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$$$getRootComponent$$$() - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
 

A

A - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
A_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Identifier for an a ion.
A_SCORE_ROW_INDEX - Static variable in class com.compomics.util.gui.protein.ModificationProfile
The a score row index.
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.
abort() - Method in class com.compomics.util.io.FTP
Send Abort command.
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
 
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 chromatogram 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.
addAll(PtmtableContent) - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
Add all.
addAnalysisSet(Sample, SampleAnalysisSet) - Method in class com.compomics.util.experiment.MsExperiment
Method to link an analysis set to an experiment
addAutomaticDeNovoSequencing(Peptide, ArrayList<IonMatch>, int, int, int, 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
 
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.
addDefaultNeutralLoss(NeutralLoss) - Method in class com.compomics.util.experiment.biology.IonFactory
Adds a default neutral loss to the default neutral losses if the corresponding loss was not here already.
addElement(MolecularElement, Integer) - Method in class com.compomics.util.protein.MolecularFormula
Method to add MolecularElements to this formula
addEnzyme(Enzyme) - Method in class com.compomics.util.experiment.biology.EnzymeFactory
Adds an enzyme in the factory.
addFilter(SpectrumFilter) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.And
Adds a filter to the and Filters will be tested iteratively so put the fast/discriminative first.
addFilter(SpectrumFilter) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.Or
Adds a filter to the or Filters will be tested iteratively so put the fast/discriminative first.
addFixedModification(PTM) - Method in class com.compomics.util.preferences.ModificationProfile
Adds a fixed modification.
addFolderContent(ArchiveOutputStream, File, WaitingHandler) - Static method in class com.compomics.util.io.TarUtils
Add content to the tar file.
addFragmentIonTypeMarkers(HashMap<String, ArrayList<XYZDataPoint>>, JFreeChart, boolean) - Static method in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Adds interval markers for all the fragment ion types.
addHit(int, PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Add a first hit.
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.
addIonMatch(int, IonMatch) - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
Method to add a match between a peak and a reporter ion
addIonType(Ion.IonType, int) - Method in class com.compomics.util.preferences.AnnotationPreferences
Adds a new ion type and subtype to annotate.
addIonType(Ion.IonType) - Method in class com.compomics.util.preferences.AnnotationPreferences
Adds a new ion type to annotate.
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.Glycon
Add a mass for this glycon.
addMatch(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Adds an identification match to the database.
addMatch(QuantificationMatch) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Adds an quantification match to the database.
addMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
Deprecated.
use the database match specific methods instead
addMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Deprecated.
use match specific mapping instead
addModification(Modification) - Method in class com.compomics.util.protein.AASequenceImpl
This method adds a modification to the list of modifications.
addModificationMatch(ModificationMatch) - Method in class com.compomics.util.experiment.biology.Peptide
Adds a modification match.
addMolecularFormula(MolecularFormula) - Method in class com.compomics.util.protein.MolecularFormula
Method to add whole formulas to this formula
addMouseListenerToHeaderInTable(JTable) - Method in class com.compomics.util.sun.TableSorter
 
addNeutralLoss(NeutralLoss) - Method in class com.compomics.util.experiment.biology.PTM
Adds a neutral loss.
addNeutralLoss(NeutralLoss, int, int) - Method in class com.compomics.util.experiment.identification.NeutralLossesMap
Adds a new neutral loss to the map.
addNeutralLoss(NeutralLoss) - Method in class com.compomics.util.preferences.AnnotationPreferences
Adds a neutral loss.
addObject(String, String, String, Object, boolean) - Method in class com.compomics.util.db.ObjectsCache
Adds an object to the cache.
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
addPeptideMatch(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Add a subordinated peptide match.
addPeptideMatch(PeptideQuantification) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Adds a peptide match to the database.
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.
addPeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Adds a peptide match parameter to the database.
addPeptideQuantification(String) - Method in class com.compomics.util.experiment.quantification.matches.ProteinQuantification
Adds a new peptide quantification in the protein quantification
addPeptideQuantification(PeptideQuantification) - Method in class com.compomics.util.experiment.quantification.Quantification
Add a peptide quantification match to the peptide quantification matches map if not already implemented.
addProteinMatch(ProteinMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Adds a protein match to the database.
addProteinMatch(ProteinQuantification) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
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.
addProteinMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Adds a protein match parameter to the database.
addProteinQuantification(ProteinQuantification) - Method in class com.compomics.util.experiment.quantification.Quantification
Add a protein quantification match to the peptide quantification matches map if not already implemented.
addProtocol(Protocol) - Method in class com.compomics.util.pride.PrideObjectsFactory
Adds a protocol in the PRIDE objects.
addPsmQuantification(String) - Method in class com.compomics.util.experiment.quantification.matches.PeptideQuantification
Adds a new psm quantification in the psm quantification map
addPsmQuantification(PsmQuantification) - Method in class com.compomics.util.experiment.quantification.Quantification
Add a spectrum quantification to the spectrum quantification matches map and overwrites if already implemented.
addQuantificationResults(Quantification.QuantificationMethod, Quantification) - Method in class com.compomics.util.experiment.ProteomicAnalysis
adds quantification results to the current analysis
addRatio(Integer, Ratio) - Method in class com.compomics.util.experiment.quantification.QuantificationMatch
Adds a new ratio to the ratio map.
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.
addRefinementModification(PTM) - Method in class com.compomics.util.preferences.ModificationProfile
Adds a refinement modification.
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.
addSelectedCharge(int) - Method in class com.compomics.util.preferences.AnnotationPreferences
Add a charge to take into account when annotating the spectrum.
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(Set<SpectrumMatch>) - Method in class com.compomics.util.experiment.identification.Identification
Add a set of spectrumMatches to the model.
addSpectrumMatch(SpectrumMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Adds a spectrum match to the database.
addSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Add a spectrum match.
addSpectrumMatch(PsmQuantification) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Adds a spectrum match to the database.
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.
addSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
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.
addUrParam(UrParameter) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Method to add a user refinement parameter.
addUserPTM(PTM) - Method in class com.compomics.util.experiment.biology.PTMFactory
Adds a new user modification.
addVariableModification(PTM) - Method in class com.compomics.util.preferences.ModificationProfile
Adds a variable modification.
addXYZDataSeries(HashMap<String, ArrayList<XYZDataPoint>>) - Static method in class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Adds the provided data series to an XYZ data set.
Advocate - Interface in com.compomics.util.experiment.identification
The advocate of a hit can be a search engine, a re-scoring algorithm, etc.
AdvocateFactory - Class in com.compomics.util.experiment.identification
This factory will provide adapted advocates when required.
Alanine - Class in com.compomics.util.experiment.biology.aminoacids
Alanine
Alanine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Alanine
 
ALANINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
Subtype int for an alanine immonium ion.
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 serie 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
Created by IntelliJ IDEA.
AlignmentBlock(int, int, int, int, String, String) - Constructor for class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
 
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
 
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 an empty pattern.
AminoAcidPattern(String) - Constructor for class com.compomics.util.experiment.biology.AminoAcidPattern
Constructor taking a sequence of targeted amino acids as input.
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.
And - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters
filter consisting of several filters.
And() - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.And
Constructor.
ANDROMEDA - Static variable in interface com.compomics.util.experiment.identification.Advocate
Andromeda index.
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
 
AndromedaIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
Constructor for an Andromeda result file reader.
AndromedaIdfileReader(File, WaitingHandler) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
Constructor for an Andromeda result file reader.
annotate(SpectrumAnnotation, Graphics, HashMap<String, Integer>) - 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 - Static 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.
AnnotationPreferences - Class in com.compomics.util.preferences
This class contains the spectrum annotation preferences.
AnnotationPreferences() - Constructor for class com.compomics.util.preferences.AnnotationPreferences
Constructor.
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.
appendDecoySequences(File) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Appends decoy sequences to the desired file.
appendDecoySequences(File, WaitingHandler) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Appends decoy sequences to the desired file while displaying progress.
appendReport(String, boolean, boolean) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Append text to the report.
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
 
appendReportEndLine() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Append a new line 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
 
appendReportNewLineNoDate() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Append two tabs 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 two tabs to the report.
appendReportNewLineNoDate() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
AQUA - Static variable in class com.compomics.util.AlternateRowColoursJTable
A rather pronounced AQUA colour (r=183, g=222, b=232).
areNeutralLossesSequenceDependant() - Method in class com.compomics.util.preferences.AnnotationPreferences
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
 
ARGININE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
Subtype int for an arginine immonium ion.
ascii() - Method in class com.compomics.util.io.FTP
Set transfer type to 'A' (ascii transfer).
aScoreCalculation() - Method in class com.compomics.util.preferences.PTMScoringPreferences
Returns a boolean indicating whether the A-score should be calculated.
asMgf() - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum
Returns the peak list as mgf bloc.
Asparagine - Class in com.compomics.util.experiment.biology.aminoacids
Asparagine
Asparagine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Asparagine
 
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
 
assignSample(int, Sample) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Assign a sample to an ion referenced by its static index.
Atom - Class in com.compomics.util.experiment.biology
This interface contains information about atoms
Atom() - Constructor for class com.compomics.util.experiment.biology.Atom
 
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.

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
 
B_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Identifier for a b ion.
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.
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.
BugReport - Class in com.compomics.util.gui.error_handlers
A simple bug report dialog.
BugReport(JFrame, String, String, String, String, File) - Constructor for class com.compomics.util.gui.error_handlers.BugReport
Creates a new BugReport dialog.
BugReport(JDialog, String, String, String, String, File) - Constructor for class com.compomics.util.gui.error_handlers.BugReport
Creates a new BugReport dialog.
buildPeptidesAndProteinQuantifications(Identification, WaitingHandler) - Method in class com.compomics.util.experiment.quantification.Quantification
Creates the peptides and protein quantification instances based on the identification and the psm quantification.
buildPeptidesAndProteins(WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Creates the peptides and protein instances based on the spectrum matches.
buildPeptidesAndProteins(String) - Method in class com.compomics.util.experiment.identification.Identification
Creates the peptides and protein instances based on the given spectrum match.
ByteArrayRenderer - Class in com.compomics.util.gui.renderers
This class
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
 
C_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
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.
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.general.ExceptionHandler
Method called whenever an exception is caught.
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.
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.
CHARGE_ESTIMATION - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
chargeValidated(Ion, int, int) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns a boolean indicating whether the given charge can be found on the given fragment ion.
checkFixedModifications(ModificationProfile, Peptide) - 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.
checkForNewVersion(String, String, String) - Static method in class com.compomics.software.CompomicsWrapper
Check if a newer version of the tool is available on GoogleCode, and closes the tool if the user decided to upgrade.
checkForNewVersion(String, String, String, boolean, String) - Static method in class com.compomics.software.CompomicsWrapper
Check if a newer version of the tool is available on GoogleCode.
checkModel() - Method in class com.compomics.util.sun.TableSorter
 
ChromatogramPanel - Class in com.compomics.util.gui.spectrum
This class provides a JPanel that can display a chromatogram.
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.
clearCharges() - Method in class com.compomics.util.preferences.AnnotationPreferences
Clears the selected charges.
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.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.
clearIonTypes() - Method in class com.compomics.util.preferences.AnnotationPreferences
Clears the ion types annotated.
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.NeutralLossesMap
Clears the mapping.
clearNeutralLosses() - Method in class com.compomics.util.preferences.AnnotationPreferences
Clears the considered neutral losses.
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.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 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.PepNovoIdfileReader
 
close() - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Closes the db connection.
close() - Method in class com.compomics.util.general.FileLoggerImplementation
This method closes the stream to the output file.
closeFile() - Method in class com.compomics.util.experiment.identification.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.
color2Hex(Color) - Static method in class com.compomics.util.Util
Converts a color to hex format for use in HTML tags.
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
 
com.compomics.software.dialogs - package com.compomics.software.dialogs
 
com.compomics.util - package com.compomics.util
This package contains general util classes.
com.compomics.util.db - package com.compomics.util.db
This package contains database related classes.
com.compomics.util.db.components - package com.compomics.util.db.components
This package contains database related components.
com.compomics.util.db.interfaces - package com.compomics.util.db.interfaces
This package contains database related interfaces.
com.compomics.util.denovo - package com.compomics.util.denovo
 
com.compomics.util.enumeration - package com.compomics.util.enumeration
This package contains enumeration used by utilties.
com.compomics.util.examples - package com.compomics.util.examples
This package contains examples of how the utilities library can can be used by other projects.
com.compomics.util.experiment - package com.compomics.util.experiment
This package contains MSExperiment main class and all sub-classes useful for the modeling of an experiment.
com.compomics.util.experiment.biology - package com.compomics.util.experiment.biology
This package contains experiement classes related to biological entities.
com.compomics.util.experiment.biology.aminoacids - package com.compomics.util.experiment.biology.aminoacids
 
com.compomics.util.experiment.biology.atoms - package com.compomics.util.experiment.biology.atoms
 
com.compomics.util.experiment.biology.ions - package com.compomics.util.experiment.biology.ions
This package contains experiment classes related to ions.
com.compomics.util.experiment.filters.massspectrometry - package com.compomics.util.experiment.filters.massspectrometry
 
com.compomics.util.experiment.filters.massspectrometry.spectrumfilters - package com.compomics.util.experiment.filters.massspectrometry.spectrumfilters
 
com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation - package com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation
 
com.compomics.util.experiment.identification - package com.compomics.util.experiment.identification
This package contains experiment classes related to identifications.
com.compomics.util.experiment.identification.advocates - package com.compomics.util.experiment.identification.advocates
This package contains experiment classes related to modeling identifications.
com.compomics.util.experiment.identification.identifications - package com.compomics.util.experiment.identification.identifications
This package contains experiment classes related to MS/MS identifications.
com.compomics.util.experiment.identification.matches - package com.compomics.util.experiment.identification.matches
This package contains experiment classes releated to matches.
com.compomics.util.experiment.identification.protein_inference - package com.compomics.util.experiment.identification.protein_inference
 
com.compomics.util.experiment.identification.ptm - package com.compomics.util.experiment.identification.ptm
 
com.compomics.util.experiment.identification.scoring - package com.compomics.util.experiment.identification.scoring
 
com.compomics.util.experiment.io - package com.compomics.util.experiment.io
 
com.compomics.util.experiment.io.identifications - package com.compomics.util.experiment.io.identifications
 
com.compomics.util.experiment.io.identifications.idfilereaders - package com.compomics.util.experiment.io.identifications.idfilereaders
This package contains experiment classes related to reading search engine files.
com.compomics.util.experiment.io.massspectrometry - package com.compomics.util.experiment.io.massspectrometry
 
com.compomics.util.experiment.massspectrometry - package com.compomics.util.experiment.massspectrometry
This package contains experiment classes related to spectra.
com.compomics.util.experiment.personalization - package com.compomics.util.experiment.personalization
This package contains experiment customization classes.
com.compomics.util.experiment.quantification - package com.compomics.util.experiment.quantification
This package contains experiment classes related to quantification.
com.compomics.util.experiment.quantification.matches - package com.compomics.util.experiment.quantification.matches
 
com.compomics.util.experiment.quantification.reporterion - package com.compomics.util.experiment.quantification.reporterion
This package contains experiment classes related to reporter ions.
com.compomics.util.experiment.quantification.spectrumcounting - package com.compomics.util.experiment.quantification.spectrumcounting
 
com.compomics.util.experiment.refinementparameters - package com.compomics.util.experiment.refinementparameters
This package contains experiment classes related to specific parametrization of experiment objects.
com.compomics.util.general - package com.compomics.util.general
The classes in this package focus mainly on very 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
This package holds the servlet representation of the classes from the general utilities package (com.compomics.util.general)
com.compomics.util.gui - package com.compomics.util.gui
This package contains basic GUI classes.
com.compomics.util.gui.error_handlers - package com.compomics.util.gui.error_handlers
 
com.compomics.util.gui.events - package com.compomics.util.gui.events
This package contains GUI event classes.
com.compomics.util.gui.export_graphics - package com.compomics.util.gui.export_graphics
 
com.compomics.util.gui.filehandling - package com.compomics.util.gui.filehandling
 
com.compomics.util.gui.interfaces - package com.compomics.util.gui.interfaces
This package contains GUI related interfaces.
com.compomics.util.gui.isotopic_calculator - package com.compomics.util.gui.isotopic_calculator
This package contains the GUI class for the Isotopic Distribution calculator.
com.compomics.util.gui.protein - package com.compomics.util.gui.protein
This package contains the GUI class related to protein sequence formatting.
com.compomics.util.gui.ptm - package com.compomics.util.gui.ptm
 
com.compomics.util.gui.renderers - package com.compomics.util.gui.renderers
This package contains GUI renderer classes.
com.compomics.util.gui.spectrum - package com.compomics.util.gui.spectrum
This package contains GUI classes related to Spectrum and Chromatogram visualization.
com.compomics.util.gui.utils - package com.compomics.util.gui.utils
 
com.compomics.util.gui.waiting - package com.compomics.util.gui.waiting
 
com.compomics.util.gui.waiting.waitinghandlers - package com.compomics.util.gui.waiting.waitinghandlers
 
com.compomics.util.interfaces - package com.compomics.util.interfaces
This package defines interfaces for the more specific implementations in the util package.
com.compomics.util.io - package com.compomics.util.io
This package contains classes related to input/output.
com.compomics.util.io.filefilters - package com.compomics.util.io.filefilters
This package contains classes related to file filters.
com.compomics.util.junit - package com.compomics.util.junit
 
com.compomics.util.math - package com.compomics.util.math
 
com.compomics.util.messages - package com.compomics.util.messages
 
com.compomics.util.nucleotide - package com.compomics.util.nucleotide
The classes in this package concern useful Objects and their operations for modelling and handling nucleotides.
com.compomics.util.pdbfinder - package com.compomics.util.pdbfinder
The classes in this package concern support for mapping between UniProt accession numbers and PDB structures.
com.compomics.util.pdbfinder.das.readers - package com.compomics.util.pdbfinder.das.readers
The classes in this package concern support for aligning and annotating PDB files when mapped to UniProt accession numbers.
com.compomics.util.pdbfinder.pdb - package com.compomics.util.pdbfinder.pdb
The classes in this package are related to paring the PDB files.
com.compomics.util.preferences - package com.compomics.util.preferences
 
com.compomics.util.preferences.gui - package com.compomics.util.preferences.gui
 
com.compomics.util.pride - package com.compomics.util.pride
 
com.compomics.util.pride.prideobjects - package com.compomics.util.pride.prideobjects
 
com.compomics.util.pride.validation - package com.compomics.util.pride.validation
 
com.compomics.util.protein - package com.compomics.util.protein
The classes in this package concern useful Objects and their operations for modelling and handling proteins.
com.compomics.util.sun - package com.compomics.util.sun
This package contains classes related to Java's Swing library.
CombDialog - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation
This dialog allows the creation of an MzFilter.
CombDialog(JFrame, Double, Double, Boolean) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.CombDialog
Constructor.
CombFilter - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters
This filter looks for a specific m/z comb in the spectrum.
CombFilter(ArrayList<Double>, double, boolean, double) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.CombFilter
Constructor.
command - Variable in class com.compomics.util.io.FTP
The last command issued.
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
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(int, int) - Method in class com.compomics.util.sun.TableSorter
 
compareRowsByColumn(int, int, int) - Method in class com.compomics.util.sun.TableSorter
 
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.
compatibilityCheck() - Method in class com.compomics.util.preferences.ModificationProfile
Checks the compatibility with older versions of the class and makes the necessary changes.
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.SequenceFactory
Returns the protein's molecular weight.
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.SequenceFactory
Indicates whether the database loaded contains decoy sequences.
Connectable - Interface in com.compomics.util.interfaces
This interface describes the behaviour for classes that can accept an incoming DB connection.
ConnectionDialog - Class in com.compomics.util.gui.utils
This class implements a dialog to gather all information concerning a DB connection.
ConnectionDialog(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.
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, 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.preferences.ModificationProfile
Indicates whether the modification is contained in the profile, looking into all modifications (fixed, variable and refinement)
contains(String) - Method in class com.compomics.util.protein.AASequenceImpl
This method reports whether a certain residu (or fixed sequence String) is found in the current sequence.
containsForbiddenCharacter(String) - Static method in class com.compomics.util.Util
Indicates whether a string contains characters forbidden in file names.
containsLoss(NeutralLoss) - Method in class com.compomics.util.experiment.identification.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.
convert(WaitingHandler, String, String, ObjectsCache, File) - Method in class com.compomics.util.experiment.identification.Identification
Converts a serialization based structure into a database based one.
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 one file to another.
CorrectionFactor - Class in com.compomics.util.experiment.quantification.reporterion
This class models the isotope correction factors given by the labels constructor.
CorrectionFactor(int, double, double, double, double) - Constructor for class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
Constructor for the correction factor
correctPrecursorMass(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets whether the precursor mass shall be corrected (TagDB setting).
correctTableName(String) - Method in class com.compomics.util.db.ObjectsDB
Surrounds the table name with quotation marks such that spaces etc are allowed.
createDefaultTableHeader() - Method in class com.compomics.util.gui.spectrum.FragmentIonTable
 
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.MutationFactory
This method creates all possible mutations for the 20 essential amino acids.
CTERM - Static variable in class com.compomics.util.protein.Enzyme
 
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
 
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
Created by IntelliJ IDEA.
DasAlignment(String) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasAlignment
 
DasAnnotationServerAlingmentReader - Class in com.compomics.util.pdbfinder.das.readers
Created by IntelliJ IDEA.
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
Created by IntelliJ IDEA.
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
Created by IntelliJ IDEA.
DasFeature(String) - Constructor for class com.compomics.util.pdbfinder.das.readers.DasFeature
 
dat - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
DAT - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
DATABASE_FILE - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead Reference for the database file
dataSetCounter - Static variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The number of 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.
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 - Variable in class com.compomics.util.experiment.quantification.QuantificationDB
The name which will be used for the database.
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.
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.
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.
DefaultSpectrumAnnotation - Class in com.compomics.util.gui.spectrum
This class provideds 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.
delete(Connection) - Method in interface com.compomics.util.db.interfaces.Deleteable
This method will physically delete the implemented object's data from the persistent store.
delete(String) - Method in class com.compomics.util.io.FTP
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.
deleteDir(File) - Static method in class com.compomics.util.Util
Deletes all files and subdirectories under dir.
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.
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.
DELTA_SCORE_ROW_INDEX - Static variable in class com.compomics.util.gui.protein.ModificationProfile
The delta score row index.
deltaMassWindow - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The size of the window to use when searcing for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
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.Glycon
Final index for deuteroacetylated masses.
DEUTEROMETHYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.Glycon
Final index for deuteromethylated masses.
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.
displayHtmlMessage(JEditorPane, String, int) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Display a given HTML containing message to the user separately from the main output.
displayHtmlMessage(JEditorPane, String, int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
displayHtmlMessage(JEditorPane, String, int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
displayHtmlMessage(JEditorPane, String, int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
displayMessage(String, String, int) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Display a given message to the user separately from the main output.
displayMessage(String, String, int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
displayMessage(String, String, int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
displayMessage(String, String, int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
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.
doNothingOnClose() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Deprecated.
replace by setUnstoppable
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.
DOTS - Static variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Drawstyle which draws a dot at the measurement height.
DOUBLE_PRECISION - Static variable in class com.compomics.util.BinaryArrayImpl
Defines the valid String indicating the correct precision for encoded doubles.
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.
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) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method draws a line, measuring the distance between two points in real mass units.
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) - 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.

E

E - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
ElementaryElement - Class in com.compomics.util.experiment.biology
This class can be used to retrieve elementary elements like a proton.
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.SequenceFactory
Empties the cache of the factory.
emptyCache() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Empties the cache.
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 - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead Reference for the 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.
enzymeCleaves() - Method in class com.compomics.util.experiment.biology.Enzyme
Returns a boolean indicating whether a cleavage site was implemented for this enzyme.
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.
equals(Object) - Method in class com.compomics.util.BinaryArrayImpl
Performs equals methods dependent on values of instance variables and class of Object o.
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.Mutation
Overwritten equals method.
equals(SearchParameters) - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns true of the search parameter objects have identical settings.
equals(Object) - Method in class com.compomics.util.experiment.massspectrometry.Charge
 
equals(ModificationProfile) - Method in class com.compomics.util.preferences.ModificationProfile
Returns true of the two profiles are identical.
equals(Object) - Method in class com.compomics.util.protein.ModificationImplementation
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class com.compomics.util.protein.ModificationTemplate
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class com.compomics.util.protein.Protein
This method will check equality between this object and another Protein instance.
error(SAXParseException) - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Receive notification of a recoverable error.
establishConnection(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.
establishConnection(String, String, boolean, ObjectsCache) - Method in class com.compomics.util.experiment.quantification.Quantification
Establishes connection to the database.
establishConnection(String, boolean, ObjectsCache) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Establishes connection to the database.
estimateAScore(boolean) - Method in class com.compomics.util.preferences.ProcessingPreferences
Deprecated.
use the PTM scoring preferences instead
estimateDensityFunction(Double[]) - Method in class com.compomics.util.gui.XYPlottingDialog.NormalKernelDensityEstimator
 
estimateDensityFunction(double[]) - Method in class com.compomics.util.gui.XYPlottingDialog.NormalKernelDensityEstimator
 
estimateTheoreticMass() - Method in class com.compomics.util.experiment.biology.Peptide
Estimates the theoretic mass of the peptide.
EVALUE_CUTOFF - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
ExceptionHandler - Class in com.compomics.util.general
Handles exception for a given application.
ExceptionHandler(JFrame) - Constructor for class com.compomics.util.general.ExceptionHandler
Constructor.
ExceptionHandler() - Constructor for class com.compomics.util.general.ExceptionHandler
Constructor without GUI
excludeNullValues(Double[]) - Method in class com.compomics.util.gui.XYPlottingDialog.NormalKernelDensityEstimator
Exclude null values from an array of Double.
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
 
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.
ExportGraphicsDialog - Class in com.compomics.util.gui.export_graphics
Simple dialog for selecting the image type to export a graphics element to.
ExportGraphicsDialog(JFrame, ExportGraphicsDialogParent, boolean, Component) - Constructor for class com.compomics.util.gui.export_graphics.ExportGraphicsDialog
Create and open a new ExportGraphicsDialog.
ExportGraphicsDialog(JFrame, ExportGraphicsDialogParent, boolean, ChartPanel) - Constructor for class com.compomics.util.gui.export_graphics.ExportGraphicsDialog
Create and open a new ExportPlot dialog.
ExportGraphicsDialog(JDialog, ExportGraphicsDialogParent, boolean, Component) - Constructor for class com.compomics.util.gui.export_graphics.ExportGraphicsDialog
Create and open a new ExportGraphicsDialog.
ExportGraphicsDialog(JDialog, ExportGraphicsDialogParent, boolean, ChartPanel) - Constructor for class com.compomics.util.gui.export_graphics.ExportGraphicsDialog
Create and open a new ExportPlot dialog.
ExportGraphicsDialogParent - Interface in com.compomics.util.gui.export_graphics
A simple interface that classes wanting to use the ExportGraphicsDialog have to implement.
extension - Static variable in class com.compomics.util.pride.PrideObjectsFactory
The extension to use when saving objects.
EXTENTION - Static variable in class com.compomics.util.experiment.identification.Identification
Deprecated.
use the database methods instead

F

F - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
factorial(int) - Static method in class com.compomics.util.math.BasicMathFunctions
returns n!
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
This class contains the index of a FASTA file.
FastaIndex(HashMap<String, Long>, String, boolean, int) - Constructor for class com.compomics.util.experiment.identification.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.
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.
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 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.
filterAnnotations(Vector<DefaultSpectrumAnnotation>, 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
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) - Constructor for class com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
 
FingerprintDialog - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation
This dialog allows the creation of an MzFilter.
FingerprintDialog(JFrame, Double, Double, Boolean) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.FingerprintDialog
Constructor.
FingerprintPattern - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters
Filters according to an m/z - intensity fingerprint.
FingerprintPattern(ArrayList<Double>, ArrayList<Double>, double, boolean, double) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.FingerprintPattern
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.
FIXED_MODIFICATIONS - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
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
This class
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.
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.
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.
FRAGMENT_ION_MASS_ACCURACY - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
FRAGMENT_ION_TYPE_1 - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
FRAGMENT_ION_TYPE_2 - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
FragmentIonTable - Class in com.compomics.util.gui.spectrum
Creates a fragment ion table with the detected fragment ions.
FragmentIonTable(Peptide, ArrayList<ArrayList<IonMatch>>, ArrayList<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>, ArrayList<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.
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.
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.
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
 
generateQuery() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns a boolean indicating whether a blast query shall be generated.
GeneratorException - Exception in com.compomics.util.db
This class wraps all exception that can occur while generating code.
GeneratorException(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.
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.SequenceFactory
Returns the occurrence of every amino acid in the database.
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.
getAbsoluteError(boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the absolute matching error in Da.
getAbsoluteError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the absolute matching error in Da without isotope removal.
getAccession() - Method in class com.compomics.util.experiment.biology.Protein
Getter for the protein accession.
getAccession() - Method in class com.compomics.util.pride.CvTerm
 
getAccession() - Method in class com.compomics.util.protein.Header
 
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.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.NeutralLossesMap
Returns an arraylist of implemented neutral losses.
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.
getAdvocate(int) - Method in class com.compomics.util.experiment.identification.AdvocateFactory
Returns an advocate of the specified index
getAdvocate(String) - Method in class com.compomics.util.experiment.identification.AdvocateFactory
returns the index of an advocate base on its name
getAdvocate() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Get the used advocate.
getAdvocates() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns all advocates used referenced by their index.
getAlignmentBlocks() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
 
getAllAlignments() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader
Get all alingment 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 search engines 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
getAllModifications() - Method in class com.compomics.util.preferences.ModificationProfile
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.preferences.ModificationProfile
Returns a list of all searched modifications but the fixed ones.
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) - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader
This methods 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) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader
 
getAllSpectrumMatches(WaitingHandler) - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
 
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.
getAminoAcidBefore() - Method in class com.compomics.util.experiment.biology.Enzyme
Getter for the amino acids potentially preceding the cleavage.
getAminoAcids() - Static method in class com.compomics.util.experiment.biology.AminoAcid
Convenience method returning an arrayList of all implemented amino-acids.
getAminoAcidsAtTarget() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Returns the targeted amino acids at position "target".
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.preferences.AnnotationPreferences
Returns the intensity limit.
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.
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, HashMap<Ion.IonType, ArrayList<Integer>>, ArrayList<Integer>, int, double) - Static method in class com.compomics.util.experiment.identification.ptm.PTMLocationScores
Returns the A-score for the best PTM location without accounting for neutral losses.
getAScore(Peptide, ArrayList<PTM>, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double) - Static method in class com.compomics.util.experiment.identification.ptm.PTMLocationScores
Returns the A-score for the best PTM location accounting for neutral losses.
getAScore(Peptide, ArrayList<PTM>, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, boolean) - Static method in class com.compomics.util.experiment.identification.ptm.PTMLocationScores
Returns the A-score for the best PTM location.
getAScorePeptideScore(Peptide, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, boolean) - Static method in class com.compomics.util.experiment.identification.scoring.PsmScores
Returns a PSM score like the peptide score calculated for the A-score.
getAsStringPattern() - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Returns the amino acid pattern as case insensitive pattern for String matching.
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.preferences.ModificationProfile
Returns the names of the backed-up PTMs.
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.
getBestAssumption() - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Getter for the best assumption.
getBinary(String) - Method in class com.compomics.util.io.FTP
GET a file from the FTP server in Binary mode.
getBlock() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
getBlocks() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
getBlockSequence(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
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.
getBStart(NeutralLoss) - Method in class com.compomics.util.experiment.identification.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).
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.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.
getChoice() - Method in class com.compomics.util.gui.SampleSelection
Getter for the users choice.
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
 
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 interface com.compomics.util.gui.interfaces.SpectrumAnnotation
This method returns the color for the annotation.
getColor() - Method in class com.compomics.util.gui.protein.ModificationProfile
Returns the PTM color.
getColor() - Method in class com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation
This method returns the color for the annotation.
getColor(String) - Method in class com.compomics.util.preferences.ModificationProfile
Returns the color used to code the given modification.
getColummnNames() - Method in class com.compomics.util.gui.XYPlottingDialog
Return the column names.
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.
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
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.
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.
getContentPane() - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
This methods gives a JPanel holding everything from this frame
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.
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:
getCorrectionFactors() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns the correction factors corresponding to the reporter ions.
getcTermGap() - Method in class com.compomics.util.denovo.PeptideAssumptionDetails
Returns the C-term Gap.
getCTerminal() - Method in class com.compomics.util.experiment.biology.Peptide
Returns the C-terminal of the peptide as a String.
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.
getCurrentAnnotation(HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the currently matched ions with the given settings.
getCurrentlyLoadedPeptide() - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the currently inspected peptide.
getCurrentlyLoadedSpectrumKey() - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the spectrum currently inspected.
getCurrentPrecursorCharge() - Method in class com.compomics.util.preferences.AnnotationPreferences
Returns the current precursor charge.
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.
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
 
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.
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).
getDecodedByteArray() - Method in class com.compomics.util.BinaryArrayImpl
Returns the contents of the binary array decoded using the Base64 algorithm.
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
Returns the default cvTerm of a modification when it exists.
getDefaultExportFolder() - Method in interface com.compomics.util.gui.export_graphics.ExportGraphicsDialogParent
Returns the default folder used for the export.
getDefaultExportFolder() - Method in class com.compomics.util.gui.XYPlottingDialog
 
getDefaultInstruments() - Static method in class com.compomics.util.pride.prideobjects.Instrument
Returns a list of predefined instruments.
getDefaultLosses(Peptide) - Static method in class com.compomics.util.experiment.identification.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.
getDefaultNeutralLosses() - Method in class com.compomics.util.experiment.biology.IonFactory
Returns the default neutral losses.
getDefaultOMSSAIndex(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns the default OMSSA index of the modification.
getDefaultProtocols() - Static method in class com.compomics.util.pride.prideobjects.Protocol
Returns a list of default protocols.
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.
getDefaultShortName(String) - Static method in class com.compomics.util.experiment.biology.PTMFactory
Returns a default short name for a given modification.
getDeisotopedIntensities() - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
returns the deisotoped intensities
getDeltaMass(double, boolean, boolean) - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Returns the precursor mass error (in ppm or Da).
getDeltaMass(double, boolean) - Method in class com.compomics.util.experiment.identification.PeptideAssumption
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.preferences.AnnotationPreferences
Returns the charge to use for the fragment ions in the de novo sequencing.
getDescription() - Method in class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter
Returns a description of the validated spectra, typically "containing a peak at m/z 114".
getDescription() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.And
 
getDescription() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.CombFilter
 
getDescription() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.FingerprintPattern
 
getDescription() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
 
getDescription() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.Or
 
getDescription() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.PeakFilter
 
getDescription() - Method in class com.compomics.util.io.filefilters.DatFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.DtaFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.FastaFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.JpegFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.MgfFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.Ms2FileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.MzDataFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.MzMlFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.MzXmlFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.OmxFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.OutFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.PdfFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.PeffFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.PepXmlFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.PklFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.PklSpoFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.PkxFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.PngFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.ProtXmlFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.SequestParamsFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.SvgFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.TiffFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.filefilters.XmlFileFilter
The description of this filter
getDescription() - Method in class com.compomics.util.io.FilenameExtensionFilter
 
getDescription() - Method in class com.compomics.util.protein.Header
 
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.
getDifference() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
 
getDifference() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
getDiscardLowQualitySpectra() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns a boolean indicating whether low quality spectra shall be discarded.
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).
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.
getElementaryFilters() - Static method in class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter
Convenience method returning the types of implemented elementary filters.
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
 
getEnd_block() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
getEnd_protein() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
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
 
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.SearchParameters
Returns the enzyme used for digestion.
getEnzyme(String) - Method in class com.compomics.util.io.MascotEnzymeReader
This method will return a copy of an Enzyme instance for the given name, or 'null' if the enzyme was not found in the current list.
getEnzymeNames() - Method in class com.compomics.util.io.MascotEnzymeReader
This method reports on all the known names for enzymes in this reader.
getEnzymes() - Method in class com.compomics.util.experiment.biology.EnzymeFactory
Get the imported enzymes.
getError(double) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Get the absolute matching error in Da.
getError(double) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.PeakFilter
Get the absolute matching error in Da.
getError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Deprecated.
replaced by getAbsoluteError() and getRelativeError()
getError(boolean, boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the error.
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.
getEValue() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Deprecated.
use getScore instead
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.
getExcludedAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Returns the excluded amino acids at a given index in the pattern.
getExpectedIons(HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, Peptide) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the expected ions in a map indexed by the possible charges.
getExpectedPTMs(ModificationProfile, Peptide, double, double) - 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(ModificationProfile, Peptide, String) - 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.das.readers.DasAlignment
 
getExperiment_type() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
getExtension() - Method in enum com.compomics.util.enumeration.ImageType
Returns the extension.
getExtension() - Method in interface com.compomics.util.experiment.io.identifications.IdfileReader
This method should return 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.PepNovoIdfileReader
 
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.denovo.PeptideAssumptionDetails
 
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.MascotScore
This method returns the family name of the parameter
getFastaFile() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the sequence database file used for identification.
getFeatureId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getFeatureLabel() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
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.experiment.identification.PeptideAssumption
Returns the file.
getFileName() - Method in class com.compomics.util.experiment.identification.FastaIndex
Returns the file name of the inspected FASTA file.
getFileName(String) - Method in class com.compomics.util.experiment.identification.Identification
Deprecated.
use the database methods instead
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, WaitingHandler) - 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.
getFilter(JFrame, Double, Double, Double, Boolean) - Static method in class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter
Allows the user to design basic filters via a GUI.
getFilter() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.CombDialog
Returns the filter created.
getFilter() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.FingerprintDialog
Returns the filter created.
getFilter() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.MzDialog
Returns the filter created.
getFilter() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.PeakDialog
Returns the filter created.
getFirstHit(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns the first hit obtained using the specified advocate.
getFixedModifications() - Method in class com.compomics.util.preferences.ModificationProfile
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.
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
 
getForwardIons() - Static method in class com.compomics.util.experiment.identification.SearchParameters
Returns the list of forward ions.
getFractionMolecularWeightRanges() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the user provided molecular weight ranges for the fractions.
getFractionMolecularWeights() - Method in class com.compomics.util.experiment.identification.SearchParameters
Deprecated.
use getFractionMolecularWeightRanges instead
getFragmentationModel() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the name of the fragmentation model.
getFragmentIonAccuracy() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the MS2 ion m/z tolerance.
getFragmentIonAccuracy() - Method in class com.compomics.util.preferences.AnnotationPreferences
Returns the fragment ion accuracy.
getFragmentIons(Peptide) - Method in class com.compomics.util.experiment.biology.IonFactory
This method returns the theoretic ions expected from a peptide.
getFragmentIonTypes() - Method in class com.compomics.util.preferences.AnnotationPreferences
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).
getGeneName() - Method in class com.compomics.util.protein.Header
 
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.
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.
getHeader(String) - Method in class com.compomics.util.experiment.identification.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
 
getHeader() - Method in class com.compomics.util.protein.Protein
This method reports on the header for the current protein.
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.
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.SearchParameters
Returns the length of the hit list for OMSSA.
getHomeFolder() - Static method in class com.compomics.util.io.FileSystemAccessor
Returns the user home folder.
getId() - Method in class com.compomics.util.experiment.biology.Enzyme
Get the enzyme id.
getId() - Method in interface com.compomics.util.experiment.identification.Advocate
Getter for the index of the advocate.
getId() - Method in class com.compomics.util.experiment.identification.advocates.PostProcessor
getter for the post-processor's index
getId() - Method in class com.compomics.util.experiment.identification.advocates.SearchEngine
Getter for the search engine index.
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
getIdentificationCharge() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Returns the charge used for identification.
getIdentificationParameters(File) - Static method in class com.compomics.util.experiment.identification.SearchParameters
Loads the identification parameters from a serialized file.
getIdentifier() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns the reference identifier.
getIdFilter() - Method in interface com.compomics.util.preferences.gui.ImportSettingsDialogParent
Returns the identification filter used.
getImplementedIonTypes() - Static method in class com.compomics.util.experiment.biology.Ion
Returns the implemented ion types.
getIndex() - Method in class com.compomics.util.denovo.PeptideAssumptionDetails
 
getIndex() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
Returns the index of a reporter ion.
getIndex(String) - Method in class com.compomics.util.experiment.identification.FastaIndex
Returns the index of the accession of interest.
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.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.MascotScore
This method returns the index of the parameter
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) - 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.FastaIndex
Returns a map of all indexes of the FASTA file (accession -> index).
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.
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.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.identification.AdvocateFactory
A static method to retrieve the factory instance
getInstance() - Static method in class com.compomics.util.experiment.identification.SequenceFactory
Static method returning the instance of the factory.
getInstance(int) - Static method in class com.compomics.util.experiment.identification.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.
getInstruments() - Method in class com.compomics.util.pride.PrideObjectsFactory
Returns the instruments.
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.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.
getIntensityLimit(double) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
Returns the intensity limit.
getIntensityPrideCvTerm() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Returns the pride CV term for the ion match intensity.
getIntensityQuantile() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Returns the intensity quantile to look into.
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.
getIonAtRow(int) - Method in class com.compomics.util.gui.spectrum.IonLabelColorTableModel
Returns the ion type at the given row.
getIonId() - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
returns the reporter ion id
getIonMassErrorPrideCvTerm() - 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.SearchParameters
Getter for the list of ion symbols used.
getIonSearched1() - Method in class com.compomics.util.experiment.identification.SearchParameters
Getter for the first kind of ion searched.
getIonSearched2() - Method in class com.compomics.util.experiment.identification.SearchParameters
Getter for the second kind of ion searched.
getIonTypes() - Method in class com.compomics.util.preferences.AnnotationPreferences
Returns the type of ions annotated.
getIsotopeNumber() - 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) - Method in class com.compomics.util.experiment.identification.PeptideAssumption
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
getJarFilePath(String, String) - Static method in class com.compomics.software.CompomicsWrapper
Returns the path to the jar file.
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.
getKey() - Method in class com.compomics.util.experiment.biology.Peptide
Returns the index 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() - Method in class com.compomics.util.experiment.quantification.matches.PeptideQuantification
 
getKey() - Method in class com.compomics.util.experiment.quantification.matches.ProteinQuantification
 
getKey() - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
 
getKey() - Method in class com.compomics.util.experiment.quantification.QuantificationMatch
Returns the key of a match.
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.
getLastSelectedFolder() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Returns the last selected folder.
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.
getLevel() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
Returns at which level the spectrum was recorded.
getLink() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getLinkHref() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
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
 
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.
getLossesMass(ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.biology.IonFactory
Convenience summing the masses of various neutral losses.
getMainMatch() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns the main match accession after protein inference.
getMainMatchKey() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Returns the key of the main match.
getMap() - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
Get the map.
getMascotMaxEvalue() - Method in class com.compomics.util.preferences.IdFilter
Returns the maximal Mascot e-value allowed.
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.Glycon
Get the glycon mass.
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 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.
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.
getMassShift() - Method in class com.compomics.util.experiment.biology.Mutation
Returns the mass shift.
getMassShift() - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the m/z shift applied to the fragment ions.
getMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
Deprecated.
use the database match specific methods instead
getMatchPArameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Deprecated.
use match specific mapping instead
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.
getMaxChargeSearched() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the maximal charge searched.
getMaxEValue() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the maximal e-value searched for.
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.
getMaximumValue() - Method in class com.compomics.util.gui.waiting.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.
getMaxMass() - Method in class com.compomics.util.gui.events.RescalingEvent
Returns the maximum mass.
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.preferences.IdFilter
Returns the maximal m/z deviation allowed.
getMaxPadding() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the max padding (distance between the axes and the border of the panel).
getMaxPepLength() - Method in class com.compomics.util.preferences.IdFilter
Returns the maximal peptide length allowed.
getMaxPeptideLength() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the maximal peptide length allowed.
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 RT for the desired file.
getMaxRT() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Returns the maximum RT for the whole project.
getMaxXAxisValue() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method reports on the largest x-axis value in the point collection accross all datasets.
getMeasureSample() - Method in class com.compomics.util.experiment.quantification.Ratio
returns the measured label indexed by its corresponding reporter ion index
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.
getMemoryPreference() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Returns the preferred upper memory limit.
getMemoryShare() - Method in class com.compomics.util.db.ObjectsCache
Returns the share of heap size which can be used before emptying the cache.
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.
getMethod() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getMethodId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
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.
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
getMgfFileName() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader
Returns the spectrum file name.
getMgfFileNames() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Returns a list of loaded mgf files.
getMinChargeSearched() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the minimal charge searched.
getMinimalChargeForMultipleChargedFragments() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.
getMinimumValue() - Method in class com.compomics.util.gui.waiting.ProgressDialog
Returns the current minimum value for the progressbar.
getMinMass() - Method in class com.compomics.util.gui.events.RescalingEvent
Returns the minimum mass.
getMinMz() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
Returns the min mz value.
getMinPepLength() - Method in class com.compomics.util.preferences.IdFilter
Returns the maximal peptide length allowed.
getMinPeptideLength() - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the minimal peptide length allowed.
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 RT for the desired file.
getMinRT() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Returns the minimum RT for the whole project.
getMinus1() - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
returns the reporter ion -1 Da amount
getMinus2() - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
returns the reporter ion -2 Da amount
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
 
getModification(int) - Method in class com.compomics.util.preferences.ModificationProfile
Returns the name of the modification indexed by the given OMSSA index.
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, String) - 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 names of the variable modifications found in the key of a peptide.
getModificationMatches() - Method in class com.compomics.util.experiment.biology.Peptide
Getter for the modifications carried by this peptide.
getModificationProfile() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the modification profile of the project.
getModifications() - Method in class com.compomics.util.protein.AASequenceImpl
Simple getter for the modifications.
getModificationSite() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Getter for the modification site, 1 is the first amino acid.
getModifiedIndexes() - Method in class com.compomics.util.experiment.biology.Peptide
Returns the indexes of the residues in the peptide that contain at least one modification.
getModifiedPeptideQuantification(String) - Method in class com.compomics.util.experiment.quantification.Quantification
This method retrieves the quantification result at the modified peptides level
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
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.
getMutation(Mutation) - Static method in class com.compomics.util.experiment.biology.MutationFactory
Returns the requested mutation by lookup in the mutation map.
getMutationsAsString() - Static method in class com.compomics.util.experiment.biology.MutationFactory
Returns the mutation as a string.
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.
getMzArray() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Returns the mzArray.
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.
getMzTolerance() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Returns the m/z tolerance to search with.
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.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.Glycon
 
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.ReporterIon
This method returns the name of the reporter ion.
getName() - Method in class com.compomics.util.experiment.biology.PTM
Getter for the modification name.
getName() - Method in class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter
Returns the name of the filter.
getName() - Method in interface com.compomics.util.experiment.identification.Advocate
Getter for the name of the Advocate.
getName() - Method in class com.compomics.util.experiment.identification.advocates.PostProcessor
getter for the name of the post-processor
getName(int) - Static method in class com.compomics.util.experiment.identification.advocates.SearchEngine
Getter for the search engine name.
getName() - Method in class com.compomics.util.experiment.identification.advocates.SearchEngine
Getter for the search engine name.
getName() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns the name of the method.
getName() - Method in class com.compomics.util.pride.CvTerm
 
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.
getnCache() - Method in class com.compomics.util.experiment.identification.SequenceFactory
Returns the size of the cache.
getNestedException() - Method in exception com.compomics.util.db.GeneratorException
This method returns the nested exception for this exception, or 'null' if none is present.
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.Ion
Returns the possible neutral losses of this ion type.
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.ElementaryIon
 
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.Glycon
 
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.ReporterIon
 
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.preferences.AnnotationPreferences
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.
getNextFeature() - Method in class com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
Get the next feature in the xml string.
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.SearchParameters
Returns the allowed number of missed cleavages.
getNModificationLocalized(String, String) - 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.
getNote() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getNPossiblePeptides(Enzyme) - Method in class com.compomics.util.experiment.biology.Protein
Returns the number of possible peptides (not accounting PTMs nor missed cleavages) with the selected enzyme.
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.
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.FastaIndex
Returns the number of target sequences in the database.
getNTargetSequences() - Method in class com.compomics.util.experiment.identification.SequenceFactory
Returns the number of target sequences in the database.
getnTermGap() - Method in class com.compomics.util.denovo.PeptideAssumptionDetails
Returns the N-term Gap.
getNTerminal() - Method in class com.compomics.util.experiment.biology.Peptide
Returns the N-terminal of the peptide as a String.
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.
getNumber() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Returns the number of the fragment in the sequence.
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.
getObject(String, String, String) - Method in class com.compomics.util.db.ObjectsCache
Returns the objects if present in the cache.
getObjectsCache() - Method in class com.compomics.util.db.ObjectsDB
Returns the cache used by this database.
getObservableLength(Enzyme, int) - Method in class com.compomics.util.experiment.biology.Protein
Returns the number of observable amino acids of the sequence.
getOccurrence() - Method in class com.compomics.util.general.IsotopicElement
Getter for the occurrence of this element
getOlsAccessionLink(String) - Method in class com.compomics.util.gui.ptm.ModificationsDialog
Returns the protein accession number as a web link to the given PSI-MOD at http://www.ebi.ac.uk/ontology-lookup.
getOmssaIndex(String) - Method in class com.compomics.util.preferences.ModificationProfile
Returns the OMSSA index of a given modification, null if not found.
getOMSSAIndexes(File) - Static method in class com.compomics.util.experiment.biology.PTMFactory
Imports the OMSSA indexes from an XML file.
getOmssaMaxEvalue() - Method in class com.compomics.util.preferences.IdFilter
Returns the OMSSA maximal e-value allowed.
getOmssaUserModBloc(String, int) - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns an MSModSpec bloc as present in the OMSSA user modification files for a given PTM.
getOntology() - Method in class com.compomics.util.pride.CvTerm
 
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.
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
 
getOrigin() - Method in class com.compomics.util.experiment.biology.Mutation
Returns the origin amino acid.
getPackageName() - Method in enum com.compomics.util.enumeration.CompomicsTools
Return the package name of the tool.
getParameterKey(UrParameter) - Static method in class com.compomics.util.experiment.personalization.ExperimentObject
Returns the key of a personalization parameter.
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.
getParametersFile() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the parameters file loaded.
getParameterTable(UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Deprecated.
use match specific mapping instead
getParentProteins() - Method in class com.compomics.util.experiment.biology.Peptide
Getter for the parent proteins.
getPathOfClass(String) - Static method in class com.compomics.util.io.FileSystemAccessor
Returns the absolute path of the underlying file system of the given class.
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
 
getPdbAccession() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
 
getPdbaccession() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
getPdbEnd() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
 
getPdbGroup() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
 
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
 
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 peak 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.
getPepNovoScore() - Method in class com.compomics.util.denovo.PeptideAssumptionDetails
Returns the pep novo score.
getPeptide() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Get the theoretic peptide.
getPeptideCount() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns the number of peptides found.
getPeptideFDR() - Method in class com.compomics.util.preferences.ProcessingPreferences
Returns the initial peptide FDR.
getPeptideIdentification() - Method in class com.compomics.util.experiment.identification.Identification
Returns a list of the keys of all encountered peptides.
getPeptideMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
Returns a peptide match.
getPeptideMatch(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the desired peptide match.
getPeptideMatch(String) - Method in class com.compomics.util.experiment.quantification.Quantification
Returns a peptide quantification match.
getPeptideMatch(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the desired peptide match.
getPeptideMatches() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Getter for the peptide matches.
getPeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
Returns the desired peptide match parameter.
getPeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the desired peptide match parameter.
getPeptideMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the desired peptide match parameter.
getPeptideParameterTable(UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the table name associated with the given peptide parameter.
getPeptideParameterTable(UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the table name associated to the given peptide parameter.
getPeptideQuantification() - Method in class com.compomics.util.experiment.quantification.matches.ProteinQuantification
Getter for the corresponding peptide quantification
getPeptideQuantification() - Method in class com.compomics.util.experiment.quantification.Quantification
This method retrieves the quantification result at the peptide level
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.
getPeptideShakerPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Returns the path to the PeptideShaker installation.
getPeptideStart(String) - Method in class com.compomics.util.experiment.biology.Protein
Returns the list of indexes where a peptide can be found in the protein sequence.
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
 
getPlus1() - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
returns the reporter ion +1 Da amount
getPlus2() - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
returns the reporter ion +2 Da amount
getPmid() - Method in class com.compomics.util.pride.prideobjects.Reference
Returns the PubMed ID of the reference.
getPosition() - Method in class com.compomics.util.protein.Enzyme
Simple getter for the cleavage position of the Enzyme.
getPossibilities() - Method in class com.compomics.util.experiment.identification.AdvocateFactory
returns all implemented advocates
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.Glycon
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.ReporterIon
Returns an arraylist of possible subtypes.
getPotentialModificationSites(PTM) - Method in class com.compomics.util.experiment.biology.Peptide
Returns the potential modification sites as an ordered list of string.
getPotentialModificationSites(String, PTM) - Static method in class com.compomics.util.experiment.biology.Peptide
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.
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) - 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.SearchParameters
Returns the precursor tolerance.
getPrecursorAccuracyType() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns the precursor accuracy type.
getPrecursorIntensity() - Method in class com.compomics.util.io.PklFile
 
getPrecursorMatch(Peak) - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Returns the ion match.
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
 
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.Glycon
 
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.ReporterIon
 
getPrimaryKeyColumns() - Method in class com.compomics.util.db.DBMetaData
This method reports on the primary key columns for the table.
getPrimaryProgressBar() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Returns the primary progress bar for updates from external processes.
getPrimaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
getPrimaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
getPrimaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
getProfile() - Method in class com.compomics.util.gui.protein.ModificationProfile
Returns the profile.
getProgress() - Method in class com.compomics.util.gui.waiting.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.
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.
getProtein(String) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Returns the desired protein.
getProteinConfidenceMwPlots() - Method in class com.compomics.util.preferences.ProcessingPreferences
Returns the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.
getProteinEvidence() - Method in class com.compomics.util.protein.Header
 
getProteinFDR() - Method in class com.compomics.util.preferences.ProcessingPreferences
Returns the initial protein FDR.
getProteinIdentification() - Method in class com.compomics.util.experiment.identification.Identification
Returns a list of the keys of all encountered proteins.
getProteinKey() - Method in class com.compomics.util.experiment.biology.Protein
Returns the key for protein indexing.
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(String) - Method in class com.compomics.util.experiment.identification.protein_inference.ProteinTree
Returns the protein mapping in the sequence factory for the given peptide sequence.
getProteinMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
Returns a protein match.
getProteinMatch(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the desired protein match.
getProteinMatch(String) - Method in class com.compomics.util.experiment.quantification.Quantification
Returns a protein quantification match.
getProteinMatch(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the desired protein match.
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) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the desired protein match parameter.
getProteinMatchPArameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the desired protein match parameter.
getProteinParameterTable(UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the table name associated with the given protein parameter.
getProteinParameterTable(UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the table name associated to the given protein parameter.
getProteinQuantification() - Method in class com.compomics.util.experiment.quantification.Quantification
This method retrieves the quantification result at the protein level
getProteomicAnalysis(int) - Method in class com.compomics.util.experiment.SampleAnalysisSet
Returns the analysis corresponding to the selected replicate
getProtocols() - Method in class com.compomics.util.pride.PrideObjectsFactory
Returns the protocols.
getPsmFDR() - Method in class com.compomics.util.preferences.ProcessingPreferences
Returns the initial PSM FDR.
getPsmIDentificationToQuantification() - Method in class com.compomics.util.experiment.quantification.Quantification
This method retrieves the quantification result at the spectrum level
getPsmQuantification() - Method in class com.compomics.util.experiment.quantification.matches.PeptideQuantification
Getter for the corresponding spectrum quantification
getPTM(ModificationProfile, int) - Method in class com.compomics.util.experiment.biology.PTMFactory
Get a PTM according to its OMSSA index.
getPTM(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns the PTM indexed by its name.
getPTM(double, String, String) - Method in class com.compomics.util.experiment.biology.PTMFactory
Deprecated.
This method can generate inconsistent results in case a measurement matches to various PTMs.
getPtm(String) - Method in class com.compomics.util.preferences.ModificationProfile
Returns the back-ed up PTM with the given name.
getPtmName() - Method in class com.compomics.util.gui.protein.ModificationProfile
Returns the PTM name.
getPTMPlotData(Peptide, PTM, int, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, double) - Static method in class com.compomics.util.experiment.identification.ptm.PTMLocationScores
Returns the PTM plot series in the JFreechart format for one PSM.
getPTMs() - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns the names of all imported PTMs.
getPTMTableContent(Peptide, PTM, int, MSnSpectrum, HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, double, double) - Static method in class com.compomics.util.experiment.identification.ptm.PTMLocationScores
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.
getQuoteType() - Static method in class com.compomics.software.CommandLineUtils
Returns the quote type to use.
getRank() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Get the identification rank.
getRatio() - Method in class com.compomics.util.experiment.quantification.Ratio
returns the estimated ratio
getRatios() - Method in class com.compomics.util.experiment.quantification.QuantificationMatch
Getter for the peptide ratios.
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.PTMLocationScores
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.PTMLocationScores
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) - Static method in class com.compomics.util.experiment.identification.scoring.PsmScores
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used.
getReducedSpectra(MSnSpectrum, double, int) - Static method in class com.compomics.util.experiment.identification.scoring.PsmScores
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used.
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.
getReferenceIntensity() - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
Returns the reference intensity used to estimate the ratios
getReferences() - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
Returns the references.
getRefinementModifications() - Method in class com.compomics.util.preferences.ModificationProfile
Return the refinement modifications used for the second pass search.
getRelativeError(boolean) - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the relative m/z matching error in ppm.
getRelativeError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the relative m/z matching error in ppm without isotope removal.
getRelimsPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Returns the path to the Relims installation.
getReplicateNumberList() - Method in class com.compomics.util.experiment.SampleAnalysisSet
Returns a list containing replicate numbers
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 ion associated to the given sample.
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.quantification.reporterion.ReporterMethod
Returns the reporter ions used.
getReporterMatches() - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
Getter for the reporter matches
getReporterMethod() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
returns the reporter method used.
getReporterPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Returns the path to the Reporter installation.
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 class com.compomics.util.experiment.biology.PTM
Deprecated.
use amino acid pattern instead
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
 
getResolution() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
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.SearchParameters
Returns the list of rewind ions.
getRoundedMassShift() - Method in class com.compomics.util.experiment.biology.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
 
getRt() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
Getter for the retention time.
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(int) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
This method returns the sample associated to the given ion.
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.
getScore() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Returns the score assigned by the advocate.
getScore() - Method in class com.compomics.util.experiment.refinementparameters.MascotScore
Getter for Mascot score
getScore() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
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
getSearchedPTM(PTM) - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns the standard search compatible PTM corresponding to this pattern.
getSearchedPTM(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns the standard search compatible PTM corresponding to this pattern, i.e., a pattern targeting a single amino-acid and not a complex pattern.
getSearchEngine(File) - Method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory
This method return the search engine corresponding to the given file.
getSearchGuiPath() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Returns the path to the SearchGUI installation.
getSearchParameters(Properties, File) - Static method in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
Conversion methods which converts an old school set of identification properties into a SearchParameters instance.
getSecondaryProgressBar() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Returns the secondary progress bar for updates from external processes.
getSecondaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
getSecondaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Returns the secondary progress bar for updates from external processes.
getSecondaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
Returns the secondary progress bar for updates from external processes.
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
getSelectedPositions() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
getSelectedType() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.TypeSelection
Returns the selected type.
getSelection() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
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.
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.
getSerializationDirectory() - Method in class com.compomics.util.experiment.identification.Identification
Returns the serialization directory.
getShortName() - Method in class com.compomics.util.experiment.biology.PTM
Getter for the short modification name.
getShortName(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns the user favorite short name, a default short name otherwise.
getSimilarNotFixedModifications(Double) - Method in class com.compomics.util.preferences.ModificationProfile
Returns a list containing all not fixed modifications with the same mass.
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
 
getSpAccession() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
 
getSparklineColor() - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Getter for the sparkline color.
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.
getSpectra(File) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
Reads an MGF file and retrieves a list of spectra.
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.
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(ArrayList<IonMatch>) - Static method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel.
getSpectrumAnnotation(HashMap<Ion.IonType, ArrayList<Integer>>, NeutralLossesMap, ArrayList<Integer>, int, MSnSpectrum, Peptide, double, double, boolean) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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.
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() - Method in class com.compomics.util.experiment.identification.Identification
Deprecated.
use file specific names instead
getSpectrumIdentification(String) - Method in class com.compomics.util.experiment.identification.Identification
Returns the spectrum identifications for a given spectrum file name.
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.
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.
getSpectrumLoaded() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Returns the key of the spectrum loaded.
getSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
Returns a spectrum match.
getSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the desired spectrum match.
getSpectrumMatch(String) - Method in class com.compomics.util.experiment.quantification.Quantification
Returns a spectrum quantification match.
getSpectrumMatch(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the desired spectrum match.
getSpectrumMatches() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Returns all spectra matched.
getSpectrumMatches(String) - Method in class com.compomics.util.experiment.quantification.Quantification
Returns a list of PSM quantification matches corresponding to the given psm identification key.
getSpectrumMatchKey() - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
Getter for the key of the spectrum match
getSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
Returns the desired spectrum match parameter.
getSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the desired spectrum match parameter.
getSpectrumMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the desired spectrum match parameter.
getSpectrumMatchTable(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Returns the table name associated with the given spectrum key.
getSpectrumMatchTable(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the table name associated to 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.
getSpectrumParameterTable(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Returns the table name associated to the given spectrum parameter.
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.
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
 
getSpStart() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
 
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.
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
 
getStart_block() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
getStart_protein() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
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
 
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.Glycon
 
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.ReporterIon
 
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.Glycon
 
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.ReporterIon
 
getSurroundingAA(String, int) - 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 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
Sets up the cell renderer for the given component.
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
Sets up the cell renderer for the given component.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer
Sets up the cell renderer for the given cell.
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.
getTaggedModifiedSequence(ModificationProfile, 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(ModificationProfile, Peptide, 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>.
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.Mutation
Returns the target amino acid.
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
 
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.
getTheoreticMass() - Method in class com.compomics.util.experiment.biology.Ion
Returns the theoretic mass.
getTheoreticMz() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Returns the theoretic m/z expected for this assumption.
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.
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 class com.compomics.util.messages.FeedBack
Returns the title.
getTitle() - Method in class com.compomics.util.pdbfinder.das.readers.DasAlignment
 
getTitle() - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
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.
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.
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.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.quantification.matches.PeptideQuantification
 
getType() - Method in class com.compomics.util.experiment.quantification.matches.ProteinQuantification
 
getType() - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
 
getType() - Method in class com.compomics.util.experiment.quantification.QuantificationMatch
Returns the type of a match
getType() - Method in class com.compomics.util.messages.FeedBack
Returns the feedback type.
getType() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
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
 
getTypeId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getTypeReference() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getTypeSubparts() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getTypeSuperparts() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
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.
getUrParam(UrParameter) - Method in class com.compomics.util.experiment.personalization.ExperimentObject
Method which returns the refinement parameter.
getUserModifications() - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns the names of the user defined modifications.
getUserSelectedFile(Component, 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.
getUtilitiesUserPreferences() - Method in interface com.compomics.software.dialogs.JavaOptionsDialogParent
Returns the utilities user preferences.
getValidatedCharges() - Method in class com.compomics.util.preferences.AnnotationPreferences
Returns the fragment ion charges considered for the desired precursor charge.
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
 
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.sun.TableMap
 
getValueAt(int, int) - Method in class com.compomics.util.sun.TableSorter
 
getVariableModifications() - Method in class com.compomics.util.preferences.ModificationProfile
Returns the expected variable modification names included in this profile.
getVersion() - Method in class com.compomics.util.examples.UtilitiesDemo
Retrieves the version number set in the pom file.
getVisibleColumns() - Method in interface com.compomics.util.gui.VisibleTableColumnsDialogParent
Returns the list of visible columns.
getVisibleColumns() - Method in class com.compomics.util.gui.XYPlottingDialog
 
getWarning(String, String) - Static method in class com.compomics.util.messages.FeedBack
Creates a warning object.
getWindow() - Method in class com.compomics.util.gui.ptm.PtmDialog
 
getX() - Method in class com.compomics.util.XYZDataPoint
 
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.
getXtandemMaxEvalue() - Method in class com.compomics.util.preferences.IdFilter
Returns the maximal X!Tandem e-value allowed.
getY() - Method in class com.compomics.util.XYZDataPoint
 
getYAxisData() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the y-axis data.
getYStart(NeutralLoss) - Method in class com.compomics.util.experiment.identification.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).
getZ() - Method in class com.compomics.util.XYZDataPoint
 
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
 
Glutamine - Class in com.compomics.util.experiment.biology.aminoacids
Glutamine
Glutamine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Glutamine
 
GLUTAMINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
Subtype int for a glutamine immonium ion.
Glycine - Class in com.compomics.util.experiment.biology.aminoacids
Glycine
Glycine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Glycine
 
GLYCINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
Subtype int for a glycine immonium ion.
Glycon - Class in com.compomics.util.experiment.biology.ions
This class will models a glycon fragment.
Glycon(String, String) - Constructor for class com.compomics.util.experiment.biology.ions.Glycon
Constructor for a glycon.
GlyconFactory - Class in com.compomics.util.experiment.biology
This factory will provide theoretic glycons.
GraphicsPanel - 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, or a chromatogram.
GraphicsPanel() - Constructor for class com.compomics.util.gui.spectrum.GraphicsPanel
 
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.
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
 
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.
hasAddenda() - Method in class com.compomics.util.protein.Header
This method reports on the presence of addenda for this header.
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)
hasFlag(String) - Method in class com.compomics.util.general.CommandLineParser
This method test whether the specified flag was set on the command line.
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.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.
hasRTWindow() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
Returns a boolean indicating whether the rt window was implemented.
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.
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) - 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) - 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) - 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
 
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
An 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
 
iAnnotations - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The Vector that holds a set of Annotation instances.
iAnnotationYAxisThreshold - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The procentual 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.
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.
iClickedIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Int that indicates which point was clicked.
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.
iCode - Variable in class com.compomics.util.protein.ModificationTemplate
The code for this modification (eg., Mox).
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.
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
 
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.
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
IdentificationParametersReader - Class in com.compomics.util.experiment.io.identifications
Deprecated.
use the SearchParameters class instead
IdentificationParametersReader() - Constructor for class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
 
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.
IdFilter - Class in com.compomics.util.preferences
This class achieves a pre-filtering of the identifications for PeptideShaker.
IdFilter() - Constructor for class com.compomics.util.preferences.IdFilter
Constructor with default settings.
IdFilter(int, int, double, double, double, double, boolean, boolean) - Constructor for class com.compomics.util.preferences.IdFilter
Constructor for an Identification filter.
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.
iDrawStyle - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This variable holds the drawing style.
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.
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.
iHighLightIndex - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Index of the point that needs to be highlighted.
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.
importEnzymes(File) - Method in class com.compomics.util.experiment.biology.EnzymeFactory
Import enzymes.
importGlycons(File) - Method in class com.compomics.util.experiment.biology.GlyconFactory
Import glycons from an xml file.
importMethods(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
Imports the methods from an xml file
importModifications(File, boolean) - Method in class com.compomics.util.experiment.biology.PTMFactory
Import modifications from a modification file.
importModifications(File, boolean, boolean) - Method in class com.compomics.util.experiment.biology.PTMFactory
Import modifications from a modification file.
ImportSettingsDialog - Class in com.compomics.util.preferences.gui
The PeptideShaker import settings dialog.
ImportSettingsDialog(JFrame, ImportSettingsDialogParent, IdFilter, boolean) - Constructor for class com.compomics.util.preferences.gui.ImportSettingsDialog
Creates a new ImportSettingsDialog.
ImportSettingsDialog(JDialog, ImportSettingsDialogParent, IdFilter, boolean) - Constructor for class com.compomics.util.preferences.gui.ImportSettingsDialog
Creates a new ImportSettingsDialog.
ImportSettingsDialogParent - Interface in com.compomics.util.preferences.gui
Interface implemented by parents of the ImportSettingsDialog.
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
 
increaseProgressValue() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Increase the progress bar value by one "counter".
increaseProgressValue(int) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Increase the progress bar value by the given number.
increaseProgressValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
increaseProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
increaseProgressValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Increase the progress bar value by one "counter".
increaseProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Increase the progress bar value by the given amount.
increaseProgressValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
increaseProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
increaseSecondaryProgressValue() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Increase the secondary progress bar value by one "counter".
increaseSecondaryProgressValue(int) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Increase the secondary progress bar value by the given amount.
increaseSecondaryProgressValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Increases the progress bar.
increaseSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Increases the value of the progress bar.
increaseSecondaryProgressValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Increase the secondary progress bar value by one "counter".
increaseSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Increase the secondary progress bar value by the given amount.
increaseSecondaryProgressValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
increaseSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
incrementValue() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Deprecated.
use waiting handler method instead
incrementValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Deprecated.
use waiting handler method instead
inDB(String, String, boolean) - Method in class com.compomics.util.db.ObjectsDB
Indicates whether an object is loaded in the given table.
initiateTree(int, int) - Method in class com.compomics.util.experiment.identification.protein_inference.ProteinTree
Initiates the tree.
initiateTree(int, int, Enzyme) - Method in class com.compomics.util.experiment.identification.protein_inference.ProteinTree
Initiates the tree.
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.
insertOLSResult(String, String, String, String, String, int, String, Map<String, String>) - Method in class com.compomics.util.gui.ptm.PtmDialog
 
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>, ArrayList<Integer>, MSnSpectrum, double, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.IntensityHistogram
Creates an IntensityHistogram plot //@TODO improve charge compatibility
INTERACTIVE_STATUS - Static 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.)
interrupt() - Method in class com.compomics.util.sun.SwingWorker
A new method that interrupts the worker thread.
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, ArrayList<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.
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.
iPrecursorMZ - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
This variable holds the precursor M/Z.
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.
isAccounted(NeutralLossesMap, NeutralLoss, Ion, Peptide) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns a boolean indicating whether the neutral loss should be accounted for.
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.
isAscendingScore(int) - Static method in class com.compomics.util.experiment.identification.advocates.SearchEngine
Indicates whether a search engine score is increasing when the quality of the match increases.
isAScoreCalculated() - Method in class com.compomics.util.preferences.ProcessingPreferences
Deprecated.
use the PTM scoring preferences instead
isaScoreNeutralLosses() - Method in class com.compomics.util.preferences.PTMScoringPreferences
Indicates whether the A-score calculation should take neutral losses into account.
isAutomatedMemoryManagement() - Method in class com.compomics.util.db.ObjectsCache
Returns whether the cache is in automated memory management mode.
isCanceled() - Method in class com.compomics.util.gui.AminoAcidPatternDialog
indicates whether the changes have been canceled
isCanceled() - Method in class com.compomics.util.gui.filehandling.FileSelectionDialog
Indicates whether the user pushed on cancel
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.
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.
isConfident() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Returns a boolean indicating whether the modification is confidently localized on the sequence.
isCorrectPrecursorMass() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).
isCterm() - 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) - Method in class com.compomics.util.experiment.biology.Protein
Returns a boolean indicating whether the protein ends with the given peptide.
isDB() - Method in class com.compomics.util.experiment.identification.Identification
Indicates whether the identification matches should be stored in a database (true, default value) or serialized files (false, deprecated default).
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.FastaIndex
Returns a boolean indicating whether the database contains decoy sequences.
isDecoy() - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Inspects whether the peptide match is a decoy hit.
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() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Is the identification decoy?
isDecoy(String) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
Returns a boolean indicating whether a protein is decoy or not based on the protein accession.
isDeleted() - Method in interface com.compomics.util.db.interfaces.DBElement
This method signals whether the DBElement has been deleted in the persistent store.
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.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.
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
isEmpty() - Method in class com.compomics.util.experiment.identification.NeutralLossesMap
Returns a boolean indicating if the mapping is empty.
isEnding(String) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Indicates whether the given amino acid sequence ends with the pattern.
isEnzymaticPeptide(String, Enzyme) - 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
 
isEstimateCharge() - Method in class com.compomics.util.experiment.identification.SearchParameters
Indicates whether the precursor charge shall be estimated for OMSSA.
isFixed() - Method in class com.compomics.util.experiment.biology.NeutralLoss
Returns a boolean indicating whether the neutral loss is fixed or not.
isIndeterminate() - Method in class com.compomics.util.gui.waiting.ProgressDialog
This method signals whether the progressdialog is currently in indeterminate ('true') or determinate ('false') mode.
isInferred() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Returns a boolean indicating whether the modification is inferred from another peptide.
isIsPpm() - Method in class com.compomics.util.preferences.IdFilter
Indicates whether the mass tolerance is in ppm (true) or Dalton (false).
isMiniature() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true if the graphics panel is to be drawn in a minature form.
isModifiable(PTM) - Method in class com.compomics.util.experiment.biology.Peptide
Indicates whether the given modification can be found on the peptide.
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, String) - 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.
isNterm() - 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) - Method in class com.compomics.util.experiment.biology.Protein
Returns a boolean indicating whether the protein starts with the given peptide.
Isoleucine - Class in com.compomics.util.experiment.biology.aminoacids
Isoleucine
Isoleucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Isoleucine
 
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
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.
iSpecPanelListeners - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The list of SpectrumPanelListeners.
isPpm() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Returns a boolean indicating whether the m/z tolerance is in ppm.
isPrecursorAccuracyTypePpm() - Method in class com.compomics.util.experiment.identification.SearchParameters
Returns true if the current precursor accuracy type is ppm.
isProgressBarValid() - Method in class com.compomics.util.gui.waiting.ProgressDialog
This method reports on whether this instance can be controlled in a multithreaded environment.
isRemovePrecursor() - Method in class com.compomics.util.experiment.identification.SearchParameters
Indicates whether the precursor shall be removed for OMSSA.
isRunCanceled() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Returns true if the run is canceled.
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
 
isRunFinished() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Returns true if the run is finished.
isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Returns true if the run is finished.
isRunFinished() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
isRunning() - Method in class com.compomics.util.io.FolderMonitor
This method can be consulted to find out whether the monitor is running.
isSameAs(AminoAcidPattern) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Indicates whether another AminoAcidPattern targets the same pattern.
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.Glycon
 
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(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(NeutralLoss) - Method in class com.compomics.util.experiment.biology.NeutralLoss
Method indicating whether another neutral loss is the same as the one considered.
isSameAs(Peptide) - Method in class com.compomics.util.experiment.biology.Peptide
A method which compares two peptides.
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
Compares two PTMs.
isSameAs(Sample) - Method in class com.compomics.util.experiment.biology.Sample
Comparator for samples.
isSameAs(Peak) - Method in class com.compomics.util.experiment.massspectrometry.Peak
Returns true if the peak has the same mz and intensity.
isSameModificationStatus(Peptide) - Method in class com.compomics.util.experiment.biology.Peptide
Indicates whether another peptide has the same variable modifications as this peptide.
isSameSequence(Peptide) - 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) - 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.
isScalePrecursor() - Method in class com.compomics.util.experiment.identification.SearchParameters
Indicates whether the precursor shall be scaled for OMSSA.
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) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Indicates whether the given amino acid sequence starts with the pattern.
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.
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.
isTruncated() - Method in class com.compomics.util.protein.Protein
This method reports on the 'truncatedness' of the protein.
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
 
isVariable() - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Returns a boolean indicating if the modification is variable.
iTemplate - Variable in class com.compomics.util.protein.ModificationImplementation
The ModificationTemplate which holds all the shared information for a modification.
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).
iTRAQ113 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion iTRAQ 113.
iTRAQ114 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion iTRAQ 114.
iTRAQ115 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion iTRAQ 115.
iTRAQ116 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion iTRAQ 116.
iTRAQ117 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion iTRAQ 117.
iTRAQ118 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion iTRAQ 118.
iTRAQ119 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion iTRAQ 119.
iTRAQ121 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion iTRAQ 121.
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.
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.
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
 
JavaOptionsDialog - Class in com.compomics.software.dialogs
A simple dialog for changing the Java options.
JavaOptionsDialog(JFrame, JavaOptionsDialogParent, JDialog, String) - Constructor for class com.compomics.software.dialogs.JavaOptionsDialog
Creates a new JavaOptionsDialog.
JavaOptionsDialogParent - Interface in com.compomics.software.dialogs
Interface for parents of JavaOptionsDialog.
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.
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
 
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
 

L

L - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
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.
letter - Variable in class com.compomics.util.experiment.biology.Atom
 
Leucine - Class in com.compomics.util.experiment.biology.aminoacids
Leucine
Leucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Leucine
 
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.
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
 
LINES - Static variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Drawstyle which draws lines connecting the X-axis with the measurement.
list() - Method in class com.compomics.util.io.FTP
LIST files on a remote FTP server.
LITTLE_ENDIAN_LABEL - Static variable in class com.compomics.util.BinaryArrayImpl
Defines the valid String indicating little endian byte order.
load(Connection, HashMap) - Method in interface com.compomics.util.db.interfaces.DBElement
This method should be called to fill the DBElement with current data as present in the database.
loadBackedUpModifications(SearchParameters, boolean) - Method in class com.compomics.util.experiment.biology.PTMFactory
Verifies that the modifications backed-up in the search parameters are loaded and alerts the user in case conflicts are found.
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.SequenceFactory
Loads a new FASTA file in the factory.
loadFastaFile(File, WaitingHandler) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Loads a new FASTA file in the factory.
loadObjects(String, WaitingHandler) - Method in class com.compomics.util.db.ObjectsDB
Loads all objects from a table in the cache.
loadObjects(String, ArrayList<String>, WaitingHandler) - Method in class com.compomics.util.db.ObjectsDB
Loads some objects from a table in the cache.
loadPeptideMatches(ArrayList<String>, WaitingHandler) - 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) - Method in class com.compomics.util.experiment.identification.Identification
Loads all peptide matches in the cache of the database.
loadPeptideMatches(ArrayList<String>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Loads the desired peptide matches of the given type in the cache of the database.
loadPeptideMatches(WaitingHandler) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Loads all peptide matches in the cache of the database.
loadPeptideMatchParameters(UrParameter, WaitingHandler) - 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) - 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) - 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) - 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.
loadProperties(File) - Static method in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
loadProteinMatches(WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Loads all protein matches in the cache of the database.
loadProteinMatches(ArrayList<String>, WaitingHandler) - 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) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Loads all protein matches in the cache of the database.
loadProteinMatches(ArrayList<String>, WaitingHandler) - 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) - 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) - 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) - 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) - 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.
loadSpectrumMatches(String, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Loads all spectrum matches of the file in the cache of the database
loadSpectrumMatches(ArrayList<String>, WaitingHandler) - Method in class com.compomics.util.experiment.identification.Identification
Loads the given spectrum matches in the cache of the database.
loadSpectrumMatches(String, WaitingHandler) - 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) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Loads all given spectrum matches in the cache of the database.
loadSpectrumMatchParameters(String, UrParameter, WaitingHandler) - 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) - 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) - 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) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Loads all desired spectrum match parameters in the cache of the database.
loadUserPreferences() - Static method in class com.compomics.util.preferences.UtilitiesUserPreferences
Convenience method retrieving the user preferences.
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 "/,user..
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.
longKeys - Variable in class com.compomics.util.experiment.identification.Identification
Deprecated.
use the database instead @TODO implement this for db keys
lossesValidated(NeutralLossesMap, Ion, Peptide) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns a boolean indicating whether the neutral losses of the given fragment ion are 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
 
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
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.UtilitiesDemo
Starts the UtilitiesDemo.
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.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.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.pdbfinder.FindPdbForUniprotAccessions
Main method.
main(String[]) - Static method in class com.compomics.util.protein.DualEnzyme
Tests the DualEnzyme by digesting a hardcoded protein.
makeSequenceIndependant() - Method in class com.compomics.util.experiment.identification.NeutralLossesMap
Makes the neutral losses sequence independant.
MASCOT - Static variable in interface com.compomics.util.experiment.identification.Advocate
Mascot index.
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.
MascotScore - Class in com.compomics.util.experiment.refinementparameters
This class will contain the mascot score.
MascotScore(double) - Constructor for class com.compomics.util.experiment.refinementparameters.MascotScore
Contructor for the Mascot score
mass - Variable in class com.compomics.util.experiment.biology.Atom
 
mass - Variable in class com.compomics.util.experiment.biology.NeutralLoss
The mass lost.
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<Integer>, ArrayList<MSnSpectrum>, double, boolean, boolean, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(ArrayList<String>, ArrayList<ArrayList<IonMatch>>, ArrayList<Integer>, ArrayList<MSnSpectrum>, double, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorBubblePlot
Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(ArrayList<String>, ArrayList<ArrayList<IonMatch>>, ArrayList<Integer>, ArrayList<MSnSpectrum>, double, double, boolean, boolean, boolean, 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>, ArrayList<Integer>, MSnSpectrum, double, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot
Creates a new MassErrorPlot.
MassErrorPlot(ArrayList<IonMatch>, ArrayList<Integer>, MSnSpectrum, double, boolean, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot
Creates a new MassErrorPlot.
matches(String) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Indicates whether the pattern 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.
matchPeak(Peptide, HashMap<Ion.IonType, ArrayList<Integer>>, ArrayList<Integer>, int, NeutralLossesMap, Peak) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
This method matches the potential fragment ions of a given peptide with a given peak.
MAX_PEPTIDE_SIZE - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
MAXIMUM_HITLIST_LENGTH - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
maxPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The maximum padding (distance between the axes and the border of the panel).
mean(ArrayList<Double>) - Static method in class com.compomics.util.math.BasicMathFunctions
Convenience method returning the mean of a list of doubles
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
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.
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).
Methionine - Class in com.compomics.util.experiment.biology.aminoacids
Methionine
Methionine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Methionine
 
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
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
 
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>, String, double, double, double, double) - 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.
MIN_PEPTIDE_SIZE - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
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.
MINUS - Static variable in class com.compomics.util.experiment.massspectrometry.Charge
Static int to modele a negative charge.
MISSED_CLEAVAGES - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
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
 
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.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
MODIFICATION_USE_SEPARATOR - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
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 modofication profile object.
ModificationProfile(String, double[][], Color) - Constructor for class com.compomics.util.gui.protein.ModificationProfile
Modification profile constructor.
ModificationProfile - Class in com.compomics.util.preferences
This class stores the information about the modification preferences (colors, names) used for the selected project.
ModificationProfile() - Constructor for class com.compomics.util.preferences.ModificationProfile
Constructor.
ModificationsDialog - Class in com.compomics.util.gui.ptm
A dialog where the modification details can be modified.
ModificationsDialog(Frame, PtmDialogParent, 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.
modifiedPeptidesQuantification - Variable in class com.compomics.util.experiment.quantification.Quantification
The modified peptides quantification
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.
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.
monoisotopicMass - Variable in class com.compomics.util.experiment.biology.AminoAcid
Monoisotopic mass of the amino acid.
MONONUCLEOTIDES - Static variable in class com.compomics.util.general.MassCalc
Index for the monoisotopic nucleotide masses.
mouseClickedInChart(ChartMouseEvent) - Method in class com.compomics.util.gui.XYPlottingDialog
Handles mouse clicks in the chart panel.
mouseMovedInChart(ChartMouseEvent) - Method in class com.compomics.util.gui.XYPlottingDialog
Handles mouse movements in the chart panel.
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
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
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
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
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.Mutation
Constructs a mutation from one amino acid (origin) to another (target).
MutationFactory - Class in com.compomics.util.experiment.biology
This class holds the all possible one-letter peptide sequence mutations.
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
 
MzDialog - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation
This dialog allows the creation of an MzFilter.
MzDialog(JFrame, Double, Double, Boolean) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.MzDialog
Constructor.
MzFilter - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters
This class checks whether a peak is present in a spectrum among the most intense peaks.
MzFilter(double, double, boolean, double) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Constructor.
MzFilter(MzFilter, double) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Creates a filter from a similar filter.
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
 
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
 
n2sort() - Method in class com.compomics.util.sun.TableSorter
 
N_TERM_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
 
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
 
name - Variable in class com.compomics.util.experiment.biology.NeutralLoss
The name of the neutral loss.
name - Variable in class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter
The name of the filter.
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, double, 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
This class contains the informations relative to the accounting of neutral losses
NeutralLossesMap() - Constructor for class com.compomics.util.experiment.identification.NeutralLossesMap
Constructor.
neutron - Static variable in class com.compomics.util.experiment.biology.ElementaryElement
A proton.
NH3 - Static variable in class com.compomics.util.experiment.biology.NeutralLoss
NH3 loss.
Nitrogen - Class in com.compomics.util.experiment.biology.atoms
A 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
noErrors() - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Returns true of there were no errors.
normalize() - Method in class com.compomics.util.experiment.identification.ptm.PtmtableContent
Normalize intesities.
NTERM - Static variable in class com.compomics.util.protein.Enzyme
 
NTERMINAL - Static variable in class com.compomics.util.protein.DualEnzyme
The code for N-terminal position in the resultant peptide.
NTERMINUS - Static variable in interface com.compomics.util.interfaces.Modification
The residue code for the N-terminus.
NTERMTRUNC - Static variable in class com.compomics.util.protein.Protein
The code for an N-terminal truncation.
NucleotideSequence - Class in com.compomics.util.nucleotide
This class combines a protein Header with a nucleotide sequence.
NucleotideSequence(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.

O

O - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
O - Static variable in class com.compomics.util.experiment.biology.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.
OMSSA - Static variable in interface com.compomics.util.experiment.identification.Advocate
OMSSA index.
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.
Or - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters
Filter consisting of several filters.
Or() - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.Or
Constructor.
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
 
outputFolderOption - Static variable in class com.compomics.software.ToolFactory
The command line argument for an output folder
Oxygen - Class in com.compomics.util.experiment.biology.atoms
An 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
 
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.
parseFromFASTA(String) - Static method in class com.compomics.util.protein.Header
Factory method that constructs a Header instance based on a FASTA header line.
parseModificationLine(String) - Static method in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
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.
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
 
PdbBlock - Class in com.compomics.util.pdbfinder.pdb
Created by IntelliJ IDEA.
PdbBlock(String, int, int, int, int) - Constructor for class com.compomics.util.pdbfinder.pdb.PdbBlock
 
PdbParameter - Class in com.compomics.util.pdbfinder.pdb
Created by IntelliJ IDEA.
PdbParameter(String, String, String, String) - Constructor for class com.compomics.util.pdbfinder.pdb.PdbParameter
 
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.
PeakDialog - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation
This dialog allows the creation of an MzFilter.
PeakDialog(JFrame, Double, Double, Boolean) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.PeakDialog
Constructor.
PeakFilter - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters
A peak filter.
PeakFilter(double, double, boolean, double, double) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.PeakFilter
Constructor.
peakList - Variable in class com.compomics.util.experiment.massspectrometry.Spectrum
Peak list.
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 interface com.compomics.util.experiment.identification.Advocate
PepNovo
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.
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<String>, ArrayList<ModificationMatch>) - Constructor for class com.compomics.util.experiment.biology.Peptide
Constructor for the peptide.
Peptide(String, Double, ArrayList<String>, ArrayList<ModificationMatch>) - Constructor for class com.compomics.util.experiment.biology.Peptide
Deprecated.
use the constructor without mass. The mass will be recalculated.
PEPTIDE_FINGERPRINTING - Static variable in class com.compomics.util.experiment.identification.IdentificationMethod
index for identification method based on peptide mass fingerprinting
PEPTIDE_SHAKER - Static variable in interface com.compomics.util.experiment.identification.Advocate
PeptideShaker.
PeptideAssumption - Class in com.compomics.util.experiment.identification
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.PeptideAssumption
Constructor for a peptide assumption.
PeptideAssumption(Peptide, int, int, Charge, double) - Constructor for class com.compomics.util.experiment.identification.PeptideAssumption
Constructor for a peptide assumption.
PeptideAssumptionDetails - Class in com.compomics.util.denovo
This class contains the de novo specific details of a spectrum match
PeptideAssumptionDetails() - Constructor for class com.compomics.util.denovo.PeptideAssumptionDetails
Constructor.
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) - 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.
peptideMatchLoaded(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Indicates whether a peptide match is loaded.
peptideMatchLoaded(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Indicates whether a peptide match is loaded.
PeptideQuantification - Class in com.compomics.util.experiment.quantification.matches
This class models quantification of a peptide.
PeptideQuantification(String) - Constructor for class com.compomics.util.experiment.quantification.matches.PeptideQuantification
Constructor for the peptide quantification
PeptideQuantification(String, ArrayList<String>) - Constructor for class com.compomics.util.experiment.quantification.matches.PeptideQuantification
Constructor for the peptide quantification
PeptideQuantification(String, ArrayList<String>, HashMap<Integer, Ratio>) - Constructor for class com.compomics.util.experiment.quantification.matches.PeptideQuantification
Constructor for the peptide quantification
peptideQuantification - Variable in class com.compomics.util.experiment.quantification.Quantification
The peptide quantification
peptideShakerFileOption - Static variable in class com.compomics.software.ToolFactory
The command line argument for a cps file for PeptideShaker.
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.
PEPTIZER - Static variable in interface com.compomics.util.experiment.identification.Advocate
Peptizer index.
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
 
PERACETYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.Glycon
Final index for peracetylated masses.
PERMETHYLATED_MASS - Static variable in class com.compomics.util.experiment.biology.ions.Glycon
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
 
PHENYLALANINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
Subtype int for a phenylananine immonium ion.
Phosphorus - Class in com.compomics.util.experiment.biology.atoms
A phosphorus atom.
Phosphorus() - Constructor for class com.compomics.util.experiment.biology.atoms.Phosphorus
Constructor.
PickUp - Interface in com.compomics.util.interfaces
This interface describes the behaviour for a class that can pick up results.
PICKUP - Static variable in class com.compomics.util.io.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
 
PostProcessor - Class in com.compomics.util.experiment.identification.advocates
This object models a tool which post-processed identifications.
PostProcessor() - Constructor for class com.compomics.util.experiment.identification.advocates.PostProcessor
contructor for a post-processor
PostProcessor(int) - Constructor for class com.compomics.util.experiment.identification.advocates.PostProcessor
constructor for a post-processor
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 modilizes the 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
Cronstructor with rt window.
Precursor(double, double, ArrayList<Charge>, double, double) - Constructor for class com.compomics.util.experiment.massspectrometry.Precursor
Cronstructor with rt window and no reference rt.
Precursor(double, double, double, ArrayList<Charge>) - Constructor for class com.compomics.util.experiment.massspectrometry.Precursor
Constructor for the precursor.
PRECURSOR_CHARGE_LOWER_BOUND - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
PRECURSOR_CHARGE_UPPER_BOUND - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
PRECURSOR_ELIMINATION - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
PRECURSOR_MASS_ACCURACY_UNIT - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
PRECURSOR_MASS_TOLERANCE - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
PRECURSOR_SCALING - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
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(Peptide) - Constructor for class com.compomics.util.experiment.biology.ions.PrecursorIon
Constructor.
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.
prideFolder - Static variable in class com.compomics.util.pride.PrideObjectsFactory
The folder where PRIDE related info is stored.
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.
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.
ProcessingPreferences - Class in com.compomics.util.preferences
This class groups the user preferences for the initial PeptideShaker processing.
ProcessingPreferences() - Constructor for class com.compomics.util.preferences.ProcessingPreferences
Constructor with default settings.
ProcessingPreferencesDialog - Class in com.compomics.util.preferences.gui
A simple dialog where the user can view/edit the PeptideShaker processing preferences.
ProcessingPreferencesDialog(Frame, boolean, ProcessingPreferences, PTMScoringPreferences) - Constructor for class com.compomics.util.preferences.gui.ProcessingPreferencesDialog
Creates a new parameters dialog.
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.
ProgressDialog - Class in com.compomics.util.gui.waiting
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.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
 
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 spectrumFile and spectrumTitle.
proteinIdentification - Variable in class com.compomics.util.experiment.identification.Identification
List of the keys of all imported proteins.
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) - Constructor for class com.compomics.util.experiment.identification.matches.ProteinMatch
Constructor for the protein match.
proteinMatchLoaded(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Indicates whether a protein match is loaded.
proteinMatchLoaded(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Indicates whether a protein match is loaded.
ProteinQuantification - Class in com.compomics.util.experiment.quantification.matches
This class models the quantification of a protein.
ProteinQuantification(String) - Constructor for class com.compomics.util.experiment.quantification.matches.ProteinQuantification
Constructor for the protein quantification
ProteinQuantification(String, ArrayList<String>) - Constructor for class com.compomics.util.experiment.quantification.matches.ProteinQuantification
Constructor for the protein quantification
ProteinQuantification(String, ArrayList<String>, HashMap<Integer, Ratio>) - Constructor for class com.compomics.util.experiment.quantification.matches.ProteinQuantification
Constructor for the protein quantification
proteinQuantification - Variable in class com.compomics.util.experiment.quantification.Quantification
The protein quantification
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
 
ProteinTree - Class in com.compomics.util.experiment.identification.protein_inference
This class sorts the proteins into groups.
ProteinTree() - Constructor for class com.compomics.util.experiment.identification.protein_inference.ProteinTree
Creates a tree based on the proteins present in the sequence factory.
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
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
 
psmIDentificationToQuantification - Variable in class com.compomics.util.experiment.quantification.Quantification
A convenience map indicating all psm quantifying an identified PSM
PsmQuantification - Class in com.compomics.util.experiment.quantification.matches
This class models the quantification of a spectrum.
PsmQuantification(String, String) - Constructor for class com.compomics.util.experiment.quantification.matches.PsmQuantification
Constructor for a spectrumQuantification
PsmScores - Class in com.compomics.util.experiment.identification.scoring
This class contains different ways of scoring a match.
PsmScores() - Constructor for class com.compomics.util.experiment.identification.scoring.PsmScores
 
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, double, ArrayList<String>) - Constructor for class com.compomics.util.experiment.biology.PTM
Deprecated.
use amino acid pattern instead
PTM(int, String, String, double, ArrayList<String>) - Constructor for class com.compomics.util.experiment.biology.PTM
Deprecated.
use amino acid pattern instead
PTM(int, String, double, AminoAcidPattern) - Constructor for class com.compomics.util.experiment.biology.PTM
Constructor for a reference modification.
PTM(int, String, String, double, AminoAcidPattern) - Constructor for class com.compomics.util.experiment.biology.PTM
Constructor for a reference modification.
PtmDialog - Class in com.compomics.util.gui.ptm
This dialog allows the user to create/edit PTMs.
PtmDialog(JDialog, PtmDialogParent, PtmToPrideMap, PTM, boolean) - Constructor for class com.compomics.util.gui.ptm.PtmDialog
Creates a new PTM dialog.
PtmDialog(JFrame, PtmDialogParent, PtmToPrideMap, PTM, boolean) - Constructor for class com.compomics.util.gui.ptm.PtmDialog
Creates a new PTM dialog.
PtmDialogParent - Interface in com.compomics.util.gui.ptm
An interface that has to be implemented by all classes using the PtmDialog.
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.
PTMLocationScores - Class in com.compomics.util.experiment.identification.ptm
This class scores PTM locations using various scores.
PTMLocationScores() - Constructor for class com.compomics.util.experiment.identification.ptm.PTMLocationScores
 
PTMScoringPreferences - Class in com.compomics.util.preferences
This class contains the PTM scoring preferences.
PTMScoringPreferences() - Constructor for class com.compomics.util.preferences.PTMScoringPreferences
Constructor.
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 PSI-MOD 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
 

Q

Q - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
Quantification - Class in com.compomics.util.experiment.quantification
This class contains quantification results.
Quantification() - Constructor for class com.compomics.util.experiment.quantification.Quantification
 
Quantification.QuantificationMethod - Enum in com.compomics.util.experiment.quantification
The implemented quantification methods.
QuantificationDB - Class in com.compomics.util.experiment.quantification
This class uses a database to manage quantification matches.
QuantificationDB(String, String, boolean, ObjectsCache) - Constructor for class com.compomics.util.experiment.quantification.QuantificationDB
Constructor creating the database and the protein and protein parameters tables.
QuantificationMatch - Class in com.compomics.util.experiment.quantification
Abstract class for a quantification match.
QuantificationMatch() - Constructor for class com.compomics.util.experiment.quantification.QuantificationMatch
 
QuantificationMatch.MatchType - Enum in com.compomics.util.experiment.quantification
The type of match.

R

R - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
Ratio - Class in com.compomics.util.experiment.quantification
This class models an object.
Ratio(int, double) - Constructor for class com.compomics.util.experiment.quantification.Ratio
constructor for the Ratio
ratios - Variable in class com.compomics.util.experiment.quantification.QuantificationMatch
The estimated ratios.
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.
readFasta(String, String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
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 serverresponse.
readUrl(String, String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
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.
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) - 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) - 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.
RelimsSetupDialog - Class in com.compomics.software.dialogs
Deprecated.
the original relims is not used anymore
RelimsSetupDialog(JFrame, boolean) - Constructor for class com.compomics.software.dialogs.RelimsSetupDialog
Deprecated.
Creates a new RelimsSetupDialog.
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.
removeAA(int) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Removes an amino acid index from the pattern.
removeAllReferenceAreasXAxis() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Removes all the x-axis reference areas.
removeAllReferenceAreasYAxis() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Removes all the y-axis reference areas.
removeAssumption(PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Removes an assumption from the mapping
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.preferences.ModificationProfile
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
removeMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
Deprecated.
it is advised to use the specific psm/peptide/protein method instead
removeMatch(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Deprecated.
it is advised to use the specific psm/peptide/protein method instead
removeMouseListenerToHeaderInTable(JTable) - Method in class com.compomics.util.sun.TableSorter
 
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.
removePeptideMatch(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
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.
removeProteinMatch(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Deletes a protein match 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.
removeRefinementModification(String) - Method in class com.compomics.util.preferences.ModificationProfile
Removes a modification from the list of refinement modifications modifications.
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.
removeSpectrumMatch(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Deletes a spectrum match from the database.
removeUnknownPTMs() - Method in class com.compomics.util.preferences.IdFilter
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.preferences.ModificationProfile
Removes a modification from the list of variable modifications.
rename(String, String) - Method in class com.compomics.util.io.FTP
Rename a file on the remote server.
repair() - Method in class com.compomics.util.preferences.ModificationProfile
Sets empty lists and maps to the values lost due to backward compatability issues.
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(int) - 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 will contain quantification results.
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 models a reporter quantification method.
ReporterMethod(String, ArrayList<ReporterIon>, ArrayList<CorrectionFactor>) - 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.
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.
resetAutomaticAnnotation() - Method in class com.compomics.util.preferences.AnnotationPreferences
Updates the neutral losses and charge annotation settings.
resetProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Reset the primary progress bar value to 0.
resetSecondaryProgressBar() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Reset the secondary progress bar value to 0.
resetSecondaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
resets the value of the progress bar.
resetSecondaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Reset the secondary progress bar value to 0.
resetSecondaryProgressBar() - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
restart() - Method in interface com.compomics.software.dialogs.JavaOptionsDialogParent
Restart the given tool with the new Java options.
Retrievable - Interface in com.compomics.util.db.interfaces
This interface indicates that the implementing class can be retrieved from permanent storage.
RetrievableCode - Class in com.compomics.util.db.components
This class generates the code to make a DBAccessor an implementation of the Retrieveable interface.
RetrievableCode(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) - Method in class com.compomics.util.db.ObjectsDB
Retrieves an object from the desired table.
rmdir(String) - Method in class com.compomics.util.io.FTP
Delete the specified directory from the ftp server file system.
roundDouble(double, int) - Static method in class com.compomics.util.Util
Rounds a double value to the wanted number of decimal places.
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.

S

S - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
S - Static variable in class com.compomics.util.experiment.biology.Atom
 
sameLists(ArrayList<Integer>, ArrayList<Integer>) - Static method in class com.compomics.util.Util
Convenience methods indicating whether the content of two lists have the same content.
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.
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
 
saveIdentificationParameters(SearchParameters, File) - Static method in class com.compomics.util.experiment.identification.SearchParameters
Saves the identification parameters to a serialized file.
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.
saveUserPreferences(UtilitiesUserPreferences) - Static method in class com.compomics.util.preferences.UtilitiesUserPreferences
Convenience method saving the user preferences.
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 timepoint when the spectrum was recorded (scan start time in mzML files).
sdf - Static variable in interface com.compomics.util.gui.waiting.WaitingHandler
Convenience date format.
SEARCH_SUFFIX - Static variable in class com.compomics.util.experiment.biology.PTMFactory
Suffix for the modifications searched but not in the factory.
SearchEngine - Class in com.compomics.util.experiment.identification.advocates
This class models a search engine.
SearchEngine() - Constructor for class com.compomics.util.experiment.identification.advocates.SearchEngine
Constructor for a search engine.
SearchEngine(int) - Constructor for class com.compomics.util.experiment.identification.advocates.SearchEngine
Constructor for a search engine.
searchGuiParametersFileOption - Static variable in class com.compomics.software.ToolFactory
The command line argument for a parameters file 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.
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
This class groups the parameters used for identification.
SearchParameters() - Constructor for class com.compomics.util.experiment.identification.SearchParameters
Constructor.
SearchParameters.PrecursorAccuracyType - Enum in com.compomics.util.experiment.identification
Possible mass accuracy types.
Selenocysteine - Class in com.compomics.util.experiment.biology.aminoacids
SeC (U) (Mascot)
Selenocysteine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Selenocysteine
 
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.
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.
Sequence - Interface in com.compomics.util.interfaces
This interface defines the default behaviour of any kind of sequence with a certain mass - be it DNA, portein or something else.
SequenceFactory - Class in com.compomics.util.experiment.identification
Factory retrieving the information of the loaded FASTA file.
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, ModificationProfile) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Deprecated.
use the panel with ion selection instead
SequenceFragmentationPanel(String, ArrayList<IonMatch>, boolean, boolean, ModificationProfile, 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, ModificationProfile, int, int) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Creates a new SequenceFragmentationPanel working with B and Y ions.
SequenceModificationPanel - Class in com.compomics.util.gui.protein
A panel for displaying modification profiles.
SequenceModificationPanel(String, ArrayList<ModificationProfile>, boolean) - Constructor for class com.compomics.util.gui.protein.SequenceModificationPanel
Creates a new SequenceFragmentationPanel.
SequestParamsFileFilter - Class in com.compomics.util.io.filefilters
File filter for sequest.params files.
SequestParamsFileFilter() - Constructor for class com.compomics.util.io.filefilters.SequestParamsFileFilter
 
serializationDirectory - Variable in class com.compomics.util.experiment.identification.Identification
The directory where matches will be serialized/the database stored.
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
 
serialVersionUID - Static variable in interface com.compomics.util.experiment.identification.Advocate
The version UID for Serialization/Deserialization compatibility.
serialVersionUID - Static variable in interface com.compomics.util.experiment.personalization.UrParameter
The version UID for Serialization/Deserialization compatibility
Serine - Class in com.compomics.util.experiment.biology.aminoacids
Serine
Serine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Serine
 
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.
setAccession(String) - Method in class com.compomics.util.pride.CvTerm
 
setAccession(String) - Method in class com.compomics.util.protein.Header
 
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
setAnnotationLevel(double) - Method in class com.compomics.util.preferences.AnnotationPreferences
Sets the annotation level.
setAnnotations(Vector) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method sets all the annotations on this instance.
setAnnotationYAxisThreshold(double) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method allows the caller to set the procentual minimal, non-inclusive y-axis value threshold (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 chromatograms and profile spectra for the dataset with the given dataset index.
setaScoreCalculation(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences
Sets whether the A-score should be calculated.
setaScoreNeutralLosses(boolean) - Method in class com.compomics.util.preferences.PTMScoringPreferences
Sets whether the A-score calculation should take neutral losses into account.
setAutomatedMemoryManagement(boolean) - Method in class com.compomics.util.db.ObjectsCache
Sets whether the cache is in automated memory management mode.
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.
setBestAssumption(PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Setter for the best assumption.
setBlock(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
setBlocks(PdbBlock[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
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.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.
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
 
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(Color) - Method in class com.compomics.util.gui.protein.ModificationProfile
Sets the PTM color.
setColor(String, Color) - Method in class com.compomics.util.preferences.ModificationProfile
Sets a new color for the given expected modification.
setConfident(boolean) - Method in class com.compomics.util.experiment.identification.matches.ModificationMatch
Sets whether the modification is confidently localized on the sequence.
setContacts(ArrayList<Contact>) - Method in class com.compomics.util.pride.prideobjects.ContactGroup
Set the contacts.
setcTermGap(double) - Method in class com.compomics.util.denovo.PeptideAssumptionDetails
Sets the C-term Gap.
setCurrentSettings(Peptide, int, boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Sets the annotation settings for the current peptide and precursor charge.
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
 
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.
setDefaultNeutralLosses() - Method in class com.compomics.util.experiment.biology.PTMFactory
Sets the default neutral losses of PTMs when not implemented.
setDefaultReporterIons() - Method in class com.compomics.util.experiment.biology.PTMFactory
Sets the default reporter ions of PTMs when not implemented.
setDeisotopedIntensities(HashMap<Integer, Double>) - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
Sets the deisotoped intensities
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.preferences.AnnotationPreferences
Set the charge to use for the fragment ions in the de novo sequencing
setDescription(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.ProgressDialog
This method sets the progressbar to determinate mode, with the specified minimum and maximum values.
setDirectory(String, boolean) - Method in class com.compomics.util.experiment.identification.Identification
Deprecated.
use establishConnection(String dbFolder) instead
setDiscardLowQualitySpectra(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets whether low quality spectra shall be discarded.
setDoi(String) - Method in class com.compomics.util.pride.prideobjects.Reference
Set the Digital Object Identifier (DOI) of the reference.
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.
setEMail(String) - Method in class com.compomics.util.pride.prideobjects.Contact
Set the contact e-mail.
setEnd(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the end value.
setEnd_block(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
setEnd_protein(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
setEnzyme(Enzyme) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the enzyme used for digestion.
setEstimateCharge(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets whether the precursor charge shall be estimated for OMSSA.
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<AminoAcid>) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Sets the amino acids excluded at a given index.
setExperiment_type(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
setFastaFile(File) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the sequence database file used for identification.
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.
setFirstHit(int, PeptideAssumption) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Sets the best peptideAssumption according to the search engine.
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.
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.SearchParameters
Set the user provided molecular weight ranges for the fractions.
setFractionMolecularWeights(HashMap<String, Double>) - Method in class com.compomics.util.experiment.identification.SearchParameters
Deprecated.
use setFractionMolecularWeightRanges instead
setFragmentationModel(String) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the name of the fragmentation model.
setFragmentIonAccuracy(Double) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the fragment ion m/z tolerance.
setFragmentIonAccuracy(double) - Method in class com.compomics.util.preferences.AnnotationPreferences
Sets the fragment ion accuracy.
setGeneName(String) - Method in class com.compomics.util.protein.Header
 
setGenerateQuery(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets a boolean indicating whether a blast query shall be generated.
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.
setHitListLength(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the length of the hit list for OMSSA.
setID(String) - Method in class com.compomics.util.protein.Header
 
setIdentifier(String) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Sets the references identifier.
setIdFilter(IdFilter) - Method in interface com.compomics.util.preferences.gui.ImportSettingsDialogParent
Sets the identification filter used.
setIndeterminate() - Method in class com.compomics.util.gui.waiting.ProgressDialog
This method makes the progressbar indeterminate.
setIndeterminate(boolean) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Sets whether the primary progress bar is indeterminate or not.
setIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
 
setIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
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.
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.
setIntensityIonTable(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Set if the intensity or m/z ion table should be shown.
setIntensityValues(double[]) - Method in class com.compomics.util.io.PklFile
 
setIntermidiate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Deprecated.
Replaced by setIndeterminate, from utilities 3.1.17.
setIonColor(Ion, Color) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Sets an annotation color for the given ion.
setIonId(int) - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
Sets the reporter ion id
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.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.SearchParameters
Setter for the second kind of ion searched, indexed by its single letter code, for example "a".
setIsDB(Boolean) - Method in class com.compomics.util.experiment.identification.Identification
Sets whether the identification matches should be stored in a database or serialized files.
setIsPpm(boolean) - Method in class com.compomics.util.preferences.IdFilter
Sets whether the mass tolerance is in ppm (true) or Dalton (false).
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.
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.
setMainMatch(String) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
Sets the main match.
setMainMatch(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Sets the main protein accession after protein inference.
setMascotMaxEvalue(double) - Method in class com.compomics.util.preferences.IdFilter
Sets the maximal Mascot e-value allowed.
setMass(double) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
Method to set the mass of the reporter ion.
setMassShift(double) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Sets an m/z shift on all ions.
setMatchChanged(QuantificationMatch) - Method in class com.compomics.util.experiment.quantification.Quantification
Indicates that a match was changed, it will thus be serialized again if needed.
setMax(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Deprecated.
use waiting handler method instead
setMaxChargeSearched(Charge) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the maximal charge searched.
setMaxEValue(Double) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the maximal e-value searched for.
setMaxIntensity(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
Sets the maximum precursor intensity in this file.
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.preferences.IdFilter
Sets the maximal m/z deviation allowed.
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).
setMaxPepLength(int) - Method in class com.compomics.util.preferences.IdFilter
Sets the maximal peptide length allowed.
setMaxPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the maximal peptide length allowed.
setMaxProgressValue(int) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Set the maximum value of the progress bar.
setMaxProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
 
setMaxProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Set the maximum value of the progress bar.
setMaxProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setMaxRT(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
Sets the maximal RT in this file.
setMaxSecondaryProgressValue(int) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Set the maximum value of the secondary progress bar.
setMaxSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Sets the maximal value of the progress bar.
setMaxSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Set the maximum value of the secondary progress bar.
setMaxSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
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.
setMessage(String) - Method in class com.compomics.util.gui.waiting.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
setMinChargeSearched(Charge) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the minimal charge searched.
setMiniature(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the graphics panel is to be drawn in a minature form.
setMinimalChargeForMultipleChargedFragments(Charge) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.
setMinPepLength(int) - Method in class com.compomics.util.preferences.IdFilter
Sets the maximal peptide length allowed.
setMinPeptideLength(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the minimal peptide length allowed.
setMinRT(Double) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
Sets the minimum RT in this file.
setMinus1(double) - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
Sets the reporter ion -1 Da amount
setMinus2(double) - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
Sets the reporter ion -2 Da amount
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
 
setModificationProfile(ModificationProfile) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the modification profile of the project.
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.
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.PTM
Sets the PTM name.
setName(String) - Method in class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter
Sets the name of the filter.
setName(String) - Method in class com.compomics.util.pride.CvTerm
 
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.
setnCache(int) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Sets the size of the cache.
setNeutralLosses(ArrayList<NeutralLoss>) - Method in class com.compomics.util.experiment.biology.PTM
Sets the neutral losses possibly encountered with this modification.
setNeutralLossesSequenceDependant(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Set whether neutral losses are considered only for amino acids of interest or not.
setnMissedCleavages(Integer) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the allowed number of missed cleavages.
setnTermGap(double) - Method in class com.compomics.util.denovo.PeptideAssumptionDetails
Sets the N-term Gap.
setObjectCache(ObjectsCache) - Method in class com.compomics.util.db.ObjectsDB
Sets the object cache to be used by this database.
setOmssaIndex(String, int) - Method in class com.compomics.util.preferences.ModificationProfile
Sets the OMSSA index for a given modification.
setOmssaMaxEvalue(double) - Method in class com.compomics.util.preferences.IdFilter
Sets the OMSSA maximal e-value allowed.
setOntology(String) - Method in class com.compomics.util.pride.CvTerm
 
setOrderedListOfSpectrumFileNames(ArrayList<String>) - Method in class com.compomics.util.experiment.identification.Identification
Set the ordered list of spectrum file names.
setParametersFile(File) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the parameter file loaded.
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 Trasfers.
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
 
setPeakList(HashMap<Double, Peak>) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
Sets the peak list.
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.
setPepNovoScore(double) - Method in class com.compomics.util.denovo.PeptideAssumptionDetails
Sets the pep novo score.
setPeptide(Peptide, int) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Sets a new peptide to match.
setPeptideFDR(double) - Method in class com.compomics.util.preferences.ProcessingPreferences
Sets the initial peptide FDR.
setPeptideShakerPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Set the path to the PeptideShaker installation.
setPercentLength(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the length of the reference area in percent.
setPlus1(double) - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
Sets the reporter ion +1 Da amount
setPlus2(double) - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
Sets the reporter ion +2 Da amount
setPmid(String) - Method in class com.compomics.util.pride.prideobjects.Reference
Set the PubMed ID of the reference.
setPointSize(Integer) - Method in class com.compomics.util.gui.spectrum.ChromatogramPanel
This method allows the caller to set the point size for the chromatogram.
setPosition(int) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to set the cleavage position for the Enzyme.
setPrecurorCharge(int) - Method in class com.compomics.util.io.PklFile
 
setPrecursorAccuracy(Double) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the precursor tolerance.
setPrecursorAccuracyType(SearchParameters.PrecursorAccuracyType) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets the precursor accuracy type.
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
 
setPreferencesFromSearchParamaers(SearchParameters) - Method in class com.compomics.util.preferences.AnnotationPreferences
Updates the annotation parameters based on the search parameters
setProfile(double[][]) - Method in class com.compomics.util.gui.protein.ModificationProfile
Sets the profile.
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.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.ProgressDialog
This method sets the progress to the specified value.
setProteinConfidenceMwPlots(Double) - Method in class com.compomics.util.preferences.ProcessingPreferences
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
 
setProteinFDR(double) - Method in class com.compomics.util.preferences.ProcessingPreferences
Sets the initial protein FDR.
setPsmFDR(double) - Method in class com.compomics.util.preferences.ProcessingPreferences
Sets the initial PSM FDR.
setPtmName(String) - Method in class com.compomics.util.gui.protein.ModificationProfile
Sets the PTM name.
setPtmToPrideMap(PtmToPrideMap) - Method in class com.compomics.util.pride.PrideObjectsFactory
Sets a new ptm to PRIDE map.
setRank(int) - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Set the rank of the PeptideAssumption.
setRatios(HashMap<Integer, Ratio>) - Method in class com.compomics.util.experiment.quantification.QuantificationMatch
Sets new peptide ratios.
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.
setReferenceIntensity(double) - Method in class com.compomics.util.experiment.quantification.matches.PsmQuantification
Sets the reference intensity used to estimate the ratios
setReferences(ArrayList<Reference>) - Method in class com.compomics.util.pride.prideobjects.ReferenceGroup
Set the reference.
setRelimsPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Set the path to the Relims installation.
setRemovePrecursor(Boolean) - Method in class com.compomics.util.experiment.identification.SearchParameters
Sets whether the precursor shall be removed for OMSSA
setRemoveUnknownPTMs(boolean) - Method in class com.compomics.util.preferences.IdFilter
Set whether unknown PTMs shall be removed.
setReporterIons(ArrayList<ReporterIon>) - Method in class com.compomics.util.experiment.biology.PTM
Sets the reporter ions possibly encountered with this modification.
setReporterPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Set the path to the PeptideShaker installation.
setResolution(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
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 interface com.compomics.util.gui.waiting.WaitingHandler
Set the analysis as canceled.
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
 
setRunFinished() - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Set the analysis as finished.
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
 
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.SearchParameters
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.
setSearchedOMSSAIndexes(ModificationProfile) - Method in class com.compomics.util.experiment.biology.PTMFactory
Set the OMSSA indexes used for this search.
setSearchGuiPath(String) - Method in class com.compomics.util.preferences.UtilitiesUserPreferences
Set the path to the SearchGUI installation.
setSecondaryProgressDialogIndeterminate(boolean) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Sets the secondary progress bar to indeterminate or not.
setSecondaryProgressDialogIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Makes the dialog indeterminate or not indeterminate.
setSecondaryProgressDialogIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Sets the secondary progress bar to indeterminate or not.
setSecondaryProgressDialogIndeterminate(boolean) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setSecondaryProgressValue(int) - Method in interface com.compomics.util.gui.waiting.WaitingHandler
Sets the secondary progress bar to the given value.
setSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Sets the value of the progress bar.
setSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog
Sets the secondary progress bar to the given value.
setSecondaryProgressValue(int) - Method in class com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl
 
setSelectedExportFolder(String) - Method in interface com.compomics.util.gui.export_graphics.ExportGraphicsDialogParent
Set the default folder to use for exporting the graphics.
setSelectedExportFolder(String) - Method in class com.compomics.util.gui.XYPlottingDialog
 
setSelectedPositions(Integer[]) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
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.
setShortName(String) - Method in class com.compomics.util.experiment.biology.PTM
Sets the short PTM name.
setShortName(String, String) - Method in class com.compomics.util.experiment.biology.PTMFactory
Sets the short name for a modification.
setShowAllPeaks(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Set if all peaks or just the annotated ones are to be shown.
setShowBars(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Set if the bars in the bubble plot are to be shown or not.
setShowForwardIonDeNovoTags(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Set if the automatic forward ion de novo tags are to be shown.
setShowPrecursorDetails(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set wheter the precursor details are to be shown.
setShowResolution(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set wheter the resolution is to be shown.
setShowRewindIonDeNovoTags(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Set if the automatic rewind ion de novo tags are to be shown.
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.
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.
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.
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
setStart(double) - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Set the start value.
setStart_block(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
setStart_protein(int) - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
setString(String) - Method in class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX
Sets the string to display in the progrss bar.
setSubscriptAnnotationNumbers(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the numbers in the peak annotations are to be subscripted.
setTarget(Integer) - Method in class com.compomics.util.experiment.biology.AminoAcidPattern
Sets the index of the amino acid of interest in the pattern.
setTargeted(int, ArrayList<AminoAcid>) - 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
 
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.
setTitle(String) - Method in class com.compomics.util.messages.FeedBack
Sets the title.
setTitle(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
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.
setType(FeedBack.FeedBackType) - Method in class com.compomics.util.messages.FeedBack
Sets the feedback 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 possble to stop nicely.
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.
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
 
setValueAt(Object, int, int) - Method in class com.compomics.util.sun.TableMap
 
setValueAt(Object, int, int) - Method in class com.compomics.util.sun.TableSorter
 
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 interface com.compomics.util.gui.waiting.WaitingHandler
Sets the text describing what is currently waited for.
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
 
setX(double) - Method in class com.compomics.util.XYZDataPoint
 
setXAxisStartAtZero(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
This method sets the start value of the x-axis to zero.
setXtandemMaxEvalue(double) - Method in class com.compomics.util.preferences.IdFilter
Sets the OMSSA maximal e-value allowed.
setY(double) - Method in class com.compomics.util.XYZDataPoint
 
setYAxisZoomExcludesBackgroundPeaks(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the automatic y-axis zoom only considers the anotated peaks.
setYAxisZoomExcludesBackgroundPeaks(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Set if the automatic y-axis zoom only considers the anotated 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
 
showAllPeaks - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If false, only the annotated peaks will be shown.
showAllPeaks() - Method in class com.compomics.util.preferences.AnnotationPreferences
If true, all peaks are shown, false displays the annotated peaks, and the non-annotated in the background.
showAnnotatedPeaksOnly(boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
If true only the annotated peaks will be drawn.
showBars() - Method in class com.compomics.util.preferences.AnnotationPreferences
If true, bars are shown in the bubble plot highlighting the ions.
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.preferences.AnnotationPreferences
Returns true if the automatic forward ion de novo tags are to be shown.
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 precuror 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.preferences.AnnotationPreferences
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.
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
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.
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
 
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 - Interface in com.compomics.util.gui.interfaces
This interface describes the behaviour for a spectrum annotation.
SpectrumAnnotator - Class in com.compomics.util.experiment.identification
The spectrum annotator annotates peaks in a spectrum.
SpectrumAnnotator() - Constructor for class com.compomics.util.experiment.identification.SpectrumAnnotator
Constructor.
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, ...).
SpectrumFilter - Class in com.compomics.util.experiment.filters.massspectrometry
This class represent all spectrum filters which will be used to filter spectra.
SpectrumFilter() - Constructor for class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter
 
spectrumIdentification - Variable in class com.compomics.util.experiment.identification.Identification
Deprecated.
use file specific mapping instead
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, PeptideAssumption) - 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.
spectrumMatchLoaded(String) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Indicates whether a spectrum match is loaded.
spectrumMatchLoaded(String) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Indicates whether a spectrum match is loaded.
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, 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, int, 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, int, 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, int, 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, int, 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, int, 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.
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
Returns a list of file names for inputs of comma separated files.
spo - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
SPO - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
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.
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
Created by IntelliJ IDEA.
StartEndPosition(int, int) - Constructor for class com.compomics.util.pdbfinder.das.readers.StartEndPosition
 
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.
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.
startRelims(JFrame) - Static method in class com.compomics.software.ToolFactory
Deprecated.
use PeptideShaker's own Reshake option instead.
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>, File, File) - 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.
strFileNameAndPath - Variable in class com.compomics.util.io.FTP
String to hold the file we are up/downloading
Sulfur - Class in com.compomics.util.experiment.biology.atoms
A sulfur atom.
Sulfur() - Constructor for class com.compomics.util.experiment.biology.atoms.Sulfur
Constructor.
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.
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.
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 - Static variable in interface com.compomics.util.gui.waiting.WaitingHandler
The tab space to add when using tab.
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.
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
 
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.
tarFolder(File, File, WaitingHandler) - Static method in class com.compomics.util.io.TarUtils
Tar a given folder in a file.
TarUtils - Class in com.compomics.util.io
This class contains convenience methods for taring files.
TarUtils() - Constructor for class com.compomics.util.io.TarUtils
 
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.
TEXTMODE - Static variable in class com.compomics.util.io.FolderMonitor
 
theoreticMass - Variable in class com.compomics.util.experiment.biology.Ion
 
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
 
THREONINE - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
Subtype int for a threonine immonium ion.
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
 
TimestampRenderer - Class in com.compomics.util.gui.renderers
This class
TimestampRenderer() - Constructor for class com.compomics.util.gui.renderers.TimestampRenderer
 
TMT0 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion TMT0.
TMT1 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion TMT1.
TMT2 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion TMT2.
TMT3 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion TMT3.
TMT4 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion TMT4.
TMT5 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Standard reporter ion TMT5.
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.
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.Mutation
 
toString() - Method in class com.compomics.util.experiment.massspectrometry.Charge
Returns a string representing the charge.
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 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 header.
toString(String) - Method in class com.compomics.util.protein.Header
This method reports on the entire 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
 
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.
Tryptophan - Class in com.compomics.util.experiment.biology.aminoacids
Tryptophan
Tryptophan() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Tryptophan
 
TRYPTOPHAN - Static variable in class com.compomics.util.experiment.biology.ions.ImmoniumIon
Subtype int for a tryptophan immonium ion.
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.
TypeSelection - Class in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation
A filter type selector dialog.
TypeSelection(Frame) - Constructor for class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.TypeSelection
Creates a new TypeSelection.
Tyrosine - Class in com.compomics.util.experiment.biology.aminoacids
Tyrosine
Tyrosine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Tyrosine
 
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.Glycon
Final index for underivated masses.
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.
unreadLine() - Method in class com.compomics.util.io.PushBackStringReader
This method 'unreads' a line of text from the Buffer.
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.
updateCache() - Method in class com.compomics.util.db.ObjectsCache
Updates the cache according to the memory settings.
updateFilterSettingsField(String) - Method in interface com.compomics.util.preferences.gui.ImportSettingsDialogParent
Sets the filter settings field to the given text.
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
updateMatch(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Updates a match.
updateMatch(QuantificationMatch) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Updates a match.
updateModifications() - Method in class com.compomics.util.gui.ptm.ModificationsDialog
Updates the modification lists and tables.
updateModifications() - Method in interface com.compomics.util.gui.ptm.PtmDialogParent
Update the ptm inforamtion in the parent.
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.
updatePeptideMatch(PeptideMatch) - Method in class com.compomics.util.experiment.identification.Identification
Updates a peptide match in the database.
updatePeptideMatch(PeptideMatch) - Method in class com.compomics.util.experiment.identification.IdentificationDB
Updates a peptide match.
updatePeptideMatch(PeptideQuantification) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
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.
updatePeptideParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Updates a peptide match parameter.
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.
updateProteinMatch(ProteinQuantification) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
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.
updateProteinParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Updates a protein match parameter.
updatePtmSelection() - Method in class com.compomics.util.gui.ptm.ModificationsDialog
Updates the PTM selection in the default table.
updateSpectrumMapping() - Method in class com.compomics.util.experiment.identification.Identification
Converts the old spectrum keys structure into the mapped version.
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.
updateSpectrumMatch(PsmQuantification) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
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.
updateSpectrumParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.QuantificationDB
Updates a spectrum match parameter.
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.
urParameters - Variable in class com.compomics.util.experiment.identification.Identification
Deprecated.
use the database instead
useAutomaticAnnotation(boolean) - Method in class com.compomics.util.preferences.AnnotationPreferences
Sets whether the default PeptideShaker annotation should be used.
useAutomaticAnnotation() - Method in class com.compomics.util.preferences.AnnotationPreferences
Returns whether PeptideShaker should automatically set the annotations.
useBoldFont() - Method in class com.compomics.util.gui.spectrum.ReferenceArea
Returns true of the label should be in bold.
useIntensityIonTable() - Method in class com.compomics.util.preferences.AnnotationPreferences
If true, the ion table is shown as an intensity versionm, false displays the standard Mascot version.
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_PREFERENCES_FILE - Static variable in class com.compomics.util.preferences.UtilitiesUserPreferences
Location of the user preferences file.
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
 
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.
validateInput() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.CombDialog
Validates the user input.
validateInput() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.FingerprintDialog
Validates the user input.
validateInput() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.MzDialog
Validates the user input.
validateInput() - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.filtercreation.PeakDialog
Validates the user input.
validateModifications(Peptide) - Method in class com.compomics.util.preferences.IdFilter
Validates the modifications of a peptide.
validatePeptideAssumption(PeptideAssumption) - Method in class com.compomics.util.preferences.IdFilter
Validates the peptide assumption based on the peptide length and maximal e-values allowed.
validatePrecursor(PeptideAssumption, String, SpectrumFactory) - Method in class com.compomics.util.preferences.IdFilter
Validates the mass deviation of a peptide assumption.
validateProteins(Peptide) - Method in class com.compomics.util.preferences.IdFilter
Validates a peptide depending on its protein inference status
validateSpectrum(MSnSpectrum) - Method in class com.compomics.util.experiment.filters.massspectrometry.SpectrumFilter
Indicates whether a spectrum passed the filter.
validateSpectrum(MSnSpectrum) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.And
Returns a boolean indicating whether all implemented filters validated the spectrum.
validateSpectrum(MSnSpectrum) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.CombFilter
Returns a boolean indicating whether the filter m/z comb was found in the spectrum.
validateSpectrum(MSnSpectrum) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.FingerprintPattern
Returns a boolean indicating whether the filter fingerprint was found in the spectrum.
validateSpectrum(MSnSpectrum) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.MzFilter
Indicates whether a peak was found in the spectrum at the desired m/z in the given intensity quartile.
validateSpectrum(MSnSpectrum) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.Or
Returns a boolean indicating whether one of the implemented filters validated the spectrum.
validateSpectrum(MSnSpectrum) - Method in class com.compomics.util.experiment.filters.massspectrometry.spectrumfilters.PeakFilter
Indicates whether a peak was found in the spectrum at the desired m/z in the given intensity quartile.
Valine - Class in com.compomics.util.experiment.biology.aminoacids
Valine
Valine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Valine
 
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.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.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.SearchParameters.PrecursorAccuracyType
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.QuantificationMatch.MatchType
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.gui.spectrum.GraphicsPanel.GraphicsPanelType
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.protein.Header.DatabaseType
Returns the enum constant of this type with the specified name.
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.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.SearchParameters.PrecursorAccuracyType
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.QuantificationMatch.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.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.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.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.protein.Header.DatabaseType
Returns an array containing the constants of this enum type, in the order they are declared.
VARIABLE_MODIFICATIONS - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Deprecated.
use the SearchParameters class instead
VERIFIER_FACTORY - Static variable in class com.compomics.util.pride.validation.PrideXmlValidator
The verifier factory.
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
 
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.
WaitingHandler - Interface in com.compomics.util.gui.waiting
An interface for code dealing with how to handle information that is displayed to the user during the loading of new projects.
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
 
warning(SAXParseException) - Method in class com.compomics.util.pride.validation.XMLValidationErrorHandler
Receive notification of a warning.
welcomeMsg - Variable in class com.compomics.util.io.FTP
Welcome message from the server, if any.
writeAplFile(File, File, String) - Static method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
Writes an apl file from an MGF file.
writeIndex(MgfIndex, File) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Writes the given mgf file index in the given directory.
writeMgf(BufferedWriter) - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum
Writes the spectrum in the mgf format using the given writer
writeObject(Object, File) - Static method in class com.compomics.util.io.SerializationUtils
Writes an object to the destination file.
writeOmssaModificationsFiles(File, File, File) - Method in class com.compomics.util.experiment.biology.PTMFactory
Write the OMSSA modification files to the given folder.
writeOmssaUserModificationFile(File) - Method in class com.compomics.util.experiment.biology.PTMFactory
Writes the OMSSA modification file corresponding to the PTMs loaded in the factory in the given file.
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
 
X_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
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 interface com.compomics.util.experiment.identification.Advocate
X!Tandem index.
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, ArrayList<String>, Image, Image, boolean) - Constructor for class com.compomics.util.gui.XYPlottingDialog
Creates a new XYPlottingDialog.
XYPlottingDialog.NormalKernelDensityEstimator - Class in com.compomics.util.gui
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.
XYPlottingDialog.NormalKernelDensityEstimator() - Constructor for class com.compomics.util.gui.XYPlottingDialog.NormalKernelDensityEstimator
 
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.
XYPlottingDialog.SelectedValuesTableFilter() - Constructor for class com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
 
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.
yAxisZoomExcludesBackgroundPeaks - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If true, the automatic y-axis zoom excludes the background peaks.
yAxisZoomExcludesBackgroundPeaks() - Method in class com.compomics.util.preferences.AnnotationPreferences
Returns true if the automatic y-axis zoom excludes 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
 
Z_ION - Static variable in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Identifier for a z ion.
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