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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_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.
addAnalysisSet(Sample, SampleAnalysisSet) - Method in class com.compomics.util.experiment.MsExperiment
Method to link an analysis set to an experiment
addAnnotation(IonMatch) - Method in class com.compomics.util.experiment.identification.PeptideAssumption
add a fragment ion annotation
addBlock(PdbBlock) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
addElement(MolecularElement, Integer) - Method in class com.compomics.util.protein.MolecularFormula
Method to add MolecularElements to this formula
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
addIonMatch(int, IonMatch) - Method in class com.compomics.util.experiment.quantification.reporterion.quantification.PsmQuantification
Method to add a match between a peak and a reporter ion
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
addMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
adds a parameter with a corresponding match key which will be loaded in the memory.
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
 
addPeak(Peak) - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
Adds a peak to the spectrum peak list
addPeptideMatch(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
add a subordinated peptide match
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.
addPeptideQuantification(String) - Method in class com.compomics.util.experiment.quantification.reporterion.quantification.ProteinQuantification
Adds a new peptide quantification in the protein quantification
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.
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.
addPsmQuantification(String) - Method in class com.compomics.util.experiment.quantification.reporterion.quantification.PeptideQuantification
Adds a new psm quantification in the psm quantification map
addQuantificationParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.Quantification
adds a parameter with a corresponding quantification key which will be loaded in the memory.
addQuantificationResults(int, 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.reporterion.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.
addSpectra(File) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Add spectra to the factory
addSpectra(File, JProgressBar) - 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
Add a spectrum match to the spectrum matches map.
addSpectrumMatch(Set<SpectrumMatch>) - Method in class com.compomics.util.experiment.identification.Identification
Add a set of spectrumMatches to the model
addSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.matches.PeptideMatch
add a spectrum match
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.
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
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 rescoring algorithm, etc.
AdvocateFactory - Class in com.compomics.util.experiment.identification
This factory will provide adapted advocates when requested.
Alanine - Class in com.compomics.util.experiment.biology.aminoacids
Alanine
Alanine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Alanine
 
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. 0 means completely see-through, 1 means opaque.
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
 
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.
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, JProgressBar) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Appends decoy sequences to the desired file while displaying progress.
AQUA - Static variable in class com.compomics.util.AlternateRowColoursJTable
A rather pronounced AQUA colour (r=183, g=222, b=232).
Arginine - Class in com.compomics.util.experiment.biology.aminoacids
Arginine
Arginine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Arginine
 
ascii() - Method in class com.compomics.util.io.FTP
Set transfer type to 'A' (ascii transfer).
AScore - Class in com.compomics.util.experiment.identification
This class scores PTM locations using the A-score.
AScore() - Constructor for class com.compomics.util.experiment.identification.AScore
 
asMgf() - Method in class com.compomics.util.experiment.massspectrometry.MSnSpectrum
return 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
 
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
 
automatedMemoryManagement - Variable in class com.compomics.util.experiment.identification.Identification
boolean indicating whether the memory management should be done automatically.
automatedMemoryManagement - Variable in class com.compomics.util.experiment.quantification.Quantification
boolean indicating whether the memory management should be done automatically.
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
 
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
 
binary() - Method in class com.compomics.util.io.FTP
Set transfer type to 'I' (binary transfer).
buildPeptidesAndProteinQuantifications(Identification) - 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() - Method in class com.compomics.util.experiment.identification.Identification
Creates the peptides and protein instances based on the spectrum matches.
ByteArrayRenderer - Class in com.compomics.util.gui.renderers
This class
ByteArrayRenderer() - Constructor for class com.compomics.util.gui.renderers.ByteArrayRenderer
 

C

C - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
C - Static variable in class com.compomics.util.experiment.biology.Atom
 
C_TERM_ENZYMATIC - Static variable in class com.compomics.util.protein.Enzyme
 
cacheSize - Variable in class com.compomics.util.experiment.identification.Identification
The cache size in number of matches. 20000 by default: should be enough to contain a velos file.
cacheSize - Variable in class com.compomics.util.experiment.quantification.Quantification
The cache size in number of matches. 20000 by default: should be enough to contain a velos file.
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.
cancelProgress() - Method in interface com.compomics.util.gui.dialogs.ProgressDialogParent
Cancel the process in the frame or dialog that opened the progress bar.
Carbon - Class in com.compomics.util.experiment.biology.atoms
Carbon
Carbon() - Constructor for class com.compomics.util.experiment.biology.atoms.Carbon
Constructor
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
CH4OS - Class in com.compomics.util.experiment.biology.neutrallosses
Neutral loss CH4OS, likely to be encountered on fragment from peptides containing an oxidized methionine.
CH4OS() - Constructor for class com.compomics.util.experiment.biology.neutrallosses.CH4OS
Constructor
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
Reference for the charge estimation
chargeValidated(PeptideFragmentIon, 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
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.
clearModificationMAtches() - Method in class com.compomics.util.experiment.biology.Peptide
Clears the list of imported modification matches
cleave(Protein) - Method in class com.compomics.util.protein.DualEnzyme
This method is the focus of the Enzyme instance.
cleave(Protein) - Method in class com.compomics.util.protein.Enzyme
This method is the focus of the Enzyme instance.
cleave(Protein, int, int) - Method in class com.compomics.util.protein.Enzyme
This method is the focus of the Enzyme instance.
cleave(Protein) - Method in class com.compomics.util.protein.RegExEnzyme
 
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.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.
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.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.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.biology.neutrallosses - package com.compomics.util.experiment.biology.neutrallosses
 
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. e.g., pepties, proteins, modifications and spectra.
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.reporterion - package com.compomics.util.experiment.quantification.reporterion
This package contains experiment classes related to reporter ions.
com.compomics.util.experiment.quantification.reporterion.quantification - package com.compomics.util.experiment.quantification.reporterion.quantification
This package contains experiment classes related to quantification by reporter ions.
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.dialogs - package com.compomics.util.gui.dialogs
This package contains GUI dialogs.
com.compomics.util.gui.events - package com.compomics.util.gui.events
This package contains GUI event classes.
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.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.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.math - package com.compomics.util.math
 
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.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.
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
This constructor requests the command-line String[] as well as a String[] with a list of options which in turn take a parameter.
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.
CompomicsTools - Enum in com.compomics.util.enumeration
This enum types all computational omics tools and libraries that make use of the utilities library.
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.dialogs
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.dialogs.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.dialogs.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.
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.protein.AASequenceImpl
This method reports whether a certain residu (or fixed sequence String) is found in the current sequence.
controlSocket - Variable in class com.compomics.util.io.FTP
Socket for communicating commands with the server.
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).
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
createDefaultTableHeader() - Method in class com.compomics.util.gui.spectrum.FragmentIonTable
 
createFastaIndex(File) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
Static method to create a fasta index for a fasta file.
createFastaIndex(File, JProgressBar) - Static method in class com.compomics.util.experiment.identification.SequenceFactory
Static method to create a fasta index for a fasta file.
createImageIcon(String) - Static method in class com.compomics.util.io.filefilters.FileFilterUtils
Returns an ImageIcon, or null if the path was invalid.
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).
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
 

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
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.dialogs
This class provides a simple date chooser.
DateChooser(JFrame) - Constructor for class com.compomics.util.gui.dialogs.DateChooser
Creates a new DataChooser object.
DateChooser(JFrame, Calendar) - Constructor for class com.compomics.util.gui.dialogs.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.
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.
decoyFlags - Static variable in class com.compomics.util.experiment.identification.SequenceFactory
Recognized flags for a decoy protein
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.
deleteDir(File) - Static method in class com.compomics.util.Util
Deletes all files and subdirectories under dir.
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
Returns the peak color to be used for the given peak label.
determineFragmentIonColor(PeptideFragmentIon) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Returns the peak color to be used for the given peak label.
determineFragmentIonColor(String) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Returns the color to use for the given fragment ion label.
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.
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.dialogs.ProgressDialogX
This method makes it impossible to close the dialog.
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.
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. for a C-terminal cutter with N-terminal specificty for 'D' and C-terminal specificity for 'R': (D)XXXXXR; for an N-terminal cutter with N-terminal specificty for 'W' and C-terminal specificity for 'K': WXXXXX(K).
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
 
ELEMENTARY_ION - Static variable in class com.compomics.util.experiment.biology.Ion
Ion family type static index for elementary ions
emptyCache(ProgressDialogX) - Method in class com.compomics.util.experiment.identification.Identification
Empties the cache and serializes everything in the specified serialization folder
emptyCache(ProgressDialogX) - Method in class com.compomics.util.experiment.quantification.Quantification
Empties the cache and serializes everything in the specified serialization folder
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
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.
EnzymeFactory - Class in com.compomics.util.experiment.biology
This factory will provide the implemented enzymes.
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.
EVALUE_CUTOFF - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the e-value cutoff
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.
EXTENTION - Static variable in class com.compomics.util.experiment.identification.Identification
Extention for a serialized hit. cuh for Compomics Utilities Hit.
EXTENTION - Static variable in class com.compomics.util.experiment.quantification.Quantification
Extention for a serialized hit. cuh for Compomics Utilities Hit.

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!
familyType - Variable in class com.compomics.util.experiment.biology.Ion
Ion attribute - the ion family name
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
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
 
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
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.
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>, ArrayList<PeptideFragmentIon.PeptideFragmentIonType>, ArrayList<NeutralLoss>, boolean, boolean, boolean) - Static method in class com.compomics.util.gui.spectrum.SpectrumPanel
Filters the annotations and returns the annotations matching the currently selected types.
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
 
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
Reference for the fixed modifications
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.
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.
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
Reference for the fragment ion mass tolerance
FRAGMENT_ION_TYPE_1 - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the type of fragment ion 1
FRAGMENT_ION_TYPE_2 - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the type of fragment ion 2
FragmentFactory - Class in com.compomics.util.experiment.biology
This factory generates the expected fragment ions from a peptide sequence.
FragmentIonTable - Class in com.compomics.util.gui.spectrum
Creates a fragment ion table with the detected fragment ions.
FragmentIonTable(Peptide, ArrayList<IonMatch>, ArrayList<PeptideFragmentIon.PeptideFragmentIonType>, HashMap<NeutralLoss, Integer>, 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<PeptideFragmentIon.PeptideFragmentIonType>, HashMap<NeutralLoss, Integer>, 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
 
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.
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.
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() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the absolute matching error in Da.
getAccession() - Method in class com.compomics.util.experiment.biology.Protein
Getter for the protein accession
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.
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 the next feature 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
getAllModificationTitles() - Static method in class com.compomics.util.protein.ModificationFactory
This method returns all modification titles known to the Factory.
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() - 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
getAllSpectrumMatches() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MascotIdfileReader
a method to get all the spectrum matches
getAllSpectrumMatches() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.OMSSAIdfileReader
returns all spectrum matches found in the inspected file
getAllSpectrumMatches() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.XTandemIdfileReader
Method which returns all spectrum matches found in the file.
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(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
getAnalysisSet(Sample) - Method in class com.compomics.util.experiment.MsExperiment
Returns the analysis set corresponding to a sample
getAnnotations() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
retrieves all fragment ion annotation
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, PTM, int, MSnSpectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType>, HashMap<NeutralLoss, Integer>, ArrayList<Integer>, double) - Static method in class com.compomics.util.experiment.identification.AScore
Returns the A-score for the best PTM location.
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.
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
 
getC13() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Returns the number of 1Da intervals between the measured mass and the theoretical mass
getCacheSize() - Method in class com.compomics.util.experiment.identification.Identification
Returns the cache size in number of matches
getCacheSize() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
returns the cache size
getCacheSize() - Method in class com.compomics.util.experiment.quantification.Quantification
Returns the cache size in number of matches
getCharge() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
Getter for the charge.
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 +.
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.
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 residus of the Enzyme.
getCleavage() - Method in class com.compomics.util.protein.Enzyme
Simple getter for the cleavagable residus 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() - 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.
getColumnClass(int) - Method in class com.compomics.util.db.DBResultSet
Returns Object.class regardless of columnIndex.
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.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.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
getContentPane() - Method in class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
This methods gives a JPanel holding everything from this frame
getControlSample() - Method in class com.compomics.util.experiment.quantification.Ratio
returns the reference label indexed by its corresponding reporter ion index
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: [ID]|[accession_string] This is mostly useful for appending this core as an addendum to another header.
getCorrectionFactors() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethod
Returns the correction factors corresponding to the reporter ions
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(ArrayList<PeptideFragmentIon.PeptideFragmentIonType>, HashMap<NeutralLoss, Integer>, 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
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
 
getDefaultLosses(Peptide, ArrayList<NeutralLoss>) - Static method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the neutral losses map by default for a given peptide and a given list of neutral losses
getDefaultLosses(Peptide) - Static method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the possible neutral losses expected by default for a given peptide
getDeltaMass(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.
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.
getDifference() - Method in class com.compomics.util.pdbfinder.das.readers.AlignmentBlock
 
getDifference() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
getElement() - Method in class com.compomics.util.general.IsotopicElement
Getter for the MolecularElement
getElement() - Method in exception com.compomics.util.general.UnknownElementMassException
Simple getter for the element variable.
getElementCount(MolecularElement) - Method in class com.compomics.util.protein.MolecularFormula
Getter for the count of a specific element
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
 
getEnzyme(String) - Method in class com.compomics.util.experiment.biology.EnzymeFactory
Returns the enzyme corresponding to the given name
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() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Deprecated. replaced by getAbsoluteError() and getRelativeError()
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].
getEValue() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
returns the e-value assigned by the advocate
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.
getExpectedIons(ArrayList<PeptideFragmentIon.PeptideFragmentIonType>, HashMap<NeutralLoss, Integer>, ArrayList<Integer>, Peptide, int) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the expected ions in a map indexed by the possible charges Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.
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(File) - Static method in class com.compomics.util.io.filefilters.FileFilterUtils
Get the extension of a file.
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
getFastaIndex(File) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Returns the file index of a fasta file.
getFastaIndex(File, JProgressBar) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Returns the file index of a fasta file.
getFeatureId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getFeatureLabel() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
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
Returns the name of the file to use for serialization/deserialization
getFileName() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.MascotIdfileReader
getter for the file name
getFileName() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.OMSSAIdfileReader
get the file name
getFileName() - Method in class com.compomics.util.experiment.io.identifications.idfilereaders.XTandemIdfileReader
getter for the file name
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(String) - Method in class com.compomics.util.experiment.quantification.Quantification
Returns the name of the file to use for serialization/deserialization
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(String) - Static method in class com.compomics.util.Util
An OS independent getName alternative.
getFileReader(File) - Method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory
This method returns the proper identification file reader depending on the format of the provided file
getFirstHit(int) - Method in class com.compomics.util.experiment.identification.matches.SpectrumMatch
Returns the first hit obtained using the specified advocate
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.
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
 
getFragmentIons(Peptide) - Method in class com.compomics.util.experiment.biology.FragmentFactory
This method returns the theoretic fragment ions expected from a peptide sequence
getFullHeaderWithAddenda() - Method in class com.compomics.util.protein.Header
This method reports on the full header, with the addenda (if present).
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.
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.
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
getIndex() - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
Getter for the ion type
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(File) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Deserializes the index of the fasta file.
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.quantification.reporterion.ReporterMethod
returns the index of the method
getIndex() - Method in class com.compomics.util.experiment.refinementparameters.MascotScore
This method returns the index of the parameter
getIndexes() - Method in class com.compomics.util.experiment.identification.FastaIndex
Returns a map of all indexes of the fasta file (accession -> index)
getIndexes() - Method in class com.compomics.util.experiment.io.massspectrometry.MgfIndex
Returns the index map
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, JProgressBar) - 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.FragmentFactory
Static method which returns the instance of the factory
getInstance() - Static method in class com.compomics.util.experiment.biology.GlyconFactory
Static method to get the factory instance.
getInstance() - Static method in class com.compomics.util.experiment.biology.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
 
getInstance() - Static method in class com.compomics.util.io.PropertiesManager
Get the singleton instance to access properties of Computational Omics tools.
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.
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.
getIonFamilyType() - Method in class com.compomics.util.experiment.biology.Ion
getter for the ion family name
getIonId() - Method in class com.compomics.util.experiment.quantification.reporterion.CorrectionFactor
returns the reporter ion id
getIonType() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Returns the ion type (a, b, c, x, y, z) as a string.
getIsotopicDistribution() - Method in class com.compomics.util.protein.AASequenceImpl
This method gives the IsotopicDistribution for the sequence
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. index = SEQUENCE_mod1_mod2 with modifications ordered alphabetically.
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.reporterion.quantification.PeptideQuantification
 
getKey() - Method in class com.compomics.util.experiment.quantification.reporterion.quantification.ProteinQuantification
 
getKey() - Method in class com.compomics.util.experiment.quantification.reporterion.quantification.PsmQuantification
 
getKey() - Method in class com.compomics.util.experiment.quantification.reporterion.QuantificationMatch
returns the key of a match
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.
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
 
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.
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
method returns the key of the main match
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.
getMatchParameter(String, UrParameter) - Method in class com.compomics.util.experiment.identification.Identification
Returns the personalization parameter of the given match
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.dialogs.ProgressDialog
Returns the current maximum value for the progressbar.
getMaxIntensity() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
Returns the max intensity value.
getMaxMass() - Method in class com.compomics.util.gui.events.RescalingEvent
Returns the maximum mass.
getMaxMz() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
Returns the max mz value.
getMaxPadding() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the max padding (distance between the axes and the border of the panel).
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.
getMeasuredMass() - Method in class com.compomics.util.experiment.identification.PeptideAssumption
Returns the measured precursor mass according to the search engine
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.
getMessage() - Method in exception com.compomics.util.db.GeneratorException
This method returns a String with the description for this exception.
getMethod() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getMethodId() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
getMethodIndex() - Method in class com.compomics.util.experiment.quantification.QuantificationMethod
getter for the method index
getMethodName() - Method in class com.compomics.util.experiment.quantification.QuantificationMethod
This method returns the method name according to the set method index
getMethods() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
 
getMethodsNames() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
 
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.MascotIdfileReader
get the spectrum file name
getMgfFileNames() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Returns a list of loaded mgf files
getMinimumValue() - Method in class com.compomics.util.gui.dialogs.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.
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(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!)
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
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.
getModifiedSequence() - Method in class com.compomics.util.protein.AASequenceImpl
This method will return the sequence with annotated modifications.
getModifiedSequenceAsHtml(HashMap<String, Color>, boolean) - Method in class com.compomics.util.experiment.biology.Peptide
Returns the modified sequence as an HTML string with modification color coding
getModifiedSequenceAsString(boolean) - Method in class com.compomics.util.experiment.biology.Peptide
Returns the modified sequence as a string, e.g., NH2-PEPTIDE-COOH
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.
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.
getMzMLFileNames() - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Returns a list of loaded mzML files
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 enum com.compomics.util.enumeration.CompomicsTools
Getter for the name of the tool or library.
getName() - Method in class com.compomics.util.experiment.biology.Enzyme
Get the enzyme name
getName() - Method in class com.compomics.util.experiment.biology.ions.Glycon
Getter for the glycons name
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 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() - Method in class com.compomics.util.experiment.identification.advocates.SearchEngine
getter for the search engine name
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.
getNeutralLoss() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Returns the neutral loss (if any), the empty string if no loss.
getNeutralLosses() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Returns the neutral losses for this fragment ion
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 amount of missed cleavages using the specified enzyme
getNMissedCleavages(String, Enzyme) - Static method in class com.compomics.util.experiment.biology.Peptide
Returns the amount of missed cleavages using the specified enzyme for the given sequence
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 key
getNProteins() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Returns the number of proteins for this match
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.
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.
getOccurrence() - Method in class com.compomics.util.general.IsotopicElement
Getter for the occurrence of this element
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.
getOrientation() - Method in class com.compomics.util.pdbfinder.das.readers.DasFeature
 
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.
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.
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 given ion match 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.
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
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.quantification.Quantification
Returns a peptide quantification match
getPeptideMatches() - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
getter for the peptide matches
getPeptideQuantification() - Method in class com.compomics.util.experiment.quantification.Quantification
This method retrieves the quantification result at the protein level
getPeptideQuantification() - Method in class com.compomics.util.experiment.quantification.reporterion.quantification.ProteinQuantification
Getter for the corresponding peptide quantification
getPeptideSequences() - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
Get the set of peptide sequences.
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
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
getPotentialModificationSites(String, PTM) - Static method in class com.compomics.util.experiment.biology.Peptide
returns the potential modification sites as an ordered list of string. 0 is the first aa.
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(RandomAccessFile, 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
getPrecursorIntensity() - Method in class com.compomics.util.io.PklFile
 
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.
getPrimaryKeyColumns() - Method in class com.compomics.util.db.DBMetaData
This method reports on the primary key columns for the table.
getProfile() - Method in class com.compomics.util.gui.protein.ModificationProfile
Returns the profile.
getProgress() - Method in class com.compomics.util.gui.dialogs.ProgressDialog
This method reports on the current progress of the progressdialog.
getProgressBar() - Method in class com.compomics.util.gui.dialogs.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.
getProtein(String) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Returns the desired protein.
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.
getProteinMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
Returns a protein match.
getProteinMatch(String) - Method in class com.compomics.util.experiment.quantification.Quantification
Returns a protein quantification match
getProteinMatchKey(Peptide) - Static method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Convenience method which returns the protein key of a peptide
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
getPsmIDentificationToQuantification() - Method in class com.compomics.util.experiment.quantification.Quantification
This method retrieves the quantification result at the protein level
getPsmQuantification() - Method in class com.compomics.util.experiment.quantification.reporterion.quantification.PeptideQuantification
Getter for the corresponding spectrum quantification
getPTM(int) - Method in class com.compomics.util.experiment.biology.PTMFactory
get a PTM according to its 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
getter for a ptm according to its measured characteristics /!
getPTMIndex(String) - Method in class com.compomics.util.experiment.biology.PTMFactory
Returns the index of the desired modification
getPtmIterator() - Method in class com.compomics.util.experiment.biology.PTMFactory
returns an iterator on the imported PTM
getPtmMap() - Method in class com.compomics.util.experiment.biology.PTMFactory
getter for the index to PTM map
getPtmName() - Method in class com.compomics.util.gui.protein.ModificationProfile
Returns the PTM name.
getQuantification(int) - Method in class com.compomics.util.experiment.ProteomicAnalysis
returns quantification results obtain with a quantification method
getQuantificationParameter(String, UrParameter) - Method in class com.compomics.util.experiment.quantification.Quantification
Returns the personalization parameter of the given quantification
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.reporterion.QuantificationMatch
Getter for the peptide ratios
getReducedSpectra(MSnSpectrum, double) - Static method in class com.compomics.util.experiment.identification.AScore
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
getReferenceLabel() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Returns the reference label indexed by the corresponding reporter ion
getRelativeError() - Method in class com.compomics.util.experiment.identification.matches.IonMatch
Get the relative matching error in ppm.
getReplicateNumberList() - Method in class com.compomics.util.experiment.SampleAnalysisSet
Returns a list containing replicate numbers
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.quantification.reporterion.ReporterMethod
Returns the reporter ions used
getReporterMatches() - Method in class com.compomics.util.experiment.quantification.reporterion.quantification.PsmQuantification
Getter for the reporter matches
getReporterMethod() - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
returns the reporter method used
getResidues() - Method in class com.compomics.util.experiment.biology.PTM
getter for the residues affected by this modification
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 residus 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.
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.sun.TableMap
 
getRt() - Method in class com.compomics.util.experiment.massspectrometry.Precursor
Getter for the retention time.
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
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.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
getSearchEngine(File) - Method in class com.compomics.util.experiment.io.identifications.IdfileReaderFactory
This method return the search engine corresponding to the given file.
getSelectedDate() - Method in class com.compomics.util.gui.dialogs.DateChooser
This method returns a Calendar set at the selected date, or 'null' if no date was selected.
getSelectedPositions() - Method in class com.compomics.util.pdbfinder.pdb.PdbBlock
 
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.
getSerializationDirectory() - Method in class com.compomics.util.experiment.identification.Identification
Returns the serialization directory
getSerializationDirectory() - Method in class com.compomics.util.experiment.quantification.Quantification
Returns the serialization directory
getShortName() - Method in class com.compomics.util.experiment.biology.ions.Glycon
Getter for the glycons short name
getShortName() - Method in class com.compomics.util.experiment.biology.PTM
getter for the short modification name
getSource() - Method in class com.compomics.util.gui.events.RescalingEvent
Returns the JPanel 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
 
getSpectra(File) - Method in class com.compomics.util.experiment.io.massspectrometry.MgfReader
Reads an mgf file and retrieves a list of spectra.
getSpectrum(RandomAccessFile, 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 spectrum desired
getSpectrum(String) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Returns the spectrum desired
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(ArrayList<PeptideFragmentIon.PeptideFragmentIonType>, HashMap<NeutralLoss, Integer>, ArrayList<Integer>, MSnSpectrum, Peptide, double, double) - Method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the spectrum annotations of a spectrum in a list of IonMatches Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.
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.
getSpectrumFileId() - Method in class com.compomics.util.io.PklFile
 
getSpectrumIdentification() - Method in class com.compomics.util.experiment.identification.Identification
Returns a list of the keys of all encountered psms.
getSpectrumKey(String, String) - Static method in class com.compomics.util.experiment.massspectrometry.Spectrum
Convenience method returning the key for a spectrum.
getSpectrumKey() - Method in class com.compomics.util.experiment.massspectrometry.Spectrum
Returns the key of the spectrum.
getSpectrumMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
Returns a spectrum match
getSpectrumMatch(String) - Method in class com.compomics.util.experiment.quantification.Quantification
Returns a spectrum quantification 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.reporterion.quantification.PsmQuantification
Getter for the key of the spectrum match
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(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
 
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
 
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.
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.
getTheoreticFragmentKey(PeptideFragmentIon, int) - Static method in class com.compomics.util.experiment.identification.SpectrumAnnotator
Returns the key of a theoretic fragment
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
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.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.
getType() - Method in class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Getter for 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.pdbfinder.das.readers.DasFeature
 
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
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.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.sun.TableMap
 
getValueAt(int, int) - Method in class com.compomics.util.sun.TableSorter
 
getVersion() - Method in class com.compomics.util.examples.UtilitiesDemo
Retrieves the version number set in the pom file.
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!
getY() - Method in class com.compomics.util.XYZDataPoint
 
getYAxisData() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns the y-axis data.
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
 
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
 
Glycine - Class in com.compomics.util.experiment.biology.aminoacids
Glycine
Glycine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Glycine
 
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
GLYCON_FRAGMENT - Static variable in class com.compomics.util.experiment.biology.Ion
Ion family type static index for glycons
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.

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
H2O - Class in com.compomics.util.experiment.biology.neutrallosses
A water loss, likely to be found on fragments from peptides containing the amino-acid D, E, S or T
H2O() - Constructor for class com.compomics.util.experiment.biology.neutrallosses.H2O
Constructor
H3PO4 - Static variable in class com.compomics.util.experiment.biology.NeutralLoss
H3PO4 loss
H3PO4 - Class in com.compomics.util.experiment.biology.neutrallosses
A phosphorylation loss, likely to be found on fragments from phosphorylated peptides on Y.
H3PO4() - Constructor for class com.compomics.util.experiment.biology.neutrallosses.H3PO4
Constructor
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.
hasFlag(String) - Method in class com.compomics.util.general.CommandLineParser
This method test whether the specified flag was set on the commandline.
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.
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.
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
 
HOST - Static variable in class com.compomics.util.io.FolderMonitor
 
HPO3 - Static variable in class com.compomics.util.experiment.biology.NeutralLoss
H3PO3 loss
HPO3 - Class in com.compomics.util.experiment.biology.neutrallosses
A phosphorylation loss, likely to be found on fragments from phosphorylated peptides on S or T.
HPO3() - Constructor for class com.compomics.util.experiment.biology.neutrallosses.HPO3
Constructor
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.
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 residus 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).
iDataPointAndLineColor - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
Colors in which the data points and peaks are rendered.
Identification - Class in com.compomics.util.experiment.identification
This class contains identification results.
Identification() - Constructor for class com.compomics.util.experiment.identification.Identification
 
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
 
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
The identification parameters reader returns the parameters used for identification from a searchGUI parameters file
IdentificationParametersReader() - Constructor for class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
 
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.
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.
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
 
importModifications(File) - Method in class com.compomics.util.experiment.biology.PTMFactory
Import modifications from a modification file
iMSLevel - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The ms level of the current spectrum.
incrementValue() - Method in class com.compomics.util.gui.dialogs.ProgressDialogX
Increases the progress value by 1
index - Variable in class com.compomics.util.experiment.quantification.QuantificationMethod
the method index
inMemory - Variable in class com.compomics.util.experiment.identification.Identification
boolean indicating whether the identification should be stored in memory or not.
inMemory - Variable in class com.compomics.util.experiment.quantification.Quantification
boolean indicating whether the identification should be stored in memory or not.
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.
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<PeptideFragmentIon.PeptideFragmentIonType>, MSnSpectrum, double, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.IntensityHistogram
Creates an IntensityHistogram plot
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
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 int 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.
iRestrict - Variable in class com.compomics.util.protein.Enzyme
This char[] holds the residus that will restrict cleavage when present after a cleavable residu.
iRestrictors - Variable in class com.compomics.util.protein.Enzyme
Lookup cache for the restricting residues.
isAccounted(HashMap<NeutralLoss, Integer>, NeutralLoss, PeptideFragmentIon, 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.
isAutomatedMemoryManagement() - Method in class com.compomics.util.experiment.identification.Identification
Returns whether the memory management is automated.
isAutomatedMemoryManagement() - Method in class com.compomics.util.experiment.quantification.Quantification
Returns whether the memory management is automated.
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.
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
methods 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.
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
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
 
isIndeterminate() - Method in class com.compomics.util.gui.dialogs.ProgressDialog
This method signals whether the progressdialog is currently in indeterminate ('true') or determinate ('false') mode.
isInMemory() - Method in class com.compomics.util.experiment.identification.Identification
Indicates whether matches will be stored in memory
isInMemory() - Method in class com.compomics.util.experiment.quantification.Quantification
Indicates whether matches will be stored in memory
isMiniature() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true if the graphics panel is to be drawn in a minature form.
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
Isoleucine - Class in com.compomics.util.experiment.biology.aminoacids
Isoleucine
Isoleucine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Isoleucine
 
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.
isProgressBarValid() - Method in class com.compomics.util.gui.dialogs.ProgressDialog
This method reports on whether this instance can be controlled in a multithreaded environment.
isRunning() - Method in class com.compomics.util.io.FolderMonitor
This method can be consutled to find put whether the monitor is running.
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 to peptides.
isSameAs(Protein) - Method in class com.compomics.util.experiment.biology.Protein
A method to compare proteins.
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.
isStandAlone() - Method in class com.compomics.util.gui.FlamableJFrame
Returns true if frame is stand alone.
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!
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.
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).
ITRAQ_113 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index iTRAQ 113
ITRAQ_114 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index iTRAQ 114
ITRAQ_115 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index iTRAQ 115
ITRAQ_116 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index iTRAQ 116
ITRAQ_117 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index iTRAQ 117
ITRAQ_118 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index iTRAQ 118
ITRAQ_119 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index iTRAQ 119
ITRAQ_121 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index iTRAQ 121
ITRAQ_4PLEX - Static variable in class com.compomics.util.experiment.quantification.QuantificationMethod
Index for ITRAQ 4Plex
ITRAQ_8PLEX - Static variable in class com.compomics.util.experiment.quantification.QuantificationMethod
Index for ITRAQ 8Plex
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

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
 
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
 
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). this is the default background colour for even numbered rows.
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.
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.
loadedMatches - Variable in class com.compomics.util.experiment.identification.Identification
List of the loaded matches with the most used matches in the end
loadedMatches - Variable in class com.compomics.util.experiment.quantification.Quantification
List of the loaded quantification matches with the most used matches in the end
loadedMatchesMap - Variable in class com.compomics.util.experiment.identification.Identification
Map of the loaded matches
loadedMatchesMap - Variable in class com.compomics.util.experiment.quantification.Quantification
Map of the loaded quantification matches
loadExperiment(File) - 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, JProgressBar) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Loads a new fasta file in the factory.
loadProperties(File) - Static method in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Loads the search properties from a SearchGUI parameters file
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
Map of long keys which will be referenced by their index for file creation
longKeys - Variable in class com.compomics.util.experiment.quantification.Quantification
Map of long keys which will be referenced by their index for file creation
lossesValidated(HashMap<NeutralLoss, Integer>, PeptideFragmentIon, 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
 

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
 
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.dialogs.DateChooser
Creates and opens a new DateChooser dialog.
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.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.
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.
MascotIdfileReader - Class in com.compomics.util.experiment.io.identifications.idfilereaders
This reader will import identifications from a Mascot dat file.
MascotIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.MascotIdfileReader
constructor for the mascotIdileReader
MascotIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.MascotIdfileReader
Constructor for the MascotIdilereader
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<PeptideFragmentIon.PeptideFragmentIonType>, 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<PeptideFragmentIon.PeptideFragmentIonType>, 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<PeptideFragmentIon.PeptideFragmentIonType>, 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<PeptideFragmentIon.PeptideFragmentIonType>, MSnSpectrum, double, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot
Creates a new MassErrorPlot.
MassErrorPlot(ArrayList<IonMatch>, ArrayList<PeptideFragmentIon.PeptideFragmentIonType>, MSnSpectrum, double, boolean, boolean, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.MassErrorPlot
Creates a new MassErrorPlot.
matchPeak(Peptide, ArrayList<PeptideFragmentIon.PeptideFragmentIonType>, ArrayList<Integer>, HashMap<NeutralLoss, Integer>, Peak, double) - 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
Reference for the maximal peptide size
MAXIMUM_HITLIST_LENGTH - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the maximum length of the hitlist
maxPadding - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The maximum padding (distance between the axes and the border of the panel).
memoryCheck() - Method in class com.compomics.util.experiment.identification.Identification
Indicates whether the memory used by the application is lower than 99% of the heap size
memoryCheck() - Method in class com.compomics.util.experiment.quantification.Quantification
Indicates whether the memory used by the application is lower than 99% of the heap size
Methionine - Class in com.compomics.util.experiment.biology.aminoacids
Methionine
Methionine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Methionine
 
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(HashMap<String, Long>, String) - 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
Reference for the minimal peptide size
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
Reference for the missed cleavages
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_SEPARATOR - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the separation of modifications
MODIFICATION_USE_SEPARATOR - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the separation of modification and its frequency
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.
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.
modifiedMatches - Variable in class com.compomics.util.experiment.identification.Identification
Map indicating whether a match is modified.
modifiedMatches - Variable in class com.compomics.util.experiment.quantification.Quantification
Map indicating whether a quantification match is modified.
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.
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, HashSet<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() - 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, HashSet<Peak>, String) - Constructor for class com.compomics.util.experiment.massspectrometry.MSnSpectrum
constructor for the spectrum
MSnSpectrum(int, Precursor, String, HashSet<Peak>, String, double) - Constructor for class com.compomics.util.experiment.massspectrometry.MSnSpectrum
constructor for the spectrum
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
 
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.quantification.QuantificationMethod
the method name
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() - Constructor for class com.compomics.util.experiment.biology.NeutralLoss
 
NH3 - Static variable in class com.compomics.util.experiment.biology.NeutralLoss
NH3 loss
NH3 - Class in com.compomics.util.experiment.biology.neutrallosses
A nitrium loss, likely to be found on fragments from peptides containing the amino-acid K, N, Q or R.
NH3() - Constructor for class com.compomics.util.experiment.biology.neutrallosses.NH3
Constructor
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
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.Atom
 
oldCleave(Protein) - Method in class com.compomics.util.protein.DualEnzyme
This cleave method will proces sequence XDYRZ solely into YR peptides.
OMSSA - Static variable in interface com.compomics.util.experiment.identification.Advocate
OMSSA index
OMSSAIdfileReader - Class in com.compomics.util.experiment.io.identifications.idfilereaders
This reader will import identifications from an OMSSA omx file.
OMSSAIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.OMSSAIdfileReader
constructor for the reader
OMSSAIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.OMSSAIdfileReader
Constructor for the reader
omx - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
OMX - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
OmxFileFilter - Class in com.compomics.util.io.filefilters
File filter for *.omx files.
OmxFileFilter() - Constructor for class com.compomics.util.io.filefilters.OmxFileFilter
 
openDataConnection(String) - Method in class com.compomics.util.io.FTP
This method will set up the networking for client-server data transfer and it will send the specified command to the server.
openServer(String) - Method in class com.compomics.util.io.FTP
open a FTP connection to host host.
openServer(String, int) - Method in class com.compomics.util.io.FTP
Open an FTP connection to host host on port port.
openURL(String) - Static method in class com.compomics.util.examples.BareBonesBrowserLaunch
Tries to opens the given URL in the default browser.
OperatingSystemEnum - Enum in com.compomics.util.enumeration
This ENUM types the distinct OS systems.
out - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
OUT - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
OutFileFilter - Class in com.compomics.util.io.filefilters
File filter for *.out files.
OutFileFilter() - Constructor for class com.compomics.util.io.filefilters.OutFileFilter
 
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, PTMFactory) - Static method in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
This method parses a modification line from a properties file.
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-YSFVATER-COOH' or 'Ace-MATHMPIR-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.
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
 
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_FINGERPRINTING - Static variable in class com.compomics.util.experiment.identification.IdentificationMethod
index for identification method based on peptide mass fingerprinting
PEPTIDE_FRAGMENT - Static variable in class com.compomics.util.experiment.biology.Ion
Ion family type static index for peptide fragments
PeptideAssumption - Class in com.compomics.util.experiment.identification
This object will models the assumption made by an advocate.
PeptideAssumption(Peptide, int, int, double, double, String) - Constructor for class com.compomics.util.experiment.identification.PeptideAssumption
Constructor for a peptide assumption
PeptideFragmentIon - Class in com.compomics.util.experiment.biology.ions
This class models a peptide fragment ion.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType, double) - Constructor for class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Construction for a peptide fragment.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType, int, double, ArrayList<NeutralLoss>) - Constructor for class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Construction for a peptide fragment with neutral loss.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType, int, double) - Constructor for class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Construction for a peptide fragment.
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType, String, double) - Constructor for class com.compomics.util.experiment.biology.ions.PeptideFragmentIon
Construction for a peptide fragment.
PeptideFragmentIon.PeptideFragmentIonType - Enum in com.compomics.util.experiment.biology.ions
An enumerator of the supported fragment ion types.
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
peptideQuantification - Variable in class com.compomics.util.experiment.quantification.Quantification
The peptide quantification
PeptideQuantification - Class in com.compomics.util.experiment.quantification.reporterion.quantification
This class models quantification at the peptide level.
PeptideQuantification(String) - Constructor for class com.compomics.util.experiment.quantification.reporterion.quantification.PeptideQuantification
Constructor for the peptide quantification
PeptideQuantification(String, ArrayList<String>) - Constructor for class com.compomics.util.experiment.quantification.reporterion.quantification.PeptideQuantification
Constructor for the peptide quantification
PeptideQuantification(String, ArrayList<String>, HashMap<Integer, Ratio>) - Constructor for class com.compomics.util.experiment.quantification.reporterion.quantification.PeptideQuantification
Constructor for the peptide quantification
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
 
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 - Class in com.compomics.util.experiment.massspectrometry
This class modilizes the precursor.
Precursor(double, double, Charge) - Constructor for class com.compomics.util.experiment.massspectrometry.Precursor
Constructor for the precursor.
Precursor(double, double, double, 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
Reference for the lower precursor charge
PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the precursor charge to start considering multiply charged fragments
PRECURSOR_CHARGE_UPPER_BOUND - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the upper precursor charge
PRECURSOR_ELIMINATION - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the precursor elimination option
PRECURSOR_MASS_ACCURACY_UNIT - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the precursor mass tolerance unit
PRECURSOR_MASS_TOLERANCE - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the precursor mass tolerance
PRECURSOR_SCALING - Static variable in class com.compomics.util.experiment.io.identifications.IdentificationParametersReader
Reference for the precursor scaling option
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.
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.dialogs
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.dialogs.ProgressDialog
Creates an indeterminate ProgressDialog by default, with the specified title and message.
ProgressDialogParent - Interface in com.compomics.util.gui.dialogs
Interface that makes it simpler to let the cancellation of the progress bar propagate to the parent frame or dialog that opened the progrss bar.
ProgressDialogX - Class in com.compomics.util.gui.dialogs
A dialog for displaying information about progress.
ProgressDialogX(Frame, ProgressDialogParent, boolean) - Constructor for class com.compomics.util.gui.dialogs.ProgressDialogX
Opens a new ProgressDialogX with a Frame as a parent
ProgressDialogX(JDialog, ProgressDialogParent, boolean) - Constructor for class com.compomics.util.gui.dialogs.ProgressDialogX
Opens a new ProgressDialog with a JDialog as a parent
ProgressDialogX(ProgressDialogParent, boolean) - Constructor for class com.compomics.util.gui.dialogs.ProgressDialogX
Opens a new ProgressDialog with a ProgressDialogParent as a parent
Proline - Class in com.compomics.util.experiment.biology.aminoacids
Proline
Proline() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Proline
 
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.
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
proteinQuantification - Variable in class com.compomics.util.experiment.quantification.Quantification
The protein quantification
ProteinQuantification - Class in com.compomics.util.experiment.quantification.reporterion.quantification
This class models the quantification results for a protein match.
ProteinQuantification(String) - Constructor for class com.compomics.util.experiment.quantification.reporterion.quantification.ProteinQuantification
Constructor for the protein quantification
ProteinQuantification(String, ArrayList<String>) - Constructor for class com.compomics.util.experiment.quantification.reporterion.quantification.ProteinQuantification
Constructor for the protein quantification
ProteinQuantification(String, ArrayList<String>, HashMap<Integer, Ratio>) - Constructor for class com.compomics.util.experiment.quantification.reporterion.quantification.ProteinQuantification
Constructor for 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
 
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
proton() - Static method in class com.compomics.util.experiment.biology.Ion
Convenience method returning a proton
Proton - Class in com.compomics.util.experiment.biology.ions
This class represents a proton
Proton() - Constructor for class com.compomics.util.experiment.biology.ions.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.reporterion.quantification
This class models the quantification at the MS2 spectrum level.
PsmQuantification(String, String) - Constructor for class com.compomics.util.experiment.quantification.reporterion.quantification.PsmQuantification
Constructor for a spectrumQuantification
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
Constructor for a reference modification
PTM(int, String, String, double, ArrayList<String>) - Constructor for class com.compomics.util.experiment.biology.PTM
Constructor for a reference modification
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.
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
pwd() - Method in class com.compomics.util.io.FTP
Get the name of the present working directory on the ftp server file system.

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
 
QuantificationMatch - Class in com.compomics.util.experiment.quantification.reporterion
abstract class for a quantification match
QuantificationMatch() - Constructor for class com.compomics.util.experiment.quantification.reporterion.QuantificationMatch
 
QuantificationMethod - Class in com.compomics.util.experiment.quantification
This class will models a quantification method.
QuantificationMethod() - Constructor for class com.compomics.util.experiment.quantification.QuantificationMethod
 

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, int, double) - Constructor for class com.compomics.util.experiment.quantification.Ratio
constructor for the Ratio
ratios - Variable in class com.compomics.util.experiment.quantification.reporterion.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.
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
 
ReferenceArea - Class in com.compomics.util.gui.spectrum
A reference area to be added to a GraphicsPanel.
ReferenceArea(String, double, double, Color, float, boolean, boolean) - Constructor for class com.compomics.util.gui.spectrum.ReferenceArea
Creates a new ReferenceArea
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.
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.
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.
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.
removeMatch(String) - Method in class com.compomics.util.experiment.identification.Identification
Removes a match from the model
removeMouseListenerToHeaderInTable(JTable) - Method in class com.compomics.util.sun.TableSorter
 
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.
removeQuantification(String) - Method in class com.compomics.util.experiment.quantification.Quantification
Removes a quantification from the model
removeReferenceAreaXAxis(String) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Removes the x-axis reference area with the given label.
removeReferenceAreaYAxis(String) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Removes the y-axis reference area with the given label.
rename(String, String) - Method in class com.compomics.util.io.FTP
Rename a file on the remote server.
replacePTM(String, PTM) - Method in class com.compomics.util.experiment.biology.PTMFactory
replaces an old ptm by a new
REPORTER_ION - Static variable in class com.compomics.util.experiment.biology.Ion
Ion family type static index for glycons
ReporterIon - Class in com.compomics.util.experiment.biology.ions
This class models a reporter ion.
ReporterIon(int) - Constructor for class com.compomics.util.experiment.biology.ions.ReporterIon
Constructor for a reporter ion
ReporterIon(int, String, double) - 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(int) - 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(int, 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.
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.
rescaleWithLeftSidePadding() - Method in class com.compomics.util.gui.spectrum.IsotopicDistributionPanel
Rescales to show all peaks, adds a minimum padding on the left side to make sure the that first peak is not too close to the y-axis.
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.
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.
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 decimalplaces.
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
 
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
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
save(Connection) - Method in interface com.compomics.util.db.interfaces.DBElement
This method can be called when changes need to be persisted.
save(File, ProgressDialogX) - Method in class com.compomics.util.experiment.identification.Identification
Saves the identification matches in the desired folder
save(File, MsExperiment) - Method in class com.compomics.util.experiment.io.ExperimentIO
Method which saves an experiment
save(File, ProgressDialogX) - Method in class com.compomics.util.experiment.quantification.Quantification
Saves the identification matches in the desired folder
saveFile(File) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
 
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)
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
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.util.experiment.identification.SpectrumAnnotator
Separator for the theoretic fragment key components
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!
SequenceFragmentationPanel(String, ArrayList<IonMatch>, boolean) - Constructor for class com.compomics.util.gui.spectrum.SequenceFragmentationPanel
Creates a new SequenceFragmentationPanel.
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
serializationDirectory - Variable in class com.compomics.util.experiment.quantification.Quantification
the directory where matches will be serialized
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
 
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.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
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.
setAutomatedMemoryManagement(boolean) - Method in class com.compomics.util.experiment.identification.Identification
Sets whether the memory management should be automated
setAutomatedMemoryManagement(boolean) - Method in class com.compomics.util.experiment.quantification.Quantification
Sets whether the memory management should be automated
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
 
setCacheSize(int) - Method in class com.compomics.util.experiment.identification.Identification
Sets the cache size
setCacheSize(int) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Sets the cache size
setCacheSize(int) - Method in class com.compomics.util.experiment.quantification.Quantification
Sets the 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 residus.
setCleavage(String) - Method in class com.compomics.util.protein.DualEnzyme
This method allows the caller to specify the cleavable residus.
setCleavage(char[], int) - Method in class com.compomics.util.protein.DualEnzyme
This method allows the caller to specify the cleavable residus.
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 residus.
setCleavage(String) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to specify the cleavable residus.
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
 
setColor(Color) - Method in class com.compomics.util.gui.protein.ModificationProfile
Sets the PTM color.
setDatabaseType(Header.DatabaseType) - Method in class com.compomics.util.protein.Header
 
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.
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.
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.
setDeterminate(int, int) - Method in class com.compomics.util.gui.dialogs.ProgressDialog
This method sets the progressbar to determinate mode, with the specified minimum and maximum values.
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.
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
 
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..
setExperiment_type(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
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
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
 
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.
setID(String) - Method in class com.compomics.util.protein.Header
 
setIndeterminate() - Method in class com.compomics.util.gui.dialogs.ProgressDialog
This method makes the progressbar indeterminate.
setIndeterminate(boolean) - Method in class com.compomics.util.gui.dialogs.ProgressDialogX
Makes the dialog indeterminate or not indeterminate.
setInMemory(boolean) - Method in class com.compomics.util.experiment.identification.Identification
Sets whether matches shall be stored in memory
setInMemory(boolean) - Method in class com.compomics.util.experiment.quantification.Quantification
Sets whether matches shall be stored in memory
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.
setIntensityValues(double[]) - Method in class com.compomics.util.io.PklFile
 
setIntermidiate(boolean) - Method in class com.compomics.util.gui.dialogs.ProgressDialogX
Deprecated. Replaced by setIndeterminate, from utilities 3.1.17.
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.
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,
setLabelDifference(int) - Method in class com.compomics.util.general.IsotopicDistribution
This method set the label dalton difference
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
methods sets the main match
setMainMatch(String) - Method in class com.compomics.util.experiment.identification.matches.ProteinMatch
Sets the main protein accession after protein inference
setMass(double) - Method in class com.compomics.util.experiment.biology.ions.ReporterIon
Method to set the mass of the reporter ion
setMatchChanged(IdentificationMatch) - Method in class com.compomics.util.experiment.identification.Identification
Indicates that a match was changed, it will thus be serialized again if needed.
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.dialogs.ProgressDialogX
Sets the maximum value of the progress bar
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).
setMessage(String) - Method in class com.compomics.util.gui.dialogs.ProgressDialog
This method allows the caller to set a message on the progressbar.
setMethod(ReporterMethod) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Sets the reporter method used
setMethodUsed(int) - Method in class com.compomics.util.experiment.quantification.Quantification
setter for the method used
setMiniature(boolean) - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Set if the graphics panel is to be drawn in a minature form.
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
 
setModifications(Vector) - Method in class com.compomics.util.protein.AASequenceImpl
Simple setter for the modifications.
setMzValues(double[]) - Method in class com.compomics.util.io.PklFile
 
setName(String) - Method in class com.compomics.util.experiment.biology.PTM
Sets the ptm name
setnCache(int) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Sets the size of the cache.
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.
setPdbaccession(String) - Method in class com.compomics.util.pdbfinder.pdb.PdbParameter
 
setPeakList(HashSet<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.
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
setPointSize(Integer) - Method in class com.compomics.util.gui.spectrum.ChromatogramPanel
This method allows the caller to set the point size for the chromatogram. b>Note that this number needs to be even, so any uneven number will be replaced by the closest, lower, even integer (e.g., 5 becomes 4, 13 becomes 12).
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
 
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
 
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.dialogs.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.dialogs.ProgressDialog
This method sets the progress to the specified value.
setPtmName(String) - Method in class com.compomics.util.gui.protein.ModificationProfile
Sets the PTM name.
setRatios(HashMap<Integer, Ratio>) - Method in class com.compomics.util.experiment.quantification.reporterion.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
setReferenceLabel(int) - Method in class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
Sets the reference label indexed by the corresponding reporter ion index
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 residus that restrict cleavage.
setRestrict(String) - Method in class com.compomics.util.protein.Enzyme
This method allows the caller to specify the residus which restrict cleavage.
setSample(int, Sample) - Method in class com.compomics.util.experiment.MsExperiment
Set a new sample
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.
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.
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.
setSerializationDirectory(String) - Method in class com.compomics.util.experiment.identification.Identification
sets the serialization directory
setSerializationDirectory(String) - Method in class com.compomics.util.experiment.quantification.Quantification
sets the serialization directory
setShortName(String) - Method in class com.compomics.util.experiment.biology.PTM
Sets the short ptm name
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.
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
 
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.dialogs.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.
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.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.
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..
setValue(int) - Method in class com.compomics.util.gui.dialogs.ProgressDialogX
Sets the progress bar value.
setValueAt(Object, int, int) - Method in class com.compomics.util.sun.TableMap
 
setValueAt(Object, int, int) - Method in class com.compomics.util.sun.TableSorter
 
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.
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.
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.
showAnnotatedPeaksOnly(boolean) - Method in class com.compomics.util.gui.spectrum.SpectrumPanel
If true only the annotated peaks will be drawn.
showFileName - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The boolean is set to 'true' if the file name is to be shown in the panel.
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.
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.
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
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, ...).
spectrumIdentification - Variable in class com.compomics.util.experiment.identification.Identification
List of the keys of all imported psms
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
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
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.
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
 
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
 
tableChanged(TableModelEvent) - Method in class com.compomics.util.sun.TableMap
 
tableChanged(TableModelEvent) - Method in class com.compomics.util.sun.TableSorter
 
TableMap - Class in com.compomics.util.sun
In a chain of data manipulators some behaviour is common.
TableMap() - Constructor for class com.compomics.util.sun.TableMap
 
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
 
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.
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
Ion attribute - the theoretic mass
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
 
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
Reporter ion index TMT 0
TMT1 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index TMT 1
TMT2 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index TMT 2
TMT2 - Static variable in class com.compomics.util.experiment.quantification.QuantificationMethod
Index for TMT2
TMT3 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index TMT 3
TMT4 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index TMT 4
TMT5 - Static variable in class com.compomics.util.experiment.biology.ions.ReporterIon
Reporter ion index TMT 5
TMT6 - Static variable in class com.compomics.util.experiment.quantification.QuantificationMethod
Index for TMT6
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.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.ions.PeptideFragmentIon
 
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() - 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
 
txt - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
TXT - Static variable in class com.compomics.util.io.filefilters.FileFilterUtils
 
Tyrosine - Class in com.compomics.util.experiment.biology.aminoacids
Tyrosine
Tyrosine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Tyrosine
 

U

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.
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.experiment.identification.Identification
updates the cache according to the memory settings.
updateCache() - Method in class com.compomics.util.experiment.quantification.Quantification
updates the cache according to the memory settings.
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
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.
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
Map of the user's parameters.
urParameters - Variable in class com.compomics.util.experiment.quantification.Quantification
Map of the user's parameters.
USER - Static variable in class com.compomics.util.io.FolderMonitor
 
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
 

V

V - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
Valine - Class in com.compomics.util.experiment.biology.aminoacids
Valine
Valine() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Valine
 
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.ions.PeptideFragmentIon.PeptideFragmentIonType
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.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.ions.PeptideFragmentIon.PeptideFragmentIonType
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.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
Reference for the variable modifications

W

W - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
welcomeMsg - Variable in class com.compomics.util.io.FTP
Welcome message from the server, if any.
writeIndex(FastaIndex, File) - Method in class com.compomics.util.experiment.identification.SequenceFactory
Serializes the fasta file index in a given directory.
writeIndex(MgfIndex, File) - Method in class com.compomics.util.experiment.massspectrometry.SpectrumFactory
Writes the given mgf file index in the given directory
writeOmssaModificationsFiles(File, File, File) - Method in class com.compomics.util.experiment.biology.PTMFactory
Write the OMSSA modification files to the given folder.
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
 
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
 
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!
XTandemIdfileReader - Class in com.compomics.util.experiment.io.identifications.idfilereaders
This reader will import identifications from an X!
XTandemIdfileReader() - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.XTandemIdfileReader
Constructor for the reader
XTandemIdfileReader(File) - Constructor for class com.compomics.util.experiment.io.identifications.idfilereaders.XTandemIdfileReader
constructor for the reader
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
 
yAxisZoomExcludesBackgroundPeaks - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If true, the automatic y-axis zoom excludes the background peaks.
yAxisZoomOnlyExcludesBackgroundPeaks() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true if the automatic y-axis zoom excludes background peaks.
yDataIsPositive - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
If set to true, all y data is assumed to be positive.
yDataIsPositive() - Method in class com.compomics.util.gui.spectrum.GraphicsPanel
Returns true of all the y-data is to be assumed as positive.
yTagCount - Variable in class com.compomics.util.gui.spectrum.GraphicsPanel
The number of Y-axis tags.

Z

Z - Static variable in class com.compomics.util.experiment.biology.AminoAcid
 
Z - Class in com.compomics.util.experiment.biology.aminoacids
Glu or Gln: Glx (Mascot)
Z() - Constructor for class com.compomics.util.experiment.biology.aminoacids.Z
 

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