a series of unmodified amino acids to the sequence.
appendDecoySequences(File) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Appends decoy sequences to the desired file.
appendDecoySequences(File, WaitingHandler) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Appends decoy sequences to the desired file while displaying progress.
appendLines(DoubleMatrix) - Method in class com.compomics.util.math.matrix.DoubleMatrix
appendNTerm(AminoAcidSequence) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Appends another sequence at the beginning of this sequence keeping the original order.
appendNTerm(String) - Method in class com.compomics.util.experiment.biology.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: Append a new line to the report.
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: Append tabs to the report.
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.Util: Appends a suffix to a file name before the file extension.
appendTerminus(SequenceSegment) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Appends a sequence segment to the terminus of sequencing.
appendTerminus(AminoAcidSequence) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Appends an amino acid sequence to the terminus of sequencing.
appendTerminus(AminoAcidPattern) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Appends an amino acid pattern to the terminus of sequencing.
appendTerminus(AminoAcid) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Appends an amino acid to the terminus of sequencing.
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.AnnotationSettings: Returns whether neutral losses are considered only for amino acids of interest or not.
Arginine - Class in com.compomics.util.experiment.biology.aminoacids: Arginine.
Arginine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Arginine: Constructor.
ARGININE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for an arginine immonium ion.
AscendingIntensityComparator - Static variable in class com.compomics.util.experiment.massspectrometry.Peak: This comparator compares two Peak instances on ascending intensity.
AscendingMzComparator - Static variable in class com.compomics.util.experiment.massspectrometry.Peak: This comparator compares two Peak instances on ascending m/z value.
ascii() - Method in class com.compomics.util.io.FTP: Set transfer type to 'A' (ascii transfer).
AScore - Class in com.compomics.util.experiment.identification.ptm.ptmscores: This class estimates the A-score as described in http://www.ncbi.nlm.nih.gov/pubmed/16964243 Note: Here the window size is adapted to mz tolerance and the score is not restricted to phosphorylation.
AScore() - Constructor for class com.compomics.util.experiment.identification.ptm.ptmscores.AScore
asMgf() - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Returns the peak list as an mgf bloc.
asMgf(HashMap<String, String>) - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Returns the peak list as an mgf bloc.
Asparagine - Class in com.compomics.util.experiment.biology.aminoacids: Asparagine.
Asparagine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Asparagine: Constructor.
ASPARAGINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for an asparagine immonium ion.
ASPARTIC_ACID - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for an aspartic acid immonium ion.
AsparticAcid - Class in com.compomics.util.experiment.biology.aminoacids: Aspartic Acid.
AsparticAcid() - Constructor for class com.compomics.util.experiment.biology.aminoacids.AsparticAcid: Constructor.
asSequence() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
asSequence(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the component of the amino acid pattern at the given index.
asSequence() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence
asSequence() - Method in class com.compomics.util.experiment.biology.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, Sample) - 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.AminoAcidPattern: Returns the sequence represented by this amino acid pattern in a new string builder.
Atom - Class in com.compomics.util.experiment.biology: This interface contains information about atoms.
Atom() - Constructor for class com.compomics.util.experiment.biology.Atom
AtomChain - Class in com.compomics.util.experiment.biology: A chain of atoms.
AtomChain() - Constructor for class com.compomics.util.experiment.biology.AtomChain: Creates an empty atom chain.
AtomChain(boolean) - Constructor for class com.compomics.util.experiment.biology.AtomChain: Creates an empty atom chain.
AtomChain(String) - Constructor for class com.compomics.util.experiment.biology.AtomChain: Constructor for a monoisotopic chain as a string of additions, e.g.
AtomChain(String, boolean) - Constructor for class com.compomics.util.experiment.biology.AtomChain: Constructor for a monoisotopic chain as a string, e.g.
atomChain - Variable in class com.compomics.util.experiment.biology.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: Class for a specific atom.
AtomImpl(Atom, Integer) - Constructor for class com.compomics.util.experiment.biology.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.
averageMass - Variable in class com.compomics.util.experiment.biology.AminoAcid: Average mass of the amino acid.
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.AminoAcid
B - Class in com.compomics.util.experiment.biology.aminoacids: Asn or Asp: Asx (Mascot).
B() - Constructor for class com.compomics.util.experiment.biology.aminoacids.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.PeptideFragmentIon: Identifier for a b ion.
B_ION - Static variable in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Identifier for a b ion.
backwardCompatibilityFix() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap: Backward compatibility fix for objects of utilities version older than 4.2.16.
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
BasicMathFunctions - Class in com.compomics.util.math: Class used to perform basic mathematical functions.
BasicMathFunctions() - Constructor for class com.compomics.util.math.BasicMathFunctions
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
BigMathUtils - Class in com.compomics.util.math: Utils for the manipulation of big numbers.
BigMathUtils() - Constructor for class com.compomics.util.math.BigMathUtils
binary() - Method in class com.compomics.util.io.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
BinomialDistribution - Class in com.compomics.util.math.statistics.distributions: Implementation of a binomial distribution.
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.
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.
buildPeptides(String, ArrayList<SequenceSegment>, String, ArrayList<SequenceSegment>, HashMap<Integer, ArrayList<ModificationMatch>>, int) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Builds the possible peptides based on the given terminal segments and the seed sequence.
buildPeptidesAndProteins(WaitingHandler, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.Identification: Creates the peptides and protein instances based on the spectrum matches.
buildPeptidesAndProteins(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.Identification: Creates the peptides and protein instances based on the given spectrum match.
buildTreeAfterClick(String) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel: Build tree after click.
buildTreeAfterSearch(String) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel: Build the ree after search.
buildTreeFromTabFile(File) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel: Build the tree from a tab file.
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
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.AminoAcid
C - Static variable in class com.compomics.util.experiment.biology.Atom: The carbon atom.
C3H9N - Static variable in class com.compomics.util.experiment.biology.NeutralLoss: C3H9N loss.
C_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Identifier for a c ion.
C_ION - Static variable in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Identifier for a c ion.
C_TERM_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
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.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli
canceled() - Method in class com.compomics.util.gui.filehandling.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: Carbon.
Carbon() - Constructor for class com.compomics.util.experiment.biology.atoms.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: CD to a specific directory on a remote FTP server.
cdup() - Method in class com.compomics.util.io.FTP: Go up one directory on remote system.
CH4OS - Static variable in class com.compomics.util.experiment.biology.NeutralLoss: CH4OS loss.
changeModificationSite(ModificationMatch, int, int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Changes the localization of a modification match.
changeModificationSite(ModificationMatch, int, int) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Changes the localization of a modification match.
charAt(int) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the amino acid at the given index on the sequence in its single letter code.
charge - Variable in class com.compomics.util.experiment.identification.matches.IonMatch: The supposed charge of the ion.
Charge - Class in com.compomics.util.experiment.massspectrometry: This class models a charge.
Charge(int, int) - Constructor for class com.compomics.util.experiment.massspectrometry.Charge: Constructor for a charge.
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.
checkDbFiles() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Removes the db files which do not exist anymore.
checkDuplicateTitles() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns if the spectra should be checked for duplicate titles or not.
checkFixedModifications(PtmSettings, Peptide, SequenceMatchingPreferences, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.PTMFactory: Removes the fixed modifications of the peptide and remaps the one searched for according to the ModificationProfile.
checkFixedModifications(PtmSettings, Tag, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.PTMFactory: Removes the fixed modifications of the given tag and remaps the one searched for according to the ModificationProfile.
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.Util: 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.preferences.UtilitiesUserPreferences: Returns if the mgf should be checked for size.
checkModel() - Method in class com.compomics.util.sun.TableSorter
checkPeakPicking() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns if the spectra should be checked for peak picking or not.
checkSetup() - Method in class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Checks that the too is properly installed.
checkTable(Collection<String>, String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Verifies that a table exists and creates it if not.
ChromatogramPanel - Class in com.compomics.util.gui.spectrum: This class provides a JPanel that can display a profileChromatogram.
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.
clearAccessions() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Clears the accessions of this node.
clearCache() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Clears the cache.
clearCache() - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Clears the cache.
clearCharges() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Clears the selected charges.
clearDatabaseSelection() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog: Clears the database selection and information.
clearDatabaseSelection() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromUniprotDialog: Clears the database selection and information.
clearFactory() - Method in class com.compomics.util.experiment.biology.PTMFactory: Clears the factory getInstance() needs to be called afterwards.
clearFactory() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Clears the factory getInstance() needs to be called afterwards.
clearFactory() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Clears the factory getInstance() needs to be called afterwards.
clearFixedModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Clears fixed modifications.
clearIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Clears the ion types annotated.
clearIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Clears the ion types annotated.
clearModificationMatches() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Clears the list of imported modification matches.
clearModificationMatches() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Clears the list of imported modification matches.
clearModificationMatches() - Method in class com.compomics.util.experiment.biology.Peptide: Clears the list of imported modification matches.
clearNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: 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.SpecificAnnotationSettings: Clears the considered neutral losses.
clearProteinTreeImportTimes() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Clears the protein tree import times.
clearRefinementModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Clears refinement modifications.
clearTagsMap() - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader: Clears the tags map.
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader
clearTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader
clearVariableModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Clears variable modifications.
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
clone() - Method in class com.compomics.util.experiment.biology.AtomChain
clone() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
clone() - Method in class com.compomics.util.experiment.biology.NeutralLoss
clone() - Method in interface com.compomics.util.experiment.filtering.Filter: Clones the filter.
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.spectrum_annotation.AnnotationSettings: 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.SpecificAnnotationSettings
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.Header: This method provides a deep copy of the Header instance.
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.util.db.ObjectsDB: Closes the db connection.
close() - Method in class com.compomics.util.experiment.identification.Identification: Closes the database connection.
close() - Method in class com.compomics.util.experiment.identification.IdentificationDB: Closes the db connection.
close() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Closes all connections to files, tries to delete corrupted and deprecated trees.
close() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Closes the factory, closes all connection and deletes the file.
close() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.HeaderIterator: Closes the connection to the file.
close() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.ProteinIterator: Closes the connection to the file.
close() - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader: Closes the file reader.
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader
close() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader
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.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.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Deletes the temp folder and closes the dialog.
closeConnection() - Static method in class com.compomics.util.db.DerbyUtil: Shuts Derby down completely thus releasing the file lock in the database folder.
closeFile() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Closes the opened file.
closeFiles() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Closes all opened files.
closeServer() - Method in class com.compomics.util.io.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.
collapseAll() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel: Collapses all found nodes in the taxonomy tree.
color2Hex(Color) - Static method in class com.compomics.util.Util: Converts a color to hex format for use in HTML tags.
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
com.compomics.software - package com.compomics.software: Helper 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.dialogs - package com.compomics.software.dialogs: Dialogs for starting compomics-utilities tools and setting their Java options.
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.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 - package com.compomics.util.experiment.biology: Experiment classes related to biological entities.
com.compomics.util.experiment.biology.aminoacids - package com.compomics.util.experiment.biology.aminoacids: The amino acid classes.
com.compomics.util.experiment.biology.atoms - package com.compomics.util.experiment.biology.atoms: The atom classes.
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.mutations - package com.compomics.util.experiment.biology.mutations: Experiment classes related to mutations.
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.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.amino_acid_tags.matchers - package com.compomics.util.experiment.identification.amino_acid_tags.matchers: Tag matching classes.
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.identification_parameters - package com.compomics.util.experiment.identification.identification_parameters: Parameters settings for the spectrum identification algorithms.
com.compomics.util.experiment.identification.identification_parameters.tool_specific - package com.compomics.util.experiment.identification.identification_parameters.tool_specific: Parameters settings for the search algorithms.
com.compomics.util.experiment.identification.identifications - package com.compomics.util.experiment.identification.identifications: Experiment classes related to MS//MS identifications.
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.parameters_cli - package com.compomics.util.experiment.identification.parameters_cli: Identification search parameters.
com.compomics.util.experiment.identification.protein_inference.proteintree - package com.compomics.util.experiment.identification.protein_inference.proteintree: Protein sequence database indexing classes.
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.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.ptm - package com.compomics.util.experiment.identification.ptm: Additional PSM scoring classes.
com.compomics.util.experiment.identification.ptm.ptmscores - package com.compomics.util.experiment.identification.ptm.ptmscores: PTM scores.
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.spectrum_annotators - package com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators: Spectrum annotation.
com.compomics.util.experiment.identification.spectrum_assumptions - package com.compomics.util.experiment.identification.spectrum_assumptions: Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.io - package com.compomics.util.experiment.io: Experiment IO classes.
com.compomics.util.experiment.io.identifications - package com.compomics.util.experiment.io.identifications: Experiment identification classes.
com.compomics.util.experiment.io.identifications.idfilereaders - package com.compomics.util.experiment.io.identifications.idfilereaders: Experiment classes related to reading search engine files.
com.compomics.util.experiment.io.massspectrometry - package com.compomics.util.experiment.io.massspectrometry: Reading and indexing of mgf files.
com.compomics.util.experiment.io.massspectrometry.export - package com.compomics.util.experiment.io.massspectrometry.export: Experiment classes related to exporting mass spectrometry files.
com.compomics.util.experiment.massspectrometry - package com.compomics.util.experiment.massspectrometry: Experiment classes related to spectra.
com.compomics.util.experiment.massspectrometry.proteowizard - package com.compomics.util.experiment.massspectrometry.proteowizard: Package containing the classes used to interact with ProteoWizard.
com.compomics.util.experiment.massspectrometry.proteowizard.gui - package com.compomics.util.experiment.massspectrometry.proteowizard.gui: Package containing the GUI classes used to interact with ProteoWizard.
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.refinementparameters - package com.compomics.util.experiment.refinementparameters: 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.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.filehandling - package com.compomics.util.gui.filehandling: File handling.
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.parameters - package com.compomics.util.gui.parameters: GUI classes for parameters, settings and preferences.
com.compomics.util.gui.parameters.identification_parameters - package com.compomics.util.gui.parameters.identification_parameters: GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.gui.parameters.identification_parameters.algorithm_settings - package com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Search algorithm settings dialogs.
com.compomics.util.gui.protein - package com.compomics.util.gui.protein: GUI class related to protein sequence formatting.
com.compomics.util.gui.ptm - package com.compomics.util.gui.ptm: PTM GUI dialogs.
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.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.export - package com.compomics.util.io.export: Classes related to exporting reports.
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.filefilters - package com.compomics.util.io.filefilters: Classes related to file filters.
com.compomics.util.io.json - package com.compomics.util.io.json: JSON marshaller.
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.maps - package com.compomics.util.maps: Classes related to maps.
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.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.preferences - package com.compomics.util.preferences: Utilities preferences classes.
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.protein_sequences_manager - package com.compomics.util.protein_sequences_manager: Classes used for the management of FASTA files.
com.compomics.util.protein_sequences_manager.enums - package com.compomics.util.protein_sequences_manager.enums: Enums used for the management of FASTA files.
com.compomics.util.protein_sequences_manager.gui - package com.compomics.util.protein_sequences_manager.gui: GUI classes used for the management of FASTA files.
com.compomics.util.protein_sequences_manager.gui.preferences - package com.compomics.util.protein_sequences_manager.gui.preferences: Classes used for the preferences for the management of FASTA files.
com.compomics.util.protein_sequences_manager.gui.sequences_import - package com.compomics.util.protein_sequences_manager.gui.sequences_import: GUI classes for importing of FASTA files.
com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy - package com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy: Classes related to FASTA taxonomy.
com.compomics.util.sun - package com.compomics.util.sun: Classes related to Java's Swing library.
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.experiment.identification.identification_parameters.tool_specific: The Comet specific parameters.
CometParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Constructor.
CometParameters.CometOutputFormat - Enum in com.compomics.util.experiment.identification.identification_parameters.tool_specific: The available output formats.
CometSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for the Comet specific settings.
CometSettingsDialog(Frame, CometParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.CometSettingsDialog: Creates a new CometSettingsDialog with a frame as owner.
CometSettingsDialog(Dialog, Frame, CometParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.CometSettingsDialog: Creates a new CometSettingsDialog with a dialog as owner.
command - Variable in class com.compomics.util.io.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.massspectrometry.proteowizard.MsFormat: 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: This class groups some convenience methods for the use of compomics tools in command line.
CommandLineUtils() - Constructor for class com.compomics.software.CommandLineUtils
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(Peak) - Method in class com.compomics.util.experiment.massspectrometry.Peak: Compare two peaks in regards to their intensity.
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
ComplementarityScore - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores: The intensity sub-score as adapted from the DirecTag manuscript (http://www.ncbi.nlm.nih.gov/pubmed/18630943).
ComplementarityScore() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.ComplementarityScore
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.
computeMolecularWeight() - Method in class com.compomics.util.experiment.biology.Protein: Returns the protein's molecular weight.
computeMolecularWeight(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the protein's molecular weight in kDa.
concatenate(ArrayList<String>) - Static method in class com.compomics.software.CommandLineUtils: Returns the list of arguments as space separated string for the command line.
concatenate(String[]) - Static method in class com.compomics.software.CommandLineUtils: Returns the list of arguments as space separated string for the command line.
concatenatedTargetDecoy() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Indicates whether the database loaded contains decoy sequences.
ConfigurationFile - Class in com.compomics.util.io: Generic configuration text file.
ConfigurationFile(File) - Constructor for class com.compomics.util.io.ConfigurationFile: Constructor.
configurationFileName - Static variable in class com.compomics.software.settings.UtilitiesPathPreferences: 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.
CONNECTION_LOG_TABLE - Static variable in class com.compomics.util.db.ObjectsDB: The name of the table to use to log connections.
ConnectionDialog - Class in com.compomics.util.gui.utils: This class implements a dialog to gather all information concerning a DB connection.
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.
ConnectionManager - Class in com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy: Connection manager.
ConnectionManager() - Constructor for class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.ConnectionManager
Constants - Class in com.compomics.util.experiment: Convenience class listing constants used throughout the library.
Constants() - Constructor for class com.compomics.util.experiment.Constants
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(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(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(ArrayList<Contact>, String) - Constructor for class com.compomics.util.pride.prideobjects.ContactGroup: Create a new ContactGroup object.
contains(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the pattern contains a subsequence of amino acids.
contains(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the pattern contains a subsequence of amino acids.
contains(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Indicates whether the modification is contained in the profile, looking into all modifications (fixed, variable and refinement)
contains(String, String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns a boolean indicating whether a protein match contains another set of matches.
contains(HashSet<String>, ArrayList<String>) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns a boolean indicating whether a protein match contains another set of matches.
contains(ProteinMatch) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns a boolean indicating whether the protein match contains another set of theoretic proteins.
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.protein.AASequenceImpl: This method reports whether a certain residu (or fixed sequence String) is found in the current sequence.
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.
containsPTM(String) - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns a boolean indicating whether the PTM is loaded in the factory.
containsSpectrum(String) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns a boolean indicating whether the spectrum title is implemented in this index.
controlSocket - Variable in class com.compomics.util.io.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.
convertPridePtm(String, PtmSettings, ArrayList<String>, boolean) - Method in class com.compomics.util.experiment.biology.PTMFactory: Tries to convert a PRIDE PTM to utilities PTM name, and add it to the modification profile.
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).
copyFile(File, File) - Static method in class com.compomics.util.Util: Copy the content of a file to another.
copyFile(File, File, boolean) - Static method in class com.compomics.util.Util: Copy the content of one file to another.
correctFastaName(String) - Static method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Corrects the name of the given FASTA file.
correctKey(String, String) - Method in class com.compomics.util.db.ObjectsDB: Indexes the long keys by a number.
correctTableName(String) - Method in class com.compomics.util.db.ObjectsDB: Surrounds the table name with quotation marks such that spaces etc are allowed.
createDefaultGeneMappingFiles(File, File, File, File, boolean) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Copies the given gene mapping files to the gene mappings folder.
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.filefilters.FileFilterUtils: Returns an ImageIcon, or null if the path was invalid.
createMutations() - Static method in class com.compomics.util.experiment.biology.mutations.MutationFactory: This method creates all possible mutations for the 20 essential amino acids.
createOptionsCLI(Options) - Method in class com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli: Provides the options left to the user.
createPeptideFilter() - Method in interface com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialogParent: Allows the creation of a peptide filter.
createProteinFilter() - Method in interface com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialogParent: Allows the creation of a protein filter.
createPsmFilter() - Method in interface com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialogParent: Allows the creation of a PSM filter.
CTERM - Static variable in class com.compomics.util.protein.Enzyme
cTermCorrection - Variable in class com.compomics.util.experiment.io.identifications.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.identifications.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.
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).
CvTerm - Class in com.compomics.util.pride: A simple CvTerm object.
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: Change working directory to a specific directory on a remote FTP server.
Cysteine - Class in com.compomics.util.experiment.biology.aminoacids: Cysteine.
Cysteine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Cysteine: Constructor.
CYSTEINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a cysteine immonium ion.

D

D - Static variable in class com.compomics.util.experiment.biology.AminoAcid
DasAlignment - Class in com.compomics.util.pdbfinder.das.readers: DasAlignment.
DasAlignment(String) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAlignment: Constructor.
DasAnnotationServerAlingmentReader - Class in com.compomics.util.pdbfinder.das.readers: DasAnnotationServerAlingmentReader.
DasAnnotationServerAlingmentReader(String) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader: Creates a new reader for a XML string.
DasAnnotationServerResultReader - Class in com.compomics.util.pdbfinder.das.readers: DasAnnotationServerResultReader
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(String) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasFeature: Constructor.
dat - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
DAT - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
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(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(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.filefilters: File filter for *.dat files.
DatFileFilter() - Constructor for class com.compomics.util.io.filefilters.DatFileFilter
DBAccessor - Class in com.compomics.util.db: This class represents an accessor class' sourcecode as generated by the DBAccessorGenerator class.
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.
dbDirectory - Variable in class com.compomics.util.experiment.identification.Identification: The directory where the database stored.
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(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.
dbName - Variable in class com.compomics.util.experiment.identification.IdentificationDB: The name which will be used for the database.
dbName - Static variable in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: The name of the db to use.
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.
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_NON_VISIBLE_MARKER_ALPHA - Static variable in class com.compomics.util.gui.spectrum.MassErrorBubblePlot: The default non-visible alpha level.
DEFAULT_VISIBLE_MARKER_ALPHA - Static variable in class com.compomics.util.gui.spectrum.MassErrorBubblePlot: The default visible alpha level.
defaultBatchSize - Variable in class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator: The default batch size.
defaultBatchSize - Variable in class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator: The default batch size.
defaultBatchSize - Variable in class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: The default batch size.
defaultMargin - Variable in class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator: The default margin to use to start batch loading before the loading index is reached.
defaultMargin - Variable in class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator: The default margin to use to start batch loading before the loading index is reached.
defaultMargin - Variable in class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: The default margin to use to start batch loading before the loading index is reached.
defaultModsSorted - Variable in class com.compomics.util.experiment.biology.PTMFactory: Set to true if the default mods are sorted alphabetically.
defaultMutationMatrices - Static variable in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the implemented default mutation 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.UtilitiesPathPreferences: Replacement for the path when not available.
DefaultSpectrumAnnotation - Class in com.compomics.util.gui.spectrum: This class provides a default implementation of the SpectrumAnnotation interface.
DefaultSpectrumAnnotation(double, double, Color, String) - Constructor for class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation: Constructor creating a DefaultSpectrumAnnotation object.
defaultStringMatching - Static variable in class com.compomics.util.preferences.SequenceMatchingPreferences: Default string matching.
DefaultStyle - Class in com.compomics.util.io.export.styles: Default style for excel sheets.
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() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Sets the currently loaded database as corrupted and tries to delete it.
delete(String) - Method in class com.compomics.util.io.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 genereates the code to make a DBAccessor class an implementation of the Deleteable interface.
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.
deleteDb() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Try to delete the current database.
deleteDir(File) - Static method in class com.compomics.util.Util: Deletes all files and subdirectories under dir and dir itself.
deleteInstrument(Instrument) - Method in class com.compomics.util.pride.PrideObjectsFactory: Delete the given instrument.
deleteObject(String, String) - Method in class com.compomics.util.db.ObjectsDB: Deletes an object from the desired table.
deleteProteinTree(ExceptionHandler) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Try to delete the default protein tree.
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.
deleteTempFolders() - Static method in class com.compomics.util.gui.filehandling.TempFilesManager: Deletes the temp folders created.
deletOutdatedTrees() - Static method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Deletes the outdated trees.
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.
derbyConnectionID - Static variable in class com.compomics.util.db.ObjectsDB: The identifier used to register the derby connection in the DerbyUtil class.
DerbyUtil - Class in com.compomics.util.db: Disable the derby log file.
DerbyUtil() - Constructor for class com.compomics.util.db.DerbyUtil
DescendingIntensityComparator - Static variable in class com.compomics.util.experiment.massspectrometry.Peak: This comparator compares two Peak instances on descending intensity.
description - Variable in enum com.compomics.util.experiment.filtering.FilterItemComparator: The description to use.
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.parameters_cli.IdentificationParametersCLIParams: Explanation for the CLI parameter.
description - Variable in enum com.compomics.util.experiment.massspectrometry.proteowizard.MsFormat: A brief description of the format.
description - Variable in enum com.compomics.util.experiment.massspectrometry.proteowizard.ProteoWizardFilter: A brief description of the filter.
description - Variable in enum com.compomics.util.io.export.ExportFormat: Description of the format.
description - Variable in enum com.compomics.util.preferences.SearchGuiOutputOption: The description of the option.
description - Variable in enum com.compomics.util.preferences.SequenceMatchingPreferences.MatchingType: The description.
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.Glycan: Final index for deuteroacetylated masses.
DEUTEROMETHYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.Glycan: Final index for deuteromethylated masses.
DI_METHYL_R_112 - Static variable in class com.compomics.util.experiment.biology.ions.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.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.ReporterIon: Standard reporter ion for di-methylation of R (PMID: 16335983).
digest(String, int, int, int) - Method in class com.compomics.util.experiment.biology.Enzyme: Digests a protein sequence in a list of expected peptide sequences.
dir() - Method in class com.compomics.util.io.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.identifications.idfilereaders: An identification file reader for Direct tag results.
DirecTagIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Default constructor for the purpose of instantiation.
DirecTagIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Constructors, parses a file but does not index the results.
DirecTagIdfileReader(File, boolean) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Constructors, parses a file.
DirecTagParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: The DirecTag specific parameters.
DirecTagParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Constructor.
DirecTagSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for editing the DirecTag advanced settings.
DirecTagSettingsDialog(Frame, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog: Creates a new DirecTagSettingsDialog with a frame as owner.
DirecTagSettingsDialog(Dialog, Frame, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog: Creates a new DirecTagSettingsDialog with a dialog as owner.
disabledDerbyLog() - Static method in class com.compomics.util.db.DerbyUtil: Returns the disabled Derby log file.
disableDerbyLog() - Static method in class com.compomics.util.db.DerbyUtil: Disable the derby log.
disconnect() - Method in class com.compomics.util.io.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(Distribution, Distribution) - Constructor for class com.compomics.util.math.roc.DistributionRoc: Constructor.
DNA_FOLDER - Static variable in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Name of the folder containing DNA translated files.
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
downloadDatabase() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromUniprotDialog: Copies the selected database to the temp folder and populates the GUI with the relevant information.
downloadFile(String, File) - Method in class com.compomics.util.io.FTPDownloader: Download the given file from the FTP server.
downloadFileFromURL(ImportSequencesFromUniprotDialog, URL, File, ProgressDialogX) - Static method in class com.compomics.util.protein_sequences_manager.DownloadingUtil: Download a file from a URL.
downloadGeneMappings(String, String, String, String, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Download the gene mappings.
downloadGeneSequences(File, String, String, String, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Download the gene sequences mappings.
downloadGoMappings(String, String, String, boolean, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Download the GO mappings.
DownloadingUtil - Class in com.compomics.util.protein_sequences_manager: Helper class for downloading a file from a URL.
DownloadingUtil() - Constructor for class com.compomics.util.protein_sequences_manager.DownloadingUtil
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.GeneFactory: 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.filefilters.FileFilterUtils
DTA - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
DtaFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.dta files.
DtaFileFilter() - Constructor for class com.compomics.util.io.filefilters.DtaFileFilter
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(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.
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.preferences: Dummy parameters used to retrieve the parameters type.
DummyParameters() - Constructor for class com.compomics.util.preferences.DummyParameters
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.AminoAcid
E - Static variable in class com.compomics.util.math.BigMathUtils: Big decimal value of E.
editFilter(Filter) - Method in interface com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialogParent: Allows the edition of a filter.
ElementaryElement - Class in com.compomics.util.experiment.biology: This class can be used to retrieve elementary elements like a neutron.
ElementaryIon - Class in com.compomics.util.experiment.biology.ions: This class represents an elementary ion.
ElementaryIon(String, double, int) - Constructor for class com.compomics.util.experiment.biology.ions.ElementaryIon: Constructor.
emptyCache() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Empties the cache.
emptyCache() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Empties the cache of the factory.
emptyCache() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Empties the cache.
emptyDir(File) - Static method in class com.compomics.util.Util: Deletes all files and subdirectories under dir.
emptyInternalCaches() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: the sequence is kept in different formats internally.
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
ENTIRELY_NOT_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
Enzyme - Class in com.compomics.util.experiment.biology: This class models an enzyme.
Enzyme(int, String, String, String, String, String) - Constructor for class com.compomics.util.experiment.biology.Enzyme: Constructor for an Enzyme.
Enzyme(int, String, String, String, String, String, Boolean, Boolean) - Constructor for class com.compomics.util.experiment.biology.Enzyme: Constructor for an Enzyme.
Enzyme - Class in com.compomics.util.protein: This class implements the functionality for an Enzyme.
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: This factory will provide the implemented enzymes.
enzymeLoaded(String) - Method in class com.compomics.util.experiment.biology.EnzymeFactory: Indicates whether an enzyme is loaded in the factory.
enzymeMapping(Enzyme) - Static method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Tries to map the utilities enzyme to the enzymes supported by MyriMatch.
EnzymeSelectionDialog - Class in com.compomics.util.gui.parameters.identification_parameters: Simple dialog for mapping a PRIDE enzyme to a utilities enzyme.
EnzymeSelectionDialog(Frame, boolean, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.EnzymeSelectionDialog: Creates a new EnzymeSelectionDialog with a frame as owner.
EnzymeSelectionDialog(Dialog, Frame, boolean, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.EnzymeSelectionDialog: Creates a new EnzymeSelectionDialog with a dialog as owner.
EnzymeSelectionDialog(JDialog, boolean, String) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.EnzymeSelectionDialog: Creates a new EnzymeSelectionDialog.
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.AminoAcid
equals(Enzyme) - Method in class com.compomics.util.experiment.biology.Enzyme: Returns true of the two enzymes are identical.
equals(Mutation) - Method in class com.compomics.util.experiment.biology.mutations.Mutation: Overwritten equals method.
equals(IdentificationAlgorithmParameter) - Method in interface com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter: Indicates whether another identificationAlgorithmParameter has the same parameters.
equals(PtmSettings) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Returns true of the two profiles are identical.
equals(SearchParameters) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns true if the search parameter objects have identical settings.
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters
equals(IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters
equals(Object) - Method in class com.compomics.util.experiment.massspectrometry.Charge
equals(Object) - Method in class com.compomics.util.experiment.massspectrometry.Peak
equals(DoubleMatrix) - Method in class com.compomics.util.math.matrix.DoubleMatrix
equals(GenePreferences) - Method in class com.compomics.util.preferences.GenePreferences: Compares these preferences to other preferences.
equals(IdentificationParameters) - Method in class com.compomics.util.preferences.IdentificationParameters: Returns true if the identification parameter objects have identical settings.
equals(IdMatchValidationPreferences) - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Returns true if the objects have identical settings.
equals(ProteinInferencePreferences) - Method in class com.compomics.util.preferences.ProteinInferencePreferences: Returns true if the objects have identical settings.
equals(PsmScoringPreferences) - Method in class com.compomics.util.preferences.PsmScoringPreferences: Returns true if the objects have identical settings.
equals(PTMScoringPreferences) - Method in class com.compomics.util.preferences.PTMScoringPreferences: Returns true if the objects have identical settings.
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.
equalsExceptValidationPreferences(IdentificationParameters) - Method in class com.compomics.util.preferences.IdentificationParameters: Returns true if the identification parameter objects have identical settings except for the validation preferences.
error(SAXParseException) - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler: Receive notification of a recoverable error.
establishConnection(String, boolean, ObjectsCache) - Method in class com.compomics.util.db.ObjectsDB: Establishes connection to the database.
establishConnection(String, boolean, ObjectsCache) - Method in class com.compomics.util.experiment.identification.Identification: Establishes a connection to the database.
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.
estimateTheoreticMass() - Method in class com.compomics.util.experiment.biology.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(File) - Constructor for class com.compomics.util.io.export.writers.ExcelWriter: Constructor.
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
excludeNullValues(Double[]) - Method in class com.compomics.util.math.statistics.distributions.NormalKernelDensityEstimator: Exclude null values from an array of double.
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.
expandAll() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel: Expands all found nodes in the taxonomy tree.
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.
ExperimentIO - Class in com.compomics.util.experiment.io: This class takes care of the saving and opening of Compomics utilities experiment objects via serialization.
ExperimentIO() - Constructor for class com.compomics.util.experiment.io.ExperimentIO: Constructor
ExperimentObject - Class in com.compomics.util.experiment.personalization: This abstract class provides customization facilities.
ExperimentObject() - Constructor for class com.compomics.util.experiment.personalization.ExperimentObject
experimentObjectName - Static variable in class com.compomics.util.experiment.MsExperiment: The name of the serialized experiment.
Export - Class in com.compomics.util: Includes export to figure formats for Components and JFreeCharts.
Export() - Constructor for class com.compomics.util.Export
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(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
extension - Static variable in class com.compomics.util.pride.PrideObjectsFactory: The extension to use when saving objects.
extention - Variable in enum com.compomics.util.io.export.ExportFormat: The extention to use for this format.
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.AminoAcid
factorial(Integer) - Static method in class com.compomics.util.math.BasicMathFunctions: Returns n! as a long.
factorial(Integer, Integer) - Static method in class com.compomics.util.math.BasicMathFunctions: Returns n!/k!, null 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.
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.filefilters.FileFilterUtils
fas - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
FASTA - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
fasta - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
FastaFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.fasta files.
FastaFileFilter() - Constructor for class com.compomics.util.io.filefilters.FastaFileFilter
FastaIndex - Class in com.compomics.util.experiment.identification.protein_sequences: This class contains the index of a FASTA file.
FastaIndex(HashMap<String, Long>, HashSet<String>, String, String, boolean, boolean, int, long, Header.DatabaseType, HashMap<Header.DatabaseType, Integer>, String, String, HashMap<String, Integer>) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Constructor.
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.
FeedBack - Class in com.compomics.util.messages: This class is used to report a message to the user.
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: Pre-defined state.
FILE_PUT - Static variable in class com.compomics.util.io.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
FileAndFileFilter - Class in com.compomics.util: Store the selected file and the file type description.
FileAndFileFilter(File, FileFilter) - Constructor for class com.compomics.util.FileAndFileFilter: Create a new FileAndFileFilter object.
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.filehandling: 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.filehandling.FileDisplayDialog: Creates a new FileSelectionDialog.
FileDisplayDialog(JDialog, ArrayList<File>, boolean) - Constructor for class com.compomics.util.gui.filehandling.FileDisplayDialog: Creates a new FileSelectionDialog.
FileFilterUtils - Class in com.compomics.util.io.filefilters: Organizes the file filters.
FileFilterUtils() - Constructor for class com.compomics.util.io.filefilters.FileFilterUtils
fileLoaded(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns a boolean indicating whether the spectrum file has been loaded.
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 - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum: Spectrum file name.
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.massspectrometry.proteowizard.MsFormat: The file name ending of the format.
FilenameExtensionFilter - Class in com.compomics.util.io: This class will implement a FilenameFilter that filters on the extension of files.
FilenameExtensionFilter(String) - Constructor for class com.compomics.util.io.FilenameExtensionFilter: This constructor takes an extension to filter on.
FilenameExtensionFilter(String, String) - Constructor for class com.compomics.util.io.FilenameExtensionFilter: This constructor takes an extension to filter on.
FileSelectionDialog - Class in com.compomics.util.gui.filehandling: A simple dialog for selecting between different files.
FileSelectionDialog(JFrame, ArrayList<File>, String) - Constructor for class com.compomics.util.gui.filehandling.FileSelectionDialog: Creates a new FileSelection dialog.
FileSelectionDialog(JDialog, ArrayList<File>, String) - Constructor for class com.compomics.util.gui.filehandling.FileSelectionDialog: Creates a new FileSelection dialog.
FileSystemAccessor - Class in com.compomics.util.io: This class serves as a fast OS independent access point to the file system.
FileSystemAccessor() - Constructor for class com.compomics.util.io.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, ArrayList<Integer>>, ArrayList<NeutralLoss>, boolean, boolean, boolean) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel: Deprecated.
don't use method based on the peak labels but on the data type
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.
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.
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.
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(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, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the first index where the amino acid pattern is found.
firstIndex(AminoAcidSequence, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the first index where the amino acid pattern is found.
firstIndex(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the first index where the amino acid pattern is found.
firstIndex(String, SequenceMatchingPreferences, int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the first index where the amino acid pattern is found.
firstIndex(AminoAcidPattern, SequenceMatchingPreferences, int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the first index where the amino acid pattern is found in the given pattern.
firstIndex(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the first index where the amino acid sequence is found in the given sequence.
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.
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.
FolderMonitor - Class in com.compomics.util.io: This class will monitor a specified folder for activity.
FolderMonitor(File, long, int, HashMap) - Constructor for class com.compomics.util.io.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.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.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.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.
folderSeparator - Static variable in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: The splitter in the key between database name and database version.
forbiddenCharacters - 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.PtmChooser
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.
FORMYL_K - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for formylation of K (PMID: 24895383).
FractionSettings - Class in com.compomics.util.preferences: Settings for the handling of fractions.
FractionSettings() - Constructor for class com.compomics.util.preferences.FractionSettings: Constructor.
FractionSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters: FractionSettingsDialog.
FractionSettingsDialog(Frame, FractionSettings, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.FractionSettingsDialog: Creates a new FractionSettingsDialog with a frame as owner.
FractionSettingsDialog(Dialog, Frame, FractionSettings, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.FractionSettingsDialog: Creates a new FractionSettingsDialog with a dialog as owner.
FragmentationMethod - Enum in com.compomics.util.experiment.massspectrometry: 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(Peptide, ArrayList<ArrayList<IonMatch>>, HashSet<Integer>, NeutralLossesMap, boolean, boolean) - 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<ArrayList<IonMatch>>, ArrayList<MSnSpectrum>, HashSet<Integer>, NeutralLossesMap, boolean, boolean) - 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(ArrayList<Integer>, Color, Color) - Constructor for class com.compomics.util.gui.renderers.FragmentIonTableCellRenderer: Creates a new FragmentIonTableCellRenderer.
FrameExceptionHandler - Class in com.compomics.util.exceptions.exception_handlers: Handles exception for a given application and displays warnings using dialogs.
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: This class was modified from a source found on the net (java.sun.com, search in developer section on 'FtpProtocolException PORT').
FTP(String) - Constructor for class com.compomics.util.io.FTP: Constructor for an FTP client connected to host host.
FTP(String, int) - Constructor for class com.compomics.util.io.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 port to use for connection.
FTP_TO_SPECIFIED_DESTINATION - Static variable in class com.compomics.util.io.FolderMonitor
FTPClient - Class in com.compomics.util.io: This class implements a 'directory listener' to listen for new files and ftp them to a remote FTP server.
FTPClient(String, String, String) - Constructor for class com.compomics.util.io.FTPClient: Constructor that takes the three parameters necessary for the FTP connection.
FtpConnectionException - Exception in com.compomics.util.io: This class handles an FTP connection exception.
FTPDownloader - Class in com.compomics.util.io: A simple FTP file downloader.
FTPDownloader(String) - Constructor for class com.compomics.util.io.FTPDownloader: Set up an anonymous FTP connection (without protocol commands printed).
FTPDownloader(String, boolean) - Constructor for class com.compomics.util.io.FTPDownloader: Set up an anonymous FTP connection.
FTPDownloader(String, String, String, boolean) - Constructor for class com.compomics.util.io.FTPDownloader: Set up an FTP connection.
FtpLoginException - Exception in com.compomics.util.io: This class handles an FTP login exception.
FtpProtocolException - Exception in com.compomics.util.io: This class handles an FTP protocol exception.
FULL_NAME - Variable in enum com.compomics.util.experiment.units.StandardUnit: The full name of the unit.
FULLY_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme

G

G - Static variable in class com.compomics.util.experiment.biology.AminoAcid
GATHER_FILES_FOR_PICKUP - Static variable in class com.compomics.util.io.FolderMonitor
GENE_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.experiment.biology.genes.GeneFactory: The suffix to use for files containing gene mappings.
GENE_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.preferences.GenePreferences: Deprecated.
use the gene factory.
GeneDetailsDialog - Class in com.compomics.util.gui.genes: This dialog displays the gene details associated to a protein match.
GeneDetailsDialog(Frame, String, GeneMaps) - Constructor for class com.compomics.util.gui.genes.GeneDetailsDialog: Creates a new GeneDetailsDialog.
GeneFactory - Class in com.compomics.util.experiment.biology.genes: Class used to map proteins to gene information.
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.
GenePreferences - Class in com.compomics.util.preferences: Contains methods for downloading gene and GO mappings.
GenePreferences() - Constructor for class com.compomics.util.preferences.GenePreferences: Create a new GenePreferences object.
GenePreferences(GenePreferences) - Constructor for class com.compomics.util.preferences.GenePreferences: Creates new gene preferences based on a GenePreferences object.
GenePreferencesDialog - Class in com.compomics.util.gui.parameters.identification_parameters: Dialog for editing the Gene Mapping Preferences.
GenePreferencesDialog(JFrame, GenePreferences, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.GenePreferencesDialog: Creates a new GenePreferencesDialog with a frame as owner.
GenePreferencesDialog(JDialog, GenePreferences, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.GenePreferencesDialog: Creates a new GenePreferencesDialog with a dialog as owner.
generateDecoy() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Returns whether a decoy database shall be created and searched against.
generateProteinTree() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns true if the protein tree will be created parallel to the searches.
generateQuery() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Returns a boolean indicating whether a blast query shall be generated.
generateTargetDecoyDatabase(File, ProgressDialogX) - Method in class com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog: Appends decoy sequences to the given target database file.
GeneratorException - Exception in com.compomics.util.db: This class wraps all exception that can occur while generating code.
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.
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.
getAAOccurrences(JProgressBar) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the occurrence of every amino acid in the database.
getAaTargeted() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the map of targeted amino acids.
getAbbreviatedFASTAHeader() - Method in class com.compomics.util.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.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.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.Protein: Getter for the protein accession.
getAccession() - Method in class com.compomics.util.pride.CvTerm: Returns the accession.
getAccession() - Method in class com.compomics.util.protein.Header
getAccessionOrRest() - Method in class com.compomics.util.protein.Header: Returns the accession or if this is null the rest.
getAccessionParsingRule() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the accession parsing rule to use for this file.
getAccessions(String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns a list of accessions from the given key.
getAccessions() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Returns the accessions attribute.
getAccessions() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the sequences present in the database.
getAccountedNeutralLosses(ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.IonFactory: Convenience method returning the possible neutral losses combination as accounted by the factory, i.e., for now up to two neutral losses per peak.
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.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Returns the activation type.
getActiveConnectionsPaths(String) - Static method in class com.compomics.util.db.DerbyUtil: Returns the paths of the active connections for the given id.
getAddenda() - Method in class com.compomics.util.protein.Header: This method allows the caller to retrieve all addenda for the current header, or 'null' if there aren't any.
getAddition() - Method in class com.compomics.util.experiment.biology.AtomChain: Returns true of the given atomic chain consists of additions, i.e., all atoms are added when calculating the mass, false, means that all atoms are subtracted.
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: Returns the advocate based on the identification file name.
getAdvocateToolTipMap() - Static method in class com.compomics.util.experiment.identification.Advocate: Returns the advocate tool tip map.
getAlgorithm() - Method in interface com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter: Returns the identification algorithm.
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters
getAlgorithm() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters
getAlgorithms() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the algorithms for which specific parameters are stored.
getAlgorithmSettingsDialog(IdentificationAlgorithmParameter) - Method in class com.compomics.util.gui.parameters.identification_parameters.SpectrumMatchingSettingsDialog: Returns the dialog to use to edit the given parameters.
getAlgorithmSpecificParameters() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
getAllAlignments() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader: Get all alignment in the XML string.
getAllAssumptions(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Return all assumptions for the specified search engine indexed by their e-value.
getAllAssumptions() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Return all assumptions for all identification algorithms as a list.
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
getAllMappings() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Returns all the protein mapping of the node.
getAllModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: 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.experiment.identification.identification_parameters.PtmSettings: Returns a list of all searched modifications but the fixed ones.
getAllPossibleSequences() - Method in class com.compomics.util.experiment.biology.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.
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(WaitingHandler, SearchParameters) - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader: Retrieves all the identifications from an identification file as a list of spectrum matches It is very important to close the file reader after creation.
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader: Retrieves all the identifications from an identification file as a list of spectrum matches It is very important to close the file reader after creation.
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader
getAllSpectrumMatches(WaitingHandler, SearchParameters, SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader
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
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.
getAminoAcid(String) - Static method in class com.compomics.util.experiment.biology.AminoAcid: Returns the amino acid corresponding to the letter given, null if not implemented.
getAminoAcid(char) - Static method in class com.compomics.util.experiment.biology.AminoAcid: Returns the amino acid corresponding to the letter given, null if not implemented.
getAminoAcidAfter() - Method in class com.compomics.util.experiment.biology.Enzyme: Getter for the amino acids potentially following the cleavage.
getAminoAcidAt(int) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the amino acid at the given index on the sequence.
getAminoAcidBefore() - Method in class com.compomics.util.experiment.biology.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.
getAminoAcidFromGeneticCode(String) - Static method in class com.compomics.util.experiment.biology.AminoAcid: Returns the amino acid from the standard genetic code.
getAminoAcids() - Static method in class com.compomics.util.experiment.biology.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.AminoAcidPattern: Returns the targeted amino acids at position "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.AminoAcid: Convenience method returning an arrayList of all implemented amino acids.
getAnalysisSet(Sample) - Method in class com.compomics.util.experiment.MsExperiment: Returns the analysis set corresponding to a sample.
getAnnotationIntensityLimit() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns the intensity percentile to consider for annotation.
getAnnotationPreferences() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the annotation preferences used for identification.
getAnnotationSettings() - Method in class com.compomics.util.gui.parameters.identification_parameters.AnnotationSettingsDialog: 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.
getArtifactId() - Method in class com.compomics.software.autoupdater.MavenJarFile: Returns the artifact id.
getAsAminoAcidPattern() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns this amino acid sequence as amino acid pattern.
getAscii(String) - Method in class com.compomics.util.io.FTP: GET a file from the FTP server in Ascii mode.
getAScore(Peptide, ArrayList<PTM>, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings, boolean, SequenceMatchingPreferences, SequenceMatchingPreferences, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore: Returns the A-score for the best PTM location.
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(SequenceMatchingPreferences, boolean) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the amino acid pattern as case insensitive pattern for String matching.
getAssumptions(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Returns the assumptions of a spectrum.
getAssumptions(String) - Method in class com.compomics.util.experiment.identification.Identification: Returns a the assumptions of a spectrum.
getAssumptions(String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the assumptions of the given spectrum in a map: advocate id → score → list of assumptions.
getAssumptionsMap() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Returns the assumptions map: advocate id → score → list of assumptions.
getAssumptionTable(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the assumptions table name associated with the given spectrum key.
getAtom(String) - Static method in class com.compomics.util.experiment.biology.Atom: Returns the atom corresponding to the given short name.
getAtom() - Method in class com.compomics.util.experiment.biology.AtomImpl: Returns the atom.
getAtom() - Method in class com.compomics.util.gui.atoms.AtomPanel: Returns the currently selected atom.
getAtomChain() - Method in class com.compomics.util.experiment.biology.AtomChain: Returns the atom chain as a list of AtomImpl.
getAtomChainAdded() - Method in class com.compomics.util.experiment.biology.PTM: 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.PTM: 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.Ion: Returns the atomic composition.
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.preferences.GenePreferences: 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.
getBackedUpPtms() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Returns the names of the backed-up PTMs.
getBackedUpPtmsMap() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Returns the PTMs backed-up as a map.
getBackgroundPeakWidth() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel: Returns the current width of the background peaks.
getBase64String() - Method in class com.compomics.util.BinaryArrayImpl
getBatchSize() - Method in class com.compomics.util.db.ObjectsCache: Returns the batch size in number of objects.
getBatchSize() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
getBinary(String) - Method in class com.compomics.util.io.FTP: GET a file from the FTP server in Binary mode.
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.
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.
getCache() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns the cache used to store the nodes.
getCachedTaxonomyID(String) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Returns the taxonomyID that was encountered for a taxonomyName.
getCacheSize() - Method in class com.compomics.util.db.ObjectsCache: Returns the cache size in number of objects.
getCacheSize() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Returns the size of the cache used for peptide mappings (note that there are two of them).
getCacheSize() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the spectrum cache size.
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() - Method in class com.compomics.util.experiment.massspectrometry.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.
getChildTaxonomies(String) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Returns the child taxonomies.
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.
getClassSizeMultiplier() - Method in class com.compomics.util.experiment.identification.identification_parameters.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
getClipNtermMethionine() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
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.PTMFactory: 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(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Returns the color used to code the given modification.
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.
getColors() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: 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.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.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.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.
getCombinations() - Method in class com.compomics.util.experiment.biology.AminoAcid: Returns the amino acids combinations which might represent this amino acid.
getCombinations(String) - Static method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns a list of all combinations which can be created from a sequence when expanding ambiguous amino acids like Xs.
getCombinationsForAminoAcid(String, ArrayList<SequenceSegment>, AminoAcid, Integer, Integer, boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Adds the possible new sequence segments generated when appending the given amino acid.
getCommandLineArgument(ArrayList<File>) - Static method in class com.compomics.software.CommandLineUtils: Returns the list of file as argument for the command line.
getCommandLineArgument(File) - Static method in class com.compomics.software.CommandLineUtils: Returns the file as argument for the command line.
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.ptm.PtmScore: Returns the different implemented scores as list of command line option.
getCommandLineOptions() - Static method in enum com.compomics.util.preferences.SearchGuiOutputOption: Convenience method returning all possibilities in a command line option description format.
getCommandLineOptions() - Static method in enum com.compomics.util.preferences.SequenceMatchingPreferences.MatchingType: Returns the different matching types as command line options description.
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.
getCommonProteins(String, String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns the common proteins between two protein groups.
getComplementMzTolerance() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the complement m/z tolerance.
getComplementScoreWeight() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the complement score weight.
getComposition() - Method in class com.compomics.util.experiment.biology.NeutralLoss: The composition of the loss.
getComputeExactPValues() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if the exact p-values are to be computed.
getComputeSpScore() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true of the SP score is to be computed.
getComputeXCorr() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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.
getConfidenceMargin() - Method in class com.compomics.util.preferences.ValidationQCPreferences: Returns the margin to the threshold to use as factor of the resolution.
getConsecutiveIonProbability() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.identifications.idfilereaders.DirecTagIdfileReader: Returns the copyright.
getCoreHeader() - Method in class com.compomics.util.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.
getCoveredAminoAcids(AnnotationSettings, SpecificAnnotationSettings, MSnSpectrum, Peptide) - 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.
getCTerminal() - Method in class com.compomics.util.experiment.biology.Peptide: Returns the C-terminal of the peptide as a String.
getCTerminal(boolean) - 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.
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
getCurrentAnnotation(MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
getCurrentAnnotation(MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
getCurrentAnnotation(MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - 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.
getCurrentFastaFile() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the currently loaded FASTA file.
getCurrentFastaIndex() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the FASTA index of the currently loaded file.
getCurrentlyLoadedPeptide() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator: Returns the currently inspected peptide.
getCurrentlyLoadedSpectrumKey() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: Returns the spectrum currently inspected.
getCurrentVennDiagramType() - Method in class com.compomics.util.gui.VennDiagramPanel: Returns the current Venn diagram type.
getCvTerm() - Method in class com.compomics.util.experiment.biology.PTM: Returns the CV term associated with this PTM.
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.
getDatabaseNames() - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the list of database names parsed from the working folder.
getDatabaseType() - Method in class com.compomics.util.experiment.biology.Protein: Getter for the protein database type.
getDatabaseType() - Method in class com.compomics.util.protein.Header
getDatabaseTypeAsString(Header.DatabaseType) - Static method in class com.compomics.util.protein.Header: Convenience method returning the database name as a String.
getDatabaseTypes() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the map of the database types and how often they occur.
getDatabaseTypesAsString() - Static method in class com.compomics.util.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.massspectrometry.proteowizard.MsFormat: 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.preferences.IdentificationParameters: Returns the absolute tolerance in Dalton corresponding to the relative tolerance in ppm at the given reference mass.
getDbFolder() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns the folder where the db in the sequence factory is stored.
getDbFolder() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the last used database folder.
getDbFolderName() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns the folder name where to store information about the protein sequence database loaded in the sequence factory.
getDecodedByteArray() - Method in class com.compomics.util.BinaryArrayImpl: Returns the contents of the binary array decoded using the Base64 algorithm.
getDecoyAccesions() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the list of decoy accessions.
getDecoyFormat() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the decoy format.
getDecoyProteinFromTarget(String, boolean) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns a decoy protein from a target protein or looks for the sequence in the cache if not found.
getDecoyProteinFromTargetSynchronized(String, boolean) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns a decoy protein from a target protein or looks for the sequence in the cache if not found.
getDecoySeed() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the decoy seed.
getDecoyTag() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the decoy tag.
getDecreasingScore(Peptide, Integer, MSnSpectrum, ShotgunProtocol, IdentificationParameters, SpecificAnnotationSettings, int) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScores: Scores the match between the given peptide and spectrum using the given score.
getDefaultColor(String) - Static method in class com.compomics.util.experiment.biology.PTMFactory: 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
getDefaultDbFolderPath() - Static method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns the default folder to use when storing the trees.
getDefaultDecoyAccession(String) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the default decoy accession for a target accession.
getDefaultDecoyAccessionSuffix() - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the default suffix for a decoy accession.
getDefaultDecoyDescription(String) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the default description for a decoy protein.
getDefaultDescription() - Method in class com.compomics.util.preferences.IdentificationParameters: Indicates whether the description is automatically generated.
getDefaultExportFolder() - Method in class com.compomics.util.gui.VennDiagramDialog
getDefaultInstruments() - Static method in class com.compomics.util.pride.prideobjects.Instrument: Returns a list of predefined instruments.
getDefaultLosses(Peptide, SequenceMatchingPreferences, SequenceMatchingPreferences) - 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, SequenceMatchingPreferences) - 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, SequenceMatchingPreferences, SequenceMatchingPreferences) - 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.PTMFactory: Returns the names of the default modifications.
getDefaultModificationsOrdered() - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns the alphabetically ordered names of the default modifications.
getDefaultNeutralLosses() - Static method in class com.compomics.util.experiment.biology.IonFactory: Returns the default neutral losses.
getDefaultPeptideFDR() - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Returns the default peptide FDR.
getDefaultProteinFDR() - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Returns the default protein FDR.
getDefaultProteinTree() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the default protein tree.
getDefaultProteinTree(WaitingHandler, ExceptionHandler) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
getDefaultProteinTree(int, WaitingHandler, ExceptionHandler) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
getDefaultProteinTree(int, WaitingHandler, ExceptionHandler, boolean) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
getDefaultProtocols() - Static method in class com.compomics.util.pride.prideobjects.Protocol: Returns a list of default protocols.
getDefaultPsmFDR() - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Returns the default PSM FDR.
getDefaultReference(String, String, int) - Static method in class com.compomics.util.experiment.identification.Identification: Returns the default reference for an identification.
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.
getDefaultSequenceMatching() - Static method in class com.compomics.util.preferences.SequenceMatchingPreferences: Returns default preferences from amino acid matching.
getDefaultTargetAccession(String) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the default target accession of a given decoy protein.
getDefaultVersion(long) - Static method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the default version based on the time the file was last modified.
getDeisotopingMode() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the deisotoping flag value.
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.
getDeNovoCharge() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns the charge to use for the fragment ions in the de novo sequencing.
getDeNovoGuiPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the path to the DeNovoGUI installation.
getDepth() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Returns the depth of the node in the tree.
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.UtilitiesPathPreferences.UtilitiesPathKey
getDescription() - Method in class com.compomics.util.experiment.biology.Enzyme: Returns the description of the cleavage of this enzyme.
getDescription() - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the description of this mutation matrix.
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 class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the description for this database.
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 class com.compomics.util.io.filefilters.DatFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.DtaFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.FastaFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.JpegFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.MgfFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.Ms2FileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.MzDataFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.MzMlFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.MzXmlFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.OmxFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.OutFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.PdfFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.PeffFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.PepXmlFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.PklFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.PklSpoFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.PkxFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.PngFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.ProtXmlFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.SequestParamsFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.SvgFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.TiffFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.filefilters.XmlFileFilter: The description of the filter.
getDescription() - Method in class com.compomics.util.io.FilenameExtensionFilter
getDescription() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the description of the parameters.
getDescription() - Method in class com.compomics.util.protein.Header
getDescriptionProteinName() - Method in class com.compomics.util.protein.Header
getDescriptionShort() - Method in class com.compomics.util.protein.Header
getDesignaledPeakList(ArrayList<IonMatch>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the peak list of this spectrum without matched peaks.
getDestinationFile() - Method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns the file where to save the identification parameters.
getDestinationFile() - Method in class com.compomics.util.io.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.Atom: Returns the mass difference between the given isotope and the monoisotopic mass.
getDigestionType() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the enzyme digestion type.
getDirecTagParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog: Returns the DirecTag parameters as set by the user.
getDiscardLowQualitySpectra() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Returns a boolean indicating whether low quality spectra shall be discarded.
getDisplayedTips() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.
getDivision(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies: Returns the division corresponding to the given NCBI taxon.
getDnaFolder() - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the folder where DNA databases are stored.
getDoi() - Method in class com.compomics.util.pride.prideobjects.Reference: Returns the Digital Object Identifier (DOI) of the reference.
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.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the window size for doubly charged ions.
getDoubleListFromString(String, String) - Static method in class com.compomics.software.CommandLineUtils: Parses a list of doubles from a command line option.
getDuplicatedSpectrumTitles() - Method in class com.compomics.util.experiment.io.massspectrometry.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.experiment.identification.identification_parameters.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.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.
getEnrichedPtms() - Method in class com.compomics.util.experiment.ShotgunProtocol: Returns the PTMs used for enrichment.
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.
getEnsemblVersion(Integer) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Returns the Ensembl version for a given species.
getEnsemblVersionFromFile(File, String) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Gets the Ensembl version of a given species from a file.
getEnsemblVersionsFile() - Static method in class com.compomics.util.experiment.biology.genes.GeneFactory: 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.EnzymeFactory: Returns the enzyme corresponding to the given name.
getEnzyme() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the enzyme used for digestion.
getEnzyme() - Method in class com.compomics.util.experiment.ShotgunProtocol: Returns the enzyme used for digestion.
getEnzyme() - Method in class com.compomics.util.gui.parameters.identification_parameters.EnzymeSelectionDialog: 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.
getEnzymeCvTerm(Enzyme) - Static method in class com.compomics.util.experiment.biology.EnzymeFactory: Tries to convert the given enzyme to a CvTerm for use in mzIdentML etc.
getEnzymeFile() - Method in class com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli: Returns the enzyme file needed to initiate the factory.
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.EnzymeFactory: Get the imported enzymes.
getEnzymeType() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.UtilitiesPathPreferences: 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.
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.
getExceptionType(Exception) - Static method in class com.compomics.util.exceptions.ExceptionHandler: Returns the exception type.
getExpectedIons(SpecificAnnotationSettings, Peptide) - 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(SpecificAnnotationSettings, Peptide, 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(SpecificAnnotationSettings) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: Returns the expected ions in a map indexed by the possible charges.
getExpectedPTMs(PtmSettings, Peptide, double, double, SequenceMatchingPreferences, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns the expected modifications based on the modification profile, the peptide found and the modification details.
getExpectedPTMs(PtmSettings, Peptide, String, Double, SequenceMatchingPreferences, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns the names of the possibly expected modification based on the name of the expected modification in a map where the PTM names are indexed by their potential site on the sequence.
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.
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) - 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.identifications.IdfileReader: Returns the extension of the file for which this IdfileReader can be used.
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader
getExtension() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader
getExtension(File) - Static method in class com.compomics.util.io.filefilters.FileFilterUtils: Get the extension of a file.
getExtension(File) - Static method in class com.compomics.util.Util: Returns the extensions of a file.
getFamilyName() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
getFamilyName() - Method in interface com.compomics.util.experiment.personalization.UrParameter: This method returns the family name of the parameter.
getFamilyName() - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails
getFastaFile() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the sequence database file used for identification.
getFastaFilePath() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns the FASTA file path.
getFastaFilePath(ObjectsDB) - Static method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns the FASTA file path.
getFastaIndex(File, boolean, WaitingHandler) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the file index of the given FASTA file.
getFastaIndex(String, String) - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the FASTA index of the given database name and version.
getFastIndexFolderName() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the name of the FASTA index folder.
getFavoriteDBs() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the last used databases.
getFeatureFamily() - Method in interface com.compomics.util.io.export.ExportFeature: Returns the family type of this export feature.
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.
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.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.FileAndFileFilter: Returns the file filter.
getFileName() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the file name of the indexed FASTA file.
getFileName() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the name of the loaded FASTA file.
getFileName() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the name of the indexed file.
getFileName() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the file name.
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() - 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
getFileName(String) - Static method in class com.compomics.util.Util: An OS independent getName alternative.
getFileName(File) - Static method in class com.compomics.util.Util: An OS independent getName alternative.
getFileReader(File) - Method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory: This method returns the proper identification file reader depending on the format of the provided file.
getFiles(String, ArrayList<String>) - Static method in class com.compomics.software.CommandLineUtils: Returns a list of files as imported from the command line option.
getFileSize(URL) - Static method in class com.compomics.util.Util: Returns the size of the file located at the given URL.
getFilter(Integer) - Static method in enum com.compomics.util.experiment.massspectrometry.proteowizard.ProteoWizardFilter: Returns the filter designed by the given number.
getFilter(String) - Static method in enum com.compomics.util.experiment.massspectrometry.proteowizard.ProteoWizardFilter: Returns the filter designed by the given name.
getFilter() - Method in class com.compomics.util.gui.parameters.identification_parameters.MatchesImportFiltersDialog: 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.
getFilters() - Method in class com.compomics.util.experiment.massspectrometry.proteowizard.MsConvertParameters: Returns the index of the filters selected.
getFiltersMap() - Method in class com.compomics.util.experiment.massspectrometry.proteowizard.MsConvertParameters: Returns the filters map, filter index - value.
getFixedModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Returns the searched fixed modifications names.
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.
getFlrThreshold() - Method in class com.compomics.util.preferences.PTMScoringPreferences: Returns the FLR threshold.
getFolder(SequenceInputType) - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the folder to be used for the given input type.
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.protein.Header
getForeignDescription() - Method in class com.compomics.util.protein.Header
getForeignID() - Method in class com.compomics.util.protein.Header
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() - Static method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the list of forward ions.
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).
getFractionMolecularWeightRanges() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the user provided molecular weight ranges for the fractions.
getFractionOfPeaksForChargeEstimation() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the fraction of peaks to be retained for charge >1 estimation.
getFractionSettings() - Method in class com.compomics.util.gui.parameters.identification_parameters.FractionSettingsDialog: Returns the fraction settings as set by the user.
getFractionSettings() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the fraction settings.
getFragmentAccuracyType() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the fragment accuracy type.
getFragmentationMethod() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the fragmentation method used.
getFragmentationMethod() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters: Returns the fragmentation method.
getFragmentationMethod() - Method in class com.compomics.util.experiment.ShotgunProtocol: Returns the fragmentation method.
getFragmentationModel() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Returns the name of the fragmentation model.
getFragmentationRule() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the fragmentation rule.
getFragmentationType() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Return the fragmentation ID.
getFragmentBinOffset() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the fragment ion bin offset.
getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the MS2 ion m/z tolerance.
getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns the fragment ion accuracy.
getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Returns the fragment ion accuracy.
getFragmentIonAccuracyInDa(Double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns the fragment ion accuracy in Da.
getFragmentIonAccuracyInDa(Double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Returns the fragment ion accuracy in Da.
getFragmentIonAccuracyInDaltons(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the absolute fragment ion tolerance in Dalton.
getFragmentIons(Peptide) - Method in class com.compomics.util.experiment.biology.IonFactory: This method returns all the theoretic ions expected from a peptide.
getFragmentIons(Peptide, SpecificAnnotationSettings) - Method in class com.compomics.util.experiment.biology.IonFactory: This method returns the theoretic ions expected from a peptide.
getFragmentIons(Tag) - Method in class com.compomics.util.experiment.biology.IonFactory: This method returns the theoretic ions expected from a tag.
getFragmentIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns the type of peptide fragment ions annotated.
getFragmentIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: 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.protein.Header: This method reports on the full header, with the addenda (if present).
getFullName() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement: Returns the full name of the unit.
getFullName() - Method in enum com.compomics.util.protein.Header.DatabaseType: Returns the full name of the database, null if not set.
getGeneMappingFile(String) - Static method in class com.compomics.util.experiment.biology.genes.GeneFactory: Returns the gene mapping file.
getGeneMappingFolder() - Static method in class com.compomics.util.experiment.biology.genes.GeneFactory: Returns the path to the folder containing the gene mapping files.
getGeneMaps(GenePreferences, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Returns the gene maps for the FASTA file loaded in the factory.
getGeneName() - Method in class com.compomics.util.protein.Header
getGeneNameForProtein(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps: Returns the gene name for a given protein accession.
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.
getGenePreferences() - Method in class com.compomics.util.gui.parameters.identification_parameters.GenePreferencesDialog: Returns the gene preferences.
getGenePreferences() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the gene preferences.
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, ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.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.Ion: Convenience method returning a generic ion based on the given ion type without neutral losses.
getGlycons() - Method in class com.compomics.util.experiment.biology.GlyconFactory: A getter to access the glycons.
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.GeneFactory: Returns the GO domains file.
getGoMappingFile(String) - Static method in class com.compomics.util.experiment.biology.genes.GeneFactory: 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.
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.
getHeader() - Static method in class com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli: IdentificationParametersCLI header message when printing the usage.
getHeader(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the desired header for the protein 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.
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.
getHeaderIterator(boolean) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns an iterator of all the headers in the FASTA file.
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.
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.experiment.identification.identification_parameters.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.ptm.PtmtableContent: Get histogram.
getHitListLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the length of the hit list for OMSSA.
getHitListLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Returns the length of the hit list.
getHomeFolder() - Static method in class com.compomics.util.io.FileSystemAccessor: Returns the user home folder.
getHtmlTooltip() - Method in class com.compomics.util.experiment.biology.PTM: Returns information about the PTM as an HTML tooltip.
getId() - Method in interface com.compomics.software.settings.PathKey: Returns the id of the path.
getId() - Method in enum com.compomics.software.settings.UtilitiesPathPreferences.UtilitiesPathKey
getId() - Method in class com.compomics.util.experiment.biology.Enzyme: Get the enzyme id.
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.ptm.PtmScore: Returns the id number of the score.
getId() - Method in class com.compomics.util.experiment.patient.Patient: Returns the patient id,
getID() - Method in class com.compomics.util.protein.Header
getIdentification(int) - Method in class com.compomics.util.experiment.ProteomicAnalysis: Returns identification results obtained with an identification method.
getIdentificationAlgorithmParameter(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
getIdentificationDB() - Method in class com.compomics.util.experiment.identification.Identification: Returns the identification database object used to interact with the back-end database.
getIdentificationFile() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: Returns the identification file.
getIdentificationParameters(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory: Returns the identification parameters corresponding to the given name.
getIdentificationParameters(File) - Static method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Loads the identification parameters from a file.
getIdentificationParameters() - Method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns the identification parameters.
getIdentificationParameters() - Method in class com.compomics.util.gui.parameters.IdentificationParametersEditionDialog: Returns the identification parameters as set by the user.
getIdentificationParameters() - Method in class com.compomics.util.gui.parameters.IdentificationParametersOverviewDialog: Returns the selected identification parameters.
getIdentificationParameters() - Method in class com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog: Deprecated.

Returns the selected identification parameters.
getIdentificationParameters(File) - Static method in class com.compomics.util.preferences.IdentificationParameters: 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_parameters.ValidationSettingsDialog: Returns the validation settings as set by the user.
getIdValidationPreferences() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the identification matches validation preferences.
getImplementedAtoms(boolean) - Static method in class com.compomics.util.experiment.biology.Atom: Returns an array of implemented atoms indicated by their short name.
getImplementedIons() - Static method in class com.compomics.util.experiment.biology.ions.ReporterIon: Returns an arraylist of possible subtypes.
getImplementedIonTypes() - Static method in class com.compomics.util.experiment.biology.Ion: Returns the implemented ion types.
getImplementedIsotopes() - Method in class com.compomics.util.experiment.biology.Atom: returns an unsorted list of isotopes for which a mass is available relative to the monoisotopic peak (+1 for carbon 13).
getImplementedPtmScores() - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore: Returns a list of the implemented scores.
getImplementedSections() - Method in interface com.compomics.util.io.export.ExportFactory: Returns the implemented sections.
getIndex() - Method in class com.compomics.util.experiment.biology.ions.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(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the index of the accession of interest.
getIndex() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
getIndex(String) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the index corresponding to the desired spectrum.
getIndex(File) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Deserializes the index of an mgf file.
getIndex() - Method in interface com.compomics.util.experiment.personalization.UrParameter: This method returns the index of the parameter.
getIndex() - Method in class com.compomics.util.experiment.ProteomicAnalysis: Get the index of the replicate.
getIndex() - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails
getIndexCache(String, Integer, boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Returns the index cache for the given segment seed, accession and index.
getIndexedFixedModifications() - Method in class com.compomics.util.experiment.biology.Peptide: Returns an indexed map of all fixed modifications amino acid, (1 is the first) > list of modification names.
getIndexes(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the indexes where the amino acid pattern was found in the input.
getIndexes(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the indexes where the amino acid pattern was found in the input.
getIndexes() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns a map of all indexes of the FASTA file (accession > index).
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.
getIndexMap(File) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Returns the index of all spectra in the given mgf file.
getIndexMap(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Returns the index of all spectra in the given MGF file.
getIndexName(String) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the name of the FASTA index corresponding to the given FASTA file name.
getIndexName(String) - Static method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the name of an index file based on the given spectrum file name.
getIndexOnProtein() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns the starting index of the segment on the protein.
getInitialSize() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Retrieves the initial tag size from the db.
getInitialTagSize() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Returns the initial tag size of the tree.
getInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.AndromedaSettingsDialog: Returns the user selection as Andromeda parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.CometSettingsDialog: Returns the user selection as Comet parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsAmandaSettingsDialog: Returns the user selection as MS Amanda parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsgfSettingsDialog: Returns the user selection as MS-GF+ parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MyriMatchSettingsDialog: Returns the user selection as MyriMatch parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.OmssaSettingsDialog: Returns the user selection as OMSSA parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.TideSettingsDialog: Returns the user selection as Tide parameters object.
getInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog: Returns the user selection as X!tandem parameters object.
getInputFile() - Method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns the input parameters file.
getInputFile() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns the spectrum file name as found in the parameters section.
getInputType(String) - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the input type of the given database.
getInstance() - Static method in class com.compomics.util.experiment.biology.EnzymeFactory: Static method to get an instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.biology.genes.GeneFactory: Static method returning the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.biology.GlyconFactory: Static method to get the factory instance.
getInstance() - Static method in class com.compomics.util.experiment.biology.IonFactory: Static method which returns the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.biology.PTMFactory: 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.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Static method returning the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Static method returning the instance of the factory.
getInstance(int) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the instance of the factory with the specified cache size.
getInstance() - Static method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory: A static method to retrieve the instance of the factory.
getInstance() - Static method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Static method returning the instance of the factory.
getInstance(int) - Static method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Static method returning the instance of the factory with a new cache size.
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.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Return the instrument ID.
getInstrumentID() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.CommandLineUtils: Parses a list of integers from a command line option.
getIntensities(int, Integer, int) - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent: Get intensity.
getIntensity() - Method in class com.compomics.util.experiment.massspectrometry.Peak: Returns the intensity.
getIntensity() - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Getter for the intensity.
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.
getIntensityCutOffIncrement() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the intensity cut-off increment.
getIntensityLimit(double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the intensity limit in intensity from a given percentile.
getIntensityMap() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the peak list in a map where peaks are indexed by their intensity.
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.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the intensity score weight.
getIntensityValues() - Method in class com.compomics.util.io.PklFile
getIntensityValuesAsArray() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the intensity values as an array.
getIntensityValuesNormalizedAsArray() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the intensity values as an array normalized against the largest peak.
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.
getIons() - Static method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Getter for the list of ion symbols used.
getIonSearched1() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Getter for the first kind of ion searched.
getIonSearched2() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Getter for the second kind of ion searched.
getIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns the type of ions annotated.
getIonTypes() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Returns the map of ions to annotate.
getIsotope() - Method in class com.compomics.util.experiment.biology.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.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the isotope correction setting.
getIsotopeMass(int) - Method in class com.compomics.util.experiment.biology.Atom: Returns the mass corresponding to the given isotope number.
getIsotopeMzTolerance() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the deisotoping m/z tolerance.
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
getIterativeReplaceEvalue() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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(String, String) - Static method in class com.compomics.software.CompomicsWrapper: Returns the path to the jar file.
getJarFilePath() - Method in class com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli: 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.preferences.UtilitiesUserPreferences: 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.
getJFreePeakList() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Format the peaks so they can be plot in JFreeChart.
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.experiment.identification.identification_parameters.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.Peptide: Returns the reference key of a peptide.
getKey(String, ArrayList<ModificationMatch>) - Static method in class com.compomics.util.experiment.biology.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() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
getKey(ArrayList<Integer>) - Static method in class com.compomics.util.maps.KeyUtils: Returns the key corresponding to a list of integers.
getKeyFromId(String) - Static method in enum com.compomics.software.settings.UtilitiesPathPreferences.UtilitiesPathKey: Returns the key from its id.
getKeyToPathMap() - Method in class com.compomics.software.settings.gui.PathSettingsDialog: 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.
getLabellingPtms() - Method in class com.compomics.util.experiment.ShotgunProtocol: Returns the PTMs used for labeling in a map: name of the PTM - boolean indicating whether the labeling is complete.
getLabelWidth() - Static method in class com.compomics.util.gui.TableProperties: Returns the label width for the sparklines.
getLastModified() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns when the file was last modified.
getLastModified() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns when the file was last modified.
getLastSelectedFolder() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Returns the last selected folder.
getLastSelectedFolder(String) - Method in class com.compomics.util.preferences.LastSelectedFolder: Returns the last selected folder according to the given use case.
getLastSelectedFolder() - Method in class com.compomics.util.preferences.LastSelectedFolder: Returns the last selected folder according to the given use case.
getLastSelectedFolder() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the last selected folder.
getLastSelectedFolder() - Method in class com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog: Returns the last selected folder.
getLastSelectedFolder() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog: 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.
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.Protein: Returns the number of amino acids in the sequence.
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.
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.Atom: Returns the single letter code of the atom.
getLevel() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns at which level the spectrum was recorded.
getLicense() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns the license information of this file.
getLimitX() - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: 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
getLineagesForTaxonomyID(String) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Returns the possible lineages for a given taxonomy.
getLineagesFromFile(File) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Returns the possible lineages for a given taxonomy
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.
getLocalPrideFolder() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.
getLocation() - Method in enum com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.QueryType: Returns the location.
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.
getLongestAminoAcidSequence() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag: Returns the longest amino acid sequence contained in this tag.
getLossesMass(ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.IonFactory: Convenience summing the masses of various neutral losses.
getLowerClearMzRange() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the lower mass value for the clear mz range.
getLowerPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Returns the lower precursor mass.
getLowIntensityCutOff() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the low intensity cut-off as percentage of the most intense ion peak.
getMainDatabaseType() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the main database type.
getMainMatch() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns the main match accession after protein inference.
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.
getMap() - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent: Get the map.
getMapping() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.PeptideIterator: Returns the protein mapping of the current peptide.
getMass() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
getMass() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence
getMass() - Method in class com.compomics.util.experiment.biology.AtomChain: Returns the mass of the atomic chain as sum of the individual atoms.
getMass() - Method in class com.compomics.util.experiment.biology.AtomImpl: Returns the mass of the atom.
getMass() - Method in class com.compomics.util.experiment.biology.ElementaryElement: Returns the mass of the element.
getMass(int) - Method in class com.compomics.util.experiment.biology.ions.Glycan: Get the glycan mass.
getMass() - Method in class com.compomics.util.experiment.biology.MassGap
getMass() - Method in class com.compomics.util.experiment.biology.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.Peptide: Getter for the mass.
getMass() - Method in class com.compomics.util.experiment.biology.PTM: Getter for the mass difference induced by this modification.
getMass() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns the mass of the segment.
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(int) - Method in class com.compomics.util.experiment.massspectrometry.Peak: Returns the mass of the compound with the given charge.
getMass(int) - Method in class com.compomics.util.experiment.massspectrometry.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.experiment.identification.identification_parameters.tool_specific.NovorParameters: Returns the mass analyzer.
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.
getMassGap() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Returns the mass gap comprised in this ion.
getMassPlusProton(int) - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Returns the mass of the precursor with the given charge plus a single proton.
getMassShift() - Method in class com.compomics.util.experiment.biology.mutations.Mutation: Returns the mass shift.
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.
getMatchedPeptideSequences(String, String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Returns a list of peptides matched using the given peptide sequence in the given protein according the provided matching settings.
getMatchingAminoAcid(String, SequenceMatchingPreferences) - Static method in class com.compomics.util.experiment.biology.AminoAcid: Returns a matching amino acid using the given preferences.
getMatchingKey(SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Returns a unique key for the peptide when considering the given matching preferences.
getMatchingSequence(String, SequenceMatchingPreferences) - Static method in class com.compomics.util.experiment.biology.AminoAcid: Returns the matching sequence of a given sequence.
getMatchingType(int) - Static method in enum com.compomics.util.preferences.SequenceMatchingPreferences.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.
getMatchType(String) - Method in class com.compomics.util.experiment.identification.Identification: Returns the kind of match pointed by the given key in the identification mappings.
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.io.massspectrometry.MgfIndex: Returns the maximal charge found in the mgf file.
getMaxCharge(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the max precursor charge encountered for the given mgf file.
getMaxCharge() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the max precursor charge encountered among all loaded mgf files.
getMaxChargeSearched() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the maximal charge searched.
getMaxCombinations() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the maximal number of combinations.
getMaxDelta() - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the maximum difference between an original amino acid and the mutated version.
getMaxDynamicMods() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the maximum number of dynamic mods.
getMaxDynamicMods() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the maximum number of variable modifications.
getMaxEValue() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the maximal e-value searched for.
getMaxEValue() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the maximum fragment ion charge.
getMaxFragmentCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the maximal fragment charge.
getMaxFragmentPerSeries() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the maximal number of fragments to retain per series.
getMaxHitsPerSpectrumPerCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.MonitorableFileInputStream: This method reports on the maximum scale for the monitor.
getMaximum() - Method in class com.compomics.util.io.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.experiment.identification.identification_parameters.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.
getMaxIntensity() - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent: Returns the max intensity.
getMaxIntensity() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the maximum precursor intensity in this file.
getMaxIntensity() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the max intensity value.
getMaxIntensity(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the maximum precursor intensity for the desired file.
getMaxIntensity() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the maximum precursor intensity for the whole project.
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.experiment.identification.identification_parameters.SearchParameters: Returns the maximal isotopic correction.
getMaxIterations() - Method in class com.compomics.util.math.clustering.KMeansClustering: Returns the maximum number of iterations.
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.
getMaxMutationsPerPeptide() - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Returns the maximal number of mutations allowed per peptide.
getMaxMz() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the maximum m/z in this file.
getMaxMz() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the max mz value.
getMaxMz(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the maximum m/z for the desired file.
getMaxMz() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the maximum m/z for the whole project.
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.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the maximal m/z ladder length.
getMaxNumberOfModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the maximum peak count.
getMaxPeakCount() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the max peak count.
getMaxPeakCount() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the maximum peak count in this file.
getMaxPeakCount(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the max peak count encountered for the given mgf file.
getMaxPeakCount() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the max peak count encountered among all loaded mgf files.
getMaxPepLength() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the maximal peptide length allowed.
getMaxPeptideLengthNoEnzyme() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the maximal peptide length to use when searching with no enzyme.
getMaxPeptideMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the maximal peptide mass.
getMaxPrecursorAdjustment() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the maximum precursor adjustment.
getMaxPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the maximum precursor mass.
getMaxPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the maxPrecursorMass precursor mass.
getMaxPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
getMaxRank() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Returns the maximum rank.
getMaxRT() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the maximal RT in this file.
getMaxRT(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the maximum retention time in seconds for the desired file.
getMaxRT() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the maximum retention time in seconds for the whole project.
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.preferences.UtilitiesUserPreferences: Returns the maximum charge added when the charge is missing for a given spectrum.
getMaxSpectrumMz() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the max spectrum m/z to search for.
getMaxTagCount() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the maximum number of tags per spectrum to be generated.
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
getMaxVariableMods() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the maximum number of variable modifications per peptide.
getMaxVariablePtmsPerPeptide() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the maximum number of variable modifications allowed on a single peptide.
getMaxVariablePtmsPerTypePerPeptide() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the maximum number of variable modifications of each modification type allowed on a single 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.
getMDScore(ArrayList<SpectrumIdentificationAssumption>, Peptide, ArrayList<String>, SequenceMatchingPreferences, Integer) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.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.
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.
getMemoryAllocation() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Returns the memory allocation.
getMemoryPreference() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the preferred upper memory limit in MB.
getMemoryShare() - Method in class com.compomics.util.db.ObjectsCache: Returns the share of heap size which can be used before emptying the cache.
getMergeSmallSubgroups() - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Indicates whether small subgroups of matches should be merged.
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.identification.Identification: Getter for the identification method used.
getMethodUsed() - Method in class com.compomics.util.experiment.quantification.Quantification: getter for the method used
getMetricsPrefix() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement: Returns the metrics prefix.
getMgfFileFromName(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the file associated to the given name.
getMgfFileName() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader: Returns the spectrum file name.
getMgfFileName() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader: Returns the spectrum file name.
getMgfFileNames() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns a list of loaded mgf files.
getMgfMaxSize() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the max mgf file size before splitting.
getMgfNSpectra() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Get the max number of spectra in an mgf file.
getMH() - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails: Returns the PepNovo mH.
getMinAnnotatedPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the minimal number of annotated peaks a peptide should have.
getMinChargeSearched() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the minimal charge searched.
getMinDelta() - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the minimum difference between an original amino acid and the mutated version.
getMinFragmentMz() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Returns the minimal fragment m/z.
getMinimalChargeForMultipleChargedFragments() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.
getMinimumValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog: Returns the current minimum value for the progressbar.
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.experiment.identification.identification_parameters.SearchParameters: Returns the minimal isotopic correction.
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.massspectrometry.Spectrum: Returns the min mz value.
getMinPeakIntensity() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the minimum peak intensity.
getMinPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the minimum number of peaks.
getMinPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the minimal number of peaks a spectrum should contain.
getMinPeaksPerSpectrum() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Sets the minimal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Sets the minimal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the minimal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Sets the minimal peptide length allowed.
getMinPeptideLengthNoEnzyme() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the minimal peptide length to use when searching with no enzyme.
getMinPrecPerSpectrum() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the minimal number of precursors per spectrum.
getMinPrecursorAdjustment() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the minimum precursor adjustment.
getMinPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the minimum precursor mass.
getMinPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the minimum precursor mass.
getMinPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the minimum precursor mass.
getMinPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Returns the minimal precursor mass.
getMinRT() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the minimum RT in this file.
getMinRT(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the minimum retention time in seconds for the desired file.
getMinRT() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the minimum retention time in seconds for the whole project.
getMinSpectrumChargeRange() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the minimum charge added when the charge is missing for a given spectrum.
getMinSpectrumMz() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Return the min spectrum m/z to search for.
getMinSpectrumPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the min number of peaks in a spectrum.
getMinTerminiCleavages() - Method in class com.compomics.util.experiment.identification.identification_parameters.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
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.
getModel() - Method in class com.compomics.util.sun.TableMap
getModelAfterClick(String) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Returns a model for a known taxonomy name (for example after node click).
getModelAfterSearch(String) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Returns a model after searching for an unknown taxonomy name (for example after a search).
getModelFromFile(File) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Returns a model after searching for an unknown taxonomy name (for example after a search).
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.
getModificationCount(String, Double) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns how many of the given modification was found in the given peptide.
getModificationFamily(String) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns a list of masses of the variable modifications found in the key of a peptide.
getModificationIndexes() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns a list of the indexes of the amino acids carrying a modification.
getModificationIndexes() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns a list of the indexes of the amino acids carrying a modification.
getModificationMatches() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Getter for the modifications carried by this sequence in a map: aa number > modification matches.
getModificationMatches() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Getter for the modifications carried by this sequence in a map: aa number > modification matches.
getModificationMatches() - Method in class com.compomics.util.experiment.biology.Peptide: Getter for the modifications carried by this peptide.
getModificationMatches() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns a map of modifications on that segment: index on the segment - modification name.
getModificationName(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the name of the modification indexed by the given index.
getModificationName(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the name of the modification indexed by the given index.
getModificationProfile() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog: Returns the modification profile corresponding to the input by the user.
getModifications() - Method in class com.compomics.util.protein.AASequenceImpl: Simple getter for the modifications.
getModificationsAt(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the modifications found at a given localization.
getModificationsAt(int) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the modifications found at a given localization.
getModificationSite() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Getter for the modification site, 1 is the first amino acid.
getModificationUseAsString(ArrayList<String>) - Static method in class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Returns a line with the most used modifications.
getModifiedIndexes() - Method in class com.compomics.util.experiment.biology.Peptide: Returns the indexes of the residues in the peptide that contain at least one variable modification.
getModifiedIndexes(boolean) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the indexes of the residues in the peptide that contain at least one modification.
getModifiedSequence() - Method in class com.compomics.util.protein.AASequenceImpl: This method will return the sequence with annotated modifications.
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.AminoAcid: Returns the monoisotopic atom chain representing this amino acid.
getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.AminoAcid: Returns the mass of the amino acid.
getMonoisotopicMass() - Method in class com.compomics.util.experiment.biology.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.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if the precursor mass is monoisotopic, false if average.
getMs1Resolution() - Method in class com.compomics.util.experiment.ShotgunProtocol: Returns the MS1 mass resolution.
getMs2Resolution() - Method in class com.compomics.util.experiment.ShotgunProtocol: Returns the MS2 resolution.
getMsConvertParameters() - Method in class com.compomics.util.experiment.massspectrometry.proteowizard.gui.MsConvertParametersDialog: Returns the parameters as created by the user.
getMsFormat() - Method in class com.compomics.util.experiment.massspectrometry.proteowizard.MsConvertParameters: Returns the format to convert to.
getMutatedAminoAcids(Character) - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the possible mutated amino acids for the given amino acid as a list of their single letter code.
getMutatedAminoAcids() - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the possible mutated amino acids.
getMutatedMasses(Character) - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the possible mutated amino acids for the given amino acid as a map where the list of their single letter code is indexed by the delta mass to the original amino acid.
getMutation(Mutation) - Static method in class com.compomics.util.experiment.biology.mutations.MutationFactory: Returns the requested mutation by lookup in the mutation map.
getMutation() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns the mutated amino acid, null if none.
getMutationIndex() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns the mutation index, null if none.
getMutationMatrix() - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Returns the mutation matrix to use.
getMutations() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns a map of mutations on that segment: index on the segment - mutated character.
getMutationsAsString() - Static method in class com.compomics.util.experiment.biology.mutations.MutationFactory: Returns the mutation as a string.
getMyriMatchFormat() - Method in class com.compomics.util.experiment.biology.Enzyme: Get the MyriMatch enzyme format.
getMz() - Method in class com.compomics.util.experiment.massspectrometry.Peak: Returns the mz.
getMz() - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Getter for the m/z.
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.
getMzAndIntensityAsArray() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the m/z and intensity values as an array in increasing order sorted on m/z value.
getMzBinOffset() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the m/z bin offset.
getMzBinWidth() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the mzFidelity score weight.
getMzidOutput() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if the mzid output is to be created.
getMzMLFileNames() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns a list of loaded mzML files.
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
getMzValuesAsArray() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the mz values as an array.
getName() - Method in class com.compomics.util.db.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.Atom: Returns the name of the atom.
getName() - Method in class com.compomics.util.experiment.biology.ElementaryElement: Returns the name of the element.
getName() - Method in class com.compomics.util.experiment.biology.Enzyme: Get the enzyme name.
getName() - Method in class com.compomics.util.experiment.biology.Ion: Returns the name of the ion.
getName() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
getName() - Method in class com.compomics.util.experiment.biology.ions.Glycan
getName() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
getName() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
getName() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
getName() - Method in class com.compomics.util.experiment.biology.ions.RelatedIon
getName() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon: This method returns the name of the reporter ion.
getName() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
getName() - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the name of this mutation matrix.
getName() - Method in class com.compomics.util.experiment.biology.PTM: 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 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 class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the name of the database.
getName() - Method in enum com.compomics.util.experiment.identification.ptm.PtmScore: Returns the name of the score.
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.preferences.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.TagFragmentIon: Returns the name with number and mass gap.
getNameWithNumber() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Returns the name with number.
getNameWithNumber() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Returns the name with number.
getnAnnotatedMostIntensePeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the minimal number of annotated most intense peaks.
getnCache() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the size of the cache.
getNCleavageSites(Enzyme) - Method in class com.compomics.util.experiment.biology.Protein: 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
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.NeutralLoss: Returns the neutral loss associated to the given name in the static map of the class.
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.Ion: Returns the possible neutral losses of this ion type.
getNeutralLosses(PtmSettings) - Static method in class com.compomics.util.experiment.biology.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.ions.ElementaryIon
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.Glycan
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.RelatedIon
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.PTM: Returns the neutral losses possibly encountered with this modification.
getNeutralLosses() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns the considered neutral losses.
getNeutralLossesAsString() - Method in class com.compomics.util.experiment.biology.Ion: Returns the neutral loss (if any), the empty string if no loss.
getNeutralLossesAsString(ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.Ion: Returns the neutral loss (if any), the empty string if no loss.
getNeutralLossesMap() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Returns the map of neutral losses to annotate.
getNeutronThreshold() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the mass after which exact neutron mass should be considered in the calculation.
getNext() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.HeaderIterator: Returns the next header in the FASTA file.
getNextFeature() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader: Get the next feature in the XML string.
getNextProtein() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.ProteinIterator: Returns the next protein.
getNLines() - Method in class com.compomics.util.math.matrix.DoubleMatrix
getNmissedCleavages(String) - Method in class com.compomics.util.experiment.biology.Enzyme: Returns the number of missed cleavages in an amino acid sequence.
getNMissedCleavages(Enzyme) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the number of missed cleavages using the specified enzyme.
getNMissedCleavages(String, Enzyme) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns the number of missed cleavages using the specified enzyme for the given sequence.
getnMissedCleavages() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the allowed number of missed cleavages.
getNModificationLocalized(String, Double) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns the list of modifications confidently localized or inferred for the peptide indexed by the given key.
getNModifications() - Method in class com.compomics.util.experiment.biology.Peptide: Returns the number of modifications carried by this peptide.
getnMutations() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns the number of mutations.
getNode(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Retrieves the node of the given tag.
getNodesInCache() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Returns the number of nodes currently loaded in cache.
getNodesInCache() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the number of nodes currently loaded in cache.
getNoModPeptide(Peptide, ArrayList<PTM>) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns a version of the peptide which does not contain the inspected PTMs.
getNonDiagonalScore() - Method in class com.compomics.util.math.matrix.DoubleMatrix: Returns a score based on the non-diagonal values.
getNoProlineRuleSeries() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
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.
getNovorParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog: Returns the Novor parameters as set by the user.
getNovorPtmMap() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters: Returns the Novor to utilities PTM map.
getnPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Returns the number of most intense peaks to consider.
getNPeaks() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the number of peaks in the spectrum.
getnPeaksInDoubleChargeWindow() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the number of peaks in doubly charged windows.
getnPeaksInSingleChargeWindow() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the number of peaks in singly charged windows.
getnProcessingNode() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns the number of processing nodes used.
getNProteins(String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns the number of proteins for the match corresponding to the given.
getNProteins() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns the number of proteins for this match.
getNSequences() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the number of sequences in the database.
getNSequences() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the number of sequences in the FASTA file.
getNSpectra() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the number of imported spectra.
getNSpectra(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the number of spectra in the desired file.
getNSpectra() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the total number of spectra in all files.
getNTarget() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the number of target sequences in the database.
getNTargetedAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the number of targeted amino acids at the given index.
getNTargetSequences() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the number of target sequences in the database.
getNTerminal() - Method in class com.compomics.util.experiment.biology.Peptide: Returns the N-terminal of the peptide as a String.
getNTerminal(boolean) - 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.
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.preferences.ProcessingPreferences: Returns the number or threads to use.
getnThreads() - Method in class com.compomics.util.preferences.PSProcessingPreferences: Deprecated.

Returns the number of threads to use.
getNumber() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Returns the number of the fragment in the sequence.
getNumber() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Returns the number of the fragment in the tag.
getNumberOfBatches() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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.
getNumberOfLines(File) - Static method in class com.compomics.util.Util: Returns the number of lines in the given file.
getNumberOfPeptides() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Returns the number of peptides to report per spectrum.
getNumberOfPtmsPerPeptide() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Returns the maximum number of PTMs per peptide.
getNumberOfSpectrumMatches() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the maximum number of spectrum matches.
getNumberOfSpectrumMatches() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Returns the maximum number of spectrum matches.
getNumberOfSpectrumMatches() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the maximum number of spectrum matches.
getNumberOfSpectrumMatches() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the number of PSMs to report per spectrum.
getNumberTolerableTermini() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Returns the number of tolerable termini.
getNumChargeStates() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the number of charge states.
getNumIntensityClasses() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the number of intensity classes.
getNumIntensityClasses() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the number of intensity classes.
getNVariableModifications(double) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the number of variable modifications found with the given mass.
getObject(String, String, String) - Method in class com.compomics.util.db.ObjectsCache: Returns the objects if present in the cache.
getObject(String, String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns an object from the database.
getObjectsCache() - Method in class com.compomics.util.db.ObjectsDB: Returns the cache used by this database.
getObjectsDB() - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the database used to store matches.
getObservableLength(Enzyme, double) - Method in class com.compomics.util.experiment.biology.Protein: Returns the number of observable amino acids in the sequence.
getOccurrence(Atom, Integer) - Method in class com.compomics.util.experiment.biology.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.ptm.ModificationsDialog: Returns a web link to the given PSI-MOD CV term at http://www.ebi.ac.uk/ontology-lookup.
getOMSSAIndexes(File) - Static method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Imports the OMSSA indexes from an XML file.
getOmssaOutputTypes() - Static method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the output types available.
getOntology() - Method in class com.compomics.util.pride.CvTerm: Returns the ontology.
getOperatingSystem() - Static method in class com.compomics.util.io.FileSystemAccessor: Get the operating system.
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() - Method in class com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli: Returns the options left to the user as a string.
getOrderedMzValues() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns a list of the m/z values sorted in ascending order.
getOrderedSpectrumFileNames() - Method in class com.compomics.util.experiment.identification.Identification: Returns the ordered list of spectrum file names.
getOrientation() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature: Returns the orientation.
getOrigin() - Method in class com.compomics.util.experiment.biology.mutations.Mutation: Returns the origin amino acid.
getOriginalAminoAcids(Character) - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the possible original amino acids for the given mutated amino acid as a list of their single letter code.
getOriginalAminoAcids() - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Returns the amino acids where a mutation has been registered.
getOriginalKey(String, String) - Method in class com.compomics.util.db.ObjectsDB: Returns the original key of the corrected long key.
getOtherProteins(String, String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns the proteins in a group (group1) which are not in another group (group2).
getOutputFolderName() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the name of the output folder.
getOutputFormat() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the output format.
getOutputOption(int) - Static method in enum com.compomics.util.preferences.SearchGuiOutputOption: Returns the output option of the given index.
getOutputOption() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the selected SearchGUI output option.
getOutputOptions() - Static method in enum com.compomics.util.preferences.SearchGuiOutputOption: Returns an array of the indexes of the different output options.
getOutputOptionsNames() - Static method in enum com.compomics.util.preferences.SearchGuiOutputOption: Returns an array of the names of the different options.
getOutputResults() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Returns the output results filter.
getOutputSuffix() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the output tags suffix.
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(UrParameter) - Static method in class com.compomics.util.experiment.personalization.ExperimentObject: Returns the key of a personalization parameter.
getParameterLine(String) - Method in class com.compomics.util.io.ConfigurationFile: Returns a parameter line corresponding to the given parameter name.
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_parameters.algorithm_settings.AndromedaSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.CometSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsAmandaSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsgfSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MyriMatchSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.OmssaSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.TideSettingsDialog
getParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog
getParameters() - Method in interface com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog: 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.
getParentFolder() - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory: Returns the parent folder.
getParentProteins(boolean, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the parent proteins and eventually remaps the peptide to the protein using the default protein tree.
getParentProteins(SequenceMatchingPreferences, ProteinTree) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set.
getParentProteins(SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set using the default protein tree of the sequence factory.
getParentProteins(boolean, SequenceMatchingPreferences, ProteinTree) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the parent proteins and eventually remaps the peptide to the protein.
getParentProteinsCreateTree(SequenceMatchingPreferences, WaitingHandler, ExceptionHandler) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set using the default protein tree of the sequence factory.
getParentProteinsNoRemapping() - Method in class com.compomics.util.experiment.biology.Peptide: Returns the parent proteins without remapping them.
getPath(String) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Returns the path at the given line.
getPath() - Method in class com.compomics.util.db.ObjectsDB: Returns the path to the database.
getPathID(String) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Returns the path id line.
getPathOfClass(String) - Static method in class com.compomics.util.io.FileSystemAccessor: Returns the absolute path of the underlying file system of the given class.
getPathPreference(UtilitiesPathPreferences.UtilitiesPathKey) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: 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.PTM: 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, Charge) - 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, Charge) - 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.
getPeakList() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the peak list.
getPeakMap() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns a peak map where peaks are indexed by their m/z.
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(double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns an array containing the intensity of all peaks above the provided threshold.
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.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Returns the PepNovo to utilities PTM map.
getPeptide() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption: Get the theoretic peptide.
getPeptideAssumptionFilter() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the filter used when importing PSMs.
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.
getPeptideFilters() - Method in class com.compomics.util.preferences.ValidationQCPreferences: Returns the list of peptide quality filters.
getPeptideIdentification() - Method in class com.compomics.util.experiment.identification.Identification: Returns a list of the keys of all encountered peptides.
getPeptideIterator() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Returns a PeptideIterator which iterates alphabetically all peptides corresponding to the end of a branch in the tree.
getPeptideMatch(String) - Method in class com.compomics.util.experiment.identification.Identification: Returns a peptide match.
getPeptideMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Returns a peptide match.
getPeptideMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the desired peptide match.
getPeptideMatches(Tag, String, String, Integer, Integer, double) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Returns the possible peptides which can be created on this sequence indexed by their start index.
getPeptideMatchesIterator(ArrayList<String>, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a peptide matches iterator.
getPeptideMatchesIterator(ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a peptide matches iterator iterating all peptides.
getPeptideMatchesKeys() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Getter for the peptide keys.
getPeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Returns the desired peptide match parameter.
getPeptideMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Returns the desired peptide match parameter.
getPeptideMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the desired peptide match parameter.
getPeptideModificationsAsString(Peptide, boolean) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns the peptide modifications as a string.
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.
getPeptideParametersTables() - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the names of the tables containing peptide parameters.
getPeptideParameterTable(UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the table name associated with the given peptide parameter.
getPeptideScoreToPositionMap(HashMap<Integer, HashMap<Integer, Double>>) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore: Estimates the peptide score for every modification localization and returns a map score > localization.
getPeptideSelected() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the color for a selected peptide.
getPeptideSequences() - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel: Get the set of peptide sequences.
getPeptidesFromTags(ProteinTree, TagMatcher, SequenceMatchingPreferences, Double, boolean, boolean) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Creates a peptide based spectrum match where peptide assumptions are deduced from tag assumptions.
getPeptideShakerPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the path to the PeptideShaker installation.
getPeptideStart(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Protein: Returns the list of indexes where a peptide can be found in the protein sequence.
getPepXmlOutput() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
getPinOutput() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if the Percolator output is to be created.
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 class com.compomics.util.pride.prideobjects.Reference: Returns the PubMed ID of the reference.
getPmid() - Method in enum com.compomics.util.protein.Header.DatabaseType: Returns the PubMed id of the database, null if not set.
getPNovoParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog: Returns the pNovo parameters as set by the user.
getPNovoPtmMap() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Returns the pNovo to utilities PTM map.
getPNovoPtmResiduesMap() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
getPositionToScoreMap(Peptide, Peptide, ArrayList<Integer>, MSnSpectrum, HashMap<Integer, MSnSpectrum>, AnnotationSettings, SpecificAnnotationSettings, PeptideSpectrumAnnotator, PTM) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore: Returns a map PTM localization > score.
getPossibilities() - Method in interface com.compomics.util.experiment.filtering.FilterItem: In case the filter has predefined values, return the possible values, null otherwise.
getPossibleCharges() - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Getter for the possible charges.
getPossibleChargesAsString() - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Returns the possible charges as a string.
getPossibleSubtypes(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.Ion: Returns an arraylist of possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.ElementaryIon: Returns an arraylist of possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.Glycan: Returns an arraylist of possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Returns an arraylist of possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Returns an arraylist of possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.PrecursorIon: Returns an arraylist of possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.RelatedIon: Returns an arraylist of possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.ReporterIon: Returns an arraylist of possible subtypes.
getPossibleSubtypes() - Static method in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Returns an arraylist 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.
getPotentialModificationSites(Double, SequenceMatchingPreferences, SequenceMatchingPreferences, PtmSettings) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the potential modification sites as an ordered list of string.
getPotentialModificationSites(PTM, SequenceMatchingPreferences, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the potential modification sites as an ordered list of string.
getPotentialModificationSites(PTM, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag: Returns the potential modification sites as an ordered list of string.
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.preferences.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(BufferedRandomAccessFile, Long, String) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Returns the next precursor starting from the given index.
getPrecursor() - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Returns the precursor.
getPrecursor(String, String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the precursor of the desired spectrum.
getPrecursor(String, String, boolean) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the precursor of the desired spectrum.
getPrecursor(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the precursor of the desired spectrum.
getPrecursor(String, boolean) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the precursor of the desired spectrum.
getPrecursorAccuracy() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the precursor tolerance.
getPrecursorAccuracyDalton() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the precursor tolerance in Dalton (for de novo searches).
getPrecursorAccuracyType() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the precursor accuracy type.
getPrecursorAdjustmentStep() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the precursor adjustment step.
getPrecursorCharge() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Returns the charge of the precursor.
getPrecursorIntensity() - Method in class com.compomics.util.io.PklFile
getPrecursorMatch(Peak) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: Returns the ion match.
getPrecursorMz(int) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the precursor mz for the spectrum at the given index.
getPrecursorMz(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the precursor mz of the desired spectrum.
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
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.Ion: Returns the pride cv term adapted to the fragment ion.
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.Glycan
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.RelatedIon
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
getPrideCvTerm() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
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.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns true if the export score is to be printed.
getPrintPeptides() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the progress indicator size.
getProbabilisticScoreThreshold() - Method in class com.compomics.util.preferences.PTMScoringPreferences: Returns the probabilistic score threshold.
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
getProcessingPreferences() - Method in class com.compomics.util.gui.parameters.ProcessingPreferencesDialog: Returns the processing preferences as set by the user.
getProcessingType() - Method in class com.compomics.util.preferences.ProcessingPreferences: 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.
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.
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.
getPrositeFormat() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the pattern in the PROSITE format.
getProtein(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns the desired 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.preferences.FractionSettings: Returns the protein confidence for inclusion in MW plots.
getProteinConfidenceMwPlots() - Method in class com.compomics.util.preferences.PSProcessingPreferences: Deprecated.

Returns the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.
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.protein.Header: Return the Uniprot protein evidence type as text.
getProteinEvidence() - Method in class com.compomics.util.protein.Header
getProteinFilters() - Method in class com.compomics.util.preferences.ValidationQCPreferences: Returns the list of protein quality 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.
getProteinInferencePreferences() - Method in class com.compomics.util.gui.parameters.identification_parameters.ProteinInferenceSettingsDialog: Returns the protein inference preferences.
getProteinInferencePreferences() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the protein inference preferences.
getProteinIterator(boolean) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns an iterator of all the proteins in the FASTA file.
getProteinKey() - Method in class com.compomics.util.experiment.biology.Protein: Returns the key for protein indexing.
getProteinLength(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Retrieves the length of a protein.
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(AminoAcidSequence, String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Returns the protein mappings for the given peptide sequence.
getProteinMapping(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Returns the protein mapping in the sequence factory for the given peptide sequence.
getProteinMapping(Tag, TagMatcher, SequenceMatchingPreferences, Double) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Returns the protein mappings for the given peptide sequence.
getProteinMatch(String) - Method in class com.compomics.util.experiment.identification.Identification: Returns a protein match.
getProteinMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Returns a protein match.
getProteinMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the desired protein match.
getProteinMatches(Peptide) - Method in class com.compomics.util.experiment.identification.Identification: Returns the keys of the protein matches where a peptide can be found.
getProteinMatchesIterator(ArrayList<String>, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a protein matches iterator.
getProteinMatchesIterator(ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a protein matches iterator iterating all protein matches.
getProteinMatchKey(Peptide) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Convenience method which returns the protein key of a peptide.
getProteinMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Returns the desired protein match parameter.
getProteinMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Returns the desired protein match parameter.
getProteinMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the desired protein match parameter.
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.
getProteinParameterTable(UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the table name associated with the given protein parameter.
getProteinPtmComplexity() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Returns the proteinPtmComplexity.
getProteinSequenceDatabase() - Method in class com.compomics.util.preferences.ProteinInferencePreferences: Returns the path to the database used.
getProteinSequencesManagerFolder() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: returns the folder to use in the protein sequences manager.
getProteinsForGoTerm(String) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps: Returns the protein accessions for a GO accession.
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.
getProteinTreeFolder() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the protein tree folder.
getProteinTreeImportTime() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the protein tree import times in a map: file size > list of import sizes.
getProteomicAnalysis(int) - Method in class com.compomics.util.experiment.SampleAnalysisSet: Returns the analysis corresponding to the selected replicate.
getProteoWizardPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the path to ProteoWizard.
getProtocol() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Returns the protocol ID.
getProtocols() - Method in class com.compomics.util.pride.PrideObjectsFactory: Returns the protocols.
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.preferences.ValidationQCPreferences: Returns the list of PSM quality filters.
getPsmIterator(String, ArrayList<String>, ArrayList<UrParameter>, boolean, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a PSM iterator.
getPsmIterator(String, ArrayList<UrParameter>, boolean, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a PSM iterator iterating all PSMs in a file.
getPsmIterator(String, boolean, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a PSM iterator iterating all PSMs in a file.
getPsmIterator(ArrayList<String>, ArrayList<UrParameter>, boolean, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a PSM iterator.
getPsmIterator(ArrayList<String>, boolean, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a PSM iterator.
getPsmIterator(boolean, ArrayList<UrParameter>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification: Returns a PSM iterator iterating all PSMs in a file.
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.
getPsmScoringPreferences() - Method in class com.compomics.util.gui.parameters.identification_parameters.PsmScoringSettingsDialog: Returns the PSM scoring preferences as set by the user.
getPsmScoringPreferences() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the scoring preferences used when scoring PSMs.
getPTM(String) - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns the PTM indexed by its name.
getPtm(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Returns the back-ed up PTM with the given name.
getPTM(PepnovoParameters, String) - Static method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader: Get a PTM.
getPtmIndex(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the index of a given modification, null if not found.
getPtmIndex(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the index of a given modification, null if not found.
getPtmIndexes() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the PTM indexes as a map.
getPtmIndexes() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the PTM indexes as a map.
getPtmName() - Method in class com.compomics.util.gui.protein.ModificationProfile: Returns the PTM name.
getPTMPlotData(Peptide, PTM, int, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Static method in class com.compomics.util.experiment.identification.ptm.PtmtableContent: Returns the PTM plot series in the JFreechart format for one PSM.
getPtmResidue(Character) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Returns the original amino acids residue corresponding to the given pNovo PTM character.
getPTMs() - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns the names of all imported PTMs.
getPtmScoringPreferences() - Method in class com.compomics.util.gui.parameters.identification_parameters.PTMLocalizationParametersDialog: Returns the PTM scoring preferences as set by the user.
getPtmScoringPreferences() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the PTM localization scoring preferences.
getPtmSettings() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the PTM settings.
getPTMTableContent(Peptide, PTM, int, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Static method in class com.compomics.util.experiment.identification.ptm.PtmtableContent: Get the PTM table content.
getPtmToPrideMap() - Method in class com.compomics.util.pride.PrideObjectsFactory: Returns the utilities PTM to pride map.
getQuantification(Quantification.QuantificationMethod) - Method in class com.compomics.util.experiment.ProteomicAnalysis: Returns quantification results obtain with a quantification method.
getQuantile(int, Integer, int, double) - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent: Get the quantile.
getQueryConnection(String, QueryType) - Static method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.ConnectionManager: Returns the query connection.
getQueryTemplate(boolean) - Method in enum com.compomics.util.pride.prideobjects.webservice.PrideQuery: Returns the actual query template.
getQueryType() - Method in class com.compomics.util.protein_sequences_manager.UniProtQuery: Returns the query type.
getQueryURL() - Method in class com.compomics.util.protein_sequences_manager.UniProtQuery: Returns the query URL.
getQuoteType() - Static method in class com.compomics.software.CommandLineUtils: Returns the quote type to use.
getRank() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: Get the identification rank.
getRankScore() - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails: Returns the PepNovo rank score.
getRawAssumptions(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Returns the raw assumptions of a spectrum.
getRawAssumptions(String) - Method in class com.compomics.util.experiment.identification.Identification: Returns a the raw assumptions of a spectrum.
getRawAssumptions(String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the raw assumptions of the given spectrum in a map: advocate id → score → list of assumptions.
getRawAssumptionTable(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the raw assumptions table name associated with the given spectrum key.
getRawHeader() - Method in class com.compomics.util.protein.Header
getRawScore() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: Returns the raw score as provided by the identification algorithm.
getReadTweets() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.
getRecalibratedPeakList(HashMap<Double, Double>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns a recalibrated peak list.
getRecalibratedPrecursor(double, double) - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Returns a recalibrated precursor.
getReducedSpectra(MSnSpectrum, double) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore: Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used.
getReducedSpectra(MSnSpectrum, double, int) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.AScore: Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used.
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.experiment.biology.Sample: Getter for the sample reference.
getReference() - Method in class com.compomics.util.experiment.MsExperiment: Returns the reference of the experiment.
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.
getReferences() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup: Returns the references.
getRefinementFixedModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Return the refinement fixed modifications used for the second pass search.
getRefinementVariableModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Return the refinement variable modifications used for the second pass search.
getRefMass() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
getRelatedIons(AminoAcid) - Static method in class com.compomics.util.experiment.biology.ions.RelatedIon: Returns the list of related ions for the given amino acid.
getRelatedIons() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Indicates whether related ions should be annotated by default.
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.preferences.UtilitiesUserPreferences: Returns the path to the Relims installation.
getRemoveMethionine() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns true if n-term methionine is to be removed.
getRemovePrecursor() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns if the precursor is to be removed.
getRemovePrecursor() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true of the precursor peak is to be removed.
getRemovePrecursorTolerance() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the precursor removal tolerance.
getRemovePrecursorTolerance() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the tolerance with which to remove the precursor peak.
getRemoveTempFolders() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if the output and index folders are to be removed when the search has completed.
getReplicateNumberList() - Method in class com.compomics.util.experiment.SampleAnalysisSet: Returns a list containing replicate numbers.
getReport(boolean) - Method in interface com.compomics.util.experiment.filtering.Filter: Returns a filter report depending on whether the condition was met.
getReport(File) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Returns the report.
getReporterIndex(Sample) - 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.ReporterIon: Returns the reporter ion indexed by the given index.
getReporterIon(String) - Static method in class com.compomics.util.experiment.biology.ions.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(PtmSettings) - Static method in class com.compomics.util.experiment.biology.IonFactory: Returns the reporter ions to annotate with the given PTM settings.
getReporterIons() - Method in class com.compomics.util.experiment.biology.PTM: Returns the reporter ions possibly encountered with this modification.
getReporterIons() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: 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.preferences.UtilitiesUserPreferences: Returns the path to the Reporter installation.
getRequireVariableMods() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns true if at least one variable modification is required per peptide.
getResidue(int) - Static method in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Returns the amino acid of the immonium ion based on the subtype index.
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: Returns all server response strings.
getResponseStringNoReset() - Method in class com.compomics.util.io.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.protein.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.Enzyme: Getter for the amino acids restricting when following the cleavage.
getRestrictionBefore() - Method in class com.compomics.util.experiment.biology.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() - Static method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the list of rewind ions.
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.
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.PTM: Getter for the rounded mass difference induced by this modification.
getRoundedMass() - Method in class com.compomics.util.experiment.biology.PTM: Getter for the rounded mass difference induced by this modification.
getRoundedMassShift() - Method in class com.compomics.util.experiment.biology.mutations.Mutation: Get rounded mass shift.
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.sun.TableMap
getRowNumber(int) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel: Returns the row number of the given view index.
getRt() - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Getter for the retention time in seconds.
getRtInMinutes() - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Returns the retention time in minutes.
getRtWindow() - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Returns an array containing the min and max of the RT window.
getSample(int) - Method in class com.compomics.util.experiment.MsExperiment: Returns a single sample accessed by its index.
getSample(String) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification: This method returns the sample associated to the given ion.
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.experiment.MsExperiment: Returns the implemented samples.
getSamples() - Method in class com.compomics.util.pride.PrideObjectsFactory: Returns the samples.
getScanNumber() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Getter for the scan number.
getScanStartTime() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the scan start time.
getScientificName(Integer) - Method in class com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies: Returns the scientific name corresponding to the given NCBI taxon.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAIntensityRankScore: Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAIntensityRankScore: Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAMS2MzFidelityScore: Scores the match between the given peptide and spectrum using an m/z fidelity score.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAMS2MzFidelityScore: Scores the match between the given peptide and spectrum using an m/z fidelity score.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.ComplementarityScore: Scores the match between the given peptide and spectrum using the complementarity of the matched peaks.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.ComplementarityScore: Scores the match between the given peptide and spectrum using the complementarity of the matched peaks.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.IntensityRankScore: Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.IntensityRankScore: Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.MS2MzFidelityScore: Scores the match between the given peptide and spectrum using an m/z fidelity score.
getScore(Peptide, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.MS2MzFidelityScore: Scores the match between the given peptide and spectrum using an m/z fidelity score.
getScore(Peptide, int, Precursor, boolean, int, int) - Static 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(int) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScores: Returns the PSM score of the given index.
getScore(Peptide, Integer, MSnSpectrum, ShotgunProtocol, IdentificationParameters, SpecificAnnotationSettings, int) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScores: Scores the match between the given peptide and spectrum using the given score.
getScore(Peptide, Integer, MSnSpectrum, ShotgunProtocol, IdentificationParameters, SpecificAnnotationSettings, PsmScores) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScores: Scores the match between the given peptide and spectrum using the given score.
getScore(int) - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore: Returns the PTM score indexed by the given id.
getScore(String) - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore: Returns the PTM score of the given name.
getScore() - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: Returns the score assigned by the advocate.
getScore() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature: Returns the score.
getScore() - Method in class com.compomics.util.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
getScoreForAlgorithm(Integer) - Method in class com.compomics.util.preferences.PsmScoringPreferences: Returns the scores set for a given algorithm.
getScoresAsList() - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore: Returns a list containing the names of the implemented scores.
getSearchGuiPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the path to the SearchGUI installation.
getSearchParameters(File, SearchParameters, String, WaitingHandler) - Static method in class com.compomics.util.experiment.io.identifications.MzIdentMLIdfileSearchParametersConverter: Constructor.
getSearchParameters() - Method in class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Returns a SearchParameters instance based on the user input in the GUI.
getSearchParameters() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the parameters used for the spectrum matching.
getSearchParametersFromGUI() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog: Returns the search parameters as set in the GUI.
getSearchParametersFromGUI() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog: Returns the search parameters as set in the GUI.
getSearchParametersFromGUI() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog: Returns the search parameters as set in the GUI.
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.
getSections() - Method in class com.compomics.util.io.export.ExportScheme: returns the list of sections to be included in the scheme.
getSegmentSequence(String) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns the sequence of this segment.
getSelectedBackgroundSpecies() - Method in class com.compomics.util.preferences.GenePreferences: Returns the taxon of the species selected as background species.
getSelectedCharges() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: 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.
getSelectedFile() - Method in class com.compomics.util.gui.filehandling.FileSelectionDialog: Returns the file selected by the user.
getSelectedFile() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromDnaDialog: Returns the file selected by the user.
getSelectedFile() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog: Returns the file selected by the user.
getSelectedFile() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromUniprotDialog: Returns the file selected by the user.
getSelectedFiles() - Method in class com.compomics.util.gui.filehandling.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.
getSelectedOutput() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the selected output type, omx, csv or pepXML.
getSelectedOutputFormat() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.preferences.PTMScoringPreferences: 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.
getSelectedTaxonomyMap() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel: Returns the selected taxonomy map.
getSelection() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock: Returns true if there is a selection.
getSeparatePeptides() - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Returns a boolean indicating whether Peptides should be grouped according to their modification status.
getSeparatePsms() - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Returns a boolean indicating whether PSMs should be grouped according to their modification status.
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.AminoAcidSequence: Returns the sequence as String.
getSequence() - Method in class com.compomics.util.experiment.biology.Peptide: Getter for the sequence.
getSequence(String) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns the sequence of the peptide indexed by the given key.
getSequence() - Method in class com.compomics.util.experiment.biology.Protein: Getter for the protein sequence.
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.
getSequenceAsAminoAcidSequence() - Method in class com.compomics.util.experiment.biology.Peptide: Returns the sequence of this peptide as AminoAcidSequence.
getSequenceAsAminoAcidSequence(String) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns the given sequence as AminoAcidSequence.
getSequenceAsPattern() - Method in class com.compomics.util.experiment.biology.Peptide: Returns the sequence of this peptide as AminoAcidPattern.
getSequenceAsPattern(String) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns the given sequence as AminoAcidPattern.
getSequenceMatchingPreferences() - Method in class com.compomics.util.gui.parameters.identification_parameters.SequenceMatchingSettingsDialog: Returns the sequence matching settings as set by the user.
getSequenceMatchingPreferences() - Method in class com.compomics.util.preferences.IdentificationParameters: Returns the sequence matching preferences.
getSequenceMatchingPreferences() - Method in class com.compomics.util.preferences.PTMScoringPreferences: Returns the sequence matching preferences to use when mapping PTMs on amino acid sequences.
getSequenceMatchingType() - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Returns the sequence matching type.
getSequenceProbabilities(Peptide, ArrayList<PTM>, MSnSpectrum, AnnotationSettings, SpecificAnnotationSettings, boolean, SequenceMatchingPreferences, SequenceMatchingPreferences, PeptideSpectrumAnnotator) - Static method in class com.compomics.util.experiment.identification.ptm.ptmscores.PhosphoRS: Returns the PhosphoRS sequence probabilities for the PTM possible locations.
getSequenceWithLowerCasePtms() - Method in class com.compomics.util.experiment.biology.Peptide: Returns the peptide sequence as a String where the modified residues are in lower case.
getSerializationFolder() - Static method in class com.compomics.util.experiment.biology.PTMFactory: Returns the folder where the factory is saved.
getSharedProteinNormalisationFactor(String) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors: Returns the shared protein normalization factor for the given sample, 1.0 if not set.
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.identification_parameters.SearchParameters: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.preferences.FractionSettings: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.preferences.GenePreferences: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.preferences.ProteinInferencePreferences: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.preferences.PsmScoringPreferences: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.preferences.PTMScoringPreferences: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Returns a short description of the parameters.
getShortDescription() - Method in class com.compomics.util.preferences.ValidationQCPreferences: Returns a short description of the parameters.
getShortName() - Method in class com.compomics.util.experiment.biology.PTM: Getter for the short modification name.
getSimilarNotFixedModifications(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Returns a list containing all not fixed modifications with the same mass.
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.protein.Header: Returns a simplified protein description for a UniProt header.
getSingleAAPTM(PTM) - Static method in class com.compomics.util.experiment.biology.PTMFactory: Returns a clone of the given PTM targeting a single amino acid instead of a pattern.
getSingleAAPTM(String) - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns a clone of the given PTM targeting a single amino acid instead of a pattern.
getSingleChargeWindow() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Returns the window size for singly charged ions.
getSingleLetterCodeAsChar() - Method in class com.compomics.util.experiment.biology.AminoAcid: Returns the single letter code as character.
getSize() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Returns the size of the node in accession*tag.
getSkylinePath() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.identifications.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.identifications.idfilereaders.AndromedaIdfileReader
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader
getSoftwareVersions() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader
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.preferences.UtilitiesUserPreferences: 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: 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.preferences.UtilitiesUserPreferences: Getter for the sparkline color.
getSparklineColorDoubtful() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the color for a doubtful sparkline bar chart plots.
getSparklineColorFalsePositives() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the color for false positives in sparkline bar chart plots.
getSparklineColorNonValidated() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Getter for the non-validated sparkline color.
getSparklineColorNotFound() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the color for a not found sparkline bar chart plots.
getSparklineColorPossible() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the color for a possible sparkline bar chart plots.
getSpecies() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the species targeted by this database.
getSpeciesDescription(HashMap<String, Integer>) - Static method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory: Returns a listing of the species occurrence map provided.
getSpecificAnnotationPreferences(String, SpectrumIdentificationAssumption, SequenceMatchingPreferences, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns the annotation preferences specific to a spectrum and an identification assumption.
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.
getSpectra(File) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Reads an MGF file and retrieves a list of spectra.
getSpectrum(BufferedReader, String) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Returns the next spectrum found in the mgf file.
getSpectrum(BufferedRandomAccessFile, long, String) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Returns the next spectrum starting from the given index.
getSpectrum(String, String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the desired spectrum.
getSpectrum(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the desired spectrum.
getSpectrumAnnotatedMirroredPeakColor() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the color to use for the annotated mirrored peaks.
getSpectrumAnnotatedPeakColor() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the color to use for the annotated peaks.
getSpectrumAnnotatedPeakWidth() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the width of the annotated peaks.
getSpectrumAnnotation(AnnotationSettings, SpecificAnnotationSettings, MSnSpectrum, Peptide) - 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(AnnotationSettings, SpecificAnnotationSettings, MSnSpectrum, Peptide, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>) - 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(AnnotationSettings, SpecificAnnotationSettings, MSnSpectrum, 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.
getSpectrumAnnotation(ArrayList<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.
getSpectrumBackgroundPeakColor() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the color to use for the background peaks.
getSpectrumBackgroundPeakWidth() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the width of the background peaks.
getSpectrumCharges() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the spectrum charges to search for.
getSpectrumComponent(int, String) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns a component in a spectrum line.
getSpectrumComponentNames() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns all the spectrum components names found in the header.
getSpectrumCount() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch: Returns the number of spectra matched.
getSpectrumFile(String) - Static method in class com.compomics.util.experiment.massspectrometry.Spectrum: Convenience method to retrieve the name of a file from the spectrum key.
getSpectrumFileFromIdName(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the spectrum file corresponding to the name of the file used for identification
getSpectrumFileId() - Method in class com.compomics.util.io.PklFile
getSpectrumFiles() - Method in class com.compomics.util.experiment.identification.Identification: Returns the names of the mgf files used in the spectrum identification map as a list.
getSpectrumIdentification(String) - Method in class com.compomics.util.experiment.identification.Identification: Returns the keys of the spectrum identifications for a given spectrum file name.
getSpectrumIdentificationAssumption() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Returns the spectrum identification assumption to annotate with.
getSpectrumIdentificationMap() - Method in class com.compomics.util.experiment.identification.Identification: Returns the keys of all identified spectra indexed by the spectrum file.
getSpectrumIdentificationSize() - Method in class com.compomics.util.experiment.identification.Identification: Returns the number of spectrum identifications.
getSpectrumIds() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns all the spectrum IDs found.
getSpectrumIndex(String) - Method in class com.compomics.util.experiment.io.massspectrometry.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.
getSpectrumIndex(String, String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the spectrum index of the given spectrum in the given file.
getSpectrumKey() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Returns the key of the spectrum to annotate.
getSpectrumKey(String, String) - Static method in class com.compomics.util.experiment.massspectrometry.Spectrum: Convenience method returning the key for a spectrum.
getSpectrumKey() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the key of the spectrum.
getSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.Identification: Returns a spectrum match.
getSpectrumMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Returns a spectrum match.
getSpectrumMatch(String, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the desired spectrum match.
getSpectrumMatchesKeys() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch: Returns the keys of all spectra matched.
getSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Returns the desired spectrum match parameter.
getSpectrumMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Returns the desired spectrum match parameter.
getSpectrumMatchParameter(String, UrParameter, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the desired spectrum match parameter.
getSpectrumMatchTable(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the PSM table name associated with the given spectrum key.
getSpectrumNumber() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Returns the spectrum number in the spectrum file.
getSpectrumParameterTable(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Returns the table name associated with the given spectrum parameter.
getSpectrumTitle(int) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns the spectrum title corresponding to the given spectrum number.
getSpectrumTitle(String) - Static method in class com.compomics.util.experiment.massspectrometry.Spectrum: Convenience method to retrieve the name of a spectrum from the spectrum key.
getSpectrumTitle() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the spectrum title.
getSpectrumTitle(String, int) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns the spectrum title of the spectrum of the given number in the given file.
getSpectrumTitles() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns an ordered list of all spectrum titles.
getSpectrumTitles(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns a list of titles from indexed spectra in the given file.
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.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if the sqt output is to be created.
getStandardGeneticCode() - Method in class com.compomics.util.experiment.biology.AminoAcid: Returns the standard genetic triplets associated to this amino acid.
getStandardGeneticCode() - Method in class com.compomics.util.experiment.biology.aminoacids.X
getStandardGeneticCodeForCombination() - Method in class com.compomics.util.experiment.biology.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.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.
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.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.experiment.identification.identification_parameters.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.preferences.SequenceMatchingPreferences: Returns preferences for simple string matching.
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.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.AminoAcid: In case of a combination of amino acids, returns the comprised amino acids or amino acid groups represented by their single letter code.
getSubMatrix(int, int, int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
getSubNode(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Returns the subnode associated to an amino acid sequence.
getSubNumber() - Method in class com.compomics.util.experiment.biology.ions.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.AminoAcidPattern: Returns a sub pattern of the pattern.
getSubPattern(int, boolean) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns a sub pattern of the pattern.
getSubSpectrum(double, double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Returns the part of the spectrum contained between mzMin (inclusive) and mzMax (exclusive) as a peak list
getSubtree() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Returns the subtree.
getSubType() - Method in class com.compomics.util.experiment.biology.Ion: Returns the ion subtype.
getSubType() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
getSubType() - Method in class com.compomics.util.experiment.biology.ions.Glycan
getSubtype(char) - Static method in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Returns the subtype identifier based on the amino acid one letter symbol.
getSubType() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
getSubType() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
getSubType() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
getSubType() - Method in class com.compomics.util.experiment.biology.ions.RelatedIon
getSubType() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
getSubType() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.Ion: Returns the subtype as string.
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.Glycan
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
getSubTypeAsString(int) - Static method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Returns the type of fragment ion as a letter.
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.RelatedIon
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
getSubTypeAsString() - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
getSubTypeAsString(int) - Static method in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Returns the type of fragment ion as a letter.
getSurroundingAA(String, int, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Protein: Returns the amino acids surrounding a peptide in the sequence of the given protein in a map: peptide start index > (amino acids before, amino acids after).
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.
getTables() - Method in class com.compomics.util.db.ObjectsDB: Returns a list of tables present in the database.
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(int, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Returns a map containing the tag assumptions of this spectrum assumptions indexed by the beginning of the longest amino acid sequence.
getTaggedModifiedSequence(PtmSettings, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, AminoAcidPattern, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, boolean, boolean) - Static method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, String, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, boolean, boolean) - Static method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, boolean, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, boolean, boolean, boolean) - Method in class com.compomics.util.experiment.biology.Peptide: Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, Peptide, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, HashMap<Integer, ArrayList<String>>, boolean, boolean, boolean) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, boolean, boolean, boolean, boolean, boolean) - 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 PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, boolean, boolean, boolean, boolean) - 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 PTM tags, e.g, <mox>.
getTaggedModifiedSequence(PtmSettings, Tag, boolean, boolean, boolean, boolean, boolean) - 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 PTM tags, e.g, <mox>.
getTaggedResidue(char, String, PtmSettings, int, boolean, boolean) - Static method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the single residue as a tagged string (HTML color or PTM tag).
getTaggingTimeSeconds() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns the tagging time in seconds as listed in the file.
getTagLength() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.identifications.idfilereaders.DirecTagIdfileReader: Returns the tagging parameter corresponding to a given parameter name.
getTagsGenerator() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns the tags generator used to create the file.
getTagsGeneratorVersion() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns the version of the tags generator used to create the file.
getTagsMap() - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader: Returns a map of all simple tags found in this file indexed by the beginning of the amino acid sequence.
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader
getTagsMap() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader
getTagsParametersNames() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns the name of the different parameters names found.
getTarget() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the index of the amino acid of interest in the pattern.
getTarget() - Method in class com.compomics.util.experiment.biology.mutations.Mutation: Returns the target amino acid.
getTargetDecoyFileNameTag() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the target-decoy file name tag.
getTargetedAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the targeted amino acids at a given index in the pattern.
getTaxonomy() - Method in class com.compomics.util.protein.Header
getTaxonomy() - Method in class com.compomics.util.protein_sequences_manager.UniProtQuery: Returns the taxonomy.
getTaxonomyID() - Method in enum com.compomics.util.protein_sequences_manager.enums.ModelOrganism: Returns the taxonomy.
getTaxonomyResult() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreeDialog: Returns the selected taxonomy ID and their corresponding name.
getTaxonomyTree() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel: Returns the taxonomy tree.
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.
getTempFolder() - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the temporary folder.
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.
getTerminalIndex() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns the index of the terminal on the protein sequence.
getTermini() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Returns the terminal mappings (they are not in the subtree).
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(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.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if the text output is to be created.
getTheoreticalFragmentIonsSumOnly() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.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(int) - Method in class com.compomics.util.experiment.biology.Ion: Returns the theoretic m/z of an ion at a given charge state.
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.
getTheoreticPeptide() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch: Getter for the theoretic peptide.
getTheoreticProteinsAccessions() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Returns the accessions of the possible theoretic proteins.
getTheoreticPtm() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Getter for the theoretic PTM name.
getTicCutoffPercentage() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the TIC cutoff in percent.
getTicCutoffPercentage() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns the TicCutoffPercentage.
getTimeEnd() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader: Returns the ending time of the tagging as given in the file.
getTimeStart() - Method in class com.compomics.util.experiment.io.identifications.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 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.
getTopPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the top peaks number.
getTopPeaksWindow() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns the top peaks window size.
getTotalIntensity() - Method in class com.compomics.util.experiment.massspectrometry.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.
getTrace() - Method in class com.compomics.util.math.matrix.DoubleMatrix
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.AminoAcidPattern: Returns the trypsin example as amino acid pattern.
getType() - Method in class com.compomics.util.experiment.biology.Ion: Returns the ion type.
getType() - Method in class com.compomics.util.experiment.biology.PTM: Getter for the modification 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.identification_parameters.SearchParameters
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.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.pdbfinder.das.readers.DasFeature: Returns the type.
getType() - Method in class com.compomics.util.preferences.DummyParameters
getType() - Method in class com.compomics.util.preferences.IdentificationParameters
getType() - Method in interface com.compomics.util.preferences.MarshallableParameter: Returns the type of marshalled parameter from an unmarshalled object.
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.Ion: Returns the type of ion as string.
getTypeAsString(Ion.IonType) - Static method in class com.compomics.util.experiment.biology.Ion: Returns the type of ion as string.
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.
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.ptm.ModificationsDialog: Returns a web link to the given Unimod CV term at http://www.ebi.ac.uk/ontology-lookup.
getUniprotFolder() - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the folder where UniProt databases are stored.
getUniprotHost() - Static method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.ConnectionManager: Returns the UniProt web site host name.
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.AminoAcid: Returns a char array of the one letter code of amino acids without combinations of amino acids.
getUniqueProteinNormalisationFactor(String) - Method in class com.compomics.util.experiment.normalization.NormalizationFactors: Returns the unique protein normalization factor for the given sample, 1.0 if not set.
getUpperClearMzRange() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Returns the upper mass value for the clear mz range.
getUpperPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.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: Method which returns the refinement parameter.
getUseFlankingPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if flanking peaks are to be used.
getUseGeneMapping() - Method in class com.compomics.util.preferences.GenePreferences: Returns a boolean indicating whether gene mappings should be used.
getUseNeutralLossPeaks() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns true if the neutral loss peaks are to be used.
getUserAdvocates() - Static method in class com.compomics.util.experiment.identification.Advocate: Returns the map of user advocates imported.
getUserFolder() - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the folder where user databases are stored.
getUserModifications() - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns the names of the user defined modifications.
getUserModificationsOrdered() - Method in class com.compomics.util.experiment.biology.PTMFactory: Returns the alphabetically ordered names of the user defined modifications.
getUserPreferencesFile() - Static method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the user preferences file to be used.
getUserPreferencesFolder() - Static method in class com.compomics.util.preferences.UtilitiesUserPreferences: Returns the user preferences file to be used.
getUserSelectedFile(Component, String, String, String, String, String, boolean) - Static method in class com.compomics.util.Util: 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.Util: 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.Util: Returns the folder selected by the user, or null if no folder was selected.
getUseSmartPlusThreeModel() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Returns true if the UseSmartPlusThreeModel is to be used.
getUseSparseMatrix() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Deprecated.
from Comet release 2015.02 all searches use this internal data representation by default
getUtilitiesEnzyme(String) - Static method in class com.compomics.util.experiment.biology.EnzymeFactory: Tries to map the enzyme name given in the PRIDE file a utilities/OMSSA enzyme.
getUtilitiesPtmName(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Returns the name of the PTM indexed by the given index.
getUtilitiesPtmName(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters: Returns the utilities PTM name corresponding to the given Novor PTM short name.
getUtilitiesPtmName(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Returns the utilities PTM name corresponding to the given PepNovo PTM name.
getUtilitiesPtmName(Character) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Returns the utilities PTM name corresponding to the given pNovo PTM character.
getUtilitiesUserPreferences() - Method in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent: Returns the utilities user preferences.
getValidationQCPreferences() - Method in class com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialog: Returns the validation QC preferences as set by the user.
getValidationQCPreferences() - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Returns the validation QC preferences.
getValue(Integer) - Method in class com.compomics.util.experiment.massspectrometry.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.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
getVariableModifications() - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Returns the expected variable modification names included in this profile.
getVennDiagramPanel() - Method in class com.compomics.util.gui.VennDiagramDialog: Returns the Venn diagram panel.
getVerbosity() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Returns the verbosity type of progress output.
getVersion() - Method in class com.compomics.util.examples.UtilitiesDemo: Retrieves the version number set in the pom file.
getVersion(ObjectsDB) - Static method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns the version.
getVersion() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns the version.
getVersion() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns the database version.
getVersionNumber() - Method in class com.compomics.software.autoupdater.MavenJarFile: Returns the version number.
getVersionsForDb(String) - Method in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Returns the list of versions for the given database name as parsed from the working folder.
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.
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.
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.experiment.biology.Enzyme: 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.filefilters.FileFilterUtils
GIF - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
GLUTAMIC_ACID - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a glutamic acid immonium ion.
GlutamicAcid - Class in com.compomics.util.experiment.biology.aminoacids: Glutamic Acid.
GlutamicAcid() - Constructor for class com.compomics.util.experiment.biology.aminoacids.GlutamicAcid: Constructor.
Glutamine - Class in com.compomics.util.experiment.biology.aminoacids: Glutamine.
Glutamine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Glutamine: Constructor.
GLUTAMINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a glutamine immonium ion.
Glycan - Class in com.compomics.util.experiment.biology.ions: This class represents a glycan.
Glycan(String, String) - Constructor for class com.compomics.util.experiment.biology.ions.Glycan: Constructor for a glycan.
Glycine - Class in com.compomics.util.experiment.biology.aminoacids: Glycine.
Glycine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Glycine: Constructor.
GLYCINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a glycine immonium ion.
GlyconFactory - Class in com.compomics.util.experiment.biology: This factory will provide theoretic glycons.
GO_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.experiment.biology.genes.GeneFactory: The suffix to use for files containing GO mappings.
GO_MAPPING_FILE_SUFFIX - Static variable in class com.compomics.util.preferences.GenePreferences: Deprecated.
use the gene factory.
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
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(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

H

H - Static variable in class com.compomics.util.experiment.biology.AminoAcid
H - Static variable in class com.compomics.util.experiment.biology.Atom: The hydrogen atom.
H2O - Static variable in class com.compomics.util.experiment.biology.NeutralLoss: H2O loss.
H3PO4 - Static variable in class com.compomics.util.experiment.biology.NeutralLoss: H3PO4 loss.
halfGbFree() - Static method in class com.compomics.util.memory.MemoryConsumptionStatus: Indicates whether a GB of memory is free.
hasAddenda() - Method in class com.compomics.util.protein.Header: This method reports on the presence of addenda for this header.
hasArgument - Variable in enum com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersCLIParams: 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.
hasAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Indicates whether the spectrum match contains a peptide assumption from a search engine.
hasAssumption(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Indicates whether the spectrum match contains a peptide assumption for the given advocate (for example a search engine, see the Advocate class)
hasCombination(String) - Static method in class com.compomics.util.experiment.biology.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.identifications.IdfileReader: Returns a boolean indicating whether the file contains de novo results as tags.
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader
hasDeNovoTags() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader
hasEnoughSequences() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Indicates whether the database contained enough protein sequences for reliability of the target/decoy based statistics.
hasEnzymaticPeptide(String, Enzyme, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Indicates whether the protein group has an enzymatic peptide when considering the given accession as main accession.
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.massspectrometry.Charge
hashCode() - Method in class com.compomics.util.experiment.massspectrometry.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.
hasLimitX() - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Indicates whether the share of X's should be limited.
hasMutationMatrix() - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Indicates whether a mutation matrix shall be used.
hasNeutralLosses() - Method in class com.compomics.util.experiment.biology.Ion: Indicates whether the ion has a neutral loss.
hasNext() - Method in class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator: Indicates whether the iterator is done iterating.
hasNext() - Method in class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator: Indicates whether the iterator is done iterating.
hasNext() - Method in class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Indicates whether the iterator is done iterating.
hasNext() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.PeptideIterator
hasNext() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.HeaderIterator: Returns true if there is a next header.
hasNext() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.ProteinIterator: Returns true if there is another protein.
hasNext() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfFileIterator: Indicates whether the file contains another spectrum.
hasNormalizationFactors() - Method in class com.compomics.util.experiment.normalization.NormalizationFactors: Indicates whether normalization factors are set.
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.
hasPtmIndexes() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Indicates whether the modification profile has PTM indexes.
hasPtmIndexes() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Indicates whether the modification profile has PTM indexes.
hasRTWindow() - Method in class com.compomics.util.experiment.massspectrometry.Precursor: Returns a boolean indicating whether the retention time window was implemented.
hasTable(String) - Method in class com.compomics.util.db.ObjectsDB: Indicates whether the database contains the given table.
He - Static variable in class com.compomics.util.experiment.biology.Atom: The helium atom.
Header - Class in com.compomics.util.protein: This class represents the header for a Protein instance.
Header.DatabaseType - Enum in com.compomics.util.protein: A list of the database types.
HeaderIterator(File, boolean) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.HeaderIterator: Constructor.
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: The helium atom.
Helium() - Constructor for class com.compomics.util.experiment.biology.atoms.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(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: Histidine.
Histidine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Histidine: Constructor.
HISTIDINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for an histidine immonium ion.
HOST - Static variable in class com.compomics.util.io.FolderMonitor
HPO3 - Static variable in class com.compomics.util.experiment.biology.NeutralLoss: H3PO3 loss.
Hydrogen - Class in com.compomics.util.experiment.biology.atoms: The hydrogen atom.
Hydrogen() - Constructor for class com.compomics.util.experiment.biology.atoms.Hydrogen: Constructor.

I

I - Static variable in class com.compomics.util.experiment.biology.AminoAcid
I - Static variable in class com.compomics.util.experiment.biology.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.util.experiment.identification.parameters_cli.IdentificationParametersCLIParams: Short Id for the CLI parameter.
id - Variable in enum com.compomics.util.preferences.SearchGuiOutputOption: 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 contains identification results.
Identification() - Constructor for class com.compomics.util.experiment.identification.Identification
IdentificationAlgorithmParameter - Interface in com.compomics.util.experiment.identification.identification_parameters: Interface for the algorithm specific parameters.
identificationCharge - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: The charge used for identification.
IdentificationDB - Class in com.compomics.util.experiment.identification: This class uses a database to manage identification matches.
IdentificationDB(String, String, boolean, ObjectsCache) - Constructor for class com.compomics.util.experiment.identification.IdentificationDB: Constructor creating the database and the protein and protein parameters tables.
identificationFile - Variable in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: The identification file.
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
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(int) - Constructor for class com.compomics.util.experiment.identification.IdentificationMethod: Constructor for the identification method
IdentificationParameters - Class in com.compomics.util.preferences: Generic class grouping the parameters used for protein identification.
IdentificationParameters() - Constructor for class com.compomics.util.preferences.IdentificationParameters: Creates empty identification parameters.
IdentificationParameters(SearchParameters) - Constructor for class com.compomics.util.preferences.IdentificationParameters: Creates default identification parameters from the given search parameters.
IdentificationParameters(String, String, SearchParameters, AnnotationSettings, SequenceMatchingPreferences, GenePreferences, PsmScoringPreferences, PeptideAssumptionFilter, PTMScoringPreferences, ProteinInferencePreferences, IdMatchValidationPreferences, FractionSettings) - Constructor for class com.compomics.util.preferences.IdentificationParameters: Constructor.
IdentificationParametersCLIParams - Enum in com.compomics.util.experiment.identification.parameters_cli: Enum class specifying the SearchParameter command line option parameters to create a SearchParameters object
IdentificationParametersEditionDialog - Class in com.compomics.util.gui.parameters: IdentificationParametersEditionDialog.
IdentificationParametersEditionDialog(Frame, IdentificationParameters, ConfigurationFile, Image, Image, LastSelectedFolder, ValidationQCPreferencesDialogParent, boolean) - Constructor for class com.compomics.util.gui.parameters.IdentificationParametersEditionDialog: Creates a new IdentificationParametersEditionDialog with a frame as owner.
IdentificationParametersEditionDialog(Dialog, Frame, IdentificationParameters, ConfigurationFile, Image, Image, LastSelectedFolder, ValidationQCPreferencesDialogParent, boolean) - Constructor for class com.compomics.util.gui.parameters.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.util.experiment.identification.parameters_cli: This class contains the parses parameters from a command line and stores them in a SearchParameters object.
IdentificationParametersInputBean(CommandLine) - Constructor for class com.compomics.util.experiment.identification.parameters_cli.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_parameters
IdentificationParametersNameDialog(Frame, IdentificationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.IdentificationParametersNameDialog: Creates a new IdentificationParametersNameDialog with a frame as owner.
IdentificationParametersNameDialog(Dialog, Frame, IdentificationParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.IdentificationParametersNameDialog: Creates a new IdentificationParametersNameDialog with a dialog as owner.
IdentificationParametersOverviewDialog - Class in com.compomics.util.gui.parameters: IdentificationParametersOverviewDialog.
IdentificationParametersOverviewDialog(Dialog) - Constructor for class com.compomics.util.gui.parameters.IdentificationParametersOverviewDialog: Constructor with a dialog as owner.
IdentificationParametersOverviewDialog(Frame) - Constructor for class com.compomics.util.gui.parameters.IdentificationParametersOverviewDialog: Constructor with a frame as owner.
IdentificationParametersSelectionDialog - Class in com.compomics.util.gui.parameters: Deprecated.
no longer used
IdentificationParametersSelectionDialog(Frame, Dialog, IdentificationParameters, IdentificationParametersSelectionDialog.StartupMode, ConfigurationFile, Image, Image, LastSelectedFolder, ValidationQCPreferencesDialogParent, boolean) - Constructor for class com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog: Deprecated.

Constructor with a dialog as owner.
IdentificationParametersSelectionDialog(Frame, IdentificationParameters, IdentificationParametersSelectionDialog.StartupMode, ConfigurationFile, Image, Image, LastSelectedFolder, ValidationQCPreferencesDialogParent, boolean) - Constructor for class com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog: Deprecated.

Constructor with a frame as owner.
IdentificationParametersSelectionDialog(Frame, ConfigurationFile, Image, Image, LastSelectedFolder, ValidationQCPreferencesDialogParent, SearchSettingsDialog) - Constructor for class com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog: Deprecated.

Constructor with a frame as owner allowing the edition and saving from a search parameters dialog.
IdentificationParametersSelectionDialog.StartupMode - Enum in com.compomics.util.gui.parameters: Deprecated.

The default edition mode to use at startup when opening a new dialog.
IdfileReader - Interface in com.compomics.util.experiment.io.identifications: This interface will retrieve spectrum matches from any identification file.
IdfileReaderFactory - Class in com.compomics.util.experiment.io.identifications: This factory will provide the appropriate identification file reader for each type of file.
IdMatchValidationPreferences - Class in com.compomics.util.preferences: Generic class grouping the identification matches validation preferences.
IdMatchValidationPreferences() - Constructor for class com.compomics.util.preferences.IdMatchValidationPreferences: Constructor for default settings.
IdMatchValidationPreferences(IdMatchValidationPreferences) - Constructor for class com.compomics.util.preferences.IdMatchValidationPreferences: 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: Represents an immonium ion.
ImmoniumIon(char) - Constructor for class com.compomics.util.experiment.biology.ions.ImmoniumIon: Constructor for an immonium ion.
ImmoniumIon(int) - Constructor for class com.compomics.util.experiment.biology.ions.ImmoniumIon: Constructor for an immonium ion.
importComplete() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns a boolean indicating whether the import was complete.
importDatabase() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog: Copies the selected database to the temp folder and populates the gui with the relevant information.
importEnzymes(File) - Method in class com.compomics.util.experiment.biology.EnzymeFactory: Import enzymes.
importFromFile(File, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.ensembl.GeneMapping: Reads go mappings from a BioMart file.
importGlycons(File) - Method in class com.compomics.util.experiment.biology.GlyconFactory: Import glycons from an xml 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.
importNewFile(File, SequenceInputType) - Method in class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Imports a file in the protein sequence manager and updates the GUI.
ImportSequencesFromDnaDialog - Class in com.compomics.util.protein_sequences_manager.gui.sequences_import: Dialog allowing the import of protein database from DNA sequences.
ImportSequencesFromDnaDialog(Frame) - Constructor for class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromDnaDialog: Constructor.
ImportSequencesFromFilesDialog - Class in com.compomics.util.protein_sequences_manager.gui.sequences_import: Dialog for importing sequences from files.
ImportSequencesFromFilesDialog(Frame, Image, Image) - Constructor for class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog: Constructor.
ImportSequencesFromUniprotDialog - Class in com.compomics.util.protein_sequences_manager.gui.sequences_import: Dialog allowing the import of sequences from UniProt.
ImportSequencesFromUniprotDialog(Frame) - Constructor for class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromUniprotDialog: Constructor.
iMSLevel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel: The ms level of the current spectrum.
inCache(String, String, String) - Method in class com.compomics.util.db.ObjectsCache: Indicates whether an object is loaded in the 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
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: Increase the progress bar value by one "counter".
increasePrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Increase the progress bar value by the given amount.
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: Increases the progress bar.
increaseSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX: Increases the value of the progress bar.
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: Increase the secondary progress bar value by the given amount.
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 amount.
increasing - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScores: Indicates whether the score increases with the quality of the match.
inDB(String, String, boolean) - Method in class com.compomics.util.db.ObjectsDB: Indicates whether an object is loaded in the given table.
index - Variable in enum com.compomics.util.experiment.biology.Ion.IonType: The index of the type.
index - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScores: The index of the score of interest.
index - Variable in enum com.compomics.util.experiment.massspectrometry.proteowizard.MsFormat: 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.preferences.SequenceMatchingPreferences.MatchingType: The index of the type as integer.
inDoubleRange(String, String, double, double) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns true if the input is a double value inside the given range.
inferProtocolFromSearchSettings(SearchParameters) - Static method in class com.compomics.util.experiment.ShotgunProtocol: Backward compatibility inferring the protocol from search settings.
inIntegerRange(String, String, int, int) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns true if the input is an integer value inside the given range.
init() - Method in class com.compomics.util.io.json.JsonMarshaller: Initializes the marshaller with (custom) type adapters and date format
init() - Method in class com.compomics.util.io.json.marshallers.PrideMarshaller
initialize(String) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Initializes the factory.
initiate(String) - Method in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory: Initiates the factory using the files of the static fields.
initiate(String[]) - Method in class com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli: Initiates the IdentificationParametersCli.
initiate() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Initiates the connection to the database and indicates whether the corresponding folder is already created.
initiateSorter() - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel: Initiates the sorter to the current order of the table.
initiateTree(int, int, int, WaitingHandler, ExceptionHandler, boolean, boolean, int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Initiates the tree.
initiateTree(int, int, int, Enzyme, WaitingHandler, ExceptionHandler, boolean, boolean, int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Initiates the tree.
insert(int, AminoAcidSequence) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Inserts another sequence in this sequence.
insert(int, String) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Inserts another sequence in this sequence.
insertObject(String, String, Object, boolean) - Method in class com.compomics.util.db.ObjectsDB: Stores an object in the desired table.
insertObjects(String, HashMap<String, Object>, WaitingHandler) - Method in class com.compomics.util.db.ObjectsDB: Inserts a set of objects in the given table.
insertObjects(String, HashMap<String, Object>, WaitingHandler, boolean) - Method in class com.compomics.util.db.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(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(String, CvTerm, CvTerm, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Instrument: Create a new Instrument object.
intensity - Variable in class com.compomics.util.experiment.massspectrometry.Peak: The intensity of the peak.
IntensityHistogram - Class in com.compomics.util.gui.spectrum: Creates an IntensityHistogram plot.
IntensityHistogram(ArrayList<IonMatch>, MSnSpectrum, 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.
intensityPeakMap - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum: Intensity indexed Peak map.
IntensityRankScore - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores: The intensity rank sub-score as adapted from the DirecTag manuscript (http://www.ncbi.nlm.nih.gov/pubmed/18630943).
IntensityRankScore() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.IntensityRankScore
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
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: Iodine.
Iodine() - Constructor for class com.compomics.util.experiment.biology.atoms.Iodine: Constructor.
Ion - Class in com.compomics.util.experiment.biology: This class models an ion.
Ion() - Constructor for class com.compomics.util.experiment.biology.Ion
ion - Variable in class com.compomics.util.experiment.identification.matches.IonMatch: The matching ion.
Ion.IonType - Enum in com.compomics.util.experiment.biology: An enumerator of the supported ion types.
IonFactory - Class in com.compomics.util.experiment.biology: This factory generates the expected ions from a peptide.
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>>, ArrayList<NeutralLoss>) - 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 will model the assignment of a peak to a theoretical ion.
IonMatch(Peak, Ion, Charge) - Constructor for class com.compomics.util.experiment.identification.matches.IonMatch: Constructor for an ion peak.
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.
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.
is64BitJava() - Static method in class com.compomics.software.CompomicsWrapper: Returns if the Java version used is 64 bit.
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.
isActiveConnection(String, String) - Static method in class com.compomics.util.db.DerbyUtil: Indicates whether a connection is active.
isActiveConnection(String) - Static method in class com.compomics.util.db.DerbyUtil: Indicates whether a connection is active.
isAdditionalOutput() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Returns if additional output is to be included.
isAdjustPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
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.
isAutomatedMemoryManagement() - Method in class com.compomics.util.db.ObjectsCache: Returns whether the cache is in automated memory management mode.
isAutomaticAnnotation() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns whether the annotation settings should be automatically inferred.
isAutoUpdate() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Indicates whether the tools should use the auto update function.
isBooleanInput(String, String) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: 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.PathSettingsDialog: Indicates whether the action was canceled by the user.
isCanceled() - Method in class com.compomics.util.experiment.massspectrometry.proteowizard.gui.MsConvertParametersDialog: 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.ExportFormatSelectionDialog: Returns true of the user canceled the dialog.
isCanceled() - Method in class com.compomics.util.gui.filehandling.FileSelectionDialog: Indicates whether the user canceled the dialog.
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.parameters.identification_parameters.AnnotationSettingsDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.FractionSettingsDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.GenePreferencesDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.IdentificationParametersNameDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.MatchesImportFiltersDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.ProteinInferenceSettingsDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.PsmScoringSettingsDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.PTMLocalizationParametersDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Indicates whether the cancel button was pressed by the user.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.SequenceMatchingSettingsDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.SpectrumMatchingSettingsDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialog: Indicates whether the preference edition was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.parameters.identification_parameters.ValidationSettingsDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.IdentificationParametersEditionDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog: Deprecated.

Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.parameters.OldProcessingPreferencesDialog: Indicates whether the cancel button was pressed by the user.
isCanceled() - Method in class com.compomics.util.gui.parameters.ProcessingPreferencesDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class com.compomics.util.gui.ptm.PtmDialog: Indicates whether the edition was canceled by the user.
isCanceled() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser: Returns a boolean indicating whether the selection was canceled by the user.
isCanceled() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromDnaDialog: Indicates whether the user has canceled the import.
isCanceled() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog: Indicates whether the user has canceled the import.
isCanceled() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromUniprotDialog: Indicates whether the user has canceled the import.
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.AndromedaSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.CometSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsAmandaSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsgfSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MyriMatchSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.OmssaSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.TideSettingsDialog
isCancelled() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog
isCancelled() - Method in interface com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog: 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.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.preferences.UtilitiesUserPreferences: Returns whether the spectra are to be checked for missing charges.
isCleavageSite(String, String) - Method in class com.compomics.util.experiment.biology.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.Enzyme: Returns a boolean indicating whether the given amino acids represent a cleavage site.
isCleaveNterMethionine() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Indicates whether N-terminal methionines should be cleaved.
isClosed() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Indicates whether the connection to the random access file has been closed.
iscombination() - Method in class com.compomics.util.experiment.biology.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.Alanine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Arginine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Asparagine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.AsparticAcid
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.B
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Cysteine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.GlutamicAcid
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Glutamine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Glycine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Histidine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Isoleucine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.J
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Leucine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Lysine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Methionine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Phenylalanine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Proline
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Pyrrolysine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Selenocysteine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Serine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Threonine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Tryptophan
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Tyrosine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Valine
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.X
iscombination() - Method in class com.compomics.util.experiment.biology.aminoacids.Z
isConcatenatedTargetDecoy() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Indicates whether the database is a concatenated target/decoy database.
isConfident() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Returns a boolean indicating whether the modification is confidently localized on the sequence.
isConnectionActive() - Static method in class com.compomics.util.db.DerbyUtil: Returns whether the connection to Derby is active.
isConnectionActive() - Method in class com.compomics.util.db.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.
isConnectionActive() - Method in class com.compomics.util.experiment.identification.IdentificationDB: Indicates whether the connection to the DB is active.
isCorrectPrecursorMass() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).
isCorrupted() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Returns a boolean indicating whether the database is corrupted.
isCterm(SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Returns a list of proteins where this peptide can be found in the C-terminus.
isCTerm(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Protein: Returns a boolean indicating whether the protein ends with the given peptide.
isCTerm() - Method in class com.compomics.util.experiment.biology.PTM: Returns true if the PTM is a c-term PTM.
isDbSize() - Method in class com.compomics.util.preferences.ValidationQCPreferences: Indicates whether the database size should be checked.
isDecoy(SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Indicates whether a peptide can be derived from a decoy protein.
isDecoy() - Method in class com.compomics.util.experiment.biology.Protein: Indicates if the protein is factice (from a decoy database for instance).
isDecoy() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Method indicates if the protein match is a decoy one.
isDecoy(String) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Convenience method indicating whether a match is decoy based on the match key.
isDecoy(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Returns true if the given accession number is a decoy.
isDecoy(String, String) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns a boolean indicating whether a protein is decoy or not based on the protein accession and a given decoy flag.
isDecoyAccession(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Indicates whether a protein is a decoy in the selected loaded FASTA file.
isDecoyInMemory() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Returns whether decoys should be kept in memory.
isDefaultReversed() - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Indicates whether the decoy sequences are reversed versions of the target and the decoy accessions built based on the sequence factory methods.
isDefaultReversed() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Indicates whether the decoy sequences are reversed versions of the target and the decoy accessions built based on the sequence factory methods.
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.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns whether neutral losses should be sequence dependent.
isDetermineChargePlusOneAlgorithmically() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns true if the argument can be parsed as a double value.
isDuplicateSpectra() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Indicates whether empirical correction should be used.
isEmpty() - Method in class com.compomics.util.db.ObjectsCache: Indicates whether the cache is empty.
isEmpty() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Indicates whether the node 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, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the given amino acid sequence ends with the pattern.
isEnding(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the given amino acid sequence ends with the pattern.
isEnzymaticPeptide(String, Enzyme, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Protein: Returns true of the peptide is non-enzymatic, i.e., has one or more end points that cannot be caused by the enzyme alone.
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
isEqualIL() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Indicates whether I and L should be considered indistinguishable.
isEstimateCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Indicates whether the precursor charge shall be estimated for OMSSA.
isEstimateCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Indicates whether the precursor charge shall be estimated for PepNovo.
isEstimateFlr() - Method in class com.compomics.util.preferences.PTMScoringPreferences: Indicates whether the threshold is FLR based.
isFirstDecoy() - Method in class com.compomics.util.preferences.ValidationQCPreferences: Indicates whether the number of hits before the first decoy should be checked.
isFixed() - Method in class com.compomics.util.experiment.biology.NeutralLoss: Returns a boolean indicating whether the neutral loss is fixed or not.
isFragmentAll() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Indicates whether the fragment all option should be used.
isFragmentIonPpm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Indicates whether the fragment ion accuracy is in ppm.
isFragmentIonPpm() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Indicates whether the fragment ion accuracy is in ppm.
isHeader() - Method in class com.compomics.util.io.export.ExportScheme: Indicates whether column header shall be used.
isHigherCharge() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Indicates whether higher charge should be considered.
isHighResolutionAnnotation() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns true if the peak annotation should be based on the most accurate mz value, false bases the annotation on the most intense peak.
isIncludeAmmonia() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Returns a boolean indicating whether ammonia losses should be accounted for.
isIncludeDateInOutputName() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.experiment.identification.identification_parameters.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.
isInferred() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Returns a boolean indicating whether the modification is inferred from another peptide.
isInList(String, String, List<String>) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns true of the input is in the provided list.
isInteger(String, String) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: 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).
isListMods() - Method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Indicates whether the modifications should be printed on the screen.
isLowMemoryMode() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Returns whether the low memory mode is used.
isMemoryMappedSequenceLibraries() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
isModifiable(PTM, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Indicates whether the given modification can be found on the peptide.
isModified() - Method in class com.compomics.util.experiment.biology.Peptide: Indicates whether a peptide carries modifications.
isModified(String) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns a boolean indicating whether the peptide has variable modifications based on its key.
isModified(String, Double) - Static method in class com.compomics.util.experiment.biology.Peptide: Returns a boolean indicating whether the peptide has the given variable modification based on its key.
isMonoIsotopic() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Returns whether monoisotopic mass values shall be used (in contrast to average mass values).
isMs1ResolutionPpm() - Method in class com.compomics.util.experiment.ShotgunProtocol: Indicates whether the MS1 resolution is in ppm.
isMs2ResolutionPpm() - Method in class com.compomics.util.experiment.ShotgunProtocol: Indicates whether the MS2 resolution is in ppm.
isMutationTarget(Character, int, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the given amino acid at the given index of the pattern is targeted when accounting for mutations.
isNeutralLossesAuto() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Indicates whether neutral losses should be automatically selected.
isNotifyStart() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Indicates whether the tools should notify their start.
isNterm(SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Returns a list of proteins where this peptide can be found in the N-terminus.
isNTerm(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Protein: Returns a boolean indicating whether the protein starts with the given peptide.
isNTerm() - Method in class com.compomics.util.experiment.biology.PTM: Returns true if the PTM is an n-term PTM.
isNumber() - Method in interface com.compomics.util.experiment.filtering.FilterItem: Indicates whether the item expects a number as threshold.
Isoleucine - Class in com.compomics.util.experiment.biology.aminoacids: Isoleucine.
Isoleucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Isoleucine: Constructor.
ISOLEUCINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for an isoleucine immonium ion.
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.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(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.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Indicates whether histograms should be written in the result file.
isOutputProteins() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Indicates whether the protein bloc should be included in the export.
isOutputSequences() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Indicate whether the spectra should be exported in the result file.
isPeakPicked() - Method in class com.compomics.util.experiment.io.massspectrometry.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.
isPositiveDouble(String, String, boolean) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns true if the argument can be parsed as a positive double value.
isPositiveInteger(String, String, boolean) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Returns true if the argument can be parsed as a positive integer value.
isPotentialModificationsForFullRefinment() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.SearchParameters: Returns true if the current precursor accuracy type is ppm.
isPrecursorChargesMissing() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Returns true if the at least one spectrum is missing the precursor charge.
isProbabilisticScoreNeutralLosses() - Method in class com.compomics.util.preferences.PTMScoringPreferences: Indicates whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score.
isProbabilitsticScoreCalculation() - Method in class com.compomics.util.preferences.PTMScoringPreferences: Indicates whether a probabilistic PTM score is required.
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.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Indicates whether the protein quick acetylation option should be triggered.
isPtm() - Method in interface com.compomics.util.experiment.filtering.FilterItem: Indicates whether the item expects a list of PTMs to filter on.
isQuickPyrolidone() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Returns whether the quick pyrolidone option should be triggered.
isRefine() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Returns whether the second pass search should be triggered.
isRefinePointMutations() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Indicates whether point mutations should be looked for during the refinement process.
isRefineSemi() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Indicates whether the semi enzymatic option of the second pass search should be triggered.
isRefineSnaps() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether snAPs should be used during the refinement process.
isRefineSpectrumSynthesis() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Indicates whether the spectrum synthesis option should be used during the refinement process.
isRefineUnanticipatedCleavages() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Returns whether the unanticipated cleavages option should be used during the refinement process.
isRemovePrecursor() - Method in class com.compomics.util.experiment.identification.identification_parameters.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: Returns true if the run is canceled.
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.FolderMonitor: This method can be consulted to find out whether the monitor is running.
isSameAs(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether another AminoAcidPattern targets the same pattern.
isSameAs(TagComponent, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
isSameAs(AminoAcidSequence, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Indicates whether another sequence has a matching sequence.
isSameAs(TagComponent, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence
isSameAs(AtomImpl) - Method in class com.compomics.util.experiment.biology.AtomImpl: Indicates whether another atom is the same as this one.
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.Ion: Returns a boolean indicating whether the ion is the same as another ion.
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.Glycan
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.ImmoniumIon
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.PrecursorIon
isSameAs(RelatedIon) - Method in class com.compomics.util.experiment.biology.ions.RelatedIon: Compares the current related ion with another one based on their composition.
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.RelatedIon
isSameAs(ReporterIon) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon: Compares the current reporter ion with another one based on their masses.
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
isSameAs(Ion) - Method in class com.compomics.util.experiment.biology.ions.TagFragmentIon
isSameAs(TagComponent, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.MassGap
isSameAs(MutationMatrix) - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Indicates whether the two MutationMatrix are the same.
isSameAs(NeutralLoss) - Method in class com.compomics.util.experiment.biology.NeutralLoss: Method indicating whether another neutral loss is the same as the one considered.
isSameAs(Protein) - Method in class com.compomics.util.experiment.biology.Protein: A method to compare proteins.
isSameAs(PTM) - Method in class com.compomics.util.experiment.biology.PTM: Returns true if the PTM is the same as another one.
isSameAs(Sample) - Method in class com.compomics.util.experiment.biology.Sample: Comparator for samples.
isSameAs(Filter) - Method in interface com.compomics.util.experiment.filtering.Filter: Indicates whether another filter is the same as the current filter.
isSameAs(Tag, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.Tag: Indicates whether this tag is the same as another tag.
isSameAs(TagComponent, SequenceMatchingPreferences) - 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(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(AnnotationSettings) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Returns a boolean indicating whether the given annotation settings are the same as these ones.
isSameAs(Peak) - Method in class com.compomics.util.experiment.massspectrometry.Peak: Returns true if the peak has the same mz and intensity.
isSameAs(UnitOfMeasurement) - Method in class com.compomics.util.experiment.units.UnitOfMeasurement: Indicates whether the given unit of measurement is the same as another.
isSameAs(FractionSettings) - Method in class com.compomics.util.preferences.FractionSettings: Returns a boolean indicating whether other given settings are the same as these.
isSameAs(SequenceMatchingPreferences) - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Indicates whether another protein inference preferences is the same as this one.
isSameAs(ValidationQCPreferences) - Method in class com.compomics.util.preferences.ValidationQCPreferences: Returns true if the two ValidationQCPreferences are the same.
isSameAtomicComposition(PTM) - Method in class com.compomics.util.experiment.biology.PTM: Returns true if the atomic composition of the PTM is the same as another one.
isSameCompositionAs(AtomChain) - Method in class com.compomics.util.experiment.biology.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.Peptide: Indicates whether another peptide has the same variable modifications as this peptide.
isSamePattern(PTM) - Method in class com.compomics.util.experiment.biology.PTM: Returns true if the targeted pattern of the PTM is the same as another one.
isSameSequence(Peptide, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Returns a boolean indicating whether another peptide has the same sequence as the given peptide
isSameSequenceAndModificationStatus(Peptide, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.Peptide: Indicates whether another peptide has the same sequence and modification status without accounting for modification localization.
isSameSequenceAndModificationStatusAs(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether another AminoAcidPattern targets the same pattern without accounting for PTM localization.
isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
isSameSequenceAndModificationStatusAs(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Indicates whether another AminoAcidPattern targets the same sequence without accounting for PTM localization.
isSameSequenceAndModificationStatusAs(AminoAcidSequence, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Indicates whether another sequence targets the same sequence without accounting for PTM localization.
isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence
isSameSequenceAndModificationStatusAs(TagComponent, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.MassGap
isSameSequenceAndModificationStatusAs(Tag, SequenceMatchingPreferences) - 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, SequenceMatchingPreferences) - 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.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Indicates whether the precursor shall be scaled for OMSSA.
isScoringNeeded(int) - Method in class com.compomics.util.preferences.PsmScoringPreferences: Indicates whether a score computation is needed for the given advocate.
isScoringNeeded(ArrayList<Integer>) - Method in class com.compomics.util.preferences.PsmScoringPreferences: 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.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Indicates whether forward ions (b1) should be searched first.
isSearchPositiveIons() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Indicates whether positive ions are searched.
isSearchRewindFragments() - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
isSemiSpecific() - Method in class com.compomics.util.experiment.biology.Enzyme: Returns true if the enzyme is semi-specific.
isSequenceMatchingType(String, String) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: 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.PTM: 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, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the given amino acid sequence starts with the pattern.
isStarting(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the given amino acid sequence starts with the pattern.
isStpBias() - Method in class com.compomics.util.experiment.identification.identification_parameters.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: This method allows the caller to issue a command to the server.
issueCommandCheck(String) - Method in class com.compomics.util.io.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.
isTargetDecoyNeededForPsmScoring(ArrayList<Integer>) - Method in class com.compomics.util.preferences.PsmScoringPreferences: Indicates whether target decoy databases are needed for PSM scoring.
isTargeted(Character, int, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.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.
isUniqueInDatabase(Peptide) - Method in class com.compomics.util.experiment.identification.Identification: Indicates whether a peptide is found in a single protein match.
isUnspecific() - Method in class com.compomics.util.experiment.biology.Enzyme: Returns true if the enzyme is unspecific, i.e., cleaves at every residue.
isUseChargeStateFromMS() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Indicates whether the charge state from the spectrum should be used.
isUseCorrelationCorrectionScore() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Indicates whether the correlation correction score should be used.
isUseNoiseSuppression() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Indicates whether noise suppression should be used when importing spectra.
isUserDefined(String) - Method in class com.compomics.util.experiment.biology.PTMFactory: Convenience method returning a boolean indicating whether a PTM is user defined or default.
isValid() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature: Returns true if valid.
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.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Verifies that modifications are correctly recognized.
isValidStartup(CommandLine, boolean) - Static method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Verifies the command line start parameters.
isVariable() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Returns a boolean indicating if the modification is variable.
isWholeProtein() - Method in class com.compomics.util.experiment.biology.Enzyme: Returns true if the enzyme does not cleave at all, i.e., the whole protein is used.
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.
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.ReporterIon: Standard reporter ion iTRAQ 4Plex 114.
iTRAQ4Plex_115 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 4Plex 115.
iTRAQ4Plex_116 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 4Plex 116.
iTRAQ4Plex_117 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 4Plex 117.
iTRAQ8Plex_113 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 8Plex 113.
iTRAQ8Plex_114 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 8Plex 114.
iTRAQ8Plex_115 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 8Plex 115.
iTRAQ8Plex_116 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 8Plex 116.
iTRAQ8Plex_117 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 8Plex 117.
iTRAQ8Plex_118 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 8Plex 118.
iTRAQ8Plex_119 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 8Plex 119.
iTRAQ8Plex_121 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ 8Plex 121.
iTRAQ_145 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion iTRAQ (reporter + balancer).
iTRAQ_305 - Static variable in class com.compomics.util.experiment.biology.ions.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.AminoAcid
J - Class in com.compomics.util.experiment.biology.aminoacids: Isoleucine or Leucine.
J() - Constructor for class com.compomics.util.experiment.biology.aminoacids.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.
JavaSettingsDialog - Class in com.compomics.software.dialogs: A dialog for showing Java memory settings.
JavaSettingsDialog(JFrame, JavaHomeOrMemoryDialogParent, JDialog, String, boolean) - Constructor for class com.compomics.software.dialogs.JavaSettingsDialog: 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.filefilters.FileFilterUtils
JPEG - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
JpegFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.jpeg files.
JpegFileFilter() - Constructor for class com.compomics.util.io.filefilters.JpegFileFilter
jpg - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
JPG - Static variable in class com.compomics.util.io.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.AminoAcid
KeyUtils - Class in com.compomics.util.maps: Converts complex keys into simpler objects.
KeyUtils() - Constructor for class com.compomics.util.maps.KeyUtils
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(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.

L

L - Static variable in class com.compomics.util.experiment.biology.AminoAcid
laodMappingFromFile(File, WaitingHandler) - Method in class com.compomics.util.experiment.biology.genes.go.GoDomains: Reads go mappings from a file.
lastFolderKey - Static variable in class com.compomics.util.io.export.ExportWriter: Key to store the last export folder.
lastFolderKey - Static variable in class com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog: The key to use to store FASTA files paths.
LastSelectedFolder - Class in com.compomics.util.preferences: Convenience class keeping class of the last selected folders.
LastSelectedFolder(String) - Constructor for class com.compomics.util.preferences.LastSelectedFolder: Constructs a new last selected folder class.
LastSelectedFolder() - Constructor for class com.compomics.util.preferences.LastSelectedFolder: Constructs a new last selected folder class.
lastSelectedFolderKey - Static variable in class com.compomics.util.gui.error_handlers.BugReport: The specific key for bug reports.
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.
length() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the length of the pattern in amino acids.
length() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the length of the sequence in amino acids.
length() - Method in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Returns the length of the segment.
letter - Variable in class com.compomics.util.experiment.biology.Atom: The single letter code of the atom.
Leucine - Class in com.compomics.util.experiment.biology.aminoacids: Leucine.
Leucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Leucine: Constructor.
LEUCINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a leucine immonium ion.
level - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum: The MS level.
Li - Static variable in class com.compomics.util.experiment.biology.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.FolderMonitor
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
linePermutation(int, int) - Method in class com.compomics.util.math.matrix.DoubleMatrix
list() - Method in class com.compomics.util.io.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(Frame, 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: The Lithium atom.
Lithium() - Constructor for class com.compomics.util.experiment.biology.atoms.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.
loadAssumptions(String, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads all spectrum matches of the file in the cache of the database.
loadAssumptions(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads the assumptions of the spectrum matches indicated by the given keys in the cache of the database.
loadAssumptions(String, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all assumptions of the given file in the cache of the database.
loadAssumptions(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all assumptions of the given spectra in the cache of the database.
loadBackedUpModifications(SearchParameters, boolean) - Method in class com.compomics.util.experiment.biology.PTMFactory: Verifies that the modifications backed-up in the search parameters are loaded and alerts the user in case conflicts are found.
loadDataForColumn(int, WaitingHandler) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel: Loads the data for a column.
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.GeneFactory: Loads the given Ensembl species file.
loadExperiment(File) - Static method in class com.compomics.util.experiment.io.ExperimentIO: Method which loads an experiment.
loadFastaFile(File) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Loads a new FASTA file in the factory.
loadFastaFile(File, WaitingHandler) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Loads a new FASTA file in the factory.
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.
loadModificationsUse(ConfigurationFile) - Static method in class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Returns a string with the modifications used.
loadNodes(ArrayList<String>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Loads nodes in the cache.
loadObjects(String, WaitingHandler, boolean) - Method in class com.compomics.util.db.ObjectsDB: Loads all objects from a table in the cache.
loadObjects(String, ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.db.ObjectsDB: Loads some objects from a table in the cache.
loadParameters() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Loads all tree parameters.
loadPathPreferenceFromLine(String) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Loads a path to be set from a line.
loadPathPreferencesFromFile(File) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Loads the path preferences from a text file.
loadPeptideMatches(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads the desired peptide matches of the given type in the cache of the database.
loadPeptideMatches(WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads all peptide matches in the cache of the database.
loadPeptideMatches(WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all peptide matches in the cache of the database.
loadPeptideMatches(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads the desired peptide matches of the given type in the cache of the database.
loadPeptideMatchParameters(UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads all peptide match parameters of the given type in the cache of the database.
loadPeptideMatchParameters(ArrayList<String>, UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads the desired peptide match parameters of the given type in the cache of the database.
loadPeptideMatchParameters(UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all peptide match parameters of the given type in the cache of the database.
loadPeptideMatchParameters(ArrayList<String>, UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads the desired peptide match parameters of the given type in the cache of the database.
loadProteinMatches(WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads all protein matches in the cache of the database.
loadProteinMatches(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads the desired protein matches of the given type in the cache of the database.
loadProteinMatches(WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all protein matches in the cache of the database.
loadProteinMatches(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads the desired protein matches of the given type in the cache of the database.
loadProteinMatchParameters(UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads all protein match parameters of the given type in the cache of the database.
loadProteinMatchParameters(ArrayList<String>, UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads the desired protein match parameters of the given type in the cache of the database.
loadProteinMatchParameters(UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all protein match parameters of the given type in the cache of the database.
loadProteinMatchParameters(ArrayList<String>, UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads the desired protein match parameters of the given type in the cache of the database.
loadPtmToPrideMap(SearchParameters) - Static method in class com.compomics.util.pride.PtmToPrideMap: Deprecated.
the CV term is now part of the PTM object
loadRawAssumptions(String, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads the raw assumptions of the spectrum matches indicated by the given keys in the cache of the database.
loadRawAssumptions(String, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all raw assumptions of the given file in the cache of the database.
loadRawAssumptions(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all raw assumptions of the given spectra in the cache of the database.
loadSpectrumMatches(String, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads all spectrum matches of the file in cache.
loadSpectrumMatches(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads the spectrum matches corresponding to the given keys in cache.
loadSpectrumMatches(String, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all spectrum matches of the given file in the cache of the database.
loadSpectrumMatches(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all given spectrum matches in the cache of the database.
loadSpectrumMatchParameters(String, UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads all spectrum match parameters of the given type in the cache of the database
loadSpectrumMatchParameters(ArrayList<String>, UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.Identification: Loads all desired spectrum match parameters in the cache of the database.
loadSpectrumMatchParameters(String, UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all spectrum match parameters of the given type in the cache of the database.
loadSpectrumMatchParameters(ArrayList<String>, UrParameter, WaitingHandler, boolean) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Loads all desired spectrum match parameters in the cache of the database.
loadTags() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Loads the tags implemented in the database.
loadUserPreferences() - Static method in class com.compomics.util.preferences.UtilitiesUserPreferences: Loads the user preferences.
loadUserPreferences() - Method in class com.compomics.util.protein_sequences_manager.gui.preferences.ProteinSequencesPreferencesDialog: Loads the user preferences.
loadUserPreferences() - Method in class com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog: Loads the user preferences.
loadUserPreferences() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog: Loads the user preferences.
loadUserPreferences() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromUniprotDialog: Loads the user preferences.
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.
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: Login user to a host with username user and password password.
login(String) - Method in class com.compomics.util.io.FTP: Login user to a host with username user and no password such as HP server which uses the form "<username>/<password>,user.<group>.
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.
LONG_KEY_PREFIX - Static variable in class com.compomics.util.db.ObjectsDB: Suffix used for long keys.
LONG_KEY_TABLE - Static variable in class com.compomics.util.db.ObjectsDB: The table where to save the long keys.
LONG_TABLE_NAMES - Static variable in class com.compomics.util.db.ObjectsDB: Name for the long table names.
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: Folder-list files on a remote FTP server.
Lysine - Class in com.compomics.util.experiment.biology.aminoacids: Lysine.
Lysine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Lysine: Constructor.
LYSINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a lysine immonium ion.

M

M - Static variable in class com.compomics.util.experiment.biology.AminoAcid
m_strDestination - Variable in class com.compomics.util.io.FTP
m_strSource - Variable in class com.compomics.util.io.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.
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.identifications.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.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.
main(String[]) - Static method in class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Main method to start a standalone version.
makeSequenceIndependant() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap: Makes the neutral losses sequence independent.
mandatory - Variable in enum com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersCLIParams: Boolean indicating whether the parameter is mandatory.
MarshallableParameter - Interface in com.compomics.util.preferences: Interface for a parameter which can be marshalled as .par file.
MarshallableParameter.Type - Enum in com.compomics.util.preferences: 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(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.
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(ArrayList<String>, ArrayList<ArrayList<IonMatch>>, ArrayList<MSnSpectrum>, double, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorBubblePlot: Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(ArrayList<String>, ArrayList<ArrayList<IonMatch>>, ArrayList<MSnSpectrum>, double, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorBubblePlot: Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(ArrayList<String>, ArrayList<ArrayList<IonMatch>>, ArrayList<MSnSpectrum>, 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(ArrayList<IonMatch>, MSnSpectrum, double) - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot: Creates a new MassErrorPlot.
MassErrorPlot(ArrayList<IonMatch>, MSnSpectrum, double, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot: Creates a new MassErrorPlot.
MassGap - Class in com.compomics.util.experiment.biology: An undefined mass gap.
MassGap(double) - Constructor for class com.compomics.util.experiment.biology.MassGap: Constructor.
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, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the pattern is matches the given amino acid sequence in .
matches(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the pattern is found in the given amino acid sequence.
matches(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
matches(AminoAcidSequence, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
MatchesImportFiltersDialog - Class in com.compomics.util.gui.parameters.identification_parameters: The PeptideShaker import settings dialog.
MatchesImportFiltersDialog(Frame, PeptideAssumptionFilter, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.MatchesImportFiltersDialog: Creates a new ImportSettingsDialog with a frame as owner.
MatchesImportFiltersDialog(Dialog, Frame, PeptideAssumptionFilter, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.MatchesImportFiltersDialog: Creates a new ImportSettingsDialog with a dialog as owner.
matchesIn(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the pattern is found in the given amino acid sequence.
matchesIn(AminoAcidPattern, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Indicates whether the pattern is found in the given amino acid sequence.
matchesIn(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Indicates whether the sequence is found in the given amino acid sequence.
matchesIn(AminoAcidSequence, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Indicates whether the sequence is found in the given amino acid sequence.
matchExists(String) - Method in class com.compomics.util.experiment.identification.Identification: Indicates whether a match indexed by the given key exists.
matchInSpectrum(Ion, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: Matches a theoretic ion in the spectrum.
matchPeak(Peptide, SpecificAnnotationSettings, Peak) - 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(SpecificAnnotationSettings, Peak) - 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.
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.ptm.ptmscores.PhosphoRS: The maximal depth to use per window (8 in the original paper).
MAX_KEY_LENGTH - Static variable in class com.compomics.util.db.ObjectsDB: The maximum key length before using the key correction for long keys.
MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH - Static variable in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: The maximum allowed length of the FASTA file name.
maxDouble - Static variable in class com.compomics.util.math.BigMathUtils: Big decimal value of the maximal value of a double.
maxIsotopicCorrection - Static variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: The maximal isotope correction.
maxPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel: The maximum padding (distance between the axes and the border of the panel).
MDScore - Class in com.compomics.util.experiment.identification.ptm.ptmscores: This class estimates the MD score as described in http://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.ptm.ptmscores.MDScore
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.
median(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions: Method to estimate the median.
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
medianSorted(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions: Method to estimate the median of a sorted list.
memoryCheck() - Method in class com.compomics.util.db.ObjectsCache: Indicates whether the memory used by the application is lower than 99% of the heap size.
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
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.AminoAcidPattern: Simple merger for two patterns.
merge(AminoAcidPattern, AminoAcidPattern) - Static method in class com.compomics.util.experiment.biology.AminoAcidPattern: Convenience method merging two different patterns (see public void merge(AminoAcidPattern otherPattern) for detailed information of the merging procedure).
MetaDataXMLParser - Class in com.compomics.software.autoupdater: MetaDataXMLParser.
MetaDataXMLParser(XMLEventReader) - Constructor for class com.compomics.software.autoupdater.MetaDataXMLParser: Create a new MetaDataXMLParser.
Methionine - Class in com.compomics.util.experiment.biology.aminoacids: Methionine.
Methionine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Methionine: Constructor.
METHIONINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a methionine immonium ion.
methodUsed - Variable in class com.compomics.util.experiment.identification.Identification: The method used.
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.ReporterIon: Standard reporter ion for methylation of R (PMID: 16335983).
METHYL_R_115 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for methylation of R (PMID: 16335983).
METHYL_R_143 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for methylation of R (PMID: 16335983).
METHYL_R_70 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for methylation of R (PMID: 16335983).
METHYL_R_87 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for methylation of R.
MetricsPrefix - Enum in com.compomics.util.experiment.units: Enumeration of the metrics prefixes.
mgf - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MGF - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MgfFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.mgf files.
MgfFileFilter() - Constructor for class com.compomics.util.io.filefilters.MgfFileFilter
MgfFileIterator - Class in com.compomics.util.experiment.io.massspectrometry: An iterator of the spectra in an mgf file.
MgfFileIterator(File) - Constructor for class com.compomics.util.experiment.io.massspectrometry.MgfFileIterator: Constructor.
MgfIndex - Class in com.compomics.util.experiment.io.massspectrometry: This class contains the indexes of an mgf file after indexing mapped with the title of the spectrum.
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.massspectrometry.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.massspectrometry.MgfIndex: Constructor.
MgfReader - Class in com.compomics.util.experiment.io.massspectrometry: This class will read an MGF file.
MgfReader() - Constructor for class com.compomics.util.experiment.io.massspectrometry.MgfReader: General constructor for an mgf reader.
mgfToApl(File, File, FragmentationMethod, int, int) - Static method in class com.compomics.util.experiment.io.massspectrometry.export.AplExporter: Writes the content of the given file name into the destination file in the APL format.
mgfToMs2(File, File, boolean) - Static method in class com.compomics.util.experiment.io.massspectrometry.export.Ms2Exporter: Writes the content of the given file name into the destination file in the ms2 format.
MIN_DEPTH - Static variable in class com.compomics.util.experiment.identification.ptm.ptmscores.PhosphoRS: The minimal depth to use per window.
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.
minIsotopicCorrection - Static variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: The minimal isotope correction.
minNormalDouble - Static variable in class com.compomics.util.math.BigMathUtils: Big decimal value of the minimal normal value of a double.
minProteinCount - Static variable in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: The minimal protein count required for reliable target/decoy based statistics.
MINUS - Static variable in class com.compomics.util.experiment.massspectrometry.Charge: Static int to modele a negative charge.
MirroredSpectraTestDialog - Class in com.compomics.util.examples: Mirrored spectra test class.
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: Create a directory on the remote system
MODAA - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at particular amino acids.
MODC - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at the C terminus of a protein.
MODCAA - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at the C terminus of a protein at particular amino acids.
MODCP - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at the C terminus of a peptide.
MODCPAA - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at the C terminus of a peptide at particular amino acids.
model - Variable in class com.compomics.util.sun.TableMap
ModelOrganism - Enum in com.compomics.util.protein_sequences_manager.enums: ModelOrganism enumerator.
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.Peptide: Separator preceding confident localization of the confident localization of a modification
MODIFICATION_SEPARATOR - Static variable in class com.compomics.util.experiment.biology.Peptide: Separator used to separate modifications in peptide keys
MODIFICATION_SEPARATOR - Static variable in class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Reference for the separation of modifications.
modificationConversionToString() - Static method in class com.compomics.util.protein.ModificationFactory: Returns a String representation of the modification title to code mappings.
ModificationFactory - Class in com.compomics.util.protein: This class can be used to generate a Modification instance from a code or title.
ModificationImplementation - Class in com.compomics.util.protein: This class implements a specific Modification.
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.
ModificationMatch - Class in com.compomics.util.experiment.identification.matches: This class models the match between theoretic PTM and identification results.
ModificationMatch(String, boolean, int) - Constructor for class com.compomics.util.experiment.identification.matches.ModificationMatch: Constructor for a modification match.
ModificationProfile - Class in com.compomics.util.gui.protein: A simple modification profile object.
ModificationProfile(String, double[][], Color) - Constructor for class com.compomics.util.gui.protein.ModificationProfile: Modification profile constructor.
ModificationsDialog - Class in com.compomics.util.gui.ptm: A dialog where the modification details can be modified.
ModificationsDialog(Frame, boolean) - Constructor for class com.compomics.util.gui.ptm.ModificationsDialog: Creates a new ModificationsDialog.
modificationsToString() - Static method in class com.compomics.util.protein.ModificationFactory: Returns a String representation of the modifications.
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(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.
MODMAX - Static variable in class com.compomics.util.experiment.biology.PTM: The max number of modification types.
MODN - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at the N terminus of a protein.
MODNAA - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at the N terminus of a protein at particular amino acids.
MODNP - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at the N terminus of a peptide.
MODNPAA - Static variable in class com.compomics.util.experiment.biology.PTM: Modification at the N terminus of a peptide at particular amino acids.
modProfileEdited() - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog: 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: 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.MonitorableFileInputStream: This constructor takes a file to load the FileInputStream from.
MonitorableFileInputStream(String) - Constructor for class com.compomics.util.io.MonitorableFileInputStream: This constructor takes a file to load the FileInputStream from.
MonitorableInputStream - Class in com.compomics.util.io: This class provides a specific FilterInputStream that can be monitored for progress.
MonitorableInputStream(InputStream) - Constructor for class com.compomics.util.io.MonitorableInputStream: A MonitorableInputStream can only be constructed around an existing InputStream.
MonitorableInputStream(InputStream, int) - Constructor for class com.compomics.util.io.MonitorableInputStream: A MonitorableInputStream can only be constructed around an existing InputStream.
MonitorableInputStream(InputStream, boolean) - Constructor for class com.compomics.util.io.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 dimmensions 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.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.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.AminoAcid: The monoisotopic atom chain.
monoisotopicMass - Variable in class com.compomics.util.experiment.biology.AminoAcid: Deprecated.
use the atomchain
monoisotopicMass - Variable in class com.compomics.util.experiment.biology.Atom: The monoisotopic mass.
MONONUCLEOTIDES - Static variable in class com.compomics.util.general.MassCalc: Index for the monoisotopic nucleotide masses.
mouseWheelMoved(MouseWheelEvent) - Method in class com.compomics.util.gui.TableMouseWheelListener
MS1Spectrum - Class in com.compomics.util.experiment.massspectrometry: This class models an MS1 spectrum.
MS1Spectrum() - Constructor for class com.compomics.util.experiment.massspectrometry.MS1Spectrum: Constructor for an MS1 spectrum.
MS1Spectrum(String, String, double, HashMap<Double, Peak>) - Constructor for class com.compomics.util.experiment.massspectrometry.MS1Spectrum: Constructor for an MS1 spectrum.
ms2 - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MS2 - Static variable in class com.compomics.util.io.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.massspectrometry.export: This converter writes spectrum files in MS2 format.
Ms2Exporter() - Constructor for class com.compomics.util.experiment.io.massspectrometry.export.Ms2Exporter
Ms2FileFilter - Class in com.compomics.util.io.filefilters: File filter for *.ms2 files.
Ms2FileFilter() - Constructor for class com.compomics.util.io.filefilters.Ms2FileFilter
Ms2Identification - Class in com.compomics.util.experiment.identification.identifications: This class models an MS2 Identification.
Ms2Identification(String) - Constructor for class com.compomics.util.experiment.identification.identifications.Ms2Identification: Constructor for MS2 identification.
MS2MzFidelityScore - Class in com.compomics.util.experiment.identification.psm_scoring.psm_scores: The m/z fidelity sub-score as adapted from the DirecTag manuscript (http://www.ncbi.nlm.nih.gov/pubmed/18630943).
MS2MzFidelityScore() - Constructor for class com.compomics.util.experiment.identification.psm_scoring.psm_scores.MS2MzFidelityScore
msAmanda - Static variable in class com.compomics.util.experiment.identification.Advocate: The MS Amanda search engine.
MsAmandaIdfileReader - Class in com.compomics.util.experiment.io.identifications.idfilereaders: This IdfileReader reads identifications from an MS Amanda csv result file.
MsAmandaIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader: Default constructor for the purpose of instantiation.
MsAmandaIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader: Constructor for an MS Amanda csv result file reader.
MsAmandaIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader: Constructor for an MS Amanda csv result file reader.
MsAmandaParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: The MS Amanda specific parameters.
MsAmandaParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Constructor.
MsAmandaSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for the MS Amanda specific settings.
MsAmandaSettingsDialog(Frame, MsAmandaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsAmandaSettingsDialog: Creates new form MsAmandaSettingsDialog with a frame as owner.
MsAmandaSettingsDialog(Dialog, Frame, MsAmandaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsAmandaSettingsDialog: Creates new form MsAmandaSettingsDialog with a dialog as owner.
MsConvertParameters - Class in com.compomics.util.experiment.massspectrometry.proteowizard: The parameters to use when running msconvert.
MsConvertParameters() - Constructor for class com.compomics.util.experiment.massspectrometry.proteowizard.MsConvertParameters: Constructor.
MsConvertParametersDialog - Class in com.compomics.util.experiment.massspectrometry.proteowizard.gui: Dialog for the creation and edition of msconvert parameters.
MsConvertParametersDialog(Frame, MsConvertParameters) - Constructor for class com.compomics.util.experiment.massspectrometry.proteowizard.gui.MsConvertParametersDialog: Constructor.
MsExperiment - Class in com.compomics.util.experiment: This class represents the experiment.
MsExperiment(String, HashMap<Integer, Sample>) - Constructor for class com.compomics.util.experiment.MsExperiment: Constructor for an experiment.
MsExperiment(String) - Constructor for class com.compomics.util.experiment.MsExperiment: Constructor for an experiment.
msFit - Static variable in class com.compomics.util.experiment.identification.Advocate: The MS-Fit search engine, old school peptide mass fingerprinting.
MsFormat - Enum in com.compomics.util.experiment.massspectrometry.proteowizard: The mass spectrometry formats supported by ProteoWizard.
msgf - Static variable in class com.compomics.util.experiment.identification.Advocate: The MS-GF+ search engine.
MsgfParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: The MS-GF+ specific parameters.
MsgfParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Constructor.
MsgfSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for the MS-GF+ specific settings.
MsgfSettingsDialog(Frame, MsgfParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsgfSettingsDialog: Creates new form MsgfSettingsDialog with a frame as owner.
MsgfSettingsDialog(Dialog, Frame, MsgfParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsgfSettingsDialog: Creates new form MsgfSettingsDialog with a dialog as owner.
MSnSpectrum - Class in com.compomics.util.experiment.massspectrometry: This class models an MSn spectrum.
MSnSpectrum() - Constructor for class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Constructor for the spectrum.
MSnSpectrum(int, Precursor, String, String) - Constructor for class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Minimal constructor for the spectrum.
MSnSpectrum(int, Precursor, String, HashMap<Double, Peak>, String) - Constructor for class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Constructor for the spectrum.
MSnSpectrum(int, Precursor, String, HashMap<Double, Peak>, String, double) - Constructor for class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Constructor for the spectrum.
Mutation - Class in com.compomics.util.experiment.biology.mutations: This class represents a mutation of one amino acid to another from the 20-letter amino acid alphabet.
Mutation(AminoAcid, AminoAcid) - Constructor for class com.compomics.util.experiment.biology.mutations.Mutation: Constructs a mutation from one amino acid (origin) to another (target).
MutationFactory - Class in com.compomics.util.experiment.biology.mutations: This class holds the all possible one-letter peptide sequence mutations.
MutationMatrix - Class in com.compomics.util.experiment.biology.mutations: This class stores and provides mutations expected for amino acids.
MutationMatrix(String, String) - Constructor for class com.compomics.util.experiment.biology.mutations.MutationMatrix: 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.experiment.identification.identification_parameters.tool_specific: The MyriMatch specific parameters.
MyriMatchParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Constructor.
MyriMatchSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for the MyriMatch specific settings.
MyriMatchSettingsDialog(Frame, MyriMatchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MyriMatchSettingsDialog: Creates new form MyriMatchSettingsDialog with a frame as owner.
MyriMatchSettingsDialog(Dialog, Frame, MyriMatchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MyriMatchSettingsDialog: Creates new form MyriMatchSettingsDialog with a dialog as owner.
mz - Variable in class com.compomics.util.experiment.massspectrometry.Peak: The mass over charge ratio of the peak.
mzdata - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
mzData - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
mzDATA - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MZDATA - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MzDataFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.mzData files.
MzDataFileFilter() - Constructor for class com.compomics.util.io.filefilters.MzDataFileFilter
MzIdentMLIdfileReader - Class in com.compomics.util.experiment.io.identifications.idfilereaders: This IdfileReader reads identifications from an mzIdentML result file.
MzIdentMLIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader: Default constructor for the purpose of instantiation.
MzIdentMLIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader: Constructor for an mzIdentML result file reader.
MzIdentMLIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader: Constructor for an mzIdentML result file reader.
MzIdentMLIdfileSearchParametersConverter - Class in com.compomics.util.experiment.io.identifications: Reads search parameters from a mzIdentML result files.
MzIdentMLIdfileSearchParametersConverter() - Constructor for class com.compomics.util.experiment.io.identifications.MzIdentMLIdfileSearchParametersConverter
mzML - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
mzml - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MZML - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MzMlFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.mzML files.
MzMlFileFilter() - Constructor for class com.compomics.util.io.filefilters.MzMlFileFilter
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.filefilters.FileFilterUtils
mzxml - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MZXML - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
MzXmlFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.mzXML files.
MzXmlFileFilter() - Constructor for class com.compomics.util.io.filefilters.MzXmlFileFilter

N

N - Static variable in class com.compomics.util.experiment.biology.AminoAcid
N - Static variable in class com.compomics.util.experiment.biology.Atom: The nitrogen atom.
n2sort() - Method in class com.compomics.util.sun.TableSorter
N_TERM_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
Na - Static variable in class com.compomics.util.experiment.biology.Atom: The sodium atom.
name - Variable in class com.compomics.util.experiment.biology.AminoAcid: Name of the amino acid.
name - Variable in class com.compomics.util.experiment.biology.Atom: The name of the atom.
name - Variable in class com.compomics.util.experiment.biology.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.matches.IonMatch.MzErrorType: The name of the error type.
name - Variable in enum com.compomics.util.experiment.identification.psm_scoring.PsmScores: The name of the score.
name - Variable in enum com.compomics.util.experiment.massspectrometry.FragmentationMethod: The name of the fragmentation method.
name - Variable in enum com.compomics.util.experiment.massspectrometry.proteowizard.MsFormat: The name of the format.
name - Variable in enum com.compomics.util.experiment.massspectrometry.proteowizard.ProteoWizardFilter: The name of the filter.
name - Variable in enum com.compomics.util.io.export.ExportFormat: The name of the format.
name - Variable in enum com.compomics.util.preferences.SearchGuiOutputOption: Name of the option.
nBins - Static variable in class com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAIntensityRankScore: The number of bins for the spectrum intensities.
needsUpdate(int, String) - Method in class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel: Indicates whether the given column needs an update, i.e.
NEUTRAL - Static variable in class com.compomics.util.experiment.massspectrometry.Charge: Static int to modele a neutral component.
NeutralLoss - Class in com.compomics.util.experiment.biology: This class represents a neutral loss.
NeutralLoss(String, AtomChain, boolean) - Constructor for class com.compomics.util.experiment.biology.NeutralLoss: Constructor for a user defined neutral loss.
NeutralLoss(String, AtomChain, boolean, boolean) - Constructor for class com.compomics.util.experiment.biology.NeutralLoss: Constructor for a user defined neutral loss.
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.ElementaryElement: A neutron.
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
newVersionExists(Integer) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: 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.PsmIterator: Returns the next match and updates the buffer.
next() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.PeptideIterator
next() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfFileIterator: Returns the next spectrum in the file.
NH3 - Static variable in class com.compomics.util.experiment.biology.NeutralLoss: NH3 loss.
Nitrogen - Class in com.compomics.util.experiment.biology.atoms: The nitrogen atom.
Nitrogen() - Constructor for class com.compomics.util.experiment.biology.atoms.Nitrogen: Constructor.
nlist() - Method in class com.compomics.util.io.FTP: NLIST files on a remote FTP server
nMutations(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns the number of mutations used to match an amino acid sequence.
nMutations(String, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Returns the number of mutations used when matching the given reference sequence.
NO_SPECIES_TAG - Static variable in class com.compomics.util.gui.genes.SpeciesDialog: Deprecated.

The text to use for no species selected.
Node - Class in com.compomics.util.experiment.identification.protein_inference.proteintree: A node of the protein tree.
Node(int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Constructor.
Node(int, HashMap<String, ArrayList<Integer>>) - Constructor for class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: 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(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(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.ptm.PtmtableContent: 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
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.identifications.idfilereaders: This IdfileReader reads identifications from a Novor csv result file.
NovorIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader: Default constructor for the purpose of instantiation.
NovorIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader: Constructor for an Novor csv result file reader.
NovorIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader: Constructor for an Novor csv result file reader.
NovorParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: Novor specific parameters.
NovorParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters: Constructor.
NovorSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for editing Novor advanced settings.
NovorSettingsDialog(Frame, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog: Creates a new NovorSettingsDialog with a frame as owner.
NovorSettingsDialog(Dialog, Frame, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog: Creates a new NovorSettingsDialog with a dialog as owner.
NTERM - Static variable in class com.compomics.util.protein.Enzyme
nTermCorrection - Variable in class com.compomics.util.experiment.io.identifications.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.identifications.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 - Variable in class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Boolean indicating whether the segment is sequencing from the N (true) or the C (false) terminus.
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(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(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.massspectrometry.proteowizard.ProteoWizardFilter: The index of the filter.

O

O - Static variable in class com.compomics.util.experiment.biology.AminoAcid
O - Static variable in class com.compomics.util.experiment.biology.Atom: The oxygen atom.
ObjectsCache - Class in com.compomics.util.db: An object cache can be combined to an ObjectDB to improve its performance.
ObjectsCache() - Constructor for class com.compomics.util.db.ObjectsCache: Constructor.
ObjectsDB - Class in com.compomics.util.db: A database which can easily be used to store objects.
ObjectsDB(String, String, boolean, ObjectsCache) - Constructor for class com.compomics.util.db.ObjectsDB: Constructor.
oldCleave(Protein) - Method in class com.compomics.util.protein.DualEnzyme: This cleave method will process sequence XDYRZ solely into YR peptides.
OldProcessingPreferencesDialog - Class in com.compomics.util.gui.parameters: A simple dialog where the user can view/edit the PeptideShaker processing preferences.
OldProcessingPreferencesDialog(Frame, boolean, IdentificationParameters, PSProcessingPreferences) - Constructor for class com.compomics.util.gui.parameters.OldProcessingPreferencesDialog: Creates a new parameters dialog.
OldProcessingPreferencesDialog(JDialog, boolean, IdentificationParameters, PSProcessingPreferences) - Constructor for class com.compomics.util.gui.parameters.OldProcessingPreferencesDialog: Creates a new parameters dialog.
omssa - Static variable in class com.compomics.util.experiment.identification.Advocate: The OMSSA search engine.
OmssaParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: The OMSSA specific parameters.
OmssaParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Constructor.
OmssaSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for the OMSSA specific parameters.
OmssaSettingsDialog(Frame, OmssaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.OmssaSettingsDialog: Creates new form OmssaParametersDialog with a frame as owner.
OmssaSettingsDialog(Dialog, Frame, OmssaParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.OmssaSettingsDialog: Creates new form OmssaParametersDialog with a dialog as owner.
omx - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
OMX - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
OmxFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.omx files.
OmxFileFilter() - Constructor for class com.compomics.util.io.filefilters.OmxFileFilter
openDataConnection(String) - Method in class com.compomics.util.io.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: open a FTP connection to host host.
openServer(String, int) - Method in class com.compomics.util.io.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.
out - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
OUT - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
OutFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.out files.
OutFileFilter() - Constructor for class com.compomics.util.io.filefilters.OutFileFilter
outputData() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Indicates whether data should be copied along with the identification files in the SearchGUI output.
outputFolderOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for an output folder.
outputFormat - Variable in enum com.compomics.util.experiment.massspectrometry.proteowizard.MsFormat: Boolean indicating if this in a format that can be used as output.
Oxygen - Class in com.compomics.util.experiment.biology.atoms: The oxygen atom.
Oxygen() - Constructor for class com.compomics.util.experiment.biology.atoms.Oxygen: Constructor.

P

P - Static variable in class com.compomics.util.experiment.biology.AminoAcid
P - Static variable in class com.compomics.util.experiment.biology.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.
parseFromFASTA(String) - Static method in class com.compomics.util.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, String) - Method in enum com.compomics.util.experiment.filtering.FilterItemComparator: Indicates whether a given value passes a threshold using this comparator.
passes(String, List<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.
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.FolderMonitor
PathKey - Interface in com.compomics.software.settings: Interface for a path key.
PathSettingsDialog - Class in com.compomics.software.settings.gui: Dialog used to set paths.
PathSettingsDialog(Frame, String, HashMap<PathKey, String>) - Constructor for class com.compomics.software.settings.gui.PathSettingsDialog: Creates a new PathSettingsDialog.
Patient - Class in com.compomics.util.experiment.patient: This class groups the information about the patient from whom the sample is taken
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(String, String) - Constructor for class com.compomics.util.experiment.patient.PatientInformation: Constructor.
PdbBlock - Class in com.compomics.util.pdbfinder.pdb: PdbBlock.
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(String, String, String, String) - Constructor for class com.compomics.util.pdbfinder.pdb.PdbParameter: Constructor.
pdf - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PDF - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PdfFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.pdf files.
PdfFileFilter() - Constructor for class com.compomics.util.io.filefilters.PdfFileFilter
peak - Variable in class com.compomics.util.experiment.identification.matches.IonMatch: The matched peak.
Peak - Class in com.compomics.util.experiment.massspectrometry: This class represents a peak.
Peak(double, double) - Constructor for class com.compomics.util.experiment.massspectrometry.Peak: Constructor for a peak.
Peak(double, double, double) - Constructor for class com.compomics.util.experiment.massspectrometry.Peak: Constructor for a peak.
peakList - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum: mz indexed Peak list.
peaks - Static variable in class com.compomics.util.experiment.identification.Advocate: The PEAKS sequencing algorithm.
PEFF - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
peff - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PeffFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.peff files.
PeffFileFilter() - Constructor for class com.compomics.util.io.filefilters.PeffFileFilter
pep_xml - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PEP_XML - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
pepnovo - Static variable in class com.compomics.util.experiment.identification.Advocate: The PepNovo+ de novo sequencing algorithm.
PepnovoAssumptionDetails - Class in com.compomics.util.experiment.refinementparameters: 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.refinementparameters.PepnovoAssumptionDetails: Constructor.
PepNovoIdfileReader - Class in com.compomics.util.experiment.io.identifications.idfilereaders: This class can be used to parse PepNovo identification files.
PepNovoIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader: Default constructor for the purpose of instantiation.
PepNovoIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader: Constructor, initiate the parser.
PepNovoIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader: Constructor, initiate the parser.
PepnovoParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: PepNovo specific parameters.
PepnovoParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Constructor.
Peptide - Class in com.compomics.util.experiment.biology: This class models a peptide.
Peptide() - Constructor for class com.compomics.util.experiment.biology.Peptide: Constructor for the peptide.
Peptide(String, ArrayList<ModificationMatch>) - Constructor for class com.compomics.util.experiment.biology.Peptide: Constructor for the peptide.
PEPTIDE_FINGERPRINTING - Static variable in class com.compomics.util.experiment.identification.IdentificationMethod: index for identification method based on peptide mass fingerprinting
PeptideAssumption - Class in com.compomics.util.experiment.identification.spectrum_assumptions: This object will models the assumption made by an advocate.
PeptideAssumption(Peptide, int, int, Charge, double, String) - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption: Constructor for a peptide assumption.
PeptideAssumption(Peptide, int, int, Charge, double) - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption: Constructor for a peptide assumption.
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.
peptideDetailsInCache(String) - Method in class com.compomics.util.experiment.identification.Identification: Indicates whether the peptide and spectrum matches corresponding to a peptide match key are loaded in the cache.
PeptideFragmentIon - Class in com.compomics.util.experiment.biology.ions: This class models a peptide fragment ion.
PeptideFragmentIon(int, int, double, ArrayList<NeutralLoss>) - Constructor for class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Constructor.
PeptideFragmentIon(int, ArrayList<NeutralLoss>) - Constructor for class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Constructor for a generic ion.
PeptideFragmentIon(int) - Constructor for class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Constructor for a generic ion without neutral losses.
peptideIdentification - Variable in class com.compomics.util.experiment.identification.Identification: List of the keys of all imported peptides.
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: Constructor for the peptide match.
PeptideMatch(Peptide, String) - 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(ArrayList<String>, Identification, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator: Constructor.
PeptideMatchesIterator(Identification, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator: Constructor.
PeptideMatchesIterator(ArrayList<String>, Identification, ArrayList<UrParameter>, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator: Constructor.
peptideMatchLoaded(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Indicates whether a peptide match is loaded.
peptideShaker - Static variable in class com.compomics.util.experiment.identification.Advocate: The PeptideShaker multiple algorithm software.
peptideShakerFileOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for a cps file for PeptideShaker.
peptideShakerPxAccessionOption - Static variable in class com.compomics.software.ToolFactory: The command line argument to open a given PX accession in PRIDE Reshake.
peptideShakerPxAccessionPrivateOption - 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.
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.
peptideShakerUrlDownloadFolderOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for the download folder for the URL for PeptideShaker.
peptideShakerUrlOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for a zipped cps URL for PeptideShaker.
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.
pepxml - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PEPXML - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PepXmlFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.pep.xml, *.pepxml and *.xml files.
PepXmlFileFilter() - Constructor for class com.compomics.util.io.filefilters.PepXmlFileFilter
PepxmlIdfileReader - Class in com.compomics.util.experiment.io.identifications.idfilereaders: Simple IdfileReader for Pepxml files.
PepxmlIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader: Blank constructor for instantiation purposes.
PepxmlIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader: Constructor.
PERACETYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.Glycan: Final index for peracetylated masses.
percentile(double[], double) - Static method in class com.compomics.util.math.BasicMathFunctions: Returns the desired percentile in a given array of double.
percentile(ArrayList<Double>, double) - Static method in class com.compomics.util.math.BasicMathFunctions: Returns the desired percentile in a given list of double.
percentileSorted(ArrayList<Double>, double) - Static method in class com.compomics.util.math.BasicMathFunctions: Returns the desired percentile in a given list of double.
percolator - Static variable in class com.compomics.util.experiment.identification.Advocate: The percolator rescoring algorithm.
PERMETHYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.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(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: Phenylalanine.
Phenylalanine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Phenylalanine: Constructor.
PHENYLALANINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a 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.ReporterIon: Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401).
PhosphoRS - Class in com.compomics.util.experiment.identification.ptm.ptmscores: This class estimates the PhosphoRS score as described in http://www.ncbi.nlm.nih.gov/pubmed/22073976.
PhosphoRS() - Constructor for class com.compomics.util.experiment.identification.ptm.ptmscores.PhosphoRS
Phosphorus - Class in com.compomics.util.experiment.biology.atoms: The phosphorus atom.
Phosphorus() - Constructor for class com.compomics.util.experiment.biology.atoms.Phosphorus: Constructor.
pickMostAccuratePeak - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: If there are more than one matching peak for a given annotation setting this value to true results in the most accurate peak being annotated, while setting this to false annotates the most intense peak.
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.FolderMonitor
pkl - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PKL - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PklFile - Class in com.compomics.util.io: Contains information about the contents of one PKL file.
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.filefilters: File filter for *.pkl files.
PklFileFilter() - Constructor for class com.compomics.util.io.filefilters.PklFileFilter
PklSpoFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.pkl.spo files.
PklSpoFileFilter() - Constructor for class com.compomics.util.io.filefilters.PklSpoFileFilter
pkx - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PKX - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PkxFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.pkx files.
PkxFileFilter() - Constructor for class com.compomics.util.io.filefilters.PkxFileFilter
PLUS - Static variable in class com.compomics.util.experiment.massspectrometry.Charge: Static int to modele a positive charge.
png - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PNG - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PngFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.png files.
PngFileFilter() - Constructor for class com.compomics.util.io.filefilters.PngFileFilter
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.identifications.idfilereaders: This class can be used to parse pNovo identification files.
PNovoIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader: Default constructor for the purpose of instantiation.
PNovoIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader: Constructor, initiate the parser.
PNovoIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader: Constructor, initiate the parser.
PNovoParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: pNovo specific parameters.
PNovoParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Constructor.
PNovoSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for editing pNovo advanced settings.
PNovoSettingsDialog(Frame, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog: Creates a new PNovoSettingsDialog with a frame as owner.
PNovoSettingsDialog(Dialog, Frame, SearchParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog: Creates a new PNovoSettingsDialog with a dialog as owner.
populateGUI() - Method in class com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog: Deprecated.

Populates the GUI using the given identification parameters.
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.
PRECURSOR - Static variable in class com.compomics.util.experiment.biology.ions.PrecursorIon: For now only one type of precursor implemented.
Precursor - Class in com.compomics.util.experiment.massspectrometry: This class models a precursor.
Precursor(double, double, ArrayList<Charge>) - Constructor for class com.compomics.util.experiment.massspectrometry.Precursor: Constructor for the precursor.
Precursor(double, double, double, ArrayList<Charge>, double, double) - Constructor for class com.compomics.util.experiment.massspectrometry.Precursor: Constructor with retention time window.
Precursor(double, double, ArrayList<Charge>, double, double) - Constructor for class com.compomics.util.experiment.massspectrometry.Precursor: Constructor with retention time window and no reference retention time.
Precursor(double, double, double, ArrayList<Charge>) - Constructor for class com.compomics.util.experiment.massspectrometry.Precursor: Constructor for the precursor.
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
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: A precursor ion.
PrecursorIon(double, ArrayList<NeutralLoss>) - Constructor for class com.compomics.util.experiment.biology.ions.PrecursorIon: Constructor.
PrecursorIon(ArrayList<NeutralLoss>) - Constructor for class com.compomics.util.experiment.biology.ions.PrecursorIon: Constructor for a generic ion.
PrecursorIon() - Constructor for class com.compomics.util.experiment.biology.ions.PrecursorIon: Constructor for a generic ion without neutral losses.
PrecursorIon(double) - Constructor for class com.compomics.util.experiment.biology.ions.PrecursorIon: Constructor for a generic ion without neutral losses.
PREFIX - Variable in enum com.compomics.util.experiment.units.MetricsPrefix: The prefix in full letters.
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.
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(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
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.
printModifications() - Method in class com.compomics.util.experiment.identification.parameters_cli.AbstractIdentificationParametersCli: Prints the available modifications on the screen.
PrivacySettingsDialog - Class in com.compomics.util.gui: The privacy settings dialog allows the user to set the privacy settings.
PrivacySettingsDialog(Frame, Image) - Constructor for class com.compomics.util.gui.PrivacySettingsDialog: 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
ProcessingPreferences - Class in com.compomics.util.preferences: ProcessingPreferences.
ProcessingPreferences() - Constructor for class com.compomics.util.preferences.ProcessingPreferences: Constructor.
ProcessingPreferences.ProcessingType - Enum in com.compomics.util.preferences: Class indicating the type of processing.
ProcessingPreferencesDialog - Class in com.compomics.util.gui.parameters: Dialog to edit the processing preferences.
ProcessingPreferencesDialog(Frame, ProcessingPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.ProcessingPreferencesDialog: Creates a new ProcessingPreferencesDialog with a frame as owner.
ProcessingPreferencesDialog(Dialog, Frame, ProcessingPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.ProcessingPreferencesDialog: 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(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.
Proline - Class in com.compomics.util.experiment.biology.aminoacids: Proline.
Proline() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Proline: Constructor.
PROLINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a proline immonium ion.
properties - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PROPERTIES - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PropertiesManager - Class in com.compomics.util.io: This class holds all user properties for ms_lims.
prot_xml - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PROT_XML - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
Protein - Class in com.compomics.util.experiment.biology: This class models a protein.
Protein() - Constructor for class com.compomics.util.experiment.biology.Protein: Constructor for a protein.
Protein(String, boolean) - Constructor for class com.compomics.util.experiment.biology.Protein: Simplistic constructor for a protein (typically used when loading identification files).
Protein(String, String, boolean) - Constructor for class com.compomics.util.experiment.biology.Protein: Constructor for a protein.
Protein(String, Header.DatabaseType, String, boolean) - Constructor for class com.compomics.util.experiment.biology.Protein: Constructor for a protein.
Protein - Class in com.compomics.util.protein: This class implements the behaviour for a Protein instance.
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.
PROTEIN_KEY_SPLITTER - Static variable in class com.compomics.util.experiment.identification.matches.ProteinMatch: The splitter in the key between protein accessions.
proteinBatchSize - Static variable in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: The number of proteins which should be imported at a time.
proteinBatchSize - Static variable in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: The number of proteins which should be imported at a time.
proteinDetailsInCache(String) - Method in class com.compomics.util.experiment.identification.Identification: Indicates whether the protein, peptide and spectrum matches corresponding to a protein match key are loaded in the cache.
proteinIdentification - Variable in class com.compomics.util.experiment.identification.Identification: List of the keys of all imported proteins.
ProteinInferencePreferences - Class in com.compomics.util.preferences: Generic class grouping the protein inference preferences.
ProteinInferencePreferences() - Constructor for class com.compomics.util.preferences.ProteinInferencePreferences
ProteinInferenceSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters: Dialog for the edition of the protein inference settings
ProteinInferenceSettingsDialog(Frame, ProteinInferencePreferences, Image, Image, LastSelectedFolder, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.ProteinInferenceSettingsDialog: Creates a new ProteinInferenceSettingsDialog with a frame as owner.
ProteinInferenceSettingsDialog(Dialog, Frame, ProteinInferencePreferences, Image, Image, LastSelectedFolder, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.ProteinInferenceSettingsDialog: Creates a new ProteinInferenceSettingsDialog with a dialog as owner.
ProteinIterator(File, boolean) - Constructor for class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.ProteinIterator: 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.Identification: 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, String) - 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(ArrayList<String>, Identification, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator: Constructor.
ProteinMatchesIterator(Identification, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, boolean, ArrayList<UrParameter>, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator: Constructor for an iterator iterating all protein keys.
proteinMatchLoaded(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Indicates whether a protein match is loaded.
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
ProteinSequencesManager - Class in com.compomics.util.protein_sequences_manager: The protein sequences manager helps the user manage FASTA files.
ProteinSequencesManager() - Constructor for class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Constructor.
ProteinSequencesManagerGUI - Class in com.compomics.util.protein_sequences_manager.gui: ProteinSequencesManager.
ProteinSequencesManagerGUI(Frame, Image, Image) - Constructor for class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Creates a new ProteinSequencesManager.
ProteinSequencesPreferencesDialog - Class in com.compomics.util.protein_sequences_manager.gui.preferences: Protein sequences preferences dialog.
ProteinSequencesPreferencesDialog(Frame) - Constructor for class com.compomics.util.protein_sequences_manager.gui.preferences.ProteinSequencesPreferencesDialog: Constructor.
ProteinTree - Class in com.compomics.util.experiment.identification.protein_inference.proteintree: This class sorts the proteins into groups.
ProteinTree(int, int) - Constructor for class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Creates a tree based on the proteins present in the sequence factory.
ProteinTree.PeptideIterator - Class in com.compomics.util.experiment.identification.protein_inference.proteintree: Alphabetical iterator for the tree.
ProteinTreeComponentsFactory - Class in com.compomics.util.experiment.identification.protein_inference.proteintree: This factory stores and returns protein trees components from databases.
ProteomicAnalysis - Class in com.compomics.util.experiment: This class models a proteomic analysis.
ProteomicAnalysis(int) - Constructor for class com.compomics.util.experiment.ProteomicAnalysis: Constructor for a proteomic analysis.
ProteoWizardFilter - Enum in com.compomics.util.experiment.massspectrometry.proteowizard: Filters which can be applied to msconvert.
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(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.ElementaryIon: Subtype int for a proton.
proton - Static variable in class com.compomics.util.experiment.biology.ions.ElementaryIon: A proton.
protxml - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
PROTXML - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
ProtXmlFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.prot.xml, *.protxml and *.xml files.
ProtXmlFileFilter() - Constructor for class com.compomics.util.io.filefilters.ProtXmlFileFilter
PsmIterator - Class in com.compomics.util.experiment.identification.matches_iterators: An iterator for spectrum matches.
PsmIterator(String, ArrayList<String>, Identification, ArrayList<UrParameter>, boolean, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmIterator(ArrayList<String>, Identification, ArrayList<UrParameter>, boolean, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmIterator(ArrayList<String>, Identification, boolean, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmIterator(String, ArrayList<String>, Identification, boolean, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmIterator(String, Identification, ArrayList<UrParameter>, boolean, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmIterator(String, Identification, boolean, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmIterator(String, Identification, boolean, ArrayList<UrParameter>, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmIterator(Identification, boolean, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmIterator(Identification, ArrayList<UrParameter>, boolean, WaitingHandler) - Constructor for class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Constructor.
PsmScores - Enum in com.compomics.util.experiment.identification.psm_scoring: Enum listing the PSM scores implemented in compomics utilities.
PsmScoringPreferences - Class in com.compomics.util.preferences: Generic class for peptide spectrum match scoring.
PsmScoringPreferences() - Constructor for class com.compomics.util.preferences.PsmScoringPreferences
PsmScoringSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters: Dialog for the edition of the PSM scoring settings.
PsmScoringSettingsDialog(Frame, PsmScoringPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.PsmScoringSettingsDialog: Creates a new PsmScoringSettingsDialog with a frame as owner.
PsmScoringSettingsDialog(Dialog, Frame, PsmScoringPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.PsmScoringSettingsDialog: Creates a new PsmScoringSettingsDialog with a dialog as owner.
PSProcessingPreferences - Class in com.compomics.util.preferences: Deprecated.
replaced by utilities processing preferences and fraction preferences
PSProcessingPreferences() - Constructor for class com.compomics.util.preferences.PSProcessingPreferences: Deprecated.

Constructor with default settings.
PTM - Class in com.compomics.util.experiment.biology: This class models a post-translational modification.
PTM() - Constructor for class com.compomics.util.experiment.biology.PTM: Constructor for the modification.
PTM(int, String, String, AtomChain, AtomChain, AminoAcidPattern) - Constructor for class com.compomics.util.experiment.biology.PTM: Constructor for a reference modification.
PTM(int, String, String, AtomChain, AtomChain, AminoAcidPattern, CvTerm) - Constructor for class com.compomics.util.experiment.biology.PTM: Constructor for a reference modification.
PTM(int, String, Double, ArrayList<String>) - Constructor for class com.compomics.util.experiment.biology.PTM: Simple constructor for a PTM.
PtmChooser - Class in com.compomics.util.gui.utils.user_choice.list_choosers: Dialog for choosing an item in a list of PTMs.
PtmChooser(Frame, ArrayList<String>, String, String, String, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.PtmChooser: Constructor.
PtmChooser(Frame, ArrayList<String>, boolean) - Constructor for class com.compomics.util.gui.utils.user_choice.list_choosers.PtmChooser: Constructor with default values.
PtmDialog - Class in com.compomics.util.gui.ptm: This dialog allows the user to create/edit PTMs.
PtmDialog(JDialog, PTM, boolean) - Constructor for class com.compomics.util.gui.ptm.PtmDialog: Creates a new PTM dialog.
PtmDialog(JFrame, PtmToPrideMap, PTM, boolean) - Constructor for class com.compomics.util.gui.ptm.PtmDialog: Creates a new PTM dialog.
PTMFactory - Class in com.compomics.util.experiment.biology: This factory will load PTM from an XML file and provide them on demand as standard class.
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.
PTMLocalizationParametersDialog - Class in com.compomics.util.gui.parameters.identification_parameters: PTMLocalizationParametersDialog.
PTMLocalizationParametersDialog(Frame, PTMScoringPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.PTMLocalizationParametersDialog: Creates a new PTMLocalizationParametersDialog with a frame as owner.
PTMLocalizationParametersDialog(Dialog, Frame, PTMScoringPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.PTMLocalizationParametersDialog: Creates a new PTMLocalizationParametersDialog with a dialog as owner.
PtmScore - Enum in com.compomics.util.experiment.identification.ptm: An enum of the PTM scores.
PTMScoringPreferences - Class in com.compomics.util.preferences: This class contains the PTM localization scoring preferences.
PTMScoringPreferences() - Constructor for class com.compomics.util.preferences.PTMScoringPreferences: Constructor.
PtmSettings - Class in com.compomics.util.experiment.identification.identification_parameters: This class stores the information about the modification preferences (colors, names) used for the selected project.
PtmSettings() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Constructor.
PtmSettings(PtmSettings) - Constructor for class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Constructor creating a new Modification profile based on the given one.
PtmSiteMapping - Class in com.compomics.util.experiment.identification.ptm: This class contains convenience methods to map ptms on potential sites.
PtmSiteMapping() - Constructor for class com.compomics.util.experiment.identification.ptm.PtmSiteMapping
PtmtableContent - Class in com.compomics.util.experiment.identification.ptm: Convenience class for the content of a PTM table.
PtmtableContent() - Constructor for class com.compomics.util.experiment.identification.ptm.PtmtableContent: 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(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: PUT a file on the FTP server in Ascii mode.
putBinary(String) - Method in class com.compomics.util.io.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: Get the name of the present working directory on the ftp server file system.
Pyrrolysine - Class in com.compomics.util.experiment.biology.aminoacids: Pyrrolysine.
Pyrrolysine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Pyrrolysine: Constructor.

Q

Q - Static variable in class com.compomics.util.experiment.biology.AminoAcid
QQ - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for SUMO-2/3 Q87R.
QQ_H2O - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for SUMO-2/3 Q87R.
QQT - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for SUMO-2/3 Q87R.
QQT_H2O - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for SUMO-2/3 Q87R.
QQTG - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for SUMO-2/3 Q87R.
QQTG_H2O - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for SUMO-2/3 Q87R.
QQTGG - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion for SUMO-2/3 Q87R.
QQTGG_H2O - Static variable in class com.compomics.util.experiment.biology.ions.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
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.GeneFactory: 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.GeneFactory: 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.GeneFactory: Sends an XML query to Ensembl and writes the result in a text file.
queryTaxonomy(String, boolean) - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Returns the query taxonomy.
QueryType - Enum in com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy: Query type.

R

R - Static variable in class com.compomics.util.experiment.biology.AminoAcid
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.massspectrometry.proteowizard.MsFormat: 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(JsonReader) - Method in class com.compomics.util.io.json.adapter.FileAdapter
read(byte[]) - Method in class com.compomics.util.io.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.MonitorableFileInputStream: Reads the next byte of data from this input stream.
read(byte[], int, int) - Method in class com.compomics.util.io.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.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.MonitorableInputStream: Reads the next byte of data from this input stream.
read(byte[], int, int) - Method in class com.compomics.util.io.MonitorableInputStream: Reads up to len bytes of data from this input stream into an array of bytes.
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.PushBackStringReader: This method reads a line of text from the buffer.
readObject(File) - Static method in class com.compomics.util.io.SerializationUtils: Reads an object from a serialized file.
readReply() - Method in class com.compomics.util.io.FTP: This method attempts to read a reply from the FTP server.
readServerResponse() - Method in class com.compomics.util.io.FTP: This method allows the caller to capture the server response.
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
reallocateIndexes() - Method in class com.compomics.util.sun.TableSorter
reduceMemoryConsumption(double, WaitingHandler) - Method in class com.compomics.util.db.ObjectsCache: Reduces the memory consumption by saving the given share of hits.
reduceNodeCacheSize(double) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Reduces the node cache size by the given share.
reduceNodeCacheSize(double) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Reduces the node cache size of the protein tree by the given share.
reference - Variable in class com.compomics.util.experiment.identification.Identification: The reference of the identification.
Reference - Class in com.compomics.util.pride.prideobjects: A simple publication reference object.
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(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(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(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.
registerIdFileReader(Class, String) - Static method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory: This method registers a new IdfileReader Class, and the file extension it can read from.
registerTempFolder(File) - Static method in class com.compomics.util.gui.filehandling.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(Double, Double, Double, Double, Double) - Constructor for class com.compomics.util.math.statistics.linear_regression.RegressionStatistics: Constructor.
RELATED_C_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for C.
RELATED_C_2 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for C.
RELATED_D_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for D.
RELATED_E_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for E.
RELATED_F_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for F.
RELATED_H_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for H (C4H5N2).
RELATED_H_2 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for H.
RELATED_K_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for K.
RELATED_K_2 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for K.
RELATED_K_3 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for K.
RELATED_M_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for M (C2H4S).
RELATED_N_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for N.
RELATED_Q_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for Q.
RELATED_Q_2 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for Q.
RELATED_R_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for R.
RELATED_R_2 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for R.
RELATED_R_3 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for R.
RELATED_R_4 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for R (C5H10N2O).
RELATED_W_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for W (C9H7N).
RELATED_Y_1 - Static variable in class com.compomics.util.experiment.biology.ions.RelatedIon: Related ion for Y (C7H7O).
RelatedIon - Class in com.compomics.util.experiment.biology.ions: Represents a related ion, i.e., an ion that is related to a given amino acid, and is its own factory.
RelatedIon(AminoAcid, AtomChain, int) - Constructor for class com.compomics.util.experiment.biology.ions.RelatedIon: Constructor for a related ion.
RelatedIon(AminoAcid, AtomChain, int, boolean) - Constructor for class com.compomics.util.experiment.biology.ions.RelatedIon: Constructor for a related ion.
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.PTMFactory: 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.AtomChain: Removes all the occurrences of the given atom.
remove() - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.PeptideIterator
removeAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Removes an amino acid index from the pattern.
removeActiveConnection(String, String) - Static method in class com.compomics.util.db.DerbyUtil: Removes a connection from the registered connections.
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.
removeAssumption(SpectrumIdentificationAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Removes an assumption from the mapping.
removeAssumptions(String) - Method in class com.compomics.util.experiment.identification.Identification: Removes the assumptions of a spectrum.
removeAssumptions(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Deletes the assumptions corresponding to a given psm from the database.
removeAssumptions() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Removes all assumptions but the best ones from the spectrum map.
removeDuplicateSpectrumTitles(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: 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.
removeExportScheme(String) - Method in interface com.compomics.util.io.export.ExportFactory: Removes a user scheme.
removeExtension(String) - Static method in class com.compomics.util.Util: Removes the extension from a file name or path.
removeFixedModification(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: 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.
removeModificationMatch(int, ModificationMatch) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Removes a modification match in the given pattern.
removeModificationMatch(int, ModificationMatch) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: Removes a modification match in the given sequence.
removeMouseListenerToHeaderInTable(JTable) - Method in class com.compomics.util.sun.TableSorter
removeNeutralLoss(String) - Static method in class com.compomics.util.experiment.biology.NeutralLoss: Removes the neutral loss associated to the given name in the static map of the class.
removeObject(String, String, String) - Method in class com.compomics.util.db.ObjectsCache: Removes an object from the cache mappings.
removePeakList() - Method in class com.compomics.util.experiment.massspectrometry.MS1Spectrum
removePeakList() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: This method will remove the peak list in order to reduce memory consumption of the model.
removePeptideMatch(String) - Method in class com.compomics.util.experiment.identification.Identification: Removes a peptide match from the model.
removePeptideMatch(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Deletes a peptide match from the database.
removeProteinMatch(String) - Method in class com.compomics.util.experiment.identification.Identification: Removes a protein match from the model.
removeProteinMatch(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Deletes a protein match from the database.
removeRawAssumptions(String) - Method in class com.compomics.util.experiment.identification.Identification: Removes the raw assumptions of a spectrum.
removeRawAssumptions(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Deletes the raw assumptions corresponding to a given psm from the database.
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.experiment.identification.identification_parameters.PtmSettings: Removes a fixed modification from the list of refinement modifications.
removeRefinementVariableModification(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: 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.
removeSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.Identification: Removes a spectrum match from the model.
removeSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Deletes a spectrum match from the database.
removeTagAssumptionsMap() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Removes the tags assumptions Map to free memory.
removeUnknownPTMs() - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Returns a boolean indicating whether unknown PTMs shall be removed.
removeUserPtm(String) - Method in class com.compomics.util.experiment.biology.PTMFactory: Removes a user PTM.
removeVariableModification(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Removes a modification from the list of variable modifications.
removeZeroes(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Removes zero intensity peaks.
rename(String, String) - Method in class com.compomics.util.io.FTP: Rename a file on the remote server.
renameDuplicateSpectrumTitles(File, WaitingHandler) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Renames duplicate spectrum titles.
renameFastaFileName(File) - Method in class com.compomics.util.protein_sequences_manager.gui.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.preferences.UtilitiesUserPreferences: Returns true if the X! Tandem file should be renamed.
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.
ReporterIon - Class in com.compomics.util.experiment.biology.ions: This class models a reporter ion and is its own factory.
ReporterIon(String, double) - Constructor for class com.compomics.util.experiment.biology.ions.ReporterIon: Constructor for a user-defined reporter ion.
ReporterIon(String, double, boolean) - Constructor for class com.compomics.util.experiment.biology.ions.ReporterIon: Constructor for a user-defined reporter ion.
ReporterIon(String, AtomChain) - Constructor for class com.compomics.util.experiment.biology.ions.ReporterIon: Constructor for a user-defined reporter ion.
ReporterIon(String, AtomChain, boolean) - Constructor for class com.compomics.util.experiment.biology.ions.ReporterIon: Constructor for a user-defined reporter ion.
ReporterIonQuantification - Class in com.compomics.util.experiment.quantification.reporterion: This class contains quantification parameters.
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(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.
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.
representativeComposition - Variable in class com.compomics.util.experiment.biology.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.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.MonitorableInputStream: Repositions this stream to the position at the time the mark method was last called on this input stream.
resetConnection() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Resets the connection to the random access file.
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: Reset the primary progress bar value to 0.
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.
resetSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX: Resets the value of the progress bar.
resetSecondaryProgressCounter() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Reset the secondary progress bar value to 0.
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.
restoreConnection(String, boolean, ObjectsCache) - Method in class com.compomics.util.experiment.identification.Identification: Restores the connection to the database.
restoreConnection(String, boolean, ObjectsCache) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Restores the connection to the database.
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(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(String, String, boolean) - Method in class com.compomics.util.db.ObjectsDB: Retrieves an object from the desired table.
retrieveObject(String, String, boolean, boolean) - Method in class com.compomics.util.db.ObjectsDB: Retrieves an object from the desired table.
reverse() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Returns an amino acid pattern which is a reversed version of the current pattern.
reverse() - Method in class com.compomics.util.experiment.biology.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: Retunrs a new TagAssumption instance where the tag is a reversed version of this tag.
reverseSequence(String) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Reverses a protein sequence.
rmdir(String) - Method in class com.compomics.util.io.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.massspectrometry.Peak: The retention time when the peak was recorded.
run() - Method in class com.compomics.util.io.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

S

S - Static variable in class com.compomics.util.experiment.biology.AminoAcid
S - Static variable in class com.compomics.util.experiment.biology.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.
sameListsFirstListSorted(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.Peptide: Indicates whether another peptide has the same modifications at the same localization as this peptide.
sameModificationsAs(Peptide) - Method in class com.compomics.util.experiment.biology.Peptide: Indicates whether another peptide has the same modifications at the same localization as this peptide.
sameSets(HashSet, HashSet) - Static method in class com.compomics.util.Util: Convenience methods indicating whether the content of two sets have the same content.
Sample - Class in com.compomics.util.experiment.biology: This class models a proteomic sample.
Sample(String) - Constructor for class com.compomics.util.experiment.biology.Sample: Constructor for a sample.
Sample - Class in com.compomics.util.pride.prideobjects: An object for storing Sample details.
Sample(String, ArrayList<CvTerm>) - Constructor for class com.compomics.util.pride.prideobjects.Sample: Create a new Sample object.
SampleAnalysisSet - Class in com.compomics.util.experiment: A sample measurement set is a set of replicates from a common sample.
SampleAnalysisSet(Sample, ProteomicAnalysis) - Constructor for class com.compomics.util.experiment.SampleAnalysisSet: Contructor for an analysis of a sample without replicates.
SampleAnalysisSet(Sample, ArrayList<ProteomicAnalysis>) - Constructor for class com.compomics.util.experiment.SampleAnalysisSet: Contructor for a set of analysis of a 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.
save(File, MsExperiment) - Static method in class com.compomics.util.experiment.io.ExperimentIO: Method which saves an experiment.
saveCache(WaitingHandler, boolean) - Method in class com.compomics.util.db.ObjectsCache: Saves the cache content in the database.
saveFactory() - Method in class com.compomics.util.experiment.biology.PTMFactory: Saves the factory in the user folder.
saveFile(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory: Save to file.
saveIdentificationParameters(SearchParameters, File) - Static method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Saves the identification parameters to a serialized file.
saveIdentificationParameters(IdentificationParameters, File) - Static method in class com.compomics.util.preferences.IdentificationParameters: Saves the identification parameters to a file.
saveIdentificationParametersAsTextFile(File) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Saves the identification parameters as a human readable text file.
saveIndex() - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Saves the index.
saveInitialSize(int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Saves the initial tag size in the parameters table of the DB.
saveMapping(File) - Method in class com.compomics.util.experiment.biology.genes.go.GoDomains: Saves the mapping to the given file.
saveModificationUse(ConfigurationFile, ArrayList<String>) - Static method in class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Saves the modification use to the given configuration file.
saveNode(String, Node) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Adds a node to the database.
saveNodes(HashMap<String, Object>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Adds nodes to the database.
saveObject(String) - Method in class com.compomics.util.db.ObjectsCache: Saves an entry in the database if modified and clears it from the cache.
saveObject(String, boolean) - Method in class com.compomics.util.db.ObjectsCache: Saves an entry in the database if modified.
saveObjects(ArrayList<String>) - Method in class com.compomics.util.db.ObjectsCache: Saves an entry in the database if modified and clears it from the cache.
saveObjects(ArrayList<String>, WaitingHandler) - Method in class com.compomics.util.db.ObjectsCache: Saves an entry in the database if modified and clears it from the cache.
saveObjects(ArrayList<String>, WaitingHandler, boolean) - Method in class com.compomics.util.db.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.
saveUrl(File, String, int, String, String, WaitingHandler) - Static method in class com.compomics.util.Util: Save a file from a URL.
saveUserPreferences(UtilitiesUserPreferences) - Static method in class com.compomics.util.preferences.UtilitiesUserPreferences: Convenience method saving the user preferences.
scaffold - Static variable in class com.compomics.util.experiment.identification.Advocate: The scaffold multiple search engine data interpretation software.
scanNumber - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum: Scan number or range.
scanStartTime - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum: The time point when the spectrum was recorded (scan start time in mzML files).
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.Atom: The selenium atom.
searchDecoyDatabase() - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Returns whether MS-GF+ is to create and search a decoy database.
SearchGuiOutputOption - Enum in com.compomics.util.preferences: This enum lists the possible output options.
searchGuiParametersFileOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for a parameters file for SearchGUI.
searchGuiRawFileOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for raw 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.
searchGuiSpectrumFileOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for mgf files for SearchGUI.
SearchParameters - Class in com.compomics.util.experiment.identification.identification_parameters: This class groups the parameters used for identification.
SearchParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Constructor.
SearchParameters(SearchParameters) - Constructor for class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Constructor.
SearchParameters.MassAccuracyType - Enum in com.compomics.util.experiment.identification.identification_parameters: Possible mass accuracy types.
SearchSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters: The search settings dialog.
SearchSettingsDialog(Frame, SearchParameters, Image, Image, boolean, boolean, ConfigurationFile, LastSelectedFolder, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Creates a new SearchSettingsDialog with a frame as owner.
SearchSettingsDialog(Dialog, Frame, SearchParameters, Image, Image, boolean, boolean, ConfigurationFile, LastSelectedFolder, String, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Creates a new SearchSettingsDialog with a dialog as owner.
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.protein_sequences_manager.gui.SequenceDbDetailsDialog: Allows the user to select a db and loads its information.
selectDB() - Method in class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog: Allows the user to select a db and loads its information.
SelectedValuesTableFilter() - Constructor for class com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
Selenium - Class in com.compomics.util.experiment.biology.atoms: Selenium.
Selenium() - Constructor for class com.compomics.util.experiment.biology.atoms.Selenium: Constructor.
Selenocysteine - Class in com.compomics.util.experiment.biology.aminoacids: SeC (U) (Mascot)-
Selenocysteine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Selenocysteine: Constructor.
SELENOCYSTEINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a 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.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.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.FTPClient: This method sends a group of files to the default FTP location on the server.
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: Sends command cmd to the server.
sendTextFile(String) - Method in class com.compomics.util.io.FTPClient: This method sends a text file to the default FTP location on the server.
SEPARATOR - Static variable in class com.compomics.software.CommandLineUtils: The command line argument separator.
separator - Static variable in class com.compomics.software.settings.UtilitiesPathPreferences: 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.GeneFactory: 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.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.maps.KeyUtils: The separator.
separator - Static variable in class com.compomics.util.Util: Separator which can be used to separate things.
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.
SequenceContentType - Enum in com.compomics.util.protein_sequences_manager.enums: SequenceContentType enumerator.
SequenceDbDetailsDialog - Class in com.compomics.util.protein_sequences_manager.gui: This dialog displays information about a sequence database.
SequenceDbDetailsDialog(Dialog, Frame, LastSelectedFolder, boolean, Image, Image) - Constructor for class com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog: Creates a new SequenceDbDetailsDialog with a dialog as owner.
SequenceDbDetailsDialog(Frame, LastSelectedFolder, boolean, Image, Image) - Constructor for class com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog: Creates a new SequenceDbDetailsDialog.
SequenceFactory - Class in com.compomics.util.experiment.identification.protein_sequences: Factory retrieving the information of the loaded FASTA file.
SequenceFactory.HeaderIterator - Class in com.compomics.util.experiment.identification.protein_sequences: Convenience iterator iterating the headers of a FASTA file without using the cache.
SequenceFactory.ProteinIterator - Class in com.compomics.util.experiment.identification.protein_sequences: Convenience iterator iterating all proteins in a FASTA file without using index or cache.
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(String, ArrayList<IonMatch>, boolean, boolean, PtmSettings) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel: Deprecated.
use the panel with ion selection instead
SequenceFragmentationPanel(String, ArrayList<IonMatch>, boolean, boolean, PtmSettings, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel: Creates a new SequenceFragmentationPanel working with B and Y ions.
SequenceFragmentationPanel(String, ArrayList<IonMatch>, boolean, PtmSettings, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel: Creates a new SequenceFragmentationPanel working with B and Y ions.
SequenceInputType - Enum in com.compomics.util.protein_sequences_manager.enums: Enum for the input types of the protein sequence manager.
SequenceMatchingPreferences - Class in com.compomics.util.preferences: The sequence matching options.
SequenceMatchingPreferences() - Constructor for class com.compomics.util.preferences.SequenceMatchingPreferences: Constructor for empty preferences.
SequenceMatchingPreferences.MatchingType - Enum in com.compomics.util.preferences: The different types of amino acid matching.
SequenceMatchingSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters: Dialog for the edition of the sequence matching settings.
SequenceMatchingSettingsDialog(Frame, SequenceMatchingPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.SequenceMatchingSettingsDialog: Creates a new SequenceMatchingSettingsDialog with a frame as owner.
SequenceMatchingSettingsDialog(Dialog, Frame, SequenceMatchingPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.SequenceMatchingSettingsDialog: Creates a new SequenceMatchingSettingsDialog with a dialog as owner.
SequenceModificationPanel - Class in com.compomics.util.gui.protein: A panel for displaying modification profiles.
SequenceModificationPanel(String, ArrayList<ModificationProfile>, boolean, String, String) - Constructor for class com.compomics.util.gui.protein.SequenceModificationPanel: Creates a new SequenceFragmentationPanel.
SequenceSegment - Class in com.compomics.util.experiment.identification.amino_acid_tags: Segment of sequence indexed on a protein sequence.
SequenceSegment(int, boolean) - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Constructor.
SequenceSegment(SequenceSegment) - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.SequenceSegment: Constructor.
sequest - Static variable in class com.compomics.util.experiment.identification.Advocate: The sequest search engine.
SequestParamsFileFilter - Class in com.compomics.util.io.filefilters: File filter for sequest.params files.
SequestParamsFileFilter() - Constructor for class com.compomics.util.io.filefilters.SequestParamsFileFilter
SerializationUtils - Class in com.compomics.util.io: This class implements convenience methods for serialization and deserialization.
SerializationUtils() - Constructor for class com.compomics.util.io.SerializationUtils
serialize(T, Type, JsonSerializationContext) - Method in class com.compomics.util.io.json.adapter.InterfaceAdapter
serialVersionUID - Static variable in interface com.compomics.util.experiment.personalization.UrParameter: The version UID for Serialization/Deserialization compatibility
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: Serine.
Serine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Serine: Constructor.
SERINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a serine immonium ion.
serverInput - Variable in class com.compomics.util.io.FTP: Buffered stream for reading replies from server.
serverIsOpen() - Method in class com.compomics.util.io.FTP: Return server connection status
serverOutput - Variable in class com.compomics.util.io.FTP: Stream for printing to the server.
serverResponse - Variable in class com.compomics.util.io.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.AminoAcidSequence: replaces the amino acid at the given position by the given amino acid represented by its single letter code.
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.pride.CvTerm: Sets the accession.
setAccession(String) - Method in class com.compomics.util.protein.Header
setAccessionParsingRule(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Sets the accession parsing rule to use for this file.
setActicationType(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Sets the activation type.
setAddition(Boolean) - Method in class com.compomics.util.experiment.biology.AtomChain: Set if the given atomic chain consists of additions, i.e., all atoms are added when calculating the mass, false, means that all atoms are subtracted.
setAdditionalOutput(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Set if additional output is to be included.
setAdjustPrecursorMass(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set if the precursor mass is to be adjusted.
setAllPathsIn(String) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: 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
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.
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.
setAnnotationSettings(AnnotationSettings) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the annotation preferences used for identification.
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.PTM: Sets the atom chain added.
setAtomChainRemoved(AtomChain) - Method in class com.compomics.util.experiment.biology.PTM: Sets the atom chain removed.
setAtomicComposition(AtomChain) - Method in class com.compomics.util.experiment.biology.Ion: Returns the atomic composition.
setAutomatedMemoryManagement(boolean) - Method in class com.compomics.util.db.ObjectsCache: Sets whether the cache is in automated memory management mode.
setAutomaticAnnotation(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Sets whether the annotation settings should be automatically inferred.
setAutoUpdate(Boolean) - Method in class com.compomics.util.preferences.GenePreferences: Sets whether the gene mappings should be automatically updated.
setAutoUpdate(Boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.
setBatchSize(int) - Method in class com.compomics.util.db.ObjectsCache: Sets the batch size in number of objects.
setBatchSize(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the batch size.
setBatchSize(int) - Method in class com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator: Set the batch size.
setBatchSize(int) - Method in class com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator: Set the batch size.
setBatchSize(int) - Method in class com.compomics.util.experiment.identification.matches_iterators.PsmIterator: Set the batch size.
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.
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.
setCacheSize(int) - Method in class com.compomics.util.db.ObjectsCache: Sets the cache size in number of objects.
setCacheSize(int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Sets the size of the cache used for peptide mappings (note that there are two of them).
setCacheSize(int) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Sets the spectrum cache size.
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.preferences.UtilitiesUserPreferences: Set if the spectra should be checked for duplicate titles or not.
setCheckMgfSize(boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set if the mgf should be checked for size.
setCheckPeakPicking(boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set if the spectra should be checked for peak picking or not.
setCheckSpectrumCharges(Boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set if the spectra are to be checked for missing charges.
setClassSizeMultiplier(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.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
setCleaveNterMethionine(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether N-terminal methionines should be cleaved.
setClipNtermMethionine(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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, Color) - Method in class com.compomics.util.experiment.biology.PTMFactory: Sets a new color for the given expected modification.
setColor(String, Color) - Method in class com.compomics.util.experiment.identification.identification_parameters.PtmSettings: Sets a new color for the given expected modification.
setColor(Color) - Method in class com.compomics.util.gui.protein.ModificationProfile: Sets the PTM color.
setColumn(int, ArrayList<Double>) - Method in class com.compomics.util.math.matrix.DoubleMatrix
setComplementMzTolerance(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets the complement m/z tolerance.
setComplementScoreWeight(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set the complement score weight.
setComposition(AtomChain) - Method in class com.compomics.util.experiment.biology.NeutralLoss: Sets the composition of the neutral loss.
setComputeExactPValues(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the exact p-values are to be computed.
setComputeSpScore(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the SP score is to be computed.
setComputeXCorr(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
setConcatenatedTargetDecoy(boolean) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Sets whether the database is a concatenated target/decoy database.
setConcatenatTargetDecoy(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the target and decoy results are to be concatenated.
setConfidenceMargin(Double) - Method in class com.compomics.util.preferences.ValidationQCPreferences: Sets the margin to the threshold to use as factor of the resolution.
setConfident(boolean) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Sets whether the modification is confidently localized on the sequence.
setConnectionActive(boolean) - Static method in class com.compomics.util.db.DerbyUtil: Sets whether the connection to Derby is active.
setConsecutiveIonProbability(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Set the consecutive ion probability.
setContacts(ArrayList<Contact>) - Method in class com.compomics.util.pride.prideobjects.ContactGroup: Set the contacts.
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.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Sets whether the precursor mass shall be corrected (TagDB setting).
setCorrupted(boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Sets whether the database is corrupted.
setCvTerm(CvTerm) - Method in class com.compomics.util.experiment.biology.PTM: Set the CV term associated with this PTM.
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(Header.DatabaseType) - Method in class com.compomics.util.protein.Header
setDatabaseTypes(HashMap<Header.DatabaseType, Integer>) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Set the database types map.
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.preferences.UtilitiesUserPreferences: Sets the last used database folder.
setDbSize(boolean) - Method in class com.compomics.util.preferences.ValidationQCPreferences: Sets whether the database size should be checked.
setDecoyFormat(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the decoy format.
setDecoyInMemory(boolean) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Sets whether decoys should be kept in memory.
setDecoySeed(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the decoy seed.
setDecoyTag(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Sets the decoy tag.
setDefaultAdvancedSettings() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Set the advanced settings to the default values.
setDefaultAdvancedSettings(SearchParameters) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
setDefaultDbFolderPath(String) - Static method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Sets the default folder to use when storing the trees.
setDefaultPeptideFDR(double) - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Sets the default peptide FDR.
setDefaultProteinFDR(double) - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Sets the default protein FDR.
setDefaultPsmFDR(double) - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Sets the default PSM FDR.
setDeisotopingMode(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
setDeNovoCharge(int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Set the charge to use for the fragment ions in the de novo sequencing
setDeNovoGuiPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the path to the DeNovoGUI installation.
setDependentLosses(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets whether neutral losses should be sequence dependent.
setDescription(String) - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Sets the description of this mutation matrix.
setDescription(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Sets the description for this database.
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.preferences.IdentificationParameters: Sets the description of the parameters.
setDescription(String) - Method in class com.compomics.util.protein.Header
setDescriptionProteinName(String) - Method in class com.compomics.util.protein.Header
setDescriptionShort(String) - Method in class com.compomics.util.protein.Header
setDestinationFile(String) - Method in class com.compomics.util.io.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.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether charge plus one should be determined algorithmically.
setDigestionType(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the enzyme digestion type.
setDiscardLowQualitySpectra(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Sets whether low quality spectra shall be discarded.
setDisplayedTips(ArrayList<String>) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.
setDoi(String) - Method in class com.compomics.util.pride.prideobjects.Reference: Set the Digital Object Identifier (DOI) of the reference.
setDoubleChargeWindow(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
setDuplicateSpectra(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets whether to use duplicate spectra option.
setDynamicRange(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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.
setEnrichedPtms(ArrayList<String>) - Method in class com.compomics.util.experiment.ShotgunProtocol: Sets the PTMs used for enrichment.
setEnsemblVersionsMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps: Sets the Ensembl version map.
setEnzyme(Enzyme) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the enzyme used for digestion.
setEnzyme(Enzyme) - Method in class com.compomics.util.experiment.ShotgunProtocol: Sets the enzyme used for digestion.
setEnzymeType(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the enzyme type.
setEqualIL(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets whether I and L should be considered indistinguishable.
setEstimateCharge(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether the precursor charge shall be estimated for OMSSA.
setEstimateCharge(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Sets whether the precursor charge shall be estimated for PepNovo.
setEstimateFlr(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences: Sets whether the threshold is FLR based.
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..
setExcluded(int, ArrayList<Character>) - Method in class com.compomics.util.experiment.biology.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.
setFastaFile(File) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the sequence database file used for identification.
setFastaFilePath(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Sets the FASTA file path.
setFastIndexFolderName(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the name of the FASTA index folder.
setFile(File) - Method in class com.compomics.util.FileAndFileFilter: Set the file.
setFileFilter(FileFilter) - Method in class com.compomics.util.FileAndFileFilter: Set the file filter.
SetFileMode(int) - Method in class com.compomics.util.io.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: 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.
setFilterFromSearchParameters(SearchParameters) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Updates the filter based on the search parameters.
setFirstDecoy(boolean) - Method in class com.compomics.util.preferences.ValidationQCPreferences: Sets whether the number of hits before the first decoy should be checked.
setFixed(boolean) - Method in class com.compomics.util.experiment.biology.NeutralLoss: Sets whether the loss is fixed or not.
setFlrThreshold(double) - Method in class com.compomics.util.preferences.PTMScoringPreferences: Sets the FLR threshold.
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.protein.Header
setForeignDescription(String) - Method in class com.compomics.util.protein.Header
setForeignID(String) - Method in class com.compomics.util.protein.Header
setFractionMolecularWeightRanges(HashMap<String, XYDataPoint>) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Set the user provided molecular weight ranges for the fractions.
setFractionOfPeaksForChargeEstimation(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the fraction of peaks to be retained for charge >1 estimation.
setFractionSettings(FractionSettings) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the fraction settings.
setFragmentAccuracyType(SearchParameters.MassAccuracyType) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the fragment accuracy type.
setFragmentAll(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets whether the fragment all option should be used.
setFragmentationMethod(FragmentationMethod) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the fragmentation method used.
setFragmentationMethod(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters: Set the fragmentation method.
setFragmentationMethod(FragmentationMethod) - Method in class com.compomics.util.experiment.ShotgunProtocol: Sets the fragmentation method.
setFragmentationModel(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Sets the name of the fragmentation model.
setFragmentationRule(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Set the fragmentation rule.
setFragmentationType(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Set the fragmentation ID.
setFragmentBinOffset(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the fragment ion bin offset.
setFragmentIonAccuracy(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the fragment ion m/z tolerance.
setFragmentIonAccuracy(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Sets the fragment ion accuracy.
setFragmentIonAccuracy(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Sets the fragment ion accuracy.
setFragmentIonPpm(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Sets whether the fragment ion accuracy is in ppm.
setFragmentIonPpm(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Sets whether the fragment ion accuracy is in ppm.
setGeneMappingFolder(String) - Static method in class com.compomics.util.experiment.biology.genes.GeneFactory: Sets the folder where gene mappings are saved.
setGeneName(String) - Method in class com.compomics.util.protein.Header
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.
setGenePreferences(GenePreferences) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the gene preferences.
setGenerateDecoyDatabase(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Set whether a decoy database shall be created and searched against.
setGenerateProteinTree(Boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set if the the protein tree will be created parallel to the searches.
setGenerateQuery(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
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.
setHigherCharge(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets whether higher charge should be considered.
setHighIntensityCutOff(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the high intensity cut-off as percentage of the most intense ion peak.
setHighResolutionAnnotation(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Set if the peak annotation should be based on the most accurate mz value, or on the most intense peak.
setHitListLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the length of the hit list for OMSSA.
setHitListLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Sets the length of the hit list.
setID(String) - Method in class com.compomics.util.protein.Header
setIdentificationAlgorithmParameter(int, IdentificationAlgorithmParameter) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Adds identification algorithm specific parameters.
setIdentificationCharge(Charge) - Method in class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption: Sets the identification charge.
setIdentificationParameters(IdentificationParameters) - Method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Sets the identification parameters.
setIdentifier(String) - Method in class com.compomics.util.gui.spectrum.ReferenceArea: Sets the references identifier.
setIdFilter(PeptideAssumptionFilter) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the filter used when importing PSMs.
setIdValidationPreferences(IdMatchValidationPreferences) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the identification matches validation preferences.
setIgnoreExceptions(boolean) - Method in class com.compomics.util.exceptions.ExceptionHandler: Sets whether exceptions should be ignored.
setImportComplete(boolean) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Sets whether the import was completed.
setIncludeAmmonia(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets whether ammonia losses should be accounted for.
setIncludeDateInOutputName(Boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets whether water losses should be accounted for.
setIndeterminate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog: This method makes the progressbar indeterminate.
setInferred(boolean) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Sets whether the modification is inferred from another peptide.
setInstitution(String) - Method in class com.compomics.util.pride.prideobjects.Contact: Set the instituttion.
setInstrumentID(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Set the instrument ID.
setInstrumentID(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Set the instrument ID.
setIntensity(double) - Method in class com.compomics.util.experiment.massspectrometry.Peak: Set the intensity.
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.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the intensity cut-off increment.
setIntensityLimit(double) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Sets the intensity percentile to consider for annotation.
setIntensityScoreWeight(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set the intensity score weight.
setIntensityValues(double[]) - Method in class com.compomics.util.io.PklFile
setIntensityValuesAsArray(double[]) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Setter for the intensityValuesAsArray.
setIonColor(Ion, Color) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel: Sets an annotation color for the given ion.
setIonMatches(ArrayList) - Method in class com.compomics.util.gui.spectrum.SequenceFragmentationPanel: Set the ArrayList with FragmentIon matches.
setIonSearched1(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Setter for the first kind of ion searched, indexed by its single letter code, for example "a".
setIonSearched2(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Setter for the second kind of ion searched, indexed by its single letter code, for example "a".
setIsotopeCorrection(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the isotope correction setting.
setIsotopeMzTolerance(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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.preferences.UtilitiesUserPreferences: Set the Java Home folder.
setKeepTerminalAminoAcids(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the option for keeping the terminal amino acids when generating the decoys
setKey(String) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch: Sets a new key for the match.
setKey(String) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Replaces the new key.
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.preferences.LastSelectedFolder: Sets the last selected folder of the given use case.
setLastSelectedFolder(String) - Method in class com.compomics.util.preferences.LastSelectedFolder: Sets the last selected folder.
setLastSelectedFolder(LastSelectedFolder) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets the last selected folder.
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.preferences.SequenceMatchingPreferences: 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.preferences.UtilitiesUserPreferences: Set the local PRIDE folder.
setLocation(int) - Method in interface com.compomics.util.interfaces.Modification: This method allows the setting of the location for this modification.
setLocation(int, int) - Method in class com.compomics.util.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 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.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the lower mass value for the clear mz range.
setLowerPrecursorMass(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Set the lower precursor mass.
setLowIntensityCutOff(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Set whether the low memory mode is used.
setMainDatabaseType(Header.DatabaseType) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Sets the main database type.
setMainMatch(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Sets the main protein accession after protein inference.
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.ReporterIon: Method to set the mass of the reporter ion.
setMass(double) - Method in class com.compomics.util.experiment.biology.MassGap: Sets the mass of the gap.
setMassAnalyzer(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters: Set the mass analyzer.
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, boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: Sets a new m/z tolerance for peak matching.
setMaxCharge(Integer) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Sets the maximum charge in this file.
setMaxChargeSearched(Charge) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the maximal charge searched.
setMaxCombinations(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the maximal number of combinations.
setMaxDynamicMods(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets the maximum number of dynamic mods.
setMaxDynamicMods(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Set the maximum number of variable modifications.
setMaxEValue(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the maximal e-value searched for.
setMaxEValue(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets the maximal e-value searched for.
setMaxFragmentCharge(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the maximum fragment ion charge.
setMaxFragmentCharge(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the maximal fragment charge.
setMaxFragmentPerSeries(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the maximal number of fragments to retain per series.
setMaxHitsPerSpectrumPerCharge(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Set the maximal number of hits searched per spectrum and per charge.
setMaximumExpectationValueRefinement(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets the maximum expectation value to use for refinement.
setMaxIntensity(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.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(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the maximal isotopic correction.
setMaxIterations(int) - Method in class com.compomics.util.math.clustering.KMeansClustering: Set the maximum number of iterations.
setMaxMissedCleavages(Integer) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Set the maximum number of missed cleavages.
setMaxMutationsPerPeptide(Integer) - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Sets the maximal number of mutations allowed per peptide.
setMaxMz(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.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(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the maximal m/z ladder length.
setMaxNumberOfModifications(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.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(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set the maximum peak count.
setMaxPeakCount(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Set the max peak count.
setMaxPeakCount(Integer) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Sets the maximum peak count in this file.
setMaxPepLength(int) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Sets the maximal peptide length allowed.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Sets the maximal peptide length allowed.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Sets the maximal peptide length allowed.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the maximal peptide length allowed.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Sets the maximal peptide length allowed.
setMaxPeptideLengthNoEnzyme(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the maximal peptide length to use when searching with no enzyme.
setMaxPeptideMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the maximal peptide mass.
setMaxPrecursorAdjustment(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set the maximum precursor adjustment.
setMaxPrecursorMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the maximum precursor mass.
setMaxPrecursorMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Sets the maximum precursor mass.
setMaxPrecursorMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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: Set the maximum value of the progress bar.
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.
setMaxRank(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters: Set the maximum rank.
setMaxRT(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Sets the maximal RT in this file.
setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX: Sets the maximal value of the progress bar.
setMaxSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Set the maximum value of the secondary progress bar.
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(Integer) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the maximum charge added when the charge is missing for a given spectrum.
setMaxSpectrumMz(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the max spectrum m/z to search for.
setMaxTagCount(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets the maximum number of tags per spectrum to be generated.
setMaxVariableMods(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the maximum number of variable modifications per peptide.
setMaxVariablePtmsPerPeptide(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the maximum number of variable modifications of allowed on a single peptide.
setMaxVariablePtmsPerTypePerPeptide(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the maximum number of variable modifications of each modification type allowed on a single peptide.
setMemoryAllocation(int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: Sets the memory allocation.
setMemoryMappedSequenceLibraries(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether sequence libraries should be mapped in memory.
setMemoryPreference(int) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets the preferred upper memory limit.
setMemoryShare(double) - Method in class com.compomics.util.db.ObjectsCache: Sets the share of heap size which can be used before emptying the cache.
setMergeSmallSubgroups(Boolean) - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Sets whether small subgroups of matches should be merged.
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.preferences.UtilitiesUserPreferences: Set the max mgf file size before splitting.
setMgfNSpectra(int) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the max number of spectra in an mgf file.
setMH(double) - Method in class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails: Sets the PepNovo provided mH.
setMinAnnotatedPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the minimal number of annotated peaks a peptide should have.
setMinChargeSearched(Charge) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the minimal charge searched.
setMinFragmentMz(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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(Charge) - Method in class com.compomics.util.experiment.identification.identification_parameters.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(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the minimum peak intensity.
setMinPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the minimum number of peaks.
setMinPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the minimal number of peaks a spectrum should contain.
setMinPeaksPerSpectrum(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.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(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Sets the minimal peptide length allowed.
setMinPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Sets the minimal peptide length allowed.
setMinPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the minimal peptide length allowed.
setMinPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Sets the minimal peptide length allowed.
setMinPeptideLengthNoEnzyme(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the minimal peptide length to use when searching with no enzyme.
setMinPrecPerSpectrum(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the minimal number of precursors per spectrum.
setMinPrecursorAdjustment(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set the minimum precursor adjustment.
setMinPrecursorMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the minimum precursor mass.
setMinPrecursorMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Sets the minimum precursor mass.
setMinPrecursorMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Sets the minimum precursor mass.
setMinPrecursorMass(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets the minimal precursor mass.
setMinRT(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Sets the minimum RT in this file.
setMinSpectrumChargeRange(Integer) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the minimum charge added when the charge is missing for a given spectrum.
setMinSpectrumMz(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the min spectrum m/z to search for.
setMinSpectrumPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the min number of peaks in a spectrum.
setMinTerminiCleavages(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
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
setModificationMatches(ArrayList<ModificationMatch>) - Method in class com.compomics.util.experiment.biology.Peptide: Sets new modification matches for the peptide.
setModifications(Vector) - Method in class com.compomics.util.protein.AASequenceImpl: Simple setter for the modifications.
setModificationSite(int) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Setter for the modification site, 1 is the first amino acid.
setMonoIsotopic(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the precursor mass is monoisotopic.
setMs1Resolution(Double) - Method in class com.compomics.util.experiment.ShotgunProtocol: Sets the MS1 mass resolution.
setMs1ResolutionPpm(boolean) - Method in class com.compomics.util.experiment.ShotgunProtocol: Sets whether the MS1 resolution is in ppm.
setMs2Resolution(Double) - Method in class com.compomics.util.experiment.ShotgunProtocol: Sets the MS2 resolution.
setMs2ResolutionPpm(boolean) - Method in class com.compomics.util.experiment.ShotgunProtocol: Sets whether the MS2 resolution is in ppm.
setMsFormat(MsFormat) - Method in class com.compomics.util.experiment.massspectrometry.proteowizard.MsConvertParameters: Sets the format to convert to.
setMutationMatrix(MutationMatrix) - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Sets the mutation matrix to use.
setMz(double) - Method in class com.compomics.util.experiment.massspectrometry.Peak: Set the mz.
setMzBinOffset(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the m/z bin offset.
setMzBinWidth(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the m/z bin width.
setMzFidelityScoreWeight(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set the mzFidelity score weight.
setMzidOutput(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the mzid output is to be created.
setMzOrdered(boolean) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Setter for the boolean that indicates whether the mzValuesAsArray is sorted.
setMzValues(double[]) - Method in class com.compomics.util.io.PklFile
setName(String) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon: Setter for the ion name.
setName(String) - Method in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Sets the name of this mutation matrix.
setName(String) - Method in class com.compomics.util.experiment.biology.PTM: Sets the PTM name.
setName(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: 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.preferences.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(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the minimal number of annotated most intense peaks.
setnCache(int) - Method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Sets the size of the cache.
setnClusters(int) - Method in class com.compomics.util.math.clustering.settings.KMeansClusteringSettings: Sets the number of clusters to use.
setNeutralLosses(ArrayList<NeutralLoss>) - Method in class com.compomics.util.experiment.biology.PTM: Sets the neutral losses possibly encountered with this modification.
setNeutralLossesAuto(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Sets whether neutral losses should be automatically selected.
setNeutralLossesMap(NeutralLossesMap) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: Sets the map of neutral losses to annotate.
setNeutralLossesSequenceAuto(Boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Sets whether neutral losses are considered only for amino acids of interest or not.
setNeutronThreshold(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.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(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the allowed number of missed cleavages.
setNoProlineRuleSeries(ArrayList<Integer>) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
setNotifyStart(Boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets whether the tools should notify their start.
setNovorPtmMap(HashMap<String, String>) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters: Set the Novor to utilities PTM map.
setnPeaks(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets the number of most intense peaks to consider.
setnPeaksInDoubleChargeWindow(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the number of peaks in doubly charged windows.
setnPeaksInSingleChargeWindow(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the number of peaks in singly charged windows.
setnThreads(int) - Method in class com.compomics.util.preferences.ProcessingPreferences: Sets the number or threads to use.
setnThreads(int) - Method in class com.compomics.util.preferences.PSProcessingPreferences: Deprecated.

Sets the number of threads to use.
setNumberOfBatches(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the number of candidates.
setNumberOfPeptides(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Set the number of peptides to report per spectrum.
setNumberOfPtmsPerPeptide(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Set the maximum number of PTMs per peptide.
setNumberOfSpectrumMarches(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Set the maximum number of spectrum matches.
setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the maximum number of spectrum matches.
setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Set the maximum number of spectrum matches.
setNumberOfSpectrumMatches(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the number of PSMs to report per spectrum.
setNumberTolerableTermini(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Set the number of tolerable termini.
setNumChargeStates(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets the number of charge states.
setNumIntensityClasses(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets the number of intensity classes.
setNumIntensityClasses(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Set the number of intensity classes.
setObjectCache(ObjectsCache) - Method in class com.compomics.util.db.ObjectsDB: Sets the object cache to be used by this database.
setOccurrence(Atom, Integer, Integer) - Method in class com.compomics.util.experiment.biology.AtomChain: Sets the occurrence of a given atom.
setOntology(String) - Method in class com.compomics.util.pride.CvTerm: Sets the ontology.
setOrderedListOfSpectrumFileNames(ArrayList<String>) - Method in class com.compomics.util.experiment.identification.Identification: Set the ordered list of spectrum file names.
setOutputData(Boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets whether data should be copied along with the identification files in the SearchGUI output.
setOutputFolderName(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the name of the output folder.
setOutputFormat(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Set the output format.
setOutputHistograms(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether histograms should be written in the result file
setOutputOption(SearchGuiOutputOption) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets how SearchGUI output files should be organized.
setOutputProteins(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether the protein bloc should be included in the export.
setOutputResults(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Set the output results filter.
setOutputSequences(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether the spectra should be exported in the result file.
setOutputSuffix(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets the output tags suffix.
setParameter(String, String) - Method in class com.compomics.util.io.ConfigurationFile: Sets the value for a given parameter.
setParametersFromSearch(SearchParameters) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets identification parameters based on given search parameters.
setParentFolder(String) - Static method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory: Set the parent folder.
setParentProteins(ArrayList<String>) - Method in class com.compomics.util.experiment.biology.Peptide: Sets the parent proteins.
setPassive(boolean) - Method in class com.compomics.util.io.FTP: Set Passive mode Transfers.
setPathPreference(UtilitiesPathPreferences.UtilitiesPathKey, String) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Sets the path according to the given key and path.
setPattern(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.PTM: Sets the amino acid pattern targeted by this modification.
setPdbaccession(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter: Set the PDB accession.
setPeakList(HashMap<Double, Peak>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Sets the peak list.
setPeakPicked(Boolean) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Set if the indexed file seems to contain only peak picked spectra or not.
setPeaks(ArrayList<Peak>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Set the peaks.
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.experiment.identification.identification_parameters.tool_specific.PepnovoParameters: Set the PepNovo to utilities PTM map.
setPeptide(Peptide, int, SpecificAnnotationSettings) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator: Sets a new peptide to match.
setPeptide(Peptide, HashMap<Integer, HashMap<Integer, ArrayList<Ion>>>, int, SpecificAnnotationSettings) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator: Sets a new peptide to match.
setPeptideFilters(ArrayList<Filter>) - Method in class com.compomics.util.preferences.ValidationQCPreferences: Sets the list of peptide quality filters.
setPeptideKeys(ArrayList<String>) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch: Sets the peptide keys for this protein match.
setPeptideShakerPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the path to the PeptideShaker installation.
setPepXmlOutput(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
setPinOutput(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Set the pNovo to utilities PTM map.
setPNovoPtmResiduesMap(HashMap<Character, Character>) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether the refinement modifications should be used for the full refinement
setPrecurorCharge(int) - Method in class com.compomics.util.io.PklFile
setPrecursor(Precursor) - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Set the precursor.
setPrecursorAccuracy(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the precursor tolerance.
setPrecursorAccuracyDalton(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the precursor tolerance in Dalton (for de novo searches).
setPrecursorAccuracyType(SearchParameters.MassAccuracyType) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the precursor accuracy type.
setPrecursorAdjustmentStep(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set the precursor adjustment step.
setPrecursorChargesMissing(Boolean) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex: Set if at least one spectrum is missing the precursor charge.
setPrecursorIntensity(double) - Method in class com.compomics.util.io.PklFile
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
setPreferencesFromSearchParameters(SearchParameters) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Updates the annotation parameters based on search parameters.
setPreferencesFromSearchParameters(SearchParameters) - Method in class com.compomics.util.preferences.GenePreferences: Sets the preferences from the given search parameters.
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: Sets the value of the progress bar.
setPrimaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Sets the primary progress bar to the given value.
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.experiment.identification.identification_parameters.tool_specific.CometParameters: Set if the export score is to be printed.
setPrintPeptides(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the progress indicator size.
setProbabilisticScoreNeutralLosses(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences: 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.preferences.PTMScoringPreferences: Sets the probabilistic score threshold.
setProbabilitsticScoreCalculation(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences: Sets whether a probabilistic PTM score is required.
setProcessingType(ProcessingPreferences.ProcessingType) - Method in class com.compomics.util.preferences.ProcessingPreferences: 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.
setProteinConfidenceMwPlots(Double) - Method in class com.compomics.util.preferences.FractionSettings: Sets the protein confidence for inclusion in MW plots.
setProteinConfidenceMwPlots(Double) - Method in class com.compomics.util.preferences.PSProcessingPreferences: Deprecated.

Sets the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.
setProteinEvidence(String) - Method in class com.compomics.util.protein.Header
setProteinFilters(ArrayList<Filter>) - Method in class com.compomics.util.preferences.ValidationQCPreferences: Sets the list of protein quality filters.
setProteinInferencePreferences(ProteinInferencePreferences) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the protein inference preferences.
setProteinPtmComplexity(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Set the proteinPtmComplexity.
setProteinQuickAcetyl(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether the protein quick acetylation option should be triggered.
setProteinSequenceDatabase(File) - Method in class com.compomics.util.preferences.ProteinInferencePreferences: Sets the path to the database used.
setProteinSequencesManagerFolder(File) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets the folder to use in the protein sequences manager.
setProteinToGoMap(HashMap<String, HashSet<String>>) - Method in class com.compomics.util.experiment.biology.genes.GeneMaps: Sets the protein to GO terms accession map.
setProteinTreeFolder(File) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets the protein tree folder.
setProteoWizardPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the path to ProteoWizard.
setProtocol(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Set the protocol ID.
setPsmFilters(ArrayList<Filter>) - Method in class com.compomics.util.preferences.ValidationQCPreferences: Sets the list of PSM quality filters.
setPsmScoringPreferences(PsmScoringPreferences) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the scoring preferences used when scoring PSMs.
setPtmIndex(String, int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the index for a given modification.
setPtmIndex(String, int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the index for a given modification.
setPtmIndexes(PtmSettings) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
setPtms(ArrayList<String>) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets the variable PTMs searched.
setPtmScoringPreferences(PTMScoringPreferences) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the PTM localization scoring preferences.
setPtmSettings(PtmSettings) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Sets the PTM settings.
setPtmToPrideMap(PtmToPrideMap) - Method in class com.compomics.util.pride.PrideObjectsFactory: Sets a new PTM to PRIDE map.
setQuickPyrolidone(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.refinementparameters.PepnovoAssumptionDetails: Sets the PepNovo rank score.
setRawHeader(String) - Method in class com.compomics.util.protein.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.ObjectsCache: Sets the cache in read only.
setReadTweets(ArrayList<String>) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.experiment.biology.Sample: Setter for the reference of a sample.
setReference(String) - Method in class com.compomics.util.experiment.MsExperiment: Sets the reference of the experiment.
setReference(String) - Method in class com.compomics.util.pride.prideobjects.Reference: Set the reference.
setReferences(ArrayList<Reference>) - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup: Set the references.
setRefine(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether the second pass search should be triggered.
setRefinePointMutations(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether point mutations should be looked for during the refinement process.
setRefineSemi(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether snAPs should be used during the refinement process.
setRefineSpectrumSynthesis(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether the spectrum synthesis option should be used during the refinement process.
setRefineUnanticipatedCleavages(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether the unanticipated cleavages option should be used during the refinement process.
setRefMass(Double) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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.AnnotationSettings: Sets whether related ions should be annotated by default.
setRelimsPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the path to the Relims installation.
setRemoveMethionine(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Sets if n-term methionine is to be removed.
setRemovePrecursor(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set if the precursor is to be removed.
setRemovePrecursor(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether the precursor shall be removed for OMSSA.
setRemovePrecursor(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the precursor peak is to be removed.
setRemovePrecursorTolerance(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the precursor removal tolerance.
setRemovePrecursorTolerance(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the tolerance with which to remove the precursor peak.
setRemoveTempFolders(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the output and index folders are to be removed when the search has completed.
setRemoveUnknownPTMs(boolean) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Set whether unknown PTMs shall be removed.
setRenameXTandemFile(Boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set if the X! Tandem file should be renamed.
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.PTM: Sets the reporter ions possibly encountered with this modification.
setReporterIons(Boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: Sets whether reporter ions should be annotated by default.
setReporterPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the path to the PeptideShaker installation.
setRequireVariableMods(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.protein.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.
setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
setRunCanceled() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Set the process as canceled.
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: Set the process as finished.
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.
setRunNotFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Set the run to not finished.
setSample(int, Sample) - Method in class com.compomics.util.experiment.MsExperiment: Set a new sample.
setScalePrecursor(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether the precursor shall be scaled for OMSSA.
setScanNumber(String) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Setter for the scan number or range.
setScanStartTime(double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum: Sets the scan start time.
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.SpectrumIdentificationAssumption: Sets the score.
setSearchDecoyDatabase(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters: Set whether MS-GF+ is to create and search a decoy database.
setSearchForwardFragmentFirst(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether forward ions (b1) should be searched first.
setSearchGuiPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the path to the SearchGUI installation.
setSearchParameters(SearchParameters) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the parameters used for the spectrum matching.
setSearchPositiveIons(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether positive ions are searched.
setSearchRewindFragments(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether C-terminal fragments should be searched.
setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX: Sets the value of the progress bar.
setSecondaryProgressCounter(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Sets the secondary progress bar to the given value.
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: Makes the dialog indeterminate or not indeterminate.
setSecondaryProgressCounterIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog: Sets the secondary progress bar to indeterminate or not.
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.
setSelectedBackgroundSpecies(Integer) - Method in class com.compomics.util.preferences.GenePreferences: Sets the taxon of the species selected as background species.
setSelectedCharges(ArrayList<Integer>) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: 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.SpecificAnnotationSettings: Sets the map of ions to annotate.
setSelectedOutput(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the output type, omx, csv or pepXML.
setSelectedOutputFormat(CometParameters.CometOutputFormat) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Sets the output format.
setSelectedPositions(Integer[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock: Set the selected positions.
setSelectedProbabilisticScore(PtmScore) - Method in class com.compomics.util.preferences.PTMScoringPreferences: 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.
setSemiSpecific(boolean) - Method in class com.compomics.util.experiment.biology.Enzyme: Set if the enzyme is semi-specific.
setSeparatePeptides(Boolean) - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Sets whether Peptides should be grouped according to their modification status.
setSeparatePsms(Boolean) - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: Sets whether PSMs should be grouped according to their modification status.
setSequence(String) - Method in class com.compomics.util.experiment.biology.AminoAcidSequence: 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.
setSequenceMatchingPreferences(SequenceMatchingPreferences) - Method in class com.compomics.util.preferences.IdentificationParameters: Sets the sequence matching preferences.
setSequenceMatchingPreferences(SequenceMatchingPreferences) - Method in class com.compomics.util.preferences.PTMScoringPreferences: Sets the sequence matching preferences to use when mapping PTMs on amino acid sequences.
setSequenceMatchingType(SequenceMatchingPreferences.MatchingType) - Method in class com.compomics.util.preferences.SequenceMatchingPreferences: Sets the sequence matching type.
setSerializationFolder(String) - Static method in class com.compomics.util.experiment.biology.PTMFactory: Sets the folder where the factory is saved.
setShortName(String) - Method in class com.compomics.util.experiment.biology.PTM: Sets the short PTM name.
setShowAllPeaks(boolean) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: 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.AnnotationSettings: 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.AnnotationSettings: Set if the automatic rewind ion de novo tags are to be shown.
setSingleChargeWindow(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets the window size for singly charged ions.
setSkylinePath(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets the skyline path.
setSortPsmsOnRt(Boolean) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: 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: This method allows to set the source for the file that is to be transferred.
setSparklineColor(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Setter for the sparkline color.
setSparklineColorDoubtful(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Setter for the doubtful sparkline color.
setSparklineColorFalsePositives(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Setter for the false positives sparkline color.
setSparklineColorNonValidated(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Setter for the non-validated sparkline color.
setSparklineColorPossible(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Setter for the possible sparkline color.
setSpecies(HashMap<String, Integer>) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: Sets the species targeted by this database.
setSpectrum(MSnSpectrum, 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.preferences.UtilitiesUserPreferences: Set the color to use for the annotated mirrored peaks.
setSpectrumAnnotatedPeakColor(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the color to use for the annotated peaks.
setSpectrumAnnotatedPeakWidth(float) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the width of the annotated peaks.
setSpectrumBackgroundPeakColor(Color) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the color to use for the background peaks.
setSpectrumBackgroundPeakWidth(float) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the width of the background peaks.
setSpectrumCharges(String) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the spectrum charges to search for.
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
setSpectrumNumber(Integer) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch: Sets the spectrum number in the spectrum file.
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.massspectrometry.Spectrum: Set the spectrum title.
setSqtOutput(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the sqt output is to be created.
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.experiment.identification.identification_parameters.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.experiment.identification.identification_parameters.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.
setSubscriptAnnotationNumbers(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel: Set if the numbers in the peak annotations are to be subscripted.
setSynchronizedIndexing(boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Sets whether the indexing of the sequence should be executed in a synchronized method.
setTag(Tag, int) - Method in class com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator: Sets a new tag to match.
setTagLength(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets the tag length.
setTarget(Integer) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Sets the index of the amino acid of interest in the pattern.
setTargetDecoyFileNameTag(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences: Set the target-decoy file name tag.
setTargeted(int, ArrayList<Character>) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern: Sets the amino acids targeted at a given index.
setTaxonomy(String) - Method in class com.compomics.util.protein.Header
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.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the text output is to be created.
setTheoreticalFragmentIonsSumOnly(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.Ion: Sets a new theoretic mass.
setTheoreticPeptide(Peptide) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch: Setter for the theoretic peptide.
setTheoreticPtm(String) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch: Sets the theoretic PTM.
setTicCutoffPercentage(double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Set the TIC cutoff in percent.
setTicCutoffPercentage(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Set the TicCutoffPercentage.
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.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the top peaks number.
setTopPeaksWindow(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters: Sets the top peaks window size.
setType() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters
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.preferences.DummyParameters
setType() - Method in class com.compomics.util.preferences.IdentificationParameters
setType() - Method in interface com.compomics.util.preferences.MarshallableParameter: Sets the parameters type.
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..
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.PathSettingsDialog: Sets up the GUI components.
setUpGui() - Method in class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Sets up the tool and populates the GUI.
setUpperClearMzRange(Double) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters: Set the upper mass value for the clear mz range.
setUpperPrecursorMass(int) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters: Set the upper precursor mass.
setUpTable() - Method in class com.compomics.util.gui.utils.user_choice.ListChooser: Updates the table content.
setUpTable() - Method in class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Sets up the design of the table.
setUseCache(boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Sets whether a cache should be used.
setUseChargeStateFromMS(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters: Sets whether the charge state from the spectrum should be used.
setUseCorrelationCorrectionScore(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters: Sets whether the correlation correction score should be used.
setUseFlankingPeaks(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if flanking peaks are to be used.
setUseGeneMapping(Boolean) - Method in class com.compomics.util.preferences.GenePreferences: 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.experiment.identification.identification_parameters.tool_specific.TideParameters: Set if the neutral loss peaks are to be used.
setUseNoiseSuppression(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Sets whether noise suppression should be used when importing spectra.
setUserAdvocates(HashMap<Integer, Advocate>) - Static method in class com.compomics.util.experiment.identification.Advocate: Returns the map of user advocates imported.
setUserPreferencesFolder(String) - Static method in class com.compomics.util.preferences.UtilitiesUserPreferences: Sets the user preferences file to be used.
setUseSmartPlusThreeModel(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters: Sets if the UseSmartPlusThreeModel is to be used.
setUseSparseMatrix(Boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.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.
setValidationQCPreferences(ValidationQCPreferences) - Method in class com.compomics.util.preferences.IdMatchValidationPreferences: 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
setVerbosity(Integer) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Set the verbosity type of progress output.
setVersion(String) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory: Sets the version.
setVersion(String) - Method in class com.compomics.util.experiment.identification.protein_sequences.FastaIndex: 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.
setWholeProtein(boolean) - Method in class com.compomics.util.experiment.biology.Enzyme: Set if the enzyme does not cleave at all, i.e., the whole protein is used.
setWorkbookStyle(WorkbookStyle) - Method in class com.compomics.util.io.export.writers.ExcelWriter: Sets the workbook style.
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.AnnotationSettings: 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.
ShotgunProtocol - Class in com.compomics.util.experiment: Generic class gathering information on a shotgun proteomics protocol.
ShotgunProtocol() - Constructor for class com.compomics.util.experiment.ShotgunProtocol
showAllPeaks() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: 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.AnnotationSettings: 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.AnnotationSettings: 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
sign - Variable in class com.compomics.util.experiment.massspectrometry.Charge: Sign of the charge according to the static fields.
signalStop() - Method in class com.compomics.util.io.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.
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
SINGLE_AA_SUFFIX - Static variable in class com.compomics.util.experiment.biology.PTMFactory: Suffix for the modification clone targeting a single amino acid instead of a pattern.
singleBaseSubstitution - Static variable in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Mutation matrix allowing for a single base mutation.
singleLetterCode - Variable in class com.compomics.util.experiment.biology.AminoAcid: Single letter code of the amino acid.
site(String) - Method in class com.compomics.util.io.FTP: Site Command
size() - Method in class com.compomics.util.experiment.biology.AtomChain: Returns the number of atoms in this atom chain.
skip(long) - Method in class com.compomics.util.io.MonitorableFileInputStream: Skips over and discards n bytes of data from the input stream.
skip(long) - Method in class com.compomics.util.io.MonitorableInputStream: Skips over and discards n bytes of data from the input stream.
Sodium - Class in com.compomics.util.experiment.biology.atoms: The sodium atom.
Sodium() - Constructor for class com.compomics.util.experiment.biology.atoms.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
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.
speciesOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for the species.
speciesTypeOption - Static variable in class com.compomics.software.ToolFactory: The command line argument for the species type.
SpecificAnnotationSettings - Class in com.compomics.util.experiment.identification.spectrum_annotation: The spectrum annotation preferences specific to a spectrum and an identification assumption.
SpecificAnnotationSettings(String, SpectrumIdentificationAssumption) - Constructor for class com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings: 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.
spectraST - Static variable in class com.compomics.util.experiment.identification.Advocate: The SpectraST spectral library search engine (TPP).
Spectrum - Class in com.compomics.util.experiment.massspectrometry: This class models a spectrum.
Spectrum() - Constructor for class com.compomics.util.experiment.massspectrometry.Spectrum
SPECTRUM_KEY_SPLITTER - Static variable in class com.compomics.util.experiment.massspectrometry.Spectrum: The splitter in the key between spectrumFile and spectrumTitle.
spectrumAnnotation - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: The spectrum annotation as a map: theoretic fragment key > ionmatch.
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
SpectrumCounting - Class in com.compomics.util.experiment.quantification.spectrumcounting: This class evaluates the spectrum counting indices for a protein.
SpectrumCounting() - Constructor for class com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCounting
SpectrumCounting.SpectrumCountingMethod - Enum in com.compomics.util.experiment.quantification.spectrumcounting: The implemented reporter ion quantification methods.
SpectrumFactory - Class in com.compomics.util.experiment.massspectrometry: This factory will provide the spectra when needed.
SpectrumFile - Interface in com.compomics.util.interfaces: This interface describes the behaviour for a spectrum file (ie., PKL file, Mascot Generic file, dat 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
spectrumIdentificationMap - Variable in class com.compomics.util.experiment.identification.Identification: List of all imported PSMs indexed by mgf file name.
spectrumLoaded(String, String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Returns a boolean indicating whether the spectrum is contained in the given spectrum file.
spectrumLoaded(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: A boolean indicating whether the spectrum is loaded in the factory.
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, SpectrumIdentificationAssumption) - Constructor for class com.compomics.util.experiment.identification.matches.SpectrumMatch: Constructor for the spectrum match.
SpectrumMatch(String) - Constructor for class com.compomics.util.experiment.identification.matches.SpectrumMatch: Constructor for the spectrum match.
SpectrumMatchingSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters: SpectrumMatchingSettingsDialog.
SpectrumMatchingSettingsDialog(Frame, String, SearchParameters, Image, Image, ConfigurationFile, LastSelectedFolder, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.SpectrumMatchingSettingsDialog: Creates a new SpectrumMatchingSettingsDialog with a frame as owner.
SpectrumMatchingSettingsDialog(Dialog, Frame, String, SearchParameters, Image, Image, ConfigurationFile, LastSelectedFolder, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.SpectrumMatchingSettingsDialog: Creates a new SpectrumMatchingSettingsDialog with a dialog as owner.
spectrumMatchLoaded(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Indicates whether a spectrum match is loaded.
spectrumMatchTableCreated(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Indicates whether the table for the given spectrum match key has been created.
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(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.
spectrumTitle - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum: Spectrum title.
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) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Splits an mgf file into smaller ones and returns the indexes of the generated files.
splitInput(String) - Static method in class com.compomics.software.CommandLineUtils: Splits the input of comma separated command line input and returns the results as an arraylist.
splitNode(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.proteintree.Node: Splits the node into subnode if its size is larger than the maxNodeSize and does the same for every sub node.
spo - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
SPO - Static variable in class com.compomics.util.io.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.AminoAcid: The standard genetic code.
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(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.
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, 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(InputStream) - Constructor for class com.compomics.util.io.StreamGobbler: Constructor.
strFileNameAndPath - Variable in class com.compomics.util.io.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(Frame, 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.AminoAcid: The sub amino acids.
subAminoAcidsWithoutCombination - Variable in class com.compomics.util.experiment.biology.AminoAcid: The sub amino acids.
subtractIsotope - Static variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: Minimal isotopic correction when matching an ion.
Sulfur - Class in com.compomics.util.experiment.biology.atoms: The sulfur atom.
Sulfur() - Constructor for class com.compomics.util.experiment.biology.atoms.Sulfur: Constructor.
sum(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions: Convenience method returning the sum of a list of doubles.
svg - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
SVG - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
SvgFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.svg files.
SvgFileFilter() - Constructor for class com.compomics.util.io.filefilters.SvgFileFilter
swap(int, int) - Method in class com.compomics.util.sun.TableSorter
swapRows(int, int) - Method in class com.compomics.util.experiment.biology.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
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.
synonymousMutation - Static variable in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Mutation matrix grouping synonymous amino acids.
syst() - Method in class com.compomics.util.io.FTP: Retrieve the system type from the remote server.

T

T - Static variable in class com.compomics.util.experiment.biology.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.
TABLE_NAME_MAX_LENGTH - Static variable in class com.compomics.util.db.ObjectsDB: The maximal length of a table name.
tableChanged(TableModelEvent) - Method in class com.compomics.util.sun.TableMap
tableChanged(TableModelEvent) - Method in class com.compomics.util.sun.TableSorter
tableContent(String) - Method in class com.compomics.util.db.ObjectsDB: Returns an arraylist with the content in the given table.
tableContentAsSet(String) - Method in class com.compomics.util.db.ObjectsDB: Returns a hashset with the content in the given table.
tableHeader - Static variable in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader: The standard format.
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
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, AminoAcidPattern, double) - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.Tag: Constructor for a tag consisting of a pattern tag between two mass tags.
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, Charge, double) - Constructor for class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption: Constructor.
TagComponent - Interface in com.compomics.util.experiment.identification.amino_acid_tags: Interface for a sequence tag component.
TagFactory - Class in com.compomics.util.experiment.identification: Convenience class for sequence tag generation.
TagFactory() - Constructor for class com.compomics.util.experiment.identification.TagFactory
TagFragmentIon - Class in com.compomics.util.experiment.biology.ions: A fragment ion obtained from a tag.
TagFragmentIon(int, int, int, double, ArrayList<NeutralLoss>, double) - Constructor for class com.compomics.util.experiment.biology.ions.TagFragmentIon: Constructor.
TagFragmentIon(int, ArrayList<NeutralLoss>) - Constructor for class com.compomics.util.experiment.biology.ions.TagFragmentIon: Constructor for a generic ion.
TagFragmentIon(int) - Constructor for class com.compomics.util.experiment.biology.ions.TagFragmentIon: Constructor for a generic ion without neutral losses.
TagMatcher - Class in com.compomics.util.experiment.identification.amino_acid_tags.matchers: This class matches tags to peptides.
TagMatcher(ArrayList<String>, ArrayList<String>, SequenceMatchingPreferences) - Constructor for class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Constructor.
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
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.
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
TaxonomyTreeDialog - Class in com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy: Taxonomy tree dialog.
TaxonomyTreeDialog(Frame, boolean) - Constructor for class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreeDialog: Creates a new TaxonomyTreeDialog.
TaxonomyTreePanel - Class in com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy: Taxonomy tree panel.
TaxonomyTreePanel() - Constructor for class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel: Constructor.
TEMP_FOLDER - Static variable in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Name of the folder containing temporary files.
TempFilesManager - Class in com.compomics.util.gui.filehandling: This class can be used to reference temp files and manage them.
TempFilesManager() - Constructor for class com.compomics.util.gui.filehandling.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.FTPClient: This method can be used to test the connection with the FTP server.
testPath(String) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Tests whether it is possible to write in a destination folder.
TEXTMODE - Static variable in class com.compomics.util.io.FolderMonitor
TextWriter - Class in com.compomics.util.io.export.writers: ExportWriter for the export to text files.
TextWriter(File, String, int) - 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.Ion: The theoretic mass.
thousand - Static variable in class com.compomics.util.math.BigMathUtils: Big decimal value of 1000.
threeLetterCode - Variable in class com.compomics.util.experiment.biology.AminoAcid: Three letter code of the amino acid.
Threonine - Class in com.compomics.util.experiment.biology.aminoacids: Threonine.
Threonine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Threonine: Constructor.
THREONINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a 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.identifications.idfilereaders: This IdfileReader reads identifications from an Tide tsv results file.
TideIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader: Default constructor for the purpose of instantiation.
TideIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader: Constructor for a Tide tsv results file reader.
TideIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader: Constructor for an Tide tsv result file reader.
TideParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: The Tide specific parameters.
TideParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters: Constructor.
TideSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for the Tide specific settings.
TideSettingsDialog(Frame, TideParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.TideSettingsDialog: Creates a new TideSettingsDialog with a frame as owner.
TideSettingsDialog(Dialog, Frame, TideParameters, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.TideSettingsDialog: Creates a new TideSettingsDialog with a dialog as owner.
tiff - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
TIFF - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
TiffFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.tiff files.
TiffFileFilter() - Constructor for class com.compomics.util.io.filefilters.TiffFileFilter
TIME_OUT - Static variable in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: The time out in milliseconds when querying the file.
timeOut - Static variable in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: The time out in milliseconds when querying the file.
TimestampRenderer - Class in com.compomics.util.gui.renderers: TimestampRenderer.
TimestampRenderer() - Constructor for class com.compomics.util.gui.renderers.TimestampRenderer
TITLED_BORDER_HORIZONTAL_PADDING - Static variable in class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: The horizontal padding used before and after the text in the titled borders.
TMT_126 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 126.
TMT_126_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 126 with ETD fragmentation.
TMT_127C - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 127C.
TMT_127C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 127C with ETD fragmentation.
TMT_127N - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 127N.
TMT_127N_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 127N with ETD fragmentation.
TMT_128C - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 128C.
TMT_128C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 128C with ETD fragmentation.
TMT_128N - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 128N.
TMT_128N_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 128N with ETD fragmentation.
TMT_129C - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 129C.
TMT_129C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 129C with ETD fragmentation.
TMT_129N - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 129N.
TMT_129N_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 129N with ETD fragmentation.
TMT_130C - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 130C.
TMT_130C_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 130C with ETD fragmentation.
TMT_130N - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 130N.
TMT_130N_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 130N with ETD fragmentation.
TMT_131 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 131.
TMT_131_ETD - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT 131 with ETD fragmentation.
TMT_226 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT (reporter + balancer).
TMT_230 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon: Standard reporter ion TMT (reporter + balancer).
toJson(Object) - Method in class com.compomics.util.io.json.JsonMarshaller: Convert an object to JSON.
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(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.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.AminoAcidPattern
toString() - Method in class com.compomics.util.experiment.biology.AminoAcidSequence
toString() - Method in class com.compomics.util.experiment.biology.AtomChain
toString() - Method in class com.compomics.util.experiment.biology.AtomImpl
toString() - Method in class com.compomics.util.experiment.biology.mutations.Mutation
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(boolean) - Method in interface com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter: Returns the parameters as a string.
toString() - Method in enum com.compomics.util.experiment.identification.identification_parameters.SearchParameters.MassAccuracyType
toString() - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.SearchParameters: Returns the search parameters as a string.
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters
toString(boolean) - Method in class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters
toString() - Method in enum com.compomics.util.experiment.identification.ptm.PtmScore
toString() - Method in class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
toString() - Method in class com.compomics.util.experiment.massspectrometry.Charge: Returns a string representing the charge.
toString() - Method in enum com.compomics.util.experiment.massspectrometry.proteowizard.MsFormat
toString() - Method in class com.compomics.util.experiment.units.UnitOfMeasurement
toString() - Method in class com.compomics.util.general.IsotopicElement: To string method
toString() - Method in interface com.compomics.util.interfaces.Modification: This method returns a String representation of the Modification.
toString() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
toString() - Method in enum com.compomics.util.preferences.SequenceMatchingPreferences.MatchingType
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.Header: This method reports on the entire processed(!) header.
toString(String) - Method in class com.compomics.util.protein.Header: This method reports on the entire processed(!) header, with the given decoy tag added.
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
transitionsSingleBaseSubstitution - Static variable in class com.compomics.util.experiment.biology.mutations.MutationMatrix: Mutation matrix allowing for a single base transitions mutation.
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.mutations.MutationMatrix: Mutation matrix allowing for a single base transversion mutation.
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: Tryptophan.
Tryptophan() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Tryptophan: Constructor.
TRYPTOPHAN - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a 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.filefilters.FileFilterUtils
TXT - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
type - Variable in class com.compomics.util.experiment.biology.Ion: Type of ion.
Tyrosine - Class in com.compomics.util.experiment.biology.aminoacids: Tyrosine.
Tyrosine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Tyrosine: Constructor.
TYROSINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a tyrosine immonium ion.

U

U - Static variable in class com.compomics.util.experiment.biology.AminoAcid
UNDERIVATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.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.
UNIPROT_FOLDER - Static variable in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Name of the folder containing UniProt files.
UNIPROT_TAXONOMY_FILENAME - Static variable in class com.compomics.util.experiment.biology.taxonomy.SpeciesFactory: The name of the UniProt taxonomy file.
UniProtQuery - Class in com.compomics.util.protein_sequences_manager: A UniProt query.
UniProtQuery(int, SequenceContentType) - Constructor for class com.compomics.util.protein_sequences_manager.UniProtQuery: Constructor.
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.
UniprotTaxonomyProvider - Class in com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy: UniProt taxonomy provider.
UniprotTaxonomyProvider(DefaultTreeModel) - Constructor for class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: GUI constructor.
UniprotTaxonomyProvider() - Constructor for class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.UniprotTaxonomyProvider: Normal constructor, GUI-less mode.
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(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.
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.
unknownPTM - Static variable in class com.compomics.util.experiment.biology.PTMFactory: Unknown modification to be returned when the modification is not found.
unmatchedIons - Variable in class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator: List of unmatched ions.
unreadLine() - Method in class com.compomics.util.io.PushBackStringReader: This method 'unreads' a line of text from the Buffer.
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(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.
updateAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>) - Method in class com.compomics.util.experiment.identification.Identification: Updates the assumptions of a spectrum.
updateAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates the map of assumptions for a given spectrum.
updateAtomComposition() - Method in class com.compomics.util.gui.atoms.AtomChainDialog: Updates the atom composition panel.
updateCache() - Method in class com.compomics.util.db.ObjectsCache: Updates the cache according to the memory settings.
updateEnsemblVersion(String, String) - Method in class com.compomics.util.experiment.biology.genes.GeneFactory: Update the Ensembl version for the given species in the local map and in the Ensembl versions file.
updateGUI() - Method in class com.compomics.util.gui.parameters.IdentificationParametersEditionDialog: Populates the GUI using the given identification parameters.
updateGUI() - Method in class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Updates the gui after the adding of new database(s).
updateIdentificationParameters(IdentificationParameters, IdentificationParameters) - Method in class com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory: Replaces old parameters by new.
updateIdentificationParameters() - Method in class com.compomics.util.experiment.identification.parameters_cli.IdentificationParametersInputBean: Updates the identification parameters according to the command line.
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.
updateMatch(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates a match.
updateModifications() - Method in class com.compomics.util.gui.ptm.ModificationsDialog: Updates the modification lists and tables.
updateObject(String, String, String, Object) - Method in class com.compomics.util.db.ObjectsCache: Sets that a match has been modified and returns true in case of success.
updateObject(String, String, Object) - Method in class com.compomics.util.db.ObjectsDB: Updates an object in the cache or in the tables if not in cache.
updateObject(String, String, Object, boolean) - Method in class com.compomics.util.db.ObjectsDB: Updates an object in the cache or in the tables if not in cache or if cache is wrong.
updateParameters(IdentificationParameters) - Method in class com.compomics.util.gui.parameters.identification_parameters.IdentificationParametersNameDialog: Updates the given identification parameters attributes.
updatePeptideMatch(PeptideMatch) - Method in class com.compomics.util.experiment.identification.Identification: Updates a peptide match in the database.
updatePeptideMatch(String, String, PeptideMatch) - Method in class com.compomics.util.experiment.identification.Identification: Updates a peptide match where the key was changed.
updatePeptideMatch(PeptideMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates a peptide match.
updatePeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Updates a peptide match parameter in the database.
updatePeptideParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates a peptide match parameter.
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.
updateProteinMatch(ProteinMatch) - Method in class com.compomics.util.experiment.identification.Identification: Updates a protein match in the database.
updateProteinMatch(ProteinMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates a protein match.
updateProteinMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Updates a protein match parameter in the database.
updateProteinParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates a protein match parameter.
updatePtmSelection() - Method in class com.compomics.util.gui.ptm.ModificationsDialog: Updates the PTM selection in the default table.
updateRawAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>) - Method in class com.compomics.util.experiment.identification.Identification: Updates the raw assumptions of a spectrum.
updateRawAssumptions(String, HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates the map of raw assumptions for a given spectrum.
updateSpectrumMatch(SpectrumMatch) - Method in class com.compomics.util.experiment.identification.Identification: Updates a spectrum match in the database.
updateSpectrumMatch(SpectrumMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates a spectrum match.
updateSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification: Updates a spectrum match parameter in the database.
updateSpectrumParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB: Updates a spectrum match parameter.
updateTable() - Method in class com.compomics.util.gui.parameters.IdentificationParametersOverviewDialog: Updates the parameters table.
updateTable() - Method in class com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog: Deprecated.

Updates the parameters table.
updateTable() - Method in class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI: Updates the 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 will be used to reference refined parameters.
useBoldFont() - Method in class com.compomics.util.gui.spectrum.ReferenceArea: Returns true of the label should be in bold.
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.FolderMonitor
USER_FOLDER - Static variable in class com.compomics.util.protein_sequences_manager.ProteinSequencesManager: Name of the folder containing user FASTA files.
usersModsSorted - Variable in class com.compomics.util.experiment.biology.PTMFactory: 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
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
UtilitiesPathPreferences - Class in com.compomics.software.settings: This class sets the path preferences for the files to read/write.
UtilitiesPathPreferences() - Constructor for class com.compomics.software.settings.UtilitiesPathPreferences
UtilitiesPathPreferences.UtilitiesPathKey - Enum in com.compomics.software.settings: Enum of the paths which can be set in utilities.
UtilitiesUserPreferences - Class in com.compomics.util.preferences: Utilities user preferences will be serialized in the user folder and provide useful information to all compomics software, well as soon as they use it of course.
UtilitiesUserPreferences() - Constructor for class com.compomics.util.preferences.UtilitiesUserPreferences: Constructor.

V

V - Static variable in class com.compomics.util.experiment.biology.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.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.AndromedaSettingsDialog: Inspects the parameter validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.CometSettingsDialog: Inspects the parameter validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsAmandaSettingsDialog: Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsgfSettingsDialog: Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MyriMatchSettingsDialog: Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.OmssaSettingsDialog: Inspects the parameters validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.TideSettingsDialog: Inspects the parameter validity.
validateInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog: Inspects the parameters validity.
validateInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.IdentificationParametersNameDialog: Validates the user input.
validateInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.PTMLocalizationParametersDialog: Validates the user input.
validateInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.SequenceMatchingSettingsDialog: Validates the user input.
validateInput() - Method in class com.compomics.util.gui.parameters.identification_parameters.ValidationSettingsDialog: Validates the user input.
validateInput() - Method in class com.compomics.util.gui.parameters.IdentificationParametersEditionDialog: Validates the user input.
validateInput() - Method in class com.compomics.util.gui.parameters.ProcessingPreferencesDialog: 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, SequenceMatchingPreferences, SequenceMatchingPreferences, PtmSettings) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Validates the modifications of a peptide.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog: Inspects the parameters validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog: Inspects the parameters validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog: Inspects the parameters validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog: Inspects the parameters validity.
validateParametersInput(boolean) - Method in class com.compomics.util.gui.parameters.IdentificationParametersEditionDialog: Inspects the search parameter validity.
validatePeptide(Peptide, SequenceMatchingPreferences, Enzyme) - 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, SpectrumFactory, SearchParameters) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Validates the mass deviation of a peptide assumption.
validateProteins(Peptide, SequenceMatchingPreferences) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Validates a peptide depending on its protein inference status.
validateProteins(Peptide, SequenceMatchingPreferences, ProteinTree) - Method in class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter: Validates a peptide depending on its protein inference status.
validateSegments(ArrayList<SequenceSegment>, ArrayList<SequenceSegment>, double, double, String, char, boolean) - Method in class com.compomics.util.experiment.identification.amino_acid_tags.matchers.TagMatcher: Removes the segments which cannot match the mass gap from the possible sequences and transfers the valid segments to the valid sequences.
ValidationQCPreferences - Class in com.compomics.util.preferences: This class lists the criteria used for quality control of the validated matches.
ValidationQCPreferences() - Constructor for class com.compomics.util.preferences.ValidationQCPreferences: Creates a validation quality control preferences object with default settings.
ValidationQCPreferences(ValidationQCPreferences) - Constructor for class com.compomics.util.preferences.ValidationQCPreferences: Creates a validation quality control preferences object based on an other ValidationQCPreferences.
ValidationQCPreferencesDialog - Class in com.compomics.util.gui.parameters.identification_parameters: Dialog for the edition of validation QC filters.
ValidationQCPreferencesDialog(Frame, ValidationQCPreferencesDialogParent, ValidationQCPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialog: Creates a new ValidationQCPreferencesDialog with a frame as owner.
ValidationQCPreferencesDialog(Dialog, Frame, ValidationQCPreferencesDialogParent, ValidationQCPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialog: Creates a new ValidationQCPreferencesDialog with a dialog as owner.
ValidationQCPreferencesDialogParent - Interface in com.compomics.util.gui.parameters.identification_parameters: Interface allowing the editing of filters from other packages.
ValidationSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters: Dialog for the edition of the sequence matching settings
ValidationSettingsDialog(Frame, IdMatchValidationPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.ValidationSettingsDialog: Creates a new ValidationSettingsDialog with a frame as owner.
ValidationSettingsDialog(Dialog, Frame, IdMatchValidationPreferences, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.ValidationSettingsDialog: Creates a new ValidationSettingsDialog with a dialog as owner.
Valine - Class in com.compomics.util.experiment.biology.aminoacids: Valine.
Valine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Valine: Constructor.
VALINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon: Subtype int for a valine immonium ion.
value - Variable in class com.compomics.util.experiment.massspectrometry.Charge: Value of the charge.
valueOf(String) - Static method in enum com.compomics.software.settings.UtilitiesPathPreferences.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.Ion.IonType: 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.identification_parameters.SearchParameters.MassAccuracyType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters.CometOutputFormat: 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.parameters_cli.IdentificationParametersCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.psm_scoring.PsmScores: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.identification.ptm.PtmScore: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.massspectrometry.FragmentationMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.massspectrometry.proteowizard.MsFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.experiment.massspectrometry.proteowizard.ProteoWizardFilter: 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.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.parameters.IdentificationParametersSelectionDialog.StartupMode: Deprecated.

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.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.preferences.MarshallableParameter.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.preferences.ProcessingPreferences.ProcessingType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.preferences.SearchGuiOutputOption: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.preferences.SequenceMatchingPreferences.MatchingType: 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.
valueOf(String) - Static method in enum com.compomics.util.protein.Header.DatabaseType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.protein_sequences_manager.enums.ModelOrganism: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.protein_sequences_manager.enums.SequenceContentType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.protein_sequences_manager.enums.SequenceInputType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.QueryType: Returns the enum constant of this type with the specified name.
values() - Static method in enum com.compomics.software.settings.UtilitiesPathPreferences.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.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.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.identification_parameters.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.experiment.identification.identification_parameters.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.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.parameters_cli.IdentificationParametersCLIParams: 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.PsmScores: 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.ptm.PtmScore: 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.massspectrometry.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.massspectrometry.proteowizard.MsFormat: 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.massspectrometry.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.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.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.parameters.IdentificationParametersSelectionDialog.StartupMode: Deprecated.

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.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.preferences.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.preferences.ProcessingPreferences.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.preferences.SearchGuiOutputOption: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.preferences.SequenceMatchingPreferences.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.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.
values() - Static method in enum com.compomics.util.protein.Header.DatabaseType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.protein_sequences_manager.enums.ModelOrganism: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.protein_sequences_manager.enums.SequenceContentType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.protein_sequences_manager.enums.SequenceInputType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.QueryType: Returns an array containing the constants of this enum type, in the order they are declared.
VARCHAR_MAX_LENGTH - Static variable in class com.compomics.util.db.ObjectsDB: The maximal length of a varchar.
VennDiagram - Class in com.compomics.util.math: Class for calculating the groups for Venn diagrams.
VennDiagram() - Constructor for class com.compomics.util.math.VennDiagram
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 - Static variable in class com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree: The version of the protein tree.
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.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(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(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
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
warning(SAXParseException) - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler: Receive notification of a warning.
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: Welcome message from the server, if any.
WorkbookStyle - Interface in com.compomics.util.io.export: This interface sets the style of a workbook export.
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(JsonWriter, Object) - Method in class com.compomics.util.io.json.adapter.FileAdapter
writeAplFile(File, File, String) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader: Writes an apl file from an MGF file.
writeConfigurationToFile(File) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Writes all path configurations to the given file.
writeConfigurationToFile(BufferedWriter) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Writes the configuration file using the provided buffered writer.
writeHeader(BufferedWriter) - Static method in class com.compomics.util.experiment.io.massspectrometry.export.Ms2Exporter: Writes the header of the file.
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
writeIndex(FastaIndex, File) - Static method in class com.compomics.util.experiment.identification.protein_sequences.SequenceFactory: Serializes the FASTA file index in a given directory.
writeIndex(MgfIndex, File) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory: Writes the given mgf file index in the given directory.
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
writeMgf(BufferedWriter) - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Writes the spectrum in the mgf format using the given writer.
writeMgf(BufferedWriter, HashMap<String, String>) - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum: Writes the spectrum in the mgf format using the given writer.
writeMsAmandaEnzymeFile(File) - Method in class com.compomics.util.experiment.biology.EnzymeFactory: Creates the MS Amanda enzyme settings file corresponding to the enzymes loaded in the factory to the given file.
writeObject(Object, File) - Static method in class com.compomics.util.io.SerializationUtils: Writes an object to the destination file.
writePathToFile(BufferedWriter, UtilitiesPathPreferences.UtilitiesPathKey) - Static method in class com.compomics.software.settings.UtilitiesPathPreferences: Writes the path of interest using the provided buffered writer.
writeSpectrum(BufferedWriter, MSnSpectrum, FragmentationMethod, int) - Static method in class com.compomics.util.experiment.io.massspectrometry.export.AplExporter: Writes the given spectrum in ms2 format.
writeSpectrum(BufferedWriter, MSnSpectrum, Integer) - Static method in class com.compomics.util.experiment.io.massspectrometry.export.Ms2Exporter: 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.AminoAcid
X - Class in com.compomics.util.experiment.biology.aminoacids: Unknown amino acid (Mascot).
X() - Constructor for class com.compomics.util.experiment.biology.aminoacids.X: Constructor.
X_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Identifier for an x ion.
X_ION - Static variable in class com.compomics.util.experiment.biology.ions.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.
xml - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
XML - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
XmlFileFilter - Class in com.compomics.util.io.filefilters: File filter for *.xml files.
XmlFileFilter() - Constructor for class com.compomics.util.io.filefilters.XmlFileFilter
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.
XtandemParameters - Class in com.compomics.util.experiment.identification.identification_parameters.tool_specific: The X!Tandem specific parameters.
XtandemParameters() - Constructor for class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters: Constructor.
XTandemSettingsDialog - Class in com.compomics.util.gui.parameters.identification_parameters.algorithm_settings: Dialog for the X!Tandem specific settings.
XTandemSettingsDialog(Frame, XtandemParameters, PtmSettings, double, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog: Creates new form XtandemParametersDialog with a frame as owner.
XTandemSettingsDialog(Dialog, Frame, XtandemParameters, PtmSettings, double, boolean) - Constructor for class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog: 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(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.AminoAcid
Y_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Identifier for a y ion.
Y_ION - Static variable in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Identifier for a y ion.
yAxisZoomExcludesBackgroundPeaks() - Method in class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings: 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.AminoAcid
Z - Class in com.compomics.util.experiment.biology.aminoacids: Glu or Gln: Glx (Mascot).
Z() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Z: Constructor.
Z_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon: Identifier for a z ion.
Z_ION - Static variable in class com.compomics.util.experiment.biology.ions.TagFragmentIon: Identifier for a z ion.
zCore - Static variable in class com.compomics.util.experiment.identification.Advocate: The ZCore search engine, ETD search engine.
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

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