Index (PeptideShaker 2.2.2 API)

A B C D E F G H I J K L M N O P Q R S T U V W

A

accessionExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether an accession export is needed.
addAdvocateContribution(int, String, boolean) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Adds an advocate contribution.
addAll(TargetDecoyMap) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Adds all the points from another target/decoy map.
addEntry(int, String, double, boolean) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Adds an entry to the input map.
addExportScheme(ExportScheme) - Method in class eu.isas.peptideshaker.export.PSExportFactory
addGoLink(String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the GO accession number as a web link to the given GO term at QuickGO.
addIdentificationFiles(File) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Adds an identification file to the list of loaded identification files.
addNote(String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Add a note to the current list of notes.
addPeptideShakerHit(String, boolean) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Adds a PeptideShaker hit for the given file.
addPoint(String, int, double, boolean) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Adds a point representing the corresponding spectrum match at a given score.
addRecentProject(String) - Method in class eu.isas.peptideshaker.preferences.UserParameters: Adds a recent project to the list and limits the list of recent projects to a size of 20.
addRecentProject(File) - Method in class eu.isas.peptideshaker.preferences.UserParameters: Adds a recent project to the list and limits the list of recent projects to a size of 20.
addSpectrumFilePath(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Attaches a spectrum file to the project.
addTip(String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Add a tip to the current list of tips.
AGREEMENT - Static variable in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Static index for the ID software agreement: the ID softwares all have the same top ranking peptide without accounting for modification localization.
AGREEMENT_WITH_MODS - Static variable in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Static index for the ID software agreement: the ID softwares all have the same top ranking peptide.
analyzeInUnipept(List<String>, boolean, boolean, boolean, File, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.UnipeptExport: Analyze the given list of peptides, with the specified configuration, using the Unipept web interface.
annotation - Variable in class eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation: The residue annotation as a string.
ANNOTATION_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The Annotation tab index.
annotationClicked(ArrayList<ResidueAnnotation>, ChartMouseEvent) - Method in interface eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanelParent
annotationClicked(ArrayList<ResidueAnnotation>, ChartMouseEvent) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel
annotationClicked(ArrayList<ResidueAnnotation>, ChartMouseEvent) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel
AnnotationPanel - Class in eu.isas.peptideshaker.gui.tabpanels: This tab contains the basic protein annotation and links to other protein resources.
AnnotationPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel: Creates a new AnnotationPanel.
applyPepWindow() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Reloads the data using the currently selected PEP window.
asMgf(Spectrum, BufferedWriter) - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Writes the given spectrum to the buffered writer.
attachDeltaScore(Identification, SpectrumMatch, SequenceMatchingParameters, ModificationProvider) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Scores the modification locations using the delta score.
attachPeptideProbabilities(Identification, FastaParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Attaches the peptide posterior error probabilities to the peptide matches.
attachProteinProbabilities(Identification, SequenceProvider, FastaParameters, Metrics, WaitingHandler, FractionParameters) - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Attaches the protein posterior error probability to the protein matches.

B

BATCH_SIZE - Static variable in class eu.isas.peptideshaker.fileimport.PsmImportRunnable: Size of the batches to use when adding objects to the database.
BestMatchSelection - Class in eu.isas.peptideshaker.scoring.psm_scoring: This class contains the method for PSM best hit selection.
BestMatchSelection(HashMap<String, Integer>, SequenceProvider, SpectrumProvider, IdentificationParameters, PeptideSpectrumAnnotator) - Constructor for class eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection: Constructor.

C

call() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLI: Calling this method will run the configured PeptideShaker process.
call() - Method in class eu.isas.peptideshaker.cmd.MzidCLI: Calling this method will run the configured PeptideShaker process.
call() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLI
call() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI
call() - Method in class eu.isas.peptideshaker.cmd.ReportCLI: Calling this method will run the configured PeptideShaker process.
catchException(Exception) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Method called whenever an exception is caught.
catchException(Exception) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
catchException(Exception) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
catchException(Exception) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
checkFastaFile() - Method in class eu.isas.peptideshaker.gui.NewDialog: Checks whether the FASTA file loaded contains mainly UniProt concatenated target decoy.
checkForNewSearchGUIVersion(String) - Method in class eu.isas.peptideshaker.gui.WelcomeDialog: Check for new version.
checkForNewVersion() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Check for new version.
checkNewsFeed() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Displays a news feed at the bottom of the GUI.
checkPeptide(Peptide, SequenceProvider, SequenceMatchingParameters) - Static method in class eu.isas.peptideshaker.protein_inference.PeptideChecker: Corrects the protein mapping based on the confident or inferred variable modifications when located at the protein termini or targeting amino acid patterns.
clean(double) - Method in class eu.isas.peptideshaker.scoring.maps.specific.ModificationSpecificMap
clean(double) - Method in class eu.isas.peptideshaker.scoring.maps.specific.SimpleSpecificMap
clean(double) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Handles sparse maps.
cleanProviders() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Cleans the SequenceProvider and ProteinDetailsProvider, please use only temporary or if you know what you do
cleanUp() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Removes empty points and clears dependent metrics if needed.
clearData(boolean, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Clear the data from the previous experiment.
clearData() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Clear all the data.
clearData() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Clear all the data.
clearData() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Clear all the data.
clearErrors(String) - Method in class eu.isas.peptideshaker.recalibration.SpectrumRecalibrator: Clears the loaded error statistics for the given file name in order to save memory.
clearGeneMappings() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Clear the gene mappings.
clearOldResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel: Clear the old results.
clearParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Clears the project parameters.
clickable - Variable in class eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation: If true the given annotation is clickable.
CLIExportMethods - Class in eu.isas.peptideshaker.cmd: This class groups standard methods used by the different command line interfaces.
CLIExportMethods() - Constructor for class eu.isas.peptideshaker.cmd.CLIExportMethods
close() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Closes the frame by first checking if the project ought to be saved.
close() - Method in class eu.isas.peptideshaker.utils.PsdbParent
closePeptideShaker(Identification) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI: Close the PeptideShaker instance.
closePeptideShaker() - Method in class eu.isas.peptideshaker.cmd.ReportCLI: Close the PeptideShaker instance by clearing up factories and cache.
confidentOnly() - Method in class eu.isas.peptideshaker.gui.export.PtmSelectionDialog: Indicates whether only the confident modifications sites are of interest.
CONFLICT - Static variable in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Static index for the ID software agreement: the ID software have different top ranking peptides.
contactAddress - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The address of the contact to annotate in the mzIdentML file.
contactEmail - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The email of the contact to annotate in the mzIdentML file.
contactFirstName - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The first name of the contact to annotate in the mzIdentML file.
contactLastName - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The last name of the contact to annotate in the mzIdentML file.
contactOrganizationAddress - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The address of the organization of the contact to annotate in the mzIdentML file.
contactOrganizationEmail - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The email of the organization of the contact to annotate in the mzIdentML file.
contactOrganizationName - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The name of the organization of the contact to annotate in the mzIdentML file.
createMzIdentMLFile(MzIdentMLVersion) - Method in class eu.isas.peptideshaker.export.MzIdentMLExport: Creates the mzIdentML file.
createOptionsCLI(Options) - Static method in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Method in class eu.isas.peptideshaker.cmd.IdentificationParametersCLI
createOptionsCLI(Options) - Static method in enum eu.isas.peptideshaker.cmd.MzidCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerIdentificationParametersCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Creates the options for the command line interface based on the possible values.
createOptionsCLI(Options) - Static method in enum eu.isas.peptideshaker.cmd.StirredOptions: Creates the options for the command line interface based on the possible values.
createPeptideFilter() - Method in class eu.isas.peptideshaker.gui.filtering.FiltersDialog: Creates a new peptide filter.
createProject() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI: Creates the PeptideShaker project based on the identification files provided in the command line input
createProject(IdentificationParameters, ProcessingParameters, SpectrumCountingParameters, SpectrumProvider, ProjectDetails, ProjectType, WaitingHandler, boolean, ExceptionHandler) - Method in class eu.isas.peptideshaker.PeptideShaker: Creates a PeptideShaker project.
createProteinFilter() - Method in class eu.isas.peptideshaker.gui.filtering.FiltersDialog: Creates a new protein filter.
createPsmFilter() - Method in class eu.isas.peptideshaker.gui.filtering.FiltersDialog: Creates a new PSM filter.
createTargetDecoyPoint(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Creates the target decoy point of the map at the given score if no other thread has done it before.

D

DARK_THEME_BACKGROUND_COLOR - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The dark theme background color.
DATA_DIRECTORY - Static variable in class eu.isas.peptideshaker.PeptideShaker: Folder where the data files are stored by default.
DatabaseHelpDialog - Class in eu.isas.peptideshaker.gui.pride: Dialog to help the user select the correct database.
DatabaseHelpDialog(PeptideShakerGUI, FastaParameters, LastSelectedFolder, boolean, String) - Constructor for class eu.isas.peptideshaker.gui.pride.DatabaseHelpDialog: Creates a new DatabaseHelpDialog.
dbFolder - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The folder where the database is stored.
decreaseDecoy() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint: Decreases the decoy counter.
decreaseTarget() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint: Decreases the target counter.
DeepLcExport - Class in eu.isas.peptideshaker.followup: Export for RT prediction using DeepLC.
DeepLcExport() - Constructor for class eu.isas.peptideshaker.followup.DeepLcExport
deepLcExport(String, Identification, ModificationParameters, SequenceMatchingParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.DeepLcExport: Exports DeepLC training files for each of the spectrum files.
deepLcExport(File, File, HashSet<Long>, Identification, ModificationParameters, SequenceMatchingParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.DeepLcExport: Exports a DeepLC training file for the given spectrum file.
deepLcExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether DeepLC export is needed.
DeepLcUtils - Class in eu.isas.peptideshaker.utils: Utils for the export and import of ms2pip results.
DeepLcUtils() - Constructor for class eu.isas.peptideshaker.utils.DeepLcUtils
DEFAULT_DATA_FOLDER - Static variable in class eu.isas.peptideshaker.export.ProjectExport: The name of the folder where to save the spectrum and FASTA files.
DEFAULT_REPORTS_FOLDER - Static variable in class eu.isas.peptideshaker.export.ProjectExport: The name of the folder where to save report files.
description - Variable in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Explanation for the CLI parameter.
description - Variable in enum eu.isas.peptideshaker.cmd.MzidCLIParams: Explanation for the CLI parameter.
description - Variable in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams: The description of the command line option.
description - Variable in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams: Explanation for the CLI parameter.
description - Variable in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Explanation for the CLI parameter.
description - Variable in enum eu.isas.peptideshaker.cmd.StirredOptions: Description for the command line argument.
description - Variable in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Description of the export.
description - Variable in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Description of the export.
description - Variable in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Description of the export.
description - Variable in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Description of the export.
description - Variable in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Description of the export.
description - Variable in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: The description to write in the report.
disableSpectrumDisplay() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Method called to disable the spectrum display.
DisplayFeaturesGenerator - Class in eu.isas.peptideshaker.utils: This class creates the display features needed for the GUI.
DisplayFeaturesGenerator(IdentificationParameters, DisplayParameters, SequenceProvider, ProteinDetailsProvider) - Constructor for class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Constructor
DisplayParameters - Class in eu.isas.peptideshaker.preferences: This class contains the display preferences for the current project.
DisplayParameters() - Constructor for class eu.isas.peptideshaker.preferences.DisplayParameters: Constructor.
displayParameters - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The display parameters.
DisplayPreferencesDialog - Class in eu.isas.peptideshaker.gui.parameters: DisplayPreferencesDialog.
DisplayPreferencesDialog(Frame, DisplayParameters) - Constructor for class eu.isas.peptideshaker.gui.parameters.DisplayPreferencesDialog: Constructor.
displayResults() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: This method will display results in all panels.
displayResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel: Update the GO mappings.
displayResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Displays the results.
displayResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Displays the results in the tables.
displayResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Display the results.
displayResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Displays the results in the result tables.
displayResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.QCPanel: This method displays results on the panel.
displayResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Displays the results in the panel.
displayResults() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: This method displays results in the panel.
distributeSharedPeptides(Identification, WaitingHandler) - Method in class eu.isas.peptideshaker.protein_inference.ProteinInference: Distribute the shared peptides among the protein groups.
documentationExportNeeded() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Indicates whether a documentation export is required by the user.
downloadPrideDatasets(String, ArrayList<String>, ArrayList<String>, String, String, String, ArrayList<Integer>) - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Download and convert a PRIDE project.
downloadSearchGUI() - Method in class eu.isas.peptideshaker.gui.WelcomeDialog: Download SearchGUI.
DummyResults() - Constructor for class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel.QuickGoTerm.DummyResults

E

editFilter(Filter) - Method in class eu.isas.peptideshaker.gui.filtering.FiltersDialog: Edits the given filter.
editPathSettings(WelcomeDialog) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Opens a dialog allowing the setting of paths.
editProteoWizardInstallation() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeSetupDialog: Opens a dialog allowing the edition of the ProteoWizard installation folder.
enableDarkTheme(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Enable or disable the dark theme.
enableSpectrumExport(boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Enable or disable the spectrum export in the overview panel.
estimateErrors(String, Identification, SequenceProvider, SpectrumProvider, IdentificationParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.recalibration.SpectrumRecalibrator: Estimates the file m/z errors and displays the progress in a waiting handler.
estimateIntermediateScoreProbabilities(Identification, InputMap, ProcessingParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer: Estimates the probabilities associated to the intermediate PSM scores.
estimateIntermediateScores(Identification, InputMap, ProcessingParameters, IdentificationParameters, WaitingHandler, ExceptionHandler) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer: Scores the PSMs contained in an identification object.
estimateIntermediateScores(Identification, SpectrumMatch, InputMap, IdentificationParameters, PeptideSpectrumAnnotator, HyperScore, WaitingHandler) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer: Scores the PSMs contained in an identification object.
estimateProbabilities(WaitingHandler) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Estimates the posterior error probability for each search engine.
estimateProbabilities(WaitingHandler) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Estimate the posterior error probabilities of the PSMs.
estimateProbabilities(WaitingHandler) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Estimates the posterior error probabilities in this map.
eu.isas.peptideshaker - package eu.isas.peptideshaker: PeptideShaker main calculations and jar wrapper.
eu.isas.peptideshaker.cmd - package eu.isas.peptideshaker.cmd: Command line usage.
eu.isas.peptideshaker.export - package eu.isas.peptideshaker.export: Exporting data from PeptideShaker.
eu.isas.peptideshaker.export.sections - package eu.isas.peptideshaker.export.sections: Export sections.
eu.isas.peptideshaker.fileimport - package eu.isas.peptideshaker.fileimport: Import of search results.
eu.isas.peptideshaker.followup - package eu.isas.peptideshaker.followup: Export for follow-up analysis.
eu.isas.peptideshaker.gui - package eu.isas.peptideshaker.gui: GUI dialogs and helper classes.
eu.isas.peptideshaker.gui.export - package eu.isas.peptideshaker.gui.export: GUI export dialogs.
eu.isas.peptideshaker.gui.filtering - package eu.isas.peptideshaker.gui.filtering: GUI filtering dialogs.
eu.isas.peptideshaker.gui.parameters - package eu.isas.peptideshaker.gui.parameters: Preferences dialogs.
eu.isas.peptideshaker.gui.pride - package eu.isas.peptideshaker.gui.pride: GUI classes for exporting to PRIDE.
eu.isas.peptideshaker.gui.protein_inference - package eu.isas.peptideshaker.gui.protein_inference: Protein inference dialogs.
eu.isas.peptideshaker.gui.protein_sequence - package eu.isas.peptideshaker.gui.protein_sequence: Protein sequence annotation.
eu.isas.peptideshaker.gui.start - package eu.isas.peptideshaker.gui.start: Getting started dialog.
eu.isas.peptideshaker.gui.tablemodels - package eu.isas.peptideshaker.gui.tablemodels: Table models.
eu.isas.peptideshaker.gui.tabpanels - package eu.isas.peptideshaker.gui.tabpanels: Main GUI panels.
eu.isas.peptideshaker.parameters - package eu.isas.peptideshaker.parameters: Parameter settings.
eu.isas.peptideshaker.preferences - package eu.isas.peptideshaker.preferences: Preferences settings.
eu.isas.peptideshaker.processing - package eu.isas.peptideshaker.processing: Classes used to create PeptideShaker projects.
eu.isas.peptideshaker.protein_inference - package eu.isas.peptideshaker.protein_inference: Protein inference classes.
eu.isas.peptideshaker.ptm - package eu.isas.peptideshaker.ptm: PTM scoring classes.
eu.isas.peptideshaker.recalibration - package eu.isas.peptideshaker.recalibration: Spectrum recalibration.
eu.isas.peptideshaker.scoring - package eu.isas.peptideshaker.scoring: Identification scoring.
eu.isas.peptideshaker.scoring.maps - package eu.isas.peptideshaker.scoring.maps: Target decoy maps.
eu.isas.peptideshaker.scoring.maps.specific - package eu.isas.peptideshaker.scoring.maps.specific: Specific target decoy maps.
eu.isas.peptideshaker.scoring.psm_scoring - package eu.isas.peptideshaker.scoring.psm_scoring: PSM scoring.
eu.isas.peptideshaker.scoring.targetdecoy - package eu.isas.peptideshaker.scoring.targetdecoy: Target/decoy related classes.
eu.isas.peptideshaker.stirred - package eu.isas.peptideshaker.stirred: Classes used to create stirred projects.
eu.isas.peptideshaker.stirred.modules - package eu.isas.peptideshaker.stirred.modules: Modules for stirred mode.
eu.isas.peptideshaker.utils - package eu.isas.peptideshaker.utils: Various utilities classes.
eu.isas.peptideshaker.validation - package eu.isas.peptideshaker.validation: Matches validation.
executeCmd(String) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel.JmolPanel: Executes the given command line on the Jmol instance.
export(File, SequenceProvider, Identification, FastaExport.ExportType, WaitingHandler, boolean) - Static method in class eu.isas.peptideshaker.followup.FastaExport: Exports the proteins of interest in a text file of the given format.
exportAccessions(FollowUpCLIInputBean, Identification, SequenceProvider, WaitingHandler, FilterParameters) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the accessions as specified in the follow-up input bean.
exportAnnotatedSpectrum() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the current spectrum annotation.
exportBubblePlotAsFigure() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the current bubble plot as a figure.
exportDeepLC(FollowUpCLIInputBean, Identification, ModificationParameters, SequenceMatchingParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports files needed by DeepLC.
exportDocumentation(ReportCLIInputBean, String, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Writes the documentation corresponding to an export given the command line arguments.
ExportFactoryMarshaller - Class in eu.isas.peptideshaker.utils: This class is a convenience class to have a DefaultJsonConverter with the ExportFactory interfaces.
ExportFactoryMarshaller() - Constructor for class eu.isas.peptideshaker.utils.ExportFactoryMarshaller: Constructor.
exportInclusionList(FollowUpCLIInputBean, Identification, IdentificationFeaturesGenerator, SpectrumProvider, SearchParameters, WaitingHandler, FilterParameters) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports an inclusion list of the validated hits.
exportInclusionList(File, Identification, IdentificationFeaturesGenerator, SpectrumProvider, ArrayList<Integer>, ArrayList<InclusionListExport.PeptideFilterType>, InclusionListExport.ExportFormat, SearchParameters, double, WaitingHandler, FilterParameters) - Static method in class eu.isas.peptideshaker.followup.InclusionListExport: Writes an inclusion list based on the validated PSMs of the validated peptides of the validated proteins.
exportIntensityHistogramAsFigure() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the current intensity histogram as a figure.
exportMassErrorPlotAsFigure() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the current mass error plot as a figure.
exportMs2pip(FollowUpCLIInputBean, Identification, SearchParameters, SequenceMatchingParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the files needed by ms2pip.
exportMzId(MzidCLIInputBean, PsdbParent, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the project in the mzIdentML format.
exportNeeded() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Indicates whether a report export is needed.
exportPercolator(FollowUpCLIInputBean, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the files needed by Percolator.
exportProgenesis(FollowUpCLIInputBean, Identification, WaitingHandler, SequenceProvider, ProteinDetailsProvider, SequenceMatchingParameters) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the identification in a Progenesis compatible format.
exportProjectAsZip(File, File, SpectrumProvider, File, boolean, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.ProjectExport: Exports the project as zip file.
exportProjectAsZip(File, File, SpectrumProvider, ArrayList<File>, ArrayList<File>, File, File, boolean, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.ProjectExport: Exports the project as zip file adding reports to it.
exportProjectAsZip() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the project as a zip file.
exportProteinSequences(FollowUpCLIInputBean, Identification, SequenceProvider, WaitingHandler, FilterParameters) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the protein details in FASTA format as specified in the follow-up input bean.
exportProteoforms(FollowUpCLIInputBean, Identification, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports proteoforms.
exportReport(ReportCLIInputBean, String, String, ProjectDetails, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, int, SpectrumCountingParameters, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Writes an export according to the command line settings contained in the reportCLIInputBean.
exportSelectedSpectraAsMgf() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the current spectrum as an mgf.
exportSequenceFragmentationAsFigure() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the current sequence fragmentation as a figure.
exportSpectra(FollowUpCLIInputBean, Identification, SpectrumProvider, WaitingHandler, SequenceMatchingParameters) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the spectra as specified in the follow-up input bean.
exportSpectra(File, WaitingHandler, SpectrumExporter.ExportType, SequenceMatchingParameters) - Method in class eu.isas.peptideshaker.followup.SpectrumExporter: Exports the spectra from different categories of PSMs according to the export type.
exportSpectrumAsFigure() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the current spectrum as a figure.
extension - Variable in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: The extension of the file.
extractAndUpdatePathOptions(String[]) - Static method in class eu.isas.peptideshaker.cmd.PathSettingsCLI: If the arguments contains changes to the paths these arguments will be extracted and the paths updated, before the remaining non-path options are returned for further processing.

F

FastaExport - Class in eu.isas.peptideshaker.followup: Export proteins in the FASTA format.
FastaExport() - Constructor for class eu.isas.peptideshaker.followup.FastaExport
FastaExport.ExportType - Enum in eu.isas.peptideshaker.followup: Enum of the different types of export implemented.
fastaFile - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The fasta file.
FeaturesExportDialog - Class in eu.isas.peptideshaker.gui.export: Dialog for exporting identification features.
FeaturesExportDialog(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.export.FeaturesExportDialog: Creates a new ExportPreferencesDialog.
FileImporter - Class in eu.isas.peptideshaker.fileimport: This class is responsible for the import of identifications.
FileImporter(Identification, IdentificationParameters, ProcessingParameters, Metrics, ProjectDetails, SpectrumProvider, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.fileimport.FileImporter: Constructor for the importer.
fileSpecificGrouping - Variable in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Map used to group keys together per file.
fileSpecificMaps - Variable in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: The map of the target decoy maps indexed by file and category.
fillPeptideMaps(Identification, Metrics, WaitingHandler, IdentificationParameters, SequenceProvider, SpectrumProvider) - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Fills the peptide specific map.
fillProteinMap(Identification, SpectrumProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Fills the protein map.
filter() - Method in class eu.isas.peptideshaker.gui.pride.ProjectsFilterDialog: Filters the projects table according to the current filter settings.
filterParameters - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The filter parameters.
FiltersDialog - Class in eu.isas.peptideshaker.gui.filtering: Displays the filters used for star/hide items.
FiltersDialog(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.filtering.FiltersDialog: Creates a new FiltersDialog.
FollowUpCLI - Class in eu.isas.peptideshaker.cmd: Command line interface to run follow-up analysis on psdb files.
FollowUpCLI(FollowUpCLIInputBean) - Constructor for class eu.isas.peptideshaker.cmd.FollowUpCLI: Construct a new FollowUpCLI runnable from a FollowUpCLI Bean.
FollowUpCLIInputBean - Class in eu.isas.peptideshaker.cmd: This class is a simple bean wrapping the CLI parameters provided in an Options instance.
FollowUpCLIInputBean(CommandLine) - Constructor for class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Construct a FollowUpCLIInputBean from an Apache CLI instance.
FollowUpCLIParams - Enum in eu.isas.peptideshaker.cmd: Enum class specifying the Command Line Parameters for follow up analysis.
FollowUpExportDialog - Class in eu.isas.peptideshaker.gui.export: This class allows generating exports for follow up analysis.
FollowUpExportDialog(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.export.FollowUpExportDialog: Creates a new FollowupPreferencesDialog.
followUpNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether follow-up tasks are required.
FractionDetailsDialog - Class in eu.isas.peptideshaker.gui: A dialog where the order of the fractions can be decided.
FractionDetailsDialog(PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.FractionDetailsDialog: Creates a new FractionDetailsDialog.

G

GARBAGE - Static variable in class eu.isas.peptideshaker.scoring.maps.specific.ModificationSpecificMap: The name of the garbage category.
GARBAGE_KEY - Static variable in class eu.isas.peptideshaker.scoring.maps.specific.ModificationSpecificMap: The key of the garbage category.
geneMaps - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The gene maps.
generateToolTip(CategoryDataset, int, int) - Method in class eu.isas.peptideshaker.gui.protein_sequence.ProteinAnnotations
getAccessionsExportFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file where to export the accessions.
getAccessionsExportTypeIndex() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the type of export needed for the accessions.
getAdvocateContribution(int, String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the contribution of validated hits of the given advocate for the given file.
getAdvocateContribution(int) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the contribution of validated hits of the given advocate for the entire dataset.
getAdvocateUniqueContribution(int, String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the contribution of unique validated hits of the given advocate for the given file.
getAdvocateUniqueContribution(int) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the contribution of unique validated hits of the given advocate for the entire dataset.
getAlgorithmNameToVersionsMap() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the different identification algorithm versions used in a map: algorithm name > versions.
getAnnotationMenuBar() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the annotation menu bar.
getBenefit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the benefit series.
getBestMatch(String, String, ArrayList<PeptideAssumption>) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection: Returns the best match for the given spectrum among the given peptide assumptions.
getBestMatch(String, String, ArrayList<PeptideAssumption>, boolean) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection: Returns the best match for the given spectrum among the given peptide assumptions.
getBestPeptideAssumption(String, String, PeptideAssumption, PeptideAssumption, boolean) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.TieBreaker: Returns the best assumption between the two given possibilities for the given spectrum.
getBubblePlot() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the bubble plot.
getBubblePlot() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Returns the bubble plot.
getBubbleScale() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the bubble plot scale value.
getCategoriesFromGroupedFiles() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns a list of categories from grouped files.
getChargeGroupingMap() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns the map of grouped categories indexed by representative category.
getCharges() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the different charges found.
getCharges() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the different charges found.
getChartPanel() - Method in class eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel: Returns the chart panel.
getColumnClass(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel
getColumnClass(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
getColumnClass(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel
getColumnClass(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel
getColumnClass(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
getColumnClass(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
getColumnCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel
getColumnCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
getColumnCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel
getColumnCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel
getColumnCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
getColumnCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
getColumnName(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel
getColumnName(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
getColumnName(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel
getColumnName(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel
getColumnName(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
getColumnName(int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
getCommandLineOptions() - Method in class eu.isas.peptideshaker.export.PSExportFactory: Returns the list of implemented reports as command line option.
getCommandLineOptions() - Static method in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Returns a description of the command line arguments.
getCommandLineOptions() - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Returns a description of the command line arguments.
getCommandLineOptions() - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Returns a description of the command line arguments.
getCommandLineOptions() - Static method in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Returns a description of the command line arguments.
getCommandLineOptions() - Static method in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Returns a description of the command line arguments.
getConfidence() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the confidence series.
getConfidenceLimit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the confidence limit.
getConfidenceLog() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the confidence log series.
getConfidenceResults(TargetDecoyResults) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Completes the results at the desired confidence threshold.
getConfidentHitsDestinationFile(String, String, boolean) - Static method in class eu.isas.peptideshaker.followup.DeepLcExport: Returns the file where to write the export for confident hits.
getContactAddress() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the contact address.
getContactAddress() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the address of the contact for the mzIdentML dataset.
getContactEmail() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the contact email.
getContactEmail() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the e-mail of the contact for the mzIdentML dataset.
getContactFirstName() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the contact first name.
getContactFirstName() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the first name of the contact for the mzIdentML dataset.
getContactLastName() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the contact last name.
getContactLastName() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the last name of the contact for the mzIdentML dataset.
getContactUrl() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the contact URL.
getContactUrl() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the URL of the contact for the mzIdentML dataset.
getCorrectedCharge(int) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: For grouped files, returns the reference category of the group.
getCreationDate() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Getter for the creation date of the project.
getCurrentMassDeltas() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Get the current delta masses for use when annotating the spectra.
getCurrentPxAccession() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns the current PX accession number.
getCurrentSpeciesList() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns the list of species for the currently selected assay or project.
getDatabaseLink(String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Transforms the protein accession number into an HTML link to the corresponding database.
getDatabaseLink(String, boolean, boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Transforms the protein accession number into an HTML link to the corresponding database.
getDatabaseLinks(String[]) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Transforms the protein accession number into an HTML link to the corresponding database.
getDatabaseLinks(String[], boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Transforms the protein accession number into an HTML link to the corresponding database.
getDatabaseText(FastaParameters, FastaSummary) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the database usage details.
getDbFolder() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the folder where the database is stored.
getDecoyType() - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the decoy sequences creation details.
getDeepLcStem() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the stem to use for the path to DeepLC files.
getDefaultDocumentation(String) - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Returns the default file name for the export of the documentation of the given report export type.
getDefaultExportScheme(String) - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Returns the desired default export scheme.
getDefaultExportSchemesNames() - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Returns a list of the default export schemes.
getDefaultPeptideSelection(long) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the default peptide, i.e., the "best" peptide for the given protein.
getDefaultPsmSelection(long) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the default PSM, i.e., the "best" PSM for the given peptide.
getDefaultReportName(String, String) - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Returns the default file name for the export of a report based on the project details
getDescription() - Method in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey
getDestinationFile(String, String, boolean) - Static method in class eu.isas.peptideshaker.followup.DeepLcExport: Returns the file where to write the export.
getDestinationFile(File, String, SpectrumExporter.ExportType) - Static method in class eu.isas.peptideshaker.followup.SpectrumExporter: Returns the destination file for the given export.
getDisplayedAssumptions() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns a list of keys of the currently displayed assumptions.
getDisplayedModifications() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Returns a list containing the names of the PTMs to display.
getDisplayedModifications(String[], HashSet<String>) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns an array containing only the modifications to display.
getDisplayedPeptides() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns a list of keys of the currently displayed peptides.
getDisplayedPeptides() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Returns a list of the keys of the currently displayed peptides.
getDisplayedPeptides() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns a list of keys of the displayed peptides
getDisplayedPeptides() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Returns a list of keys of the displayed peptides.
getDisplayedPeptides() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Returns a list of keys of the displayed peptides.
getDisplayedProteinMatches() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Returns a list of the keys of the proteins of the currently displayed peptides.
getDisplayedProteins() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns a list of keys of the currently displayed proteins.
getDisplayedProteins() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns a list of keys of the displayed proteins
getDisplayedProteins() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Returns a list of keys of the displayed proteins.
getDisplayedProteins() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Returns a list of keys of the displayed proteins.
getDisplayedSpectrumMatches() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns a list of keys of the currently displayed spectrum matches.
getDisplayedSpectrumMatches() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Returns a list of the PSM keys of the currently displayed assumptions.
getDisplayedSpectrumMatches() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns a list of keys of the displayed PSMs
getDisplayFeaturesGenerator() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the display features generator.
getDisplayParameters() - Method in class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog: Returns the display preferences.
getDisplayParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Return the display parameters to use.
getDisplayParameters() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the GUI display parameters.
getDisplayParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the display preferences.
getDisplayPreferences() - Method in class eu.isas.peptideshaker.gui.parameters.DisplayPreferencesDialog: Returns the new display preferences as set by the user.
getDocumentationTypes() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Returns the type of documentation required by the user.
getErrorKeys() - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Returns a list containing the keys of the paths where the tool is not able to write.
getExceptionHandler() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the exception handler.
getExperimentID() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the experiment name.
getExportedFiles(String, Identification) - Static method in class eu.isas.peptideshaker.followup.DeepLcExport: Returns an ArrayList of all the files that will be written by the export.
getExportFeatures(String, boolean) - Method in class eu.isas.peptideshaker.export.PSExportFactory
getExportScheme(String) - Method in class eu.isas.peptideshaker.export.PSExportFactory
getExportTypeFromCommandLineOption(int) - Method in class eu.isas.peptideshaker.export.PSExportFactory: Returns the export type based on the number used in command line.
getExtendedProjectReport() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns an extended HTML project report.
getExtendedProjectReport(String) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns an extended HTML project report.
getFastaFile() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the FASTA file.
getFastaFile() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the path to the FASTA file.
getFastaMapper() - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Returns the fasta mapper.
getFDR() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the FDR series.
getFdrLimit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the FDR limit.
getFDRResults(TargetDecoyResults) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Completes the results at the desired FDR threshold.
getfeature(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, IdentificationParameters, int, String, PeptideMatch, PsPeptideFeature, boolean, boolean, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.sections.PsPeptideSection: Returns the component of the section corresponding to the given feature.
getFeature(IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, GeneMaps, IdentificationParameters, int, long, ProteinMatch, PSParameter, PsProteinFeature, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.sections.PsProteinSection: Returns the part of the desired section.
getFeature(IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, GeneMaps, IdentificationParameters, int, long, ProteinMatch, String, PSParameter, PsProteinFeature, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.sections.PsProteinSection: Returns the part of the desired section.
getFeature(Identification, IdentificationFeaturesGenerator, IdentificationParameters, String, SpectrumMatch, PSParameter, PsPsmFeature, boolean, boolean, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.sections.PsPsmSection: Writes the given feature of the current section.
getFilesAtCategory(int) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns the files at the given category, an empty list if not found.
getFilesTable() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns the files table.
getFilteredAmbiguousModificationsRepresentativeSites(PSModificationScores, HashSet<String>, int) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Exports the ambiguously localized modification representative sites in a map: site > mapped modifications.
getFilteredAmbiguousModificationsSecondarySites(PSModificationScores, HashSet<String>, int) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Exports the ambiguously localized modification secondary sites in a map: site > mapped modifications.
getFilteredConfidentModificationsSites(PSModificationScores, HashSet<String>, int) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Exports the confidently localized modification sites in a map: site > mapped modifications.
getFilterParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Return the filter parameters to use.
getFilterParameters() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the GUI display parameters.
getFilterParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the filter preferences.
getFNR() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the probabilistic FNR series.
getFnrLimit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the FNR limit.
getFNRResults(TargetDecoyResults) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Completes the results at the desired FNR threshold.
getFollowUpCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the follow-up options required.
getFragmentMzError(double, double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation: Returns the fragment error at the given retention time and fragment m/z.
getFragmentMZList(double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation: Returns the list for fragment ion m/z bins at a given retention time point.
getGeneAnnotation() - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the gene annotation method usage details.
getGeneMaps() - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Returns the gene maps.
getGeneMaps() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the gene maps.
getGeneMaps() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the gene maps.
getGeneMaps() - Method in class eu.isas.peptideshaker.PeptideShaker: Returns the gene maps.
getGeneMaps() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the gene maps.
getGoAccessionLink(String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the GO accession number as a web link to the given GO term at QuickGO.
getGOPanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the GO Panel.
getGroupedCategories() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns a list of grouped categories from grouped files.
getHeader(SearchParameters, Boolean) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the header of the Percolator training file.
getHeaderHeight() - Method in class eu.isas.peptideshaker.export.PsExportStyle
getHeaderStyle() - Method in class eu.isas.peptideshaker.export.PsExportStyle
getHeaderStyle(int) - Method in class eu.isas.peptideshaker.export.PsExportStyle
getId() - Method in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey
getIdentification() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the identification displayed.
getIdentification() - Method in class eu.isas.peptideshaker.PeptideShaker: Returns the identification object.
getIdentification() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the identification object.
getIdentificationAlgorithms() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns a list of identification algorithms used based on the identification files of the project.
getIdentificationAlgorithmsForFile(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the identification algorithms used to create the id file in map: algorithm name > algorithm version.
getIdentificationFeaturesCache() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the identification features cache used by the identification features generator before saving the file.
getIdentificationFeaturesGenerator() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the identification features generator.
getIdentificationFeaturesGenerator() - Method in class eu.isas.peptideshaker.PeptideShaker: Returns the identification features generator used when loading the files.
getIdentificationFeaturesGenerator() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the identification features generator object.
getIdentificationFiles(String) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns a list of identification files as imported from the command line option.
getIdentificationFiles() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Getter for all identification files loaded.
getIdentificationParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the identification parameters.
getIdentificationParameters() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the identification parameters.
getIdentificationParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the identification parameters.
getIdentificationParametersFile() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the identification parameters file.
getIdentificationParametersInputBean() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the identification parameters provided by the user.
getIdentificationSettings(SearchParameters) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the identification settings details.
getIdFileReader() - Method in class eu.isas.peptideshaker.stirred.modules.IdImporter: Returns the identification file reader used.
getIdFiles() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the identification files.
getImplementedSections() - Method in class eu.isas.peptideshaker.export.PSExportFactory
getIncludeProteinSequences() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns true if the protein sequences are to be included in the mzid export.
getIncludeProteinSequences() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns true if the protein sequences are to be included in the mzid export.
getInclusionFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file for the inclusion list generation.
getInclusionFormat() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the format for inclusion list generation.
getInclusionPeptideFilter() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the peptide filters to use for inclusion list generation.
getInclusionProteinFilter() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the protein inference filters to use for inclusion list generation.
getInclusionRtWindow() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the retention time window to use for inclusion list generation.
getIndexOfSelectedItem() - Method in class eu.isas.peptideshaker.gui.JumpToPanel: Returns the index of the selected item.
getInputAlgorithms() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns a set containing the indexes of the algorithms scored in this input map.
getInputAlgorithmsSorted() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the indexes of the algorithms scored in this input map.
getInputMap() - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Returns the input map.
getInputMap() - Method in class eu.isas.peptideshaker.scoring.PSMaps: Returns the target decoy map of all search engine scores.
getInputType() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the type of input.
getInstance() - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Static method to get the instance of the factory.
getIntensityHistogramPlot() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the intensity histogram plot panel.
getIntermediateScoreInputAlgorithms(String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the algorithms having an intermediate score for the given spectrum file.
getIntermediateScoreMap(String, int, int) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the target decoy map associated to a given spectrum file, advocate and score type.
getJarFilePath() - Method in class eu.isas.peptideshaker.cmd.IdentificationParametersCLI: Returns the path to the jar file.
getJarFilePath() - Static method in class eu.isas.peptideshaker.PeptideShaker: Retrieves the path to the jar file.
getJsonFile() - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Returns the file where to save the implemented export schemes.
getJsonFolder() - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Returns the folder where to save the implemented export schemes.
getKeyFromId(String) - Static method in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey: Returns the key from its id.
getLastSelectedFolder() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the last selected folder.
getLastSelectedFolder(LastSelectedFolder) - Method in class eu.isas.peptideshaker.gui.pride.DatabaseHelpDialog: Returns the last selected folder.
getLogFileMessage() - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI: Returns the "see the log file" message.
getLogFolder() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLIInputBean: Returns the folder where to save the log files.
getLogScoreLimit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the score limit obtained with the current validation settings.
getMainTitleRowHeight() - Method in class eu.isas.peptideshaker.export.PsExportStyle
getMainTitleStyle() - Method in class eu.isas.peptideshaker.export.PsExportStyle
getMap() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the first target/decoy map of the input map in case a single algorithm was used.
getMapSize() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the size of the map.
getMapsSize() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns the overall number of points across all maps.
getMassErrorPlot() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the mass error plot panel.
getMatchesDirectoryParent() - Static method in class eu.isas.peptideshaker.PeptideShaker: Returns the matches directory parent.
getMatchesDirectoryParentFile() - Static method in class eu.isas.peptideshaker.PeptideShaker: Returns the matches directory parent.
getMatchesDirectorySubPath() - Static method in class eu.isas.peptideshaker.PeptideShaker: Returns the directory used to store the identification matches.
getMatchesFolder() - Static method in class eu.isas.peptideshaker.PeptideShaker: Returns the path to the matches folder according to the user path settings.
getMaxPeptideErrorDa() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the maximal peptide mass error found in Da.
getMaxPeptideErrorDa() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the maximal peptide mass error found in Da.
getMaxPeptideErrorPpm() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the maximal peptide mass error found in ppm.
getMaxPeptideErrorPpm() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the maximal peptide mass error found in ppm.
getMaxTagErrorDa() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the maximal tag mass error found in Da.
getMaxTagErrorDa() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the maximal tag mass error found in Da.
getMaxTagErrorPpm() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the maximal tag mass error found in ppm.
getMaxTagErrorPpm() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the maximal tag mass error found in ppm.
getMetrics() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the metrics saved while loading the files.
getMetrics() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the metrics saved when loading the files.
getMetrics() - Method in class eu.isas.peptideshaker.PeptideShaker: Returns the metrics picked-up while loading the files.
getMetrics() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the metrics object.
getMgfExport() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: When exporting the project to a zip file, returns whether mgf file/s should be written apart from it, into the same folder.
getMinFdr() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the minimal FDR which can be achieved in this dataset.
getMissingProteins() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the number of PSMs where a protein was missing.
getMissingProteins() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the number of PSMs where a protein was missing.
getModificationIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the number of PSMs which did not pass the import filters due to a modification parsing issue.
getModificationIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmImportRunnable: Returns the number of PSMs which did not pass the import filters due to a modification parsing issue.
getModifications(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, ModificationFactory) - Static method in class eu.isas.peptideshaker.utils.DeepLcUtils: Returns the modifications of the peptides encoded as required by DeepLc.
getModificationsPanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the modification panel.
getMs2pipFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file where to write the peptides for ms2pip.
getMs2pipModels() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the models for which to write an ms2pip config file.
getMzidCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the mzid export options required.
getMzIdentMLOutputFile() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the mzIdentML output file.
getMzIdentMLVersion() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the mzIdentML version to use for this file.
getN() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the number of retained hits.
getnAASurroundingPeptides() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Returns the number of amino acids surrounding a peptide sequence (1 by default).
getNalgorithms() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the number of algorithms in the input map.
getNcbiAccessionLink(String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the protein accession number as a web link to the given protein at https://www.ncbi.nlm.nih.gov/protein.
getNDecoy(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the number of decoy hits found at the given score.
getnDecoy() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the decoy series of the target decoy histogram.
getNEntries() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the number of entries in the input map.
getNEntriesSpecific() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the number of entries in the specific input map.
getNewFiles() - Method in class eu.isas.peptideshaker.gui.IdToSpectrumFileMappingDialog: Returns the new file mapping.
getNextProtAccessionLink(String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the protein accession number as a web link to the given protein at https://www.nextprot.org.
getnFP() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the estimated number of false positives.
getnMax() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the Nmax metric.
getnModificationIssues() - Method in class eu.isas.peptideshaker.stirred.modules.StirRunnable: Returns the number of peptides where the modification could not be parsed.
getNormalIcon() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the normal icon.
getnPeptideAssumptionsTotal() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the total number of peptide assumptions parsed.
getnPeptideAssumptionsTotal() - Method in class eu.isas.peptideshaker.fileimport.PsmImportRunnable: Returns the total number of peptide assumptions parsed.
getnPeptides() - Method in class eu.isas.peptideshaker.stirred.modules.StirRunnable: Returns the total number of peptides processed.
getnPSMs() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the number of PSMs processed.
getnPSMs() - Method in class eu.isas.peptideshaker.fileimport.PsmImportRunnable: Returns the number of PSMs processed.
getnRetained() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the number of PSMs retained after filtering.
getnRetained() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the number of PSMs retained after filtering.
getNTarget(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the number of target hits found at the given score.
getnTarget() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the target series of the target decoy histogram.
getnTargetOnly() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the number of target hits before the first decoy hit.
getnThreads() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the number of threads to use.
getnTP() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the estimated number of retained True positives.
getnTPTotal() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the estimated total number of True positives.
getOffset(double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation: Returns the precursor m/z deviation offset at a given retention time point.
getOptionIDs() - Static method in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams: Returns the list of supported command line options.
getOptionsAsString() - Static method in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Returns the options as a string.
getOptionsAsString() - Method in class eu.isas.peptideshaker.cmd.IdentificationParametersCLI
getOptionsAsString() - Static method in enum eu.isas.peptideshaker.cmd.MzidCLIParams: Returns the options as a string.
getOptionsAsString() - Static method in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams: Returns the options as a string.
getOptionsAsString() - Static method in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams: Returns the options as a string.
getOptionsAsString() - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerIdentificationParametersCLIParams: Returns the options as a string.
getOptionsAsString() - Static method in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Returns the options as a string.
getOptionsAsString() - Static method in enum eu.isas.peptideshaker.cmd.StirredOptions: Returns the options as a string.
getOrganizationAddress() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the organization address.
getOrganizationAddress() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the address of the organization for the mzIdentML dataset.
getOrganizationEmail() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the e-mail of the organization for the mzIdentML dataset.
getOrganizationMail() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the organization mail.
getOrganizationName() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the organization name.
getOrganizationName() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the name of the organization for the mzIdentML dataset.
getOrganizationUrl() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the organization URL.
getOrganizationUrl() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the URL of the organization for the mzIdentML dataset.
getOutput() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the psdb output file.
getOutputFile() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the file where to mzIdentML export will be stored.
getOutputOptionsAsString() - Static method in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Returns the output options as a string.
getOutputOptionsAsString() - Static method in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Returns the output options as a string.
getOverviewPanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the OverviewPanel.
getParameterKey() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters
getParameterKey() - Method in class eu.isas.peptideshaker.scoring.PSMaps
getParametersOptionsAsString() - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerIdentificationParametersCLIParams: Returns the options as a string.
getPassword() - Method in class eu.isas.peptideshaker.gui.pride.PridePrivateDataDialog: Returns the password.
getPassword() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns the current password.
getPathPreference(PeptideShakerPathParameters.PeptideShakerPathKey) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Sets the path according to the given key and path.
getPaths() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLIInputBean: Returns the specific paths provided by the user in a map: Path id > path.
getPathSettingsCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the path settings provided by the user.
getPathSettingsCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the path settings input.
getPathSettingsCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the path settings provided by the user.
getPathSettingsCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Returns the path settings provided by the user.
getPDBAccesionLink(String) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Returns the PDB accession number as a web link to the given structure at https://www.rcsb.org.
getPEP() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the score series.
getPeptideAssumptionFeature(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, IdentificationParameters, String, int, PeptideAssumption, String, String, PSParameter, PsIdentificationAlgorithmMatchesFeature, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection: Writes the feature associated to the match of the given peptide assumption.
getPeptideData(PeptideAssumption, double, ModificationParameters, SequenceProvider, SequenceMatchingParameters, ModificationFactory) - Static method in class eu.isas.peptideshaker.utils.DeepLcUtils: Gets the peptide data to provide to ms2pip.
getPeptideData(PeptideAssumption, ModificationParameters, SequenceProvider, SequenceMatchingParameters, ModificationFactory) - Static method in class eu.isas.peptideshaker.utils.Ms2PipUtils: Gets the peptide data to provide to ms2pip.
getPeptideData(SpectrumMatch, PeptideAssumption, Boolean, ArrayList<Double>, SearchParameters, SequenceProvider, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationFactory, SpectrumProvider) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Gets the peptide data to provide to percolator.
getPeptideEvidenceKey(String, int, long) - Static method in class eu.isas.peptideshaker.export.MzIdentMLExport: Returns the peptide evidence key as string for the given peptide attributes.
getPeptideIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the number of PSMs which did not pass the import filters due to a peptide issue.
getPeptideIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the number of PSMs which did not pass the import filters due to a peptide issue.
getPeptideIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmImportRunnable: Returns the number of PSMs which did not pass the import filters due to a peptide issue.
getPeptideKey(String) - Static method in class eu.isas.peptideshaker.utils.DeepLcUtils: Returns a unique key corresponding to the given peptide.
getPeptideKey(String) - Static method in class eu.isas.peptideshaker.utils.Ms2PipUtils: Returns a unique key corresponding to the given peptide.
getPeptideKey(String) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns a unique key corresponding to the given peptide.
getPeptideLocalizationText(String, int[]) - Static method in class eu.isas.peptideshaker.export.sections.PsPeptideSection: Returns the peptide localization on the given protein as text in the form accession (site1,site2).
getPeptideMap() - Method in class eu.isas.peptideshaker.scoring.PSMaps: Returns the target decoy map at the peptide level.
getPeptideMap() - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Returns the peptide scoring specific map.
getPeptideModificationLocationConfidence(PeptideMatch, ModificationParameters) - Static method in class eu.isas.peptideshaker.export.sections.PsPeptideSection: Returns the peptide modification location confidence as a string.
getPeptideModificationLocationConfidence(SpectrumMatch, ModificationParameters) - Static method in class eu.isas.peptideshaker.export.sections.PsPsmSection: Returns the peptide modification location confidence as a string.
getPeptideModificationTooltipAsHtml(SpectrumMatch) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns a string with the HTML tooltip for the peptide indicating the modification details.
getPeptideModificationTooltipAsHtml(PeptideMatch) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns a string with the HTML tooltip for the peptide indicating the modification details.
getPeptideModificationTooltipAsHtml(Peptide, PSModificationScores) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns a string with the HTML tooltip for the peptide indicating the modification details.
getPeptideModificationTooltipAsHtml(Peptide) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns a string with the HTML tooltip for the peptide indicating the modification details.
getPeptideShaker() - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the PeptideShaker usage details.
getPeptideShakerGUI() - Method in class eu.isas.peptideshaker.gui.export.FollowUpExportDialog: Returns the references to the PeptideShakerGUI.
getPeptideShakerGUI() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns a reference to the main GUI.
getPeptideShakerHits(String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the number of validated hits for the given file.
getPeptideShakerHits() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the number of PeptideShaker validated hits for the entire dataset.
getPeptideShakerUniqueContribution(String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the contribution of unique validated hits from PeptideShaker for the given file.
getPeptideShakerUniqueContribution() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the contribution of unique validated hits by PeptideShaker for the entire dataset.
getPeptideShakerVersion() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PeptideShaker version used to create the project.
getPeptideTable() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Returns the peptide table.
getPercolatorFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file where to write the training file for Percolator.
getPercolatorFragmentationFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file with fragmentation values for Percolator.
getPercolatorRtFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file with retention time values for Percolator.
getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Returns all possibilities descriptions in an array of string.
getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Returns all possibilities descriptions in an array of string.
getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Returns all possibilities descriptions in an array of string.
getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Returns all possibilities descriptions in an array of string.
getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Returns all possibilities descriptions in an array of string.
getPossibilitiesDescriptions() - Method in class eu.isas.peptideshaker.gui.JumpToPanel: Returns a list of descriptions corresponding to every item matching the search.
getPossibleCategories() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns the categories found in the map
getPrecursorIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the number of PSMs which did not pass the import filters due to a precursor issue.
getPrecursorIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the number of PSMs which did not pass the import filters due to a precursor issue.
getPrecursorMzCorrection(double, double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation: Returns an interpolation of the median error in the bins surrounding the given precursor m/z when recalibrating with m/z only.
getPrecursorRTList() - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation: Returns the list of precursor retention time bins.
getPreferredAccessionColumnWidth(JTable, int, int, Integer) - Static method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel: Gets the preferred width of the column specified by colIndex.
getPreferredColumnWidth(JTable, int, int) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Gets the preferred width of the column specified by colIndex.
getPrideAccessionLink(String) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the project accession number as a web link to the given project in PRIDE.
getPrideAssayArchiveLink(String, String) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the assay accession number as a web link to the given assay in the PRIDE archive.
getPrideContactGroup() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE contact group.
getPrideExperimentDescription() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE experiment project description.
getPrideExperimentLabel() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE experiment label.
getPrideExperimentProjectTitle() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE experiment project title.
getPrideExperimentTitle() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE experiment title.
getPrideFile() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the pride file.
getPrideInstrument() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE instrument.
getPrideOutputFolder() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE output folder.
getPrideProjectArchiveLink(String) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the project accession number as a web link to the given project in the PRIDE archive.
getPrideProtocol() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE protocol.
getPrideReferenceGroup() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE reference group.
getPrideSample() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the PRIDE sample.
getProbability(int, double) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: returns the posterior error probability associated to the given e-value for the given search-engine (indexed by its utilities index)
getProbability(String, int, double) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns the probability of the given spectrum match at the given score.
getProbability(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the posterior error probability estimated at the given score.
getProcessingParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the initial processing preferences.
getProgenesisExportFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the Progenesis file.
getProgenesisExportTypeIndex() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the type of export needed for the Progenesis export.
getProgenesisTargetedPTMs() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the list of PTMs targeted for the Progenesis PTM export.
getProjectAccession() - Method in class eu.isas.peptideshaker.gui.pride.PridePrivateDataDialog: Returns the project accession.
getProjectDetails() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the project details.
getProjectDetails() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the project details.
getProjectDetails() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the project details.
getProjectParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the project parameters.
getProjectParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the project parameters.
getProjectsTable() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns the projects table.
getProjectType() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the project type.
getProjectType() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the project type.
getProjectType() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the project type.
getProjectType() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the project type.
getProteinCount() - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Returns the occurrence of proteins.
getProteinCount() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the occurrence of each protein.
getProteinCount() - Method in class eu.isas.peptideshaker.fileimport.PsmImportRunnable: Returns the occurrence of each protein.
getProteinDetailsProvider() - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Returns the details provider.
getProteinDetailsProvider() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the protein details provider.
getProteinDetailsProvider() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the protein details provider.
getProteinDetailsProvider() - Method in class eu.isas.peptideshaker.PeptideShaker: Returns the protein details provider.
getProteinDetailsProvider() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the protein details provider.
getProteinFiltersCommandLineOptions() - Static method in class eu.isas.peptideshaker.followup.InclusionListExport: Returns a description of the command line arguments for the protein filters.
getProteinFractionsPanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the fractions panel.
getProteinGroupText(long, Identification) - Static method in class eu.isas.peptideshaker.export.sections.PsPeptideSection: Returns a description of the given protein group in the form proteinA,proteinB(confidence).
getProteinGroupText(long, Identification) - Static method in class eu.isas.peptideshaker.export.sections.PsPsmSection: Returns a description of the given protein group in the form proteinA,proteinB(confidence).
getProteinIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the number of PSMs which did not pass the import filters due to a protein issue.
getProteinIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the number of PSMs which did not pass the import filters due to a protein issue.
getProteinMap() - Method in class eu.isas.peptideshaker.scoring.PSMaps: Returns the target decoy map at the protein level.
getProteinMap() - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Returns the protein scoring map.
getProteins() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel: Returns the list of protein groups in the model.
getProteinSequencesExportFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file where to export the protein details.
getProteinSequencesExportTypeIndex() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the type of export needed for the protein details.
getProteinStructurePanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the ProteinStructurePanel.
getProteinTable() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the protein table.
getProteinTable() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Returns the protein table.
getProteoformsFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the proteoforms file.
getProteomeXchange() - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the ProteomeXchange upload details.
getPsdbFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: The psdb file selected by the user.
getPsdbFile() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns the psdb file.
getPsdbFile() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Returns the psdb file from which the information can be obtained.
getPsdbFile() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the psdb file.
getPsdbImportFromZip() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the psdb import from zip.
getPsmMap() - Method in class eu.isas.peptideshaker.scoring.PSMaps: Returns the target decoy map at the psm level.
getPsmMap() - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Returns the PSM scoring specific map.
getPsmsRejected() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Returns the number of PSMs which did not pass the import filters.
getPsmsRejected() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Returns the number of PSMs which did not pass the import filters.
getPtmScoring(ModificationLocalizationParameters) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the PTM scoring methods used.
getRecalibratedFileName(String) - Static method in class eu.isas.peptideshaker.followup.RecalibrationExporter: Returns the name of the recalibrated file.
getRecalibrationFolder() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: The folder where to export recalibrated spectra.
getRecalibrationMode() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: The recalibration mode.
getRecentProjects() - Method in class eu.isas.peptideshaker.preferences.UserParameters: Returns the paths of the recent projects.
getReport() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the report created during the loading of the project.
getReportCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the report export options required.
getReportNamePrefix() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Returns the report name prefix.
getReportOutputFolder() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Returns the report output folder.
getReportStyle(ExcelWriter) - Static method in class eu.isas.peptideshaker.export.PsExportStyle: Returns the style attached to that writer or create a new one if none found.
getReportTypes() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Returns the types of output required by the user.
getReshakeableFiles() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns the list of reshakable file types.
getResidueAnnotation(long, SequenceMatchingParameters, IdentificationFeaturesGenerator, Metrics, Identification, boolean, SearchParameters, boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the residue annotation for a given protein in a map for enzymatic or not enzymatic peptides only.
getResolution() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the minimal detectable PEP variation in percent.
getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel
getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel
getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel
getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
getRunMzDeviations(String) - Method in class eu.isas.peptideshaker.recalibration.SpectrumRecalibrator: Returns the mz deviation statistics class for the spectrum file of interest.
getScoreAndConfidenceDecimalFormat() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the decimal format used for the score and confidence columns.
getScoreLimit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the score limit obtained with the current validation settings.
getScores() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the sorted scores implemented in this map.
getScores() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the score series.
getScoresLog() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the log score series.
getSearchEnginesText(ProjectDetails) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the search engines usage details.
getSearchGUIText() - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the SearchGUI usage details.
getSearchSettingsFiles() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns the list of files that search settings can be extracted from.
getSelectedIdentificationAssumptions() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption
getSelectedIdentificationAssumptions() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption
getSelectedIdentificationAssumptions() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption
getSelectedModification() - Method in class eu.isas.peptideshaker.gui.ModificationDialog: Returns the selected modification.
getSelectedModification() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Returns the selected modification name.
getSelectedPeptideKey() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the key of the selected peptide.
getSelectedProteinKey() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the key of the selected protein.
getSelectedPsmKeys() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the keys of the selected spectra in the PSM table.
getSelectedPsmsKeys() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Returns the keys of the selected PSMs.
getSelectedSpectrumFile() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the currently selected spectrum file.
getSelectedSpectrumTabIndex() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the current selected tab in the spectrum and fragment ions tabbed pane.
getSelectedSpectrumTitle() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the currently selected spectrum title.
getSelectedSpectrumTitle() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Returns the title of the currently selected spectrum.
getSelectedSpectrumTitles() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Returns the titles of the selected spectra in the PSM table in a map by file name.
getSelectedSpectrumTitles() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the titles of the selected spectra in the PSM table in a map by file name.
getSelectedSpectrumTitles() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Returns the titles of the selected spectra in the PSM table in a map by file name.
getSelectedTab() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the selected tab as indexed by the static fields.
getSequenceFragmentationPlot() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the sequence fragmentation plot panel.
getSequencePlot(ProteinSequencePanelParent, JSparklinesDataset, HashMap<Integer, ArrayList<ResidueAnnotation>>, boolean, boolean) - Method in class eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel: Returns a sequence plot as a ChartPanel.
getSequenceProvider() - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Returns the sequence provider.
getSequenceProvider() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the sequence provider.
getSequenceProvider() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the sequence provider saved when loading the files.
getSequenceProvider() - Method in class eu.isas.peptideshaker.PeptideShaker: Returns the sequence provider.
getSequenceProvider() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the sequence provider.
getSlope(double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation: Returns the precursor m/z deviation slope at a given retention time point.
getSparklineColor() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Get the sparklines color.
getSparklineColorNonValidated() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Get the non-validated sparklines color.
getSparklineColorNotFound() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Get the not found sparklines color.
getSparklineColorPossible() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Get the possible sparklines color.
getSparkLineDataSeriesCoverage(double[], int[], HashMap<Integer, Color>) - Static method in class eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel: Returns an array list with the coverage.
getSpecificAnnotationParameters(String, String, SpectrumIdentificationAssumption) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the specific annotation parameters corresponding to the given spectrum, hit, and the menu selections.
getSpectrum() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Returns the spectrum panel.
getSpectrum() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the spectrum panel.
getSpectrum() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Returns the spectrum panel.
getSpectrumAndPlots() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns the extended spectrum panel.
getSpectrumCounting(SpectrumCountingParameters) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the spectrum counting method usage details.
getSpectrumCountingParameters() - Method in class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog: Returns the spectrum counting preferences.
getSpectrumCountingParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the spectrum counting parameters.
getSpectrumCountingParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the spectrum counting preferences.
getSpectrumCountingPreferences() - Method in class eu.isas.peptideshaker.gui.parameters.SpectrumCountingSettingsDialog: Returns the spectrum counting preferences as set by the user.
getSpectrumCountingPreferences() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Returns the spectrum counting preferences of the project.
getSpectrumExportFolder() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the folder where to export the spectrum files.
getSpectrumExportTypeIndex() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the type of export needed for the spectra.
getSpectrumFileNames() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the name of the input spectrum files as a set.
getSpectrumFilePath(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the path to the file corresponding to the given name.
getSpectrumFiles() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the spectrum files.
getSpectrumFiles(String) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns a list of spectrum files as imported from the command line option.
getSpectrumIdentificationPanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the SpectrumIdentificationPanel.
getSpectrumProvider() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the spectrum provider.
getSpectrumProvider() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the spectrum provider.
getSrsAccessionLink(String, String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the protein accession number as a web link to the given protein at https://srs.ebi.ac.uk.
getStandardHeight() - Method in class eu.isas.peptideshaker.export.PsExportStyle
getStandardStyle() - Method in class eu.isas.peptideshaker.export.PsExportStyle
getStandardStyle(int) - Method in class eu.isas.peptideshaker.export.PsExportStyle
getStarHider() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the object responsible for starring/hiding matches.
getSuffix(SpectrumExporter.ExportType) - Static method in class eu.isas.peptideshaker.followup.SpectrumExporter: Returns the suffix for a spectrum file name.
getTagAssumptionFeature(Identification, IdentificationFeaturesGenerator, SpectrumProvider, IdentificationParameters, String, TagAssumption, String, String, PSParameter, PsIdentificationAlgorithmMatchesFeature, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection: Writes the feature associated to the match of the given tag assumption.
getTaggedPeptideSequence(PeptideMatch, boolean, boolean, boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on PeptideShaker site inference results for the given peptide match.
getTaggedPeptideSequence(SpectrumMatch, boolean, boolean, boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on PeptideShaker site inference results for the best assumption of the given spectrum match.
getTaggedPeptideSequence(Peptide, PSModificationScores, boolean, boolean, boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on the provided modification localization scores.
getTagModificationTooltipAsHtml(Tag) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns a string with the HTML tooltip for the tag indicating the modification details.
getTargetDecoyMap(int) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the target decoy map attached to the given algorithm.
getTargetDecoyMap(int, String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the target decoy map attached to the given algorithm for a specific spectrum file.
getTargetDecoyMap(int, String) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns the desired target decoy map.
getTargetDecoyMaps() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns a list of all target decoy maps contained in this mapping.
getTargetDecoyMaps() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Returns a list of the target decoy maps used for scoring.
getTargetDecoyResults() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the current target decoy results.
getTargetDecoySeries() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the target decoy series.
getTdBins() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the target decoy bins to use for the histogram.
getTempFolder() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLIInputBean: Returns the temp folder, an empty string if not set.
getTempFolderName(String) - Static method in class eu.isas.peptideshaker.utils.PsZipUtils: Returns the temp folder name to use when unzipping a zip file.
GettingStartedDialog - Class in eu.isas.peptideshaker.gui.start: A dialog containing basic information on how to use PeptideShaker.
GettingStartedDialog(PeptideShakerGUI, WelcomeDialog, boolean) - Constructor for class eu.isas.peptideshaker.gui.start.GettingStartedDialog: Creates a new GettingStartedDialog.
getTips() - Static method in class eu.isas.peptideshaker.utils.Tips: Returns the tips of the day.
getTypeFromIndex(int) - Static method in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Returns the export type corresponding to a given index.
getTypeFromIndex(int) - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Returns the export type corresponding to a given index.
getTypeFromIndex(int) - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Returns the parameter type corresponding to a given index.
getTypeFromIndex(int) - Static method in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Returns the export type corresponding to a given index.
getTypeFromIndex(int) - Static method in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Returns the export type corresponding to a given index.
getUniProtAccessionLink(String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns the protein accession number as a web link to the given protein at https://www.uniprot.org/uniprot.
getUnzipParentFolder() - Static method in class eu.isas.peptideshaker.utils.PsZipUtils: Returns the parent folder where to unzip files.
getUnzipSubFolder() - Static method in class eu.isas.peptideshaker.utils.PsZipUtils: Returns the sub-folder where to unzip files.
getUserAdvocateMapping() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the user advocates used in this project.
getUserInput() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns the user input.
getUserName() - Method in class eu.isas.peptideshaker.gui.pride.PridePrivateDataDialog: Returns the user name.
getUserName() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Returns the current user name.
getUserParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the user parameters.
getUserParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Returns the user preferences.
getUserPreferencesFile() - Static method in class eu.isas.peptideshaker.PeptideShaker: Returns the file used for user preferences storage.
getUserPreferencesFolder() - Static method in class eu.isas.peptideshaker.PeptideShaker: Returns the folder used for user preferences storage.
getUserSchemesNames() - Method in class eu.isas.peptideshaker.export.PSExportFactory: Returns a list of the name of the available user schemes.
getUserSelectedFile(String, String, String, String, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the file selected by the user, or null if no file was selected.
getUtilitiesUserParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI
getValidation(IdMatchValidationParameters) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods: Returns the validation thresholds used.
getValidationPanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the validation panel.
getValueAt(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel
getValueAt(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
getValueAt(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel
getValueAt(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel
getValueAt(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
getValueAt(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
getVersion() - Static method in class eu.isas.peptideshaker.PeptideShaker: Retrieves the version number set in the pom file.
getVersion() - Method in class eu.isas.peptideshaker.utils.Properties: Retrieves the version number set in the pom file.
getViewer() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel.JmolPanel: Returns the JmolViewer.
getWaitingIcon() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns the waiting icon.
getWindowSize() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the window size used for pep estimation.
getZipExport() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the file where to export the project as zip file.
getZipFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: The zip file selected by the user.
getZipFile() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: The zip file selected by the user.
getZipFile() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: The zip file selected by the user.
GO_ANALYSIS_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The GO Analysis tab index.
GOEAPanel - Class in eu.isas.peptideshaker.gui.tabpanels: The PeptideShaker GO Enrichment Analysis tab.
GOEAPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel: Creates a new GOEAPanel.
GOEAPanel.QuickGoTerm - Class in eu.isas.peptideshaker.gui.tabpanels: Dummy class to get the aspect element from a QuickGO term JSON file.
GOEAPanel.QuickGoTerm.DummyResults - Class in eu.isas.peptideshaker.gui.tabpanels: The aspect object from the results.
groupedMaps - Variable in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: The map of the target decoy maps indexed by category.
grouping - Variable in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Map used to group keys together in the grouped maps.
GroupSimplification - Class in eu.isas.peptideshaker.protein_inference: This class handles the simplification of redundant groups based on the protein inference settings.
GroupSimplification() - Constructor for class eu.isas.peptideshaker.protein_inference.GroupSimplification

H

hasAdvocateContribution() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Indicates whether the advocate contributions are present in this map.
hasArg - Variable in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Boolean indicating whether the parameter has arguments.
hasArgument - Variable in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Indicates whether user input is expected.
hasArgument - Variable in enum eu.isas.peptideshaker.cmd.MzidCLIParams: Indicates whether user input is expected.
hasIdentificationAlgorithms() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns true if the identification algorithms are stored.
hasInput() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLIInputBean: Indicates whether the user gave some path configuration input.
hasValue - Variable in enum eu.isas.peptideshaker.cmd.StirredOptions: If true this command line argument needs a value.
hidePeptide(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Hides a peptide match.
hideProtein(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Hides a protein match.
hidePsm(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Hides a PSM match.

I

id - Variable in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Short Id for the CLI parameter.
id - Variable in enum eu.isas.peptideshaker.cmd.MzidCLIParams: Short Id for the CLI parameter.
id - Variable in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams: The id of the command line option.
id - Variable in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams: Short Id for the CLI parameter.
id - Variable in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Short Id for the CLI parameter.
identification - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The identification.
identificationFeaturesGenerator - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The identification features generator.
identificationParameters - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The identification parameters.
IdentificationParametersCLI - Class in eu.isas.peptideshaker.cmd: The SearchParametersCLI allows creating search parameters files using command line arguments.
IdentificationParametersCLI(String[]) - Constructor for class eu.isas.peptideshaker.cmd.IdentificationParametersCLI: Construct a new SearchParametersCLI runnable from a list of arguments.
identificationParametersFile - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The identification parameters file.
identifier - Variable in class eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation: A unique (external) identifier for the annotation.
IdImporter - Class in eu.isas.peptideshaker.stirred.modules: This class imports the ids from a file.
IdImporter(File, CliLogger) - Constructor for class eu.isas.peptideshaker.stirred.modules.IdImporter: Constructor.
IdToSpectrumFileMappingDialog - Class in eu.isas.peptideshaker.gui: A dialog for selecting missing mgf files.
IdToSpectrumFileMappingDialog(WaitingDialog, HashMap<File, String>) - Constructor for class eu.isas.peptideshaker.gui.IdToSpectrumFileMappingDialog: Creates a new MgfFilesNotFoundDialog.
ImageIconPanel - Class in eu.isas.peptideshaker.gui: This class extends JPanel to be able to display an ImageIcon object inside a JPanel.
ImageIconPanel(ImageIcon) - Constructor for class eu.isas.peptideshaker.gui.ImageIconPanel: Create a new ImageIconPanel.
importFiles(ArrayList<File>) - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Imports the identifications from the files.
importFiles(WaitingHandler, ArrayList<File>, SpectrumProvider, IdentificationParameters, ProjectDetails, ProcessingParameters, ExceptionHandler) - Method in class eu.isas.peptideshaker.PeptideShaker: Imports identification results from result files.
importGenes() - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Imports the gene information for this project.
importPeptideShakerFile(File, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Imports information from a PeptideShaker file.
importPeptideShakerZipFile(File) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Imports information from a PeptideShaker zip file.
importPeptideShakerZipFromURL(String, String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Imports a PeptideShaker zip file from a URL.
importPsms(File) - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Imports the PSMs from an identification file.
importPsms(ArrayList<SpectrumMatch>, Identification, IdentificationParameters, InputMap, IdfileReader, File, SequenceProvider, SpectrumProvider, FastaMapper, int, WaitingHandler, ExceptionHandler) - Method in class eu.isas.peptideshaker.fileimport.PsmImporter: Imports PSMs.
importSearchParameters(File, ArrayList<File>, ProgressDialogX) - Method in class eu.isas.peptideshaker.gui.NewDialog: Imports the search parameters from a file.
importSequences(SequenceMatchingParameters, SearchParameters, FastaParameters, PeptideVariantsParameters, WaitingHandler, ExceptionHandler) - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Imports sequences from a FASTA file and sets the sequence provider and protein details provider fields.
include(String, String, Identification, SequenceMatchingParameters, SpectrumExporter.ExportType) - Static method in class eu.isas.peptideshaker.followup.SpectrumExporter: Indicates whether a spectrum should be exported.
InclusionListExport - Class in eu.isas.peptideshaker.followup: This class exports identifications in an inclusion list.
InclusionListExport() - Constructor for class eu.isas.peptideshaker.followup.InclusionListExport
InclusionListExport.ExportFormat - Enum in eu.isas.peptideshaker.followup: Enum of the different types of export implemented.
InclusionListExport.PeptideFilterType - Enum in eu.isas.peptideshaker.followup: Enum of the peptide filters implemented.
InclusionListExportDialog - Class in eu.isas.peptideshaker.gui.export: Dialog for setting the inclusion list export settings.
InclusionListExportDialog(FollowUpExportDialog, InclusionListExport.ExportFormat, boolean) - Constructor for class eu.isas.peptideshaker.gui.export.InclusionListExportDialog: Creates a new InclusionListExportDialog.
inclusionListNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether an inclusion list generation is needed.
increaseDecoy() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint: Increases the decoy counter.
increaseTarget() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint: Increases the target counter.
index - Variable in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Index for the export type.
index - Variable in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Index for the export type.
index - Variable in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Index for the export type.
index - Variable in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Index for the export type.
index - Variable in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Index for the export type.
index - Variable in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: The index of the option.
inferPiStatus(Identification, Metrics, TargetDecoyMap, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.protein_inference.ProteinInference: Selects the leading protein of protein groups and infers PI status of peptide and proteins.
inferPiStatus(ProteinMatch, Identification, Metrics, TargetDecoyMap, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.protein_inference.ProteinInference: Selects the leading protein of protein groups and infers PI status of peptide and proteins.
initiateDisplay() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Initiate the display by displaying the data in the currently selected tab.
inputFile - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The input file.
InputMap - Class in eu.isas.peptideshaker.scoring.maps: This class contains basic information about the hits as imported from the various search engine result files.
InputMap() - Constructor for class eu.isas.peptideshaker.scoring.maps.InputMap: Constructor.
instantiateFacories(UtilitiesUserParameters) - Static method in class eu.isas.peptideshaker.PeptideShaker: Instantiates the spectrum, sequence, and PTM factories with caches adapted to the memory available as set in the user preferences.
isBestPsmEqualForAllIdSoftware(SpectrumMatch, SequenceMatchingParameters, Integer) - Static method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Returns true if all the used id software tools agree on the top PSM without accounting for modification localization, false otherwise.
isCanceled() - Method in class eu.isas.peptideshaker.gui.ModificationDialog: Cancels the selection.
isCanceled() - Method in class eu.isas.peptideshaker.gui.parameters.DisplayPreferencesDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog: Returns whether the user canceled the edition of the preferences.
isCanceled() - Method in class eu.isas.peptideshaker.gui.parameters.SpectrumCountingSettingsDialog: Indicates whether the user canceled the editing.
isCanceled() - Method in class eu.isas.peptideshaker.gui.pride.PrideDataTypeSelectionDialog: Returns true if the dialog was canceled by the user.
isCellEditable(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel
isCellEditable(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
isCellEditable(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel
isCellEditable(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel
isCellEditable(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
isCellEditable(int, int) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
isDisplayedPTM(String) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Indicates whether a PTM shall be displayed on the interface.
isFileGrouped(int, String) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Indicates whether the given file was grouped for the given category.
isGUI() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Indicates whether a GUI shall be used to display the progress.
isGzip() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Returns a boolean indicating whether the export should be gzipped.
isGzip() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Returns a boolean indicating whether the export should be gzipped.
isInitiated() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Returns true if the tab has been loaded at least once.
isInstantiated() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel: Indicates whether the table content was instantiated.
isInstantiated() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel: Indicates whether the table content was instantiated.
isInstantiated() - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel: Indicates whether the table content was instantiated.
isLowerEvidence(String, String[], ProteinDetailsProvider) - Static method in class eu.isas.peptideshaker.protein_inference.GroupSimplification: Returns a boolean indicating whether the protein is considered as uncharacterized compared to the others.
isModelInitiated() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel: Returns true if the real model has been iniitated.
isMultipleAlgorithms() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns true for multiple search engines investigations.
isPeptideHidden(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Tests whether a peptide match should be hidden according to the implemented filters.
isPeptideStarred(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Tests whether a peptide match should be starred according to the implemented filters.
isProteinHidden(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Tests whether a protein match should be hidden according to the implemented filters.
isProteinStarred(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Tests whether a protein match should be starred according to the implemented filters.
isPsmHidden(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Tests whether a PSM match should be hidden according to the implemented filters.
isPsmStarred(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Tests whether a PSM match should be starred according to the implemented filters.
isPublic() - Method in class eu.isas.peptideshaker.gui.pride.PrideDataTypeSelectionDialog: Returns true of public data is to be loaded, false means load private data.
isSpectrumEnabled() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Returns true of the spectrum tab is enabled.
isValidationChanged() - Method in class eu.isas.peptideshaker.gui.MatchValidationDialog: Indicates whether the validation level changed.
isValidStartup(CommandLine) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Verifies the command line start parameters.

J

JumpToPanel - Class in eu.isas.peptideshaker.gui: A Jump To panel for use in the menu bar in the main frame.
JumpToPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.JumpToPanel: Creates a new JumpToPanel.
JumpToPanel.JumpType - Enum in eu.isas.peptideshaker.gui: Enum of the types of data to jump to.
jumpToTab(int) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Jumps to the desired tab

K

KEY - Static variable in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: The key of the object when stored in settings table of a psdb file.
KEYWORDS_UNCHARACTERIZED - Static variable in class eu.isas.peptideshaker.protein_inference.ProteinInference: Key words used to flag uncharacterized proteins.

L

loadDataForRows(ArrayList<Integer>, WaitingHandler) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
loadDataForRows(ArrayList<Integer>, WaitingHandler) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
loadDataForRows(ArrayList<Integer>, WaitingHandler) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
loadFastaFile(WaitingHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Loads the FASTA file.
loadFromFile(File) - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Loads an export factory from a file.
LOADING_MESSAGE - Static variable in class eu.isas.peptideshaker.preferences.DisplayParameters: The text displayed in the cell of a table in case the data is not loaded.
loadModifications(SearchParameters) - Static method in class eu.isas.peptideshaker.PeptideShaker: Verifies that the modifications backed-up in the search parameters are loaded and returns an error message if one was already loaded, null otherwise.
loadPathParametersFromFile(File) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Loads the path preferences from a text file.
loadPathParametersFromLine(String) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Loads a path to be set from a line.
loadPsdbFile(File, WaitingHandler, boolean) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Loads the information from a psdb file.
loadPsdbFromZipFile(File, File, WaitingHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Loads the information from a psdb file.
loadRecentProjectsList(JPopupMenu, WelcomeDialog) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Add the list of recently used files to the file menu.
loadSpectrumFile(String, ArrayList<File>, WaitingHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Loads the spectrum file.
loadSpectrumFile(File, WaitingHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Adds a spectrum file to the spectrum provider.
loadSpectrumFiles(WaitingHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Loads the spectra in the spectrum factory.
loadSpectrumFiles(File, WaitingHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Loads the spectrum files.
loadSpectrumMatches(IdentificationParameters, SpectrumProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.stirred.modules.IdImporter: Parses the spectrum matches and returns them in an ArrayList.
loadUserParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Loads the user parameters.
loadUserParameters() - Method in class eu.isas.peptideshaker.preferences.UserPreferencesParent: Loads the user preferences.
logFile - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The log file.
longOpt - Variable in enum eu.isas.peptideshaker.cmd.StirredOptions: Key for the command line argument.
lostOwnership(Clipboard, Transferable) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

M

main(String[]) - Static method in class eu.isas.peptideshaker.cmd.FollowUpCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.peptideshaker.cmd.IdentificationParametersCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.peptideshaker.cmd.MzidCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.peptideshaker.cmd.PathSettingsCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.peptideshaker.cmd.ReportCLI: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.peptideshaker.cmd.StirredCLI: Main method.
main(String[]) - Static method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The main method used to start PeptideShaker.
main(String[]) - Static method in class eu.isas.peptideshaker.PeptideShakerWrapper: Starts the launcher by calling the launch method.
main(String[]) - Static method in class eu.isas.peptideshaker.PeptideShakerZipFileChecker: Start PeptideShakerZipFileChecker.
mandatory - Variable in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Boolean indicating whether the parameter is mandatory.
mandatory - Variable in enum eu.isas.peptideshaker.cmd.MzidCLIParams: Boolean indicating whether the parameter is mandatory.
mandatory - Variable in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams: Boolean indicating whether the parameter is mandatory.
mandatory - Variable in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Boolean indicating whether the parameter is mandatory.
mandatory - Variable in enum eu.isas.peptideshaker.cmd.StirredOptions: If true the parameter is mandatory.
mapTags(ArrayList<SpectrumMatch>, FastaMapper, WaitingHandler) - Method in class eu.isas.peptideshaker.protein_inference.TagMapper: Maps the tags to the proteins in the sequence factory.
MatchesValidator - Class in eu.isas.peptideshaker.validation: This class validates the quality of identification matches.
MatchesValidator(TargetDecoyMap, TargetDecoyMap, TargetDecoyMap) - Constructor for class eu.isas.peptideshaker.validation.MatchesValidator: Constructor.
MatchValidationDialog - Class in eu.isas.peptideshaker.gui: This class displays information about the validation of a match.
MatchValidationDialog(Frame, Identification, TargetDecoyMap, long, IdentificationParameters, String, MatchValidationDialog.MatchType) - Constructor for class eu.isas.peptideshaker.gui.MatchValidationDialog: Constructor for a protein match validation dialog.
MatchValidationDialog.MatchType - Enum in eu.isas.peptideshaker.gui: Type of match selected.
MethodsSectionDialog - Class in eu.isas.peptideshaker.gui.export: A dialog for drafting the methods section for a publication based on PeptideShaker results.
MethodsSectionDialog(PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.export.MethodsSectionDialog: Creates a new MethodsSectionDialog.
metrics - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The metrics stored during processing.
ModificationDialog - Class in eu.isas.peptideshaker.gui: A dialog for mapping unknown modifications to the list of supported modifications.
ModificationDialog(Frame, boolean, Modification) - Constructor for class eu.isas.peptideshaker.gui.ModificationDialog: Creates a new ModificationDialog dialog.
ModificationLocalizationScorer - Class in eu.isas.peptideshaker.ptm: This class scores the PSM PTMs using the scores implemented in compomics utilities.
ModificationLocalizationScorer() - Constructor for class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Constructor.
MODIFICATIONS_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The Modifications tab index.
modificationSiteInference(SpectrumMatch, SequenceProvider, ModificationProvider, IdentificationParameters) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Infers the modification site of the best peptide assumption of the given spectrum match.
ModificationSiteInferenceDialog - Class in eu.isas.peptideshaker.gui: This dialog allows the user to verify/update the modification site.
ModificationSiteInferenceDialog(PeptideShakerGUI, long, Modification) - Constructor for class eu.isas.peptideshaker.gui.ModificationSiteInferenceDialog: Constructor.
ModificationsPanel - Class in eu.isas.peptideshaker.gui.tabpanels: The Modifications tab.
ModificationsPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Creates a new Modifications tab.
ModificationSpecificMap - Class in eu.isas.peptideshaker.scoring.maps.specific: Modification specific target decoy map.
ModificationSpecificMap() - Constructor for class eu.isas.peptideshaker.scoring.maps.specific.ModificationSpecificMap
moveRows(DefaultTableModel, int, int, int) - Static method in class eu.isas.peptideshaker.gui.FractionDetailsDialog: Moves all rows contained between the positions start and end to the position specified by destination.
Ms2PipExport - Class in eu.isas.peptideshaker.followup: Export training files for ms2pip.
Ms2PipExport() - Constructor for class eu.isas.peptideshaker.followup.Ms2PipExport
ms2pipExport(File, String[], Identification, SearchParameters, SequenceMatchingParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.Ms2PipExport: Exports ms2pip config and peprec files.
ms2pipExport(File, Identification, ModificationParameters, SequenceMatchingParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.Ms2PipExport: Exports a ms2pip training file for the given spectrum file.
ms2pipExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether DeepLC export is needed.
Ms2PipUtils - Class in eu.isas.peptideshaker.utils: Utils for the export and import of ms2pip results.
Ms2PipUtils() - Constructor for class eu.isas.peptideshaker.utils.Ms2PipUtils
msFileHandler - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The mass spectrometry file handler.
mzBinSize - Static variable in class eu.isas.peptideshaker.recalibration.RunMzDeviation: The bin size in m/z in number of MS/MS spectra.
MzidCLI - Class in eu.isas.peptideshaker.cmd: Command line interface to export mzid files from psdb files.
MzidCLI(MzidCLIInputBean) - Constructor for class eu.isas.peptideshaker.cmd.MzidCLI: Construct a new MzidCLI runnable from a MzidCLI input bean.
MzidCLIInputBean - Class in eu.isas.peptideshaker.cmd: This class is a simple bean wrapping the CLI parameters provided in an Options instance.
MzidCLIInputBean(CommandLine) - Constructor for class eu.isas.peptideshaker.cmd.MzidCLIInputBean: Parses a MzidCLI command line and stores the input in the attributes.
MzidCLIParams - Enum in eu.isas.peptideshaker.cmd: Enum class specifying the Command Line Parameters for mzid export.
MzIdentMLExport - Class in eu.isas.peptideshaker.export: The class that takes care of converting the data to mzIdentML.
MzIdentMLExport(String, Identification, ProjectDetails, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, ModificationProvider, FastaSummary, IdentificationFeaturesGenerator, File, boolean, WaitingHandler, boolean) - Constructor for class eu.isas.peptideshaker.export.MzIdentMLExport: Constructor.
MzIdentMLExportDialog - Class in eu.isas.peptideshaker.gui.export: A dialog where the user can export the project to mzIdentML.
MzIdentMLExportDialog(PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.export.MzIdentMLExportDialog: Create a new MzIdentMLExportDialog.

N

nDecoy - Variable in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint: The number of decoy hits at this point.
NewDialog - Class in eu.isas.peptideshaker.gui: A dialog for selecting the files to load.
NewDialog(PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.NewDialog: Creates a new open dialog.
NewDialog(WelcomeDialog, PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.NewDialog: Creates a new open dialog.
newItemSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Provides to the PeptideShakerGUI instance the currently selected peptide and PSM.
newItemSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.
newItemSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.
newItemSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.
NO_ID - Static variable in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Static index for the ID software agreement: no psm found.
NO_MODIFICATION - Static variable in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: The modification name for no modification.
nonValidatedDecoyValues - Variable in class eu.isas.peptideshaker.gui.tabpanels.QCPanel: Values of the non validated decoy hits.
nonValidatedValues - Variable in class eu.isas.peptideshaker.gui.tabpanels.QCPanel: Values of the non validated target hits.
notificationClicked(String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI
noValidated() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Returns a boolean indicating that everything was validated.
nTarget - Variable in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint: The number of target hits at this point.
nThreads - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The number of threads to use.

O

openExampleFile() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Open the PeptideShaker example dataset.
openProteinLinks(String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Opens one or more protein links in the default web browser.
opt - Variable in enum eu.isas.peptideshaker.cmd.StirredOptions: Short key for the command line argument.
outputFolder - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The output folder.
OVER_VIEW_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The Overview tab index.
OverviewPanel - Class in eu.isas.peptideshaker.gui.tabpanels: The overview panel displaying the proteins, the peptides and the spectra.
OverviewPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Creates a new OverviewPanel.

P

p - Variable in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint: The posterior error probability associated to this point.
paint(Graphics) - Method in class eu.isas.peptideshaker.gui.ImageIconPanel
paint(Graphics) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel.JmolPanel
paintVertex(RenderContext<String, String>, Layout<String, String>, String) - Method in class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphPanel.ProteinInferenceVertexRenderer
PARTIALLY_MISSING - Static variable in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Static index for the ID software agreement: one or more of the softwares did not identify the spectrum, while one or more of the others did.
PathSettingsCLI - Class in eu.isas.peptideshaker.cmd: Allows the user to set the path settings in command line.
PathSettingsCLI(PathSettingsCLIInputBean) - Constructor for class eu.isas.peptideshaker.cmd.PathSettingsCLI: Constructor.
PathSettingsCLIInputBean - Class in eu.isas.peptideshaker.cmd: Parses the command line and retrieves the user input.
PathSettingsCLIInputBean(CommandLine) - Constructor for class eu.isas.peptideshaker.cmd.PathSettingsCLIInputBean: Construct a FollowUpCLIInputBean from an Apache CLI instance.
PathSettingsCLIParams - Enum in eu.isas.peptideshaker.cmd: Enum of the command line parameters for path setting.
PeptideChecker - Class in eu.isas.peptideshaker.protein_inference: This class checks that the peptide to protein mapping is compatible with the modification status of the peptide.
PeptideChecker() - Constructor for class eu.isas.peptideshaker.protein_inference.PeptideChecker
PeptideFractionTableModel - Class in eu.isas.peptideshaker.gui.tablemodels: This table model shows a fraction view of the peptides given in the constructor
PeptideFractionTableModel(Identification, DisplayFeaturesGenerator, ArrayList<Long>, ArrayList<String>) - Constructor for class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel: Constructor which sets a new table.
peptideMapChanged(Identification, WaitingHandler, IdentificationParameters, SequenceProvider, SpectrumProvider) - Method in class eu.isas.peptideshaker.PeptideShaker: Processes the identifications if a change occurred in the peptide map.
PeptideShaker - Class in eu.isas.peptideshaker: This class will be responsible for the identification import and the associated calculations.
PeptideShaker(ProjectParameters) - Constructor for class eu.isas.peptideshaker.PeptideShaker: Constructor without mass specification.
PEPTIDESHAKER_CONFIGURATION_FILE - Static variable in class eu.isas.peptideshaker.PeptideShaker: Default PeptideShaker modifications.
PeptideShakerCLI - Class in eu.isas.peptideshaker.cmd: A command line interface to run PeptideShaker.
PeptideShakerCLI() - Constructor for class eu.isas.peptideshaker.cmd.PeptideShakerCLI: Construct a new PeptideShakerCLI runnable.
PeptideShakerCLIInputBean - Class in eu.isas.peptideshaker.cmd: This class is a simple bean wrapping the CLI parameters provided in an Options instance.
PeptideShakerCLIInputBean(CommandLine) - Constructor for class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Construct a PeptideShakerCLIInputBean from an Apache CLI instance.
PeptideShakerCLIInputBean() - Constructor for class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Empty constructor for API usage via other tools.
PeptideShakerCLIParams - Enum in eu.isas.peptideshaker.cmd: Enum class specifying the Command Line Parameters for PeptideShaker.
PeptideShakerGUI - Class in eu.isas.peptideshaker.gui: The main PeptideShaker frame.
PeptideShakerGUI() - Constructor for class eu.isas.peptideshaker.gui.PeptideShakerGUI: Creates a new PeptideShaker frame.
PeptideShakerGUI(File, String, String, String, boolean, boolean) - Constructor for class eu.isas.peptideshaker.gui.PeptideShakerGUI: Creates a new PeptideShaker frame.
PeptideShakerIdentificationParametersCLIParams - Class in eu.isas.peptideshaker.cmd: This class provides the parameters which can be used for the identification parameters cli in PeptideShaker.
PeptideShakerIdentificationParametersCLIParams() - Constructor for class eu.isas.peptideshaker.cmd.PeptideShakerIdentificationParametersCLIParams
PeptideShakerMethods - Class in eu.isas.peptideshaker.export: This class generates the text needed to for the identification section of the methods section of a paper.
PeptideShakerMethods() - Constructor for class eu.isas.peptideshaker.export.PeptideShakerMethods
PeptideShakerParameters - Class in eu.isas.peptideshaker.parameters: This class stores parameters for a PeptideShaker project.
PeptideShakerParameters() - Constructor for class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Empty default constructor.
PeptideShakerParameters(IdentificationParameters, SpectrumCountingParameters, ProjectDetails, FilterParameters, DisplayParameters, Metrics, SequenceProvider, ProteinDetailsProvider, GeneMaps, ProjectType, IdentificationFeaturesCache) - Constructor for class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Constructor for a PeptideShaker Settings class.
PeptideShakerPathParameters - Class in eu.isas.peptideshaker.preferences: This class sets the path preferences for the files to read/write.
PeptideShakerPathParameters() - Constructor for class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters
PeptideShakerPathParameters.PeptideShakerPathKey - Enum in eu.isas.peptideshaker.preferences: Enum of the paths which can be set in PeptideShaker.
PeptideShakerWrapper - Class in eu.isas.peptideshaker: A wrapper class used to start the jar file with parameters.
PeptideShakerWrapper() - Constructor for class eu.isas.peptideshaker.PeptideShakerWrapper: Starts the launcher by calling the launch method.
PeptideShakerWrapper(String[]) - Constructor for class eu.isas.peptideshaker.PeptideShakerWrapper: Starts the launcher by calling the launch method.
PeptideShakerZipFileChecker - Class in eu.isas.peptideshaker: A wrapper class used to check if the jar file is attempted started from within an unzipped zip file.
PeptideShakerZipFileChecker(String[]) - Constructor for class eu.isas.peptideshaker.PeptideShakerZipFileChecker: Checks if the jar file is started from within an unzipped zip file.
PeptideTableModel - Class in eu.isas.peptideshaker.gui.tablemodels: Table model for a set of peptide matches.
PeptideTableModel() - Constructor for class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel: Constructor for an empty table.
PeptideTableModel(Identification, IdentificationFeaturesGenerator, DisplayFeaturesGenerator, String, long[], boolean, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel: Constructor which sets a new table.
pepWindowApplied() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Returns true of the data has been reloaded with the currently selected PEP window.
PepXmlExport - Class in eu.isas.peptideshaker.followup: Export to PepXML.
PepXmlExport() - Constructor for class eu.isas.peptideshaker.followup.PepXmlExport: Constructor.
PercolatorExport - Class in eu.isas.peptideshaker.followup: Export for Percolator.
PercolatorExport() - Constructor for class eu.isas.peptideshaker.followup.PercolatorExport
percolatorExport(File, File, File, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PercolatorExport: Exports a Percolator training file for each of the spectrum files.
percolatorExport(File, HashMap<String, ArrayList<Double>>, HashMap<String, ArrayList<Spectrum>>, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PercolatorExport: Exports a Percolator training file.
percolatorExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether DeepLC export is needed.
PercolatorUtils - Class in eu.isas.peptideshaker.utils: Utils for the export and import of Percolator results.
PercolatorUtils() - Constructor for class eu.isas.peptideshaker.utils.PercolatorUtils
PrideDataTypeSelectionDialog - Class in eu.isas.peptideshaker.gui.pride: A dialog for selecting if public or private data is to be loaded.
PrideDataTypeSelectionDialog(JFrame, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideDataTypeSelectionDialog: Creates a new PrideDataTypeSelectionDialog.
PrideFreeTextSearchDialog - Class in eu.isas.peptideshaker.gui.pride: A dialog for using PRIDE free text search via https://www.ebi.ac.uk/pride/archive/simpleSearch.
PrideFreeTextSearchDialog(JDialog, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideFreeTextSearchDialog: Creates a new PrideFreeTextSearchDialog.
PridePrivateDataDialog - Class in eu.isas.peptideshaker.gui.pride: A dialog for getting the PRIDE private project access information from the user.
PridePrivateDataDialog(Frame, boolean, String) - Constructor for class eu.isas.peptideshaker.gui.pride.PridePrivateDataDialog: Creates a new PridePrivateDataDialog.
PrideReshakeGUI - Class in eu.isas.peptideshaker.gui.pride: Frame for talking to the PRIDE Archive web service to select projects for reshaking.
PrideReshakeGUI(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Creates a new PrideReShakeGUI frame.
PrideReshakeGUI(PeptideShakerGUI, String, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Creates a new PrideReShakeGUI frame.
PrideReshakeSetupDialog - Class in eu.isas.peptideshaker.gui.pride: Dialog for setting up the PRIDE Reshake.
PrideReshakeSetupDialog(PrideReshakeGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideReshakeSetupDialog: Creates a new PrideReshakeSetupDialog.
PrideSearchParametersDialog - Class in eu.isas.peptideshaker.gui.pride: Display the extracted search settings to the user.
PrideSearchParametersDialog(PrideReshakeGUI, File, String, ArrayList<File>, ArrayList<File>, File, String, String, String, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideSearchParametersDialog: Creates a new PrideSearchParametersDialog.
process(File, File, File, FMIndex, FastaSummary, MsFileHandler, IdentificationParameters) - Method in class eu.isas.peptideshaker.stirred.Stirred: Runs the stirred process.
processProteins(ModificationLocalizationScorer, Metrics, ModificationProvider, WaitingHandler, ExceptionHandler, ProcessingParameters) - Method in class eu.isas.peptideshaker.processing.ProteinProcessor: Scores the PTMs of all protein matches contained in an identification object, estimates spectrum counting and summary statistics.
processPsms(InputMap, IdentificationParameters, MatchesValidator, ModificationLocalizationScorer, SequenceProvider, SpectrumProvider, ModificationProvider, HashMap<String, Integer>, int, WaitingHandler, ExceptionHandler) - Method in class eu.isas.peptideshaker.processing.PsmProcessor: Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.
ProgenesisExport - Class in eu.isas.peptideshaker.followup: This class exports identifications for post-processing with Non-Linear Progenesis.
ProgenesisExport() - Constructor for class eu.isas.peptideshaker.followup.ProgenesisExport
ProgenesisExport.ExportType - Enum in eu.isas.peptideshaker.followup: Enum of the different types of export implemented.
progenesisExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether a Progenesis export is needed.
progressCancelled() - Method in class eu.isas.peptideshaker.gui.export.MzIdentMLExportDialog: Returns true if the user has canceled the progress.
ProjectDetails - Class in eu.isas.peptideshaker.preferences: This class contains the details about a project.
ProjectDetails() - Constructor for class eu.isas.peptideshaker.preferences.ProjectDetails: Constructor.
projectDetails - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The project details.
ProjectDetailsDialog - Class in eu.isas.peptideshaker.gui.parameters: This dialog displays the project properties.
ProjectDetailsDialog(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.parameters.ProjectDetailsDialog: Creates a dialog to display the project properties.
ProjectExport - Class in eu.isas.peptideshaker.export: This class takes care of exporting the entire project as a single file.
ProjectExport() - Constructor for class eu.isas.peptideshaker.export.ProjectExport
projectParameters - Variable in class eu.isas.peptideshaker.utils.PsdbParent: All parameters of a project.
ProjectParametersDialog - Class in eu.isas.peptideshaker.gui.parameters: A dialog where the user can edit the PeptideShaker preferences.
ProjectParametersDialog(Frame, Dialog, SpectrumCountingParameters, DisplayParameters) - Constructor for class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog: Creates a new PreferencesDialog with a dialog as owner.
ProjectParametersDialog(Frame, SpectrumCountingParameters, DisplayParameters) - Constructor for class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog: Creates a new PreferencesDialog with a frame as owner.
ProjectsFilterDialog - Class in eu.isas.peptideshaker.gui.pride: A dialog displaying various filters that can be applied to the PRIDE project table.
ProjectsFilterDialog(PrideReshakeGUI, boolean, String[], boolean, boolean, ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Constructor for class eu.isas.peptideshaker.gui.pride.ProjectsFilterDialog: Creates a new ProjectsFilterDialog.
projectType - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The project type.
Properties - Class in eu.isas.peptideshaker.utils: This class provides the PeptideShaker version number.
Properties() - Constructor for class eu.isas.peptideshaker.utils.Properties: Creates a new empty Properties object.
PROTEIN_FRACTIONS_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The Protein Fractions tab index.
ProteinAnnotations - Class in eu.isas.peptideshaker.gui.protein_sequence: This class generates the tooltips for a ProteinSequencePanel.
ProteinAnnotations(HashMap<Integer, ArrayList<ResidueAnnotation>>) - Constructor for class eu.isas.peptideshaker.gui.protein_sequence.ProteinAnnotations: Create a new ProteinAnnotations object.
proteinDetailsProvider - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The protein details provider.
ProteinFractionsPanel - Class in eu.isas.peptideshaker.gui.tabpanels: Displays information about which fractions the peptides and proteins were detected in.
ProteinFractionsPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Creates a new ProteinFractionsPanel.
ProteinFractionTableModel - Class in eu.isas.peptideshaker.gui.tablemodels: This table model displays the protein confidence in every fraction.
ProteinFractionTableModel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel: Constructor which sets a new table.
ProteinFractionTableModel() - Constructor for class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel: Constructor which sets a new empty table.
ProteinGoTableModel - Class in eu.isas.peptideshaker.gui.tablemodels: Model for a the GO mappings protein table.
ProteinGoTableModel(Identification, ProteinDetailsProvider, IdentificationFeaturesGenerator, DisplayFeaturesGenerator, ArrayList<Long>, boolean) - Constructor for class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel: Constructor which sets a new table.
ProteinInference - Class in eu.isas.peptideshaker.protein_inference: This class groups the methods for protein inference.
ProteinInference() - Constructor for class eu.isas.peptideshaker.protein_inference.ProteinInference
ProteinInference.GroupSimplificationOption - Enum in eu.isas.peptideshaker.protein_inference
ProteinInferenceDialog - Class in eu.isas.peptideshaker.gui.protein_inference: This dialog allows the user to resolve manually some protein inference issues.
ProteinInferenceDialog(PeptideShakerGUI, GeneMaps, long, Identification) - Constructor for class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceDialog: Creates new form ProteinInferenceDialog.
ProteinInferenceGraphLegendDialog - Class in eu.isas.peptideshaker.gui.protein_inference: Dialog for displaying the protein inference graph legend.
ProteinInferenceGraphLegendDialog(JDialog, boolean) - Constructor for class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphLegendDialog: Creates a new ProteinInferenceGraphLegendDialog.
ProteinInferenceGraphPanel - Class in eu.isas.peptideshaker.gui.protein_inference: A panel to display protein inference graphs.
ProteinInferenceGraphPanel(JDialog, JPanel, Image, Image, LastSelectedFolder, ArrayList<String>, HashMap<String, ArrayList<String>>, HashMap<String, String>, HashMap<String, String>, HashMap<String, String>, ArrayList<String>) - Constructor for class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphPanel: Creates a new ProteinInferenceGraphPanel.
ProteinInferenceGraphPanel.ProteinInferenceVertexRenderer - Class in eu.isas.peptideshaker.gui.protein_inference: The protein inference vertex renderer.
ProteinInferenceGraphSelectionDialog - Class in eu.isas.peptideshaker.gui.protein_inference: Dialog for displaying the selected nodes in a ProteinInferenceGraphPanel.
ProteinInferenceGraphSelectionDialog(JDialog, boolean, String) - Constructor for class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphSelectionDialog: Creates a new ProteinInferenceGraphSelectionJDialog.
ProteinInferencePeptideLevelDialog - Class in eu.isas.peptideshaker.gui.protein_inference: A simple dialog for showing the list of proteins a given peptide can map to.
ProteinInferencePeptideLevelDialog(PeptideShakerGUI, boolean, long, Long, GeneMaps) - Constructor for class eu.isas.peptideshaker.gui.protein_inference.ProteinInferencePeptideLevelDialog: Create a new ProteinInferencePeptideLevelDialog.
ProteinInferenceVertexRenderer() - Constructor for class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphPanel.ProteinInferenceVertexRenderer
proteinMapChanged(Identification, WaitingHandler, IdentificationParameters, SequenceProvider) - Method in class eu.isas.peptideshaker.PeptideShaker: Processes the identifications if a change occurred in the protein map.
ProteinProcessor - Class in eu.isas.peptideshaker.processing: Scores modification localization on proteins, estimates spectrum counting and summary statistics values.
ProteinProcessor(Identification, IdentificationParameters, IdentificationFeaturesGenerator, SequenceProvider) - Constructor for class eu.isas.peptideshaker.processing.ProteinProcessor: Constructor.
ProteinSequencePanel - Class in eu.isas.peptideshaker.gui.protein_sequence: This class can be used to create a protein sequence plot.
ProteinSequencePanel(Color) - Constructor for class eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel: Creates a new ProteinSequencePanel object.
ProteinSequencePanelParent - Interface in eu.isas.peptideshaker.gui.protein_sequence: An interface implemented by parents of ProteinSequencePanel plots/charts.
proteinSequencesExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether protein details (in FASTA format) export is needed.
ProteinStructurePanel - Class in eu.isas.peptideshaker.gui.tabpanels: The Protein Structure tab.
ProteinStructurePanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Creates a new ProteinPanel.
ProteinStructurePanel.JmolPanel - Class in eu.isas.peptideshaker.gui.tabpanels: A simple class for displaying a Jmol viewer in a JPanel.
ProteinTableModel - Class in eu.isas.peptideshaker.gui.tablemodels: Model for the protein table.
ProteinTableModel() - Constructor for class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel: Constructor for an empty table
ProteinTableModel(Identification, IdentificationFeaturesGenerator, ProteinDetailsProvider, SequenceProvider, GeneMaps, DisplayFeaturesGenerator, ExceptionHandler, long[]) - Constructor for class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel: Constructor.
ProteoformExport - Class in eu.isas.peptideshaker.followup: Export for PathwayMatcher.
ProteoformExport() - Constructor for class eu.isas.peptideshaker.followup.ProteoformExport
proteoformsNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether a list of proteoforms is needed.
PsAnnotationSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the annotation related export features.
PsAnnotationSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsAnnotationSection: Constructor.
PsdbExporter - Class in eu.isas.peptideshaker.export: This class exports a PeptideShaker project as pdsb file.
PsdbExporter() - Constructor for class eu.isas.peptideshaker.export.PsdbExporter
psdbFile - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The currently loaded psdb file.
PsdbParent - Class in eu.isas.peptideshaker.utils: Implementing this abstract class allows interacting with a psdb files.
PsdbParent() - Constructor for class eu.isas.peptideshaker.utils.PsdbParent: Empty constructor for instantiation purposes.
PsdbParent(File) - Constructor for class eu.isas.peptideshaker.utils.PsdbParent: Constructor.
PSExportFactory - Class in eu.isas.peptideshaker.export: The PeptideShaker export factory.
PsExportStyle - Class in eu.isas.peptideshaker.export: This class contains the style for a PeptideShaker excel export.
PsFragmentSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the PSM related export features.
PsFragmentSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsFragmentSection: Constructor.
PsIdentificationAlgorithmMatchesSection - Class in eu.isas.peptideshaker.export.sections: This report section contains the results of the identification algorithms.
PsIdentificationAlgorithmMatchesSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection: Constructor.
PsInputFilterSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the annotation related export features.
PsInputFilterSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsInputFilterSection: Constructor.
PSMaps - Class in eu.isas.peptideshaker.scoring: This class contains all scoring maps from PeptideShaker and will be used to store the information.
PSMaps() - Constructor for class eu.isas.peptideshaker.scoring.PSMaps: Constructor.
PSMaps(InputMap, TargetDecoyMap, TargetDecoyMap, TargetDecoyMap) - Constructor for class eu.isas.peptideshaker.scoring.PSMaps: Constructor for the PSMaps.
PsmFirstHitRunnable - Class in eu.isas.peptideshaker.fileimport: This class tries to find a best hit per search engine for each spectrum match.
PsmFirstHitRunnable(ConcurrentLinkedQueue<SpectrumMatch>, IdentificationParameters, SequenceProvider, SpectrumProvider, InputMap, HashMap<String, Integer>, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable: Constructor.
PsmImporter - Class in eu.isas.peptideshaker.fileimport: This class can be used to import PSMs from search engine results.
PsmImporter() - Constructor for class eu.isas.peptideshaker.fileimport.PsmImporter: Constructor.
PsmImportRunnable - Class in eu.isas.peptideshaker.fileimport: Runnable for the import of PSMs.
PsmImportRunnable(ConcurrentLinkedQueue<SpectrumMatch>, IdentificationParameters, IdfileReader, File, Identification, SequenceProvider, FastaMapper, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.fileimport.PsmImportRunnable: Constructor.
PsmProcessor - Class in eu.isas.peptideshaker.processing: Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.
PsmProcessor(Identification) - Constructor for class eu.isas.peptideshaker.processing.PsmProcessor: Constructor.
PsmProcessorRunnable - Class in eu.isas.peptideshaker.processing: This class processes PSMs.
PsmProcessorRunnable(ConcurrentLinkedQueue<Long>, Identification, IdentificationParameters, InputMap, MatchesValidator, ModificationLocalizationScorer, SequenceProvider, SpectrumProvider, ModificationProvider, HashMap<String, Integer>, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.processing.PsmProcessorRunnable: Constructor.
PsmScorer - Class in eu.isas.peptideshaker.scoring.psm_scoring: This class scores peptide spectrum matches.
PsmScorer(FastaParameters, SequenceProvider, SpectrumProvider) - Constructor for class eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer: Constructor.
PsmTableModel - Class in eu.isas.peptideshaker.gui.tablemodels: Table model for a set of peptide to spectrum matches.
PsmTableModel() - Constructor for class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel: Constructor for an empty table.
PsmTableModel(Identification, DisplayFeaturesGenerator, SpectrumProvider, IdentificationParameters, long[], boolean, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel: Constructor which sets a new table.
PsPeptideSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the peptide related export features.
PsPeptideSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsPeptideSection: Constructor.
PsProjectSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the project related export features.
PsProjectSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsProjectSection: Constructor
PsProteinSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the protein related export features.
PsProteinSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsProteinSection: Constructor.
PsPsmSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the PSM level export features.
PsPsmSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsPsmSection: Constructor.
PsPtmScoringSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the project related export features.
PsPtmScoringSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsPtmScoringSection: Constructor.
PsSearchParametersSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the search parameters related export features.
PsSearchParametersSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsSearchParametersSection: Constructor.
PsSpectrumCountingSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the spectrum counting related export features.
PsSpectrumCountingSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsSpectrumCountingSection: Constructor.
PsValidationSection - Class in eu.isas.peptideshaker.export.sections: This class outputs the validation related export features.
PsValidationSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsValidationSection: Constructor.
PsZipUtils - Class in eu.isas.peptideshaker.utils: This class contains information and methods to zip and unzip files from PeptideShaker.
PsZipUtils() - Constructor for class eu.isas.peptideshaker.utils.PsZipUtils
PtmSelectionDialog - Class in eu.isas.peptideshaker.gui.export: PTM location dialog for the Progenesis export.
PtmSelectionDialog(Frame, ArrayList<String>) - Constructor for class eu.isas.peptideshaker.gui.export.PtmSelectionDialog: Creates a new PtmSelectionDialog.
put(double, boolean) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Puts a new point in the target/decoy map at the given score.

Q

QC_PLOTS_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The QC Plots tab index.
QCPanel - Class in eu.isas.peptideshaker.gui.tabpanels: This panel will display QC statistics for the current project.
QCPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.QCPanel: Creates a new QCPanel.
QuickGoTerm() - Constructor for class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel.QuickGoTerm

R

recalibrateFragmentMz(double, double[]) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation: Recalibrate an m/z array.
recalibrateSpectra(FollowUpCLIInputBean, Identification, SequenceProvider, SpectrumProvider, IdentificationParameters, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Recalibrates spectra as specified in the follow-up input bean.
recalibrateSpectra() - Method in class eu.isas.peptideshaker.gui.export.FollowUpExportDialog: Lets the user select an output folder and starts the recalibration of spectra.
recalibrateSpectrum(String, String, SpectrumProvider, boolean, boolean) - Method in class eu.isas.peptideshaker.recalibration.SpectrumRecalibrator: Recalibrates a spectrum.
RecalibrationExporter - Class in eu.isas.peptideshaker.followup: This class exports recalibrated spectra.
RecalibrationExporter() - Constructor for class eu.isas.peptideshaker.followup.RecalibrationExporter
recalibrationNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether a recalibration is needed.
redirectErrorStream(File) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI: Redirects the error stream to the PeptideShaker.log of a given folder.
remove(double, boolean) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Removes a point in the target/decoy map at the given score.
removeExportScheme(String) - Method in class eu.isas.peptideshaker.export.PSExportFactory
removeRecentProject(String) - Method in class eu.isas.peptideshaker.preferences.UserParameters: Removes a recent project from the list.
removeRedundantGroups(Identification, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.protein_inference.GroupSimplification: Remove groups that can be explained by a simpler group.
removeRedundantGroups(Identification, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, ProteinMatch, HashMap<Long, long[]>, HashSet<Long>, SimpleSemaphore, WaitingHandler) - Method in class eu.isas.peptideshaker.protein_inference.GroupSimplification: Removes the redundant groups for the given protein shared group.
renameFastaFileName() - Method in class eu.isas.peptideshaker.gui.pride.DatabaseHelpDialog: Copies the content of the FASTA file to a new file and replaces any white space in the file name with '_' instead.
ReportCLI - Class in eu.isas.peptideshaker.cmd: This class performs the command line export of reports in command line.
ReportCLI(ReportCLIInputBean) - Constructor for class eu.isas.peptideshaker.cmd.ReportCLI: Construct a new ReportCLI runnable from a ReportCLI Bean.
ReportCLIInputBean - Class in eu.isas.peptideshaker.cmd: This class is a simple bean wrapping the CLI parameters provided in an Options instance.
ReportCLIInputBean(CommandLine) - Constructor for class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Construct a FollowUpCLIInputBean from an Apache CLI instance.
ReportCLIParams - Enum in eu.isas.peptideshaker.cmd: This class provides the available reports as command line parameters.
reportExportNeeded() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Indicates whether a report export is required by the user.
reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel: Reset the peptide keys.
reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel: Resets the peptide keys.
reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel: Reset the protein keys.
reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel: Reset the protein keys.
reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel: Reset the protein keys.
reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel: Resets the peptide keys.
resetAdvocateContributions(String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Resets the advocate contribution mappings for the given file.
resetAdvocateContributions() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Resets the advocate contribution mappings.
resetAllThresholds() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Resets all thresholds to the last validated value.
resetDisplayFeaturesGenerator() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Resets the display features generator.
resetFrameTitle() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Reset the frame title.
resetIdentificationFeaturesGenerator() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Resets the feature generator.
resetIdentificationFeaturesGenerator() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Resets the feature generator.
resetModificationFactory() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Resets the modification factory.
resetSelectedItems() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Resets the items selection.
resetThreshold(String) - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Resets the threshold of the given group to the last validated value.
ResidueAnnotation - Class in eu.isas.peptideshaker.gui.protein_sequence: Annotation for a given protein residue.
ResidueAnnotation(String, long, boolean) - Constructor for class eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation: Create a new ResidueAnnotation object.
restart() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Closes and restarts PeptideShaker.
revalidateData() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Revalidates the data using the currently selected threshold.
rtBinSize - Static variable in class eu.isas.peptideshaker.recalibration.RunMzDeviation: The bin size in retention time in number of MS/MS spectra.
run() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable
run() - Method in class eu.isas.peptideshaker.fileimport.PsmImportRunnable
run() - Method in class eu.isas.peptideshaker.processing.PsmProcessorRunnable
run() - Method in class eu.isas.peptideshaker.stirred.modules.StirRunnable
run() - Method in class eu.isas.peptideshaker.stirred.Stirred: Runs the stirred process.
RunMzDeviation - Class in eu.isas.peptideshaker.recalibration: This class computes the mz deviations for a a given run (i.e.
RunMzDeviation(String, Identification, SequenceProvider, SpectrumProvider, IdentificationParameters, WaitingHandler) - Constructor for class eu.isas.peptideshaker.recalibration.RunMzDeviation: Creates a map of m/z deviations for a given run.

S

saveAs(File, WaitingHandler, Identification, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumCountingParameters, ProjectDetails, FilterParameters, Metrics, GeneMaps, ProjectType, IdentificationFeaturesCache, boolean, DisplayParameters, File) - Static method in class eu.isas.peptideshaker.export.PsdbExporter: Saves the given data in a psdb file.
SaveDialog - Class in eu.isas.peptideshaker.gui: A dialog for displaying the various save/export options.
SaveDialog(PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.SaveDialog: Create a new SaveDialog.
saveFactory(PSExportFactory) - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Saves the factory in the user folder.
saveProject(boolean, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Saves the modifications made to the project.
saveProject(WaitingHandler, boolean) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Saves the project in the psdb file.
saveProjectAs(boolean, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Save the project to a new location.
saveUserParameters() - Method in class eu.isas.peptideshaker.preferences.UserPreferencesParent: Saves the user preferences.
scorePeptidePtms(Identification, ModificationProvider, WaitingHandler, IdentificationParameters) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Scores the PTMs of all peptide matches contained in an identification object.
scorePsms(Identification, InputMap, ProcessingParameters, IdentificationParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer: Attaches a score to the PSMs.
scorePTMs(Identification, SpectrumMatch, SequenceProvider, SpectrumProvider, ModificationProvider, IdentificationParameters, WaitingHandler, PeptideSpectrumAnnotator) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Scores PTM locations for a desired spectrum match.
scorePTMs(Identification, PeptideMatch, IdentificationParameters, ModificationProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Scores the PTMs for a peptide match.
scorePTMs(Identification, ProteinMatch, IdentificationParameters, boolean, ModificationProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Scores PTMs in a protein match.
SEARCHGUI_INPUT - Static variable in class eu.isas.peptideshaker.gui.NewDialog: A file where the input FASTA and mgf files are stored.
selectBestHit(SpectrumMatch, InputMap, TargetDecoyMap, Identification) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection: Selects the best hit.
selectedModifications() - Method in class eu.isas.peptideshaker.gui.export.PtmSelectionDialog: Returns a list of selected modifications.
selectTextField() - Method in class eu.isas.peptideshaker.gui.JumpToPanel: Move the focus to the Jump To text field and select all the content.
selfUpdating(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Deactivates the self updating tables.
selfUpdating(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Deactivates the self updating tables.
selfUpdating(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Deactivates the self updating tables.
SEPARATOR - Static variable in class eu.isas.peptideshaker.followup.ProgenesisExport: The separator (tab by default).
sequenceProvider - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The sequence provider.
setAccuracySliderValue(int) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Set the accuracy slider value.
setAccuracySliderValue(int) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Set the accuracy slider value.
setAccuracySliderValue(int) - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Set the accuracy slider value.
setAllPathsIn(String) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Sets all the paths inside a given folder.
setBackground(Color) - Method in class eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel: Set the background color.
setColor(Color) - Method in class eu.isas.peptideshaker.gui.JumpToPanel: Set the color for the hits.
setConfidenceLimit(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the confidence limit.
setContactAddress(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: SEt the address of the contact for the mzIdentML dataset.
setContactEmail(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the e-mail of the contact for the mzIdentML dataset.
setContactFirstName(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the first name of the contact for the mzIdentML dataset.
setContactLastName(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the last name of the contact for the mzIdentML dataset.
setContactUrl(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the first URL of the contact for the mzIdentML dataset.
setCreationDate(Date) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Setter the creation date of the project.
setCurentNotes(ArrayList<String>) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set the list of current notes.
setCurentTips(ArrayList<String>) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set the list of current tips.
setCurrentFilterValues(String[], boolean) - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Set the current filter values.
setDataSaved(boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set whether the current data has been saved to a psdb file or not.
setDbFolder(File) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the folder where the database is stored.
setDefaultMatchesQCFilters(ValidationQcParameters) - Static method in class eu.isas.peptideshaker.validation.MatchesValidator: Sets the default matches quality control filters.
setDefaultParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set the default parameters.
setDefaultParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the default preferences.
setDefaultSelection(ArrayList<String>) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Set the list of visible modifications.
setDisplayedModification(String, boolean) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Sets whether a PTM shall be displayed on the sequences or not.
setDisplayOptions(boolean, boolean, boolean, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the display options for the overview tab.
setDisplayOptions(boolean, boolean, boolean, boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Sets the whether the protein coverage and the spectrum shall be displayed.
setDisplayParameters(DisplayParameters) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the display parameters to use.
setDisplayParameters(DisplayParameters) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the display preferences.
setEnabled(boolean) - Method in class eu.isas.peptideshaker.gui.JumpToPanel
setExperimentID(String) - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Sets the experiment name.
setFastaFile(File) - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Sets the FASTA file.
setFastaFile(File) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the path to the FASTA file.
setFdrLimit(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the FDR limit.
setFilterParameters(FilterParameters) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the filter parameters to use.
setFilterParameters(FilterParameters) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the filter preferences.
setFnrLimit(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the FNR limit.
setGeneMaps(GeneMaps) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the gene maps.
setGeneMaps(GeneMaps) - Method in class eu.isas.peptideshaker.PeptideShaker: Sets the gene maps.
setGeneMaps(GeneMaps) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the gene maps.
setIconImage(Image) - Method in class eu.isas.peptideshaker.gui.NewDialog
setIconImage(Image) - Method in class eu.isas.peptideshaker.gui.WelcomeDialog
setIdentification(Identification) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the identification.
setIdentification(Identification) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the identification object.
setIdentificationAlgorithmsForFile(String, HashMap<String, ArrayList<String>>) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Sets the identification algorithms used to create an identification file.
setIdentificationFeaturesGenerator(IdentificationFeaturesGenerator) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the feature generator.
setIdentificationFeaturesGenerator(IdentificationFeaturesGenerator) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the identification feature generator.
setIdentificationParameters(IdentificationParameters) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the identification parameters.
setIdentificationParameters(IdentificationParameters) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets new identification parameters.
setIdFiles(ArrayList<File>) - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Sets the identification files.
setIncludeProteinSequences(Boolean) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set if the protein sequences are to be included in the mzid export.
setInputType(int) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the type of input.
setIntensityIonTable(boolean) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Set if the intensity or m/z ion table should be shown.
setIntensitySliderValue(int) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Set the intensity slider value.
setIntensitySliderValue(int) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Set the intensity slider value.
setIntensitySliderValue(int) - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Set the intensity slider value.
setIntermediateScore(String, int, int, double, boolean, PsmScoringParameters) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Adds an intermediate score for a given match.
setJsonFolder(String) - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Sets the file where to save the implemented export schemes.
setLastSelectedFolder(LastSelectedFolder) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set the last selected folder.
setMatchesDirectoryParent(String) - Static method in class eu.isas.peptideshaker.PeptideShaker: Sets the matches directory parent.
setMetrics(Metrics) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the metrics saved while loading the files.
setMetrics(Metrics) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the metrics.
setModelInitiated(boolean) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel: Set if the real model has been initiated.
setMsFileHandler(MsFileHandler) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the mass spectrometry file handler.
setMsFileHandler(MsFileHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the mass spectrometry file handler.
setMzIdentOutputFile(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the mzIdentML output file.
setn(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the number of retained hits.
setnAASurroundingPeptides(int) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Sets the number of amino acids surrounding a peptide sequence.
setnFP(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the estimated number of false positives.
setNoValidated(boolean) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets whether everything was validated.
setnTPTotal(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the estimated total number of True positives.
setOrganizationAddress(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the address of the organization for the mzIdentML dataset.
setOrganizationEmail(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the name of the organization for the mzIdentML dataset.
setOrganizationName(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the name of the organization for the mzIdentML dataset.
setOrganizationUrl(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the URL of the organization for the mzIdentML dataset.
setOutput(File) - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Sets the psdb output file.
setPathParameters(PathKey, String) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Sets the path according to the given key and path.
setPathPreference(PeptideShakerPathParameters.PeptideShakerPathKey, String) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Sets the path according to the given key and path.
setPathSettings() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLI: Sets the path settings according to the pathSettingsCLIInputBean.
setPeptideMap(TargetDecoyMap) - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Sets the peptide scoring specific map.
setPeptideShakerCLIInputBean(PeptideShakerCLIInputBean) - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI: Set the PeptideShakerCLIInputBean.
setPeptideShakerVersion(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Sets the PeptideShaker version used to create the project.
setPrideContactGroup(ContactGroup) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the PRIDE contact group.
setPrideExperimentDescription(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the PRIDE experiment project description.
setPrideExperimentLabel(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Sets the PRIDE experiment label.
setPrideExperimentProjectTitle(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the PRIDE experiment project title.
setPrideExperimentTitle(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Sets the PRIDE experiment title.
setPrideFile(File) - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Sets the pride file.
setPrideInstrument(Instrument) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the the PRIDE instrument.
setPrideOutputFolder(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the PRIDE output folder.
setPrideProtocol(Protocol) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the PRIDE protocol.
setPrideReferenceGroup(ReferenceGroup) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the PRIDE reference group.
setPrideSample(Sample) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the PRIDE sample.
setProcessingParameters(ProcessingParameters) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the initial processing preferences.
setProject(ProjectParameters) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the project.
setProject(ProjectParameters) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the project parameters.
setProjectDetails(ProjectDetails) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the project details.
setProjectDetails(ProjectDetails) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the project details.
setProjectType(ProjectType) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the project type.
setProjectType(ProjectType) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the project type.
setProteinDetailsProvider(ProteinDetailsProvider) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the protein details provider.
setProteinDetailsProvider(ProteinDetailsProvider) - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Setter for the protein details provider
setProteinDetailsProvider(ProteinDetailsProvider) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the protein details provider.
setProteinMap(TargetDecoyMap) - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Sets the protein scoring map.
setProteinTableProperties(JTable, Color, Color, Color, Color, DecimalFormat, Class, Integer) - Static method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel: Set up the properties of the protein table.
setPsdbFile(File) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the psdb file.
setPsdbImportFromZip(boolean) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets that the psdb file is imported from a zip file.
setPsmMap(TargetDecoyMap) - Method in class eu.isas.peptideshaker.validation.MatchesValidator: Sets the PSM scoring specific map.
setReferenceLine(double, Color) - Method in class eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel: Set the reference line properties.
setReport(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Set the report created during the loading of the project.
setReportNamePrefix(String) - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Set the report name prefix.
setReportOutputFolder(File) - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean: Set the report output folder.
setScoreLimit(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the score limit obtained with the current validation settings.
setSelectedItem(int) - Method in class eu.isas.peptideshaker.gui.JumpToPanel: Sets the index of the selected item.
setSelectedItems(long, long, String, String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the keys of the selected protein, peptide and PSM.
setSelectedItems() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the selected item based on the selected tab.
setSequenceProvider(SequenceProvider) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the sequence provider.
setSequenceProvider(SequenceProvider) - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters: Setter for the sequence provider
setSequenceProvider(SequenceProvider) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the sequence provider.
setShowBars(boolean) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Set if the bars in the bubble plot are to be shown or not.
setShowSliders(boolean) - Method in class eu.isas.peptideshaker.preferences.UserParameters: Sets whether sliders should be displayed.
setSparklineColor(Color) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set the sparklines color.
setSparklineColorNonValidated(Color) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set the non-validated sparklines color.
setSparklineColorPossible(Color) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set the possible sparklines color.
setSpectrumCountingParameters(SpectrumCountingParameters) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets new spectrum counting parameters.
setSpectrumCountingParameters(SpectrumCountingParameters) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Sets the spectrum counting preferences.
setSpectrumFile(String) - Method in class eu.isas.peptideshaker.gui.JumpToPanel: Sets the spectrum file inspected.
setSpectrumFiles(ArrayList<File>) - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Sets the spectrum files.
setType(JumpToPanel.JumpType) - Method in class eu.isas.peptideshaker.gui.JumpToPanel: Changes the type of jumpToPanel.
setUnzipParentFolder(String) - Static method in class eu.isas.peptideshaker.utils.PsZipUtils: Sets the parent folder where to unzip files to.
setUpdated(int, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets that the tab was updated.
setUpLogFile(boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set up the log file.
setUserAdvocateMapping(HashMap<Integer, Advocate>) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Sets the user advocates used in this project.
setUserInput(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Sets the user input.
setUserPreferencesFolder(String) - Static method in class eu.isas.peptideshaker.PeptideShaker: Sets the file used for user preferences storage.
setUtilitiesUserParameters(UtilitiesUserParameters) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Set the utilities user parameters.
setVisible(boolean) - Method in class eu.isas.peptideshaker.gui.WelcomeDialog: Make sure that the dummy frame is hidden when the dialog is not visible.
setWindowSize(int) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Sets the window size used for pep estimation.
showBars() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: If true, bars are shown in the bubble plot highlighting the ions.
showHiddenProteins(boolean) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Sets whether hidden proteins should be displayed.
showHiddenProteins() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Returns whether hidden proteins should be displayed.
showNotesNotification() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Show a note notification pop up.
showProjectFilterRemovalOption(boolean) - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Show/hide the clear projects filters option.
showScores(boolean) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel: Sets whether the scores should be displayed.
showScores(boolean) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel: Sets whether the scores should be displayed.
showScores(boolean) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel: Sets whether the scores should be displayed.
showScores(boolean) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Sets whether scores should be displayed.
showScores() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Returns whether scores should be displayed.
showSeparators(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Enable or disable the separators.
showSliders() - Method in class eu.isas.peptideshaker.preferences.UserParameters: Returns whether sliders should be displayed.
showSparklines() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Returns true if the sparklines are to be shown.
showSparkLines(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel: Displays or hide sparklines in the tables.
showSparkLines(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Displays or hide sparklines in tables.
showSparkLines(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Displays or hide sparklines in the tables.
showSparkLines(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Displays or hide sparklines in the tables.
showSparkLines(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Displays or hide sparklines in the tables.
showSparkLines(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Displays or hide sparklines in the tables.
showSpectrumAnnotationMenu() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Makes sure that the annotation menu bar is visible.
showSpectrumAnnotationMenu() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Makes sure that the annotation menu bar is shown in the currently visible spectrum and fragment ions tabbed pane.
showSpectrumAnnotationMenu() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Makes sure that the annotation menu bar is visible.
showTipsNotification() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Show a tip notification pop up.
showValidatedProteinsOnly(boolean) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Sets whether only the validated proteins should be displayed.
showValidatedProteinsOnly() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Returns whether only the validated proteins should be displayed.
SimpleSpecificMap - Class in eu.isas.peptideshaker.scoring.maps.specific: Specific target decoy map where the highest value with enough values is kept.
SimpleSpecificMap() - Constructor for class eu.isas.peptideshaker.scoring.maps.specific.SimpleSpecificMap
SOFTWARE_NAME - Variable in class eu.isas.peptideshaker.stirred.Stirred: The name of the software to annotate in the mzIdentML file.
SOFTWARE_URL - Variable in class eu.isas.peptideshaker.stirred.Stirred: The URL of the software to annotate in the mzIdentML file.
SOFTWARE_VERSION - Variable in class eu.isas.peptideshaker.stirred.Stirred: The version of the software to annotate in the mzIdentML file.
SpecificTargetDecoyMap - Class in eu.isas.peptideshaker.scoring.maps: This stores target decoy maps grouped by file and category.
SpecificTargetDecoyMap() - Constructor for class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap: Constructor.
SPECTRUM_ID_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The SpectrumID tab index.
SpectrumColorsDialog - Class in eu.isas.peptideshaker.gui.parameters: Dialog for user selection of spectrum annotation colors.
SpectrumColorsDialog(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.parameters.SpectrumColorsDialog: Creates a new SpectrumColorsDialog.
spectrumCountingParameters - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The spectrum counting preferences.
SpectrumCountingSettingsDialog - Class in eu.isas.peptideshaker.gui.parameters: SpectrumCountingSettingsDialog.
SpectrumCountingSettingsDialog(Frame, SpectrumCountingParameters) - Constructor for class eu.isas.peptideshaker.gui.parameters.SpectrumCountingSettingsDialog: Constructor.
SpectrumExporter - Class in eu.isas.peptideshaker.followup: This class can be used to export spectra.
SpectrumExporter(Identification, SpectrumProvider) - Constructor for class eu.isas.peptideshaker.followup.SpectrumExporter: Constructor.
SpectrumExporter.ExportType - Enum in eu.isas.peptideshaker.followup: Enum of the different types of export implemented.
spectrumExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether a spectrum export is needed.
spectrumFile - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The spectrum file.
spectrumFileSelectionChanged(String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the new spectrum file selected.
SpectrumIdentificationPanel - Class in eu.isas.peptideshaker.gui.tabpanels: The Spectrum ID panel.
SpectrumIdentificationPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Create a new SpectrumIdentificationPanel.
spectrumMapChanged(Identification, WaitingHandler, ProcessingParameters, IdentificationParameters, SequenceProvider, SpectrumProvider, ProjectType) - Method in class eu.isas.peptideshaker.PeptideShaker: Processes the identifications if a change occurred in the PSM map.
SpectrumRecalibrator - Class in eu.isas.peptideshaker.recalibration: This class recalibrates spectra.
SpectrumRecalibrator() - Constructor for class eu.isas.peptideshaker.recalibration.SpectrumRecalibrator: Constructor.
spinModel(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Turns the spinning of the model on or off.
starHide() - Method in class eu.isas.peptideshaker.utils.StarHider: Updates the star/hide status of all identification items.
StarHider - Class in eu.isas.peptideshaker.utils: This class provides information whether a hit should be hidden or starred.
StarHider(Identification, FilterParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, Metrics, ProgressDialogX, int, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.utils.StarHider: Constructor.
starPeptide(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Stars a peptide match.
starProtein(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Stars a protein match.
starPsm(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Stars a PSM match.
Stirred - Class in eu.isas.peptideshaker.stirred: This class imports the results of a search engine from SearchGUI in the utilities model.
Stirred(File, File, File, File, File, File, CliLogger, int, int, String, String, String, String, String, String, String) - Constructor for class eu.isas.peptideshaker.stirred.Stirred: Constructor.
StirredCLI - Class in eu.isas.peptideshaker.cmd: Command line to manage the modifications.
StirredCLI() - Constructor for class eu.isas.peptideshaker.cmd.StirredCLI
StirredOptions - Enum in eu.isas.peptideshaker.cmd: Enum class specifying the ModificationsCLI parameters.
StirredOptionsBean - Class in eu.isas.peptideshaker.cmd: This class parses the parameters from an ModificationsCLI.
StirredOptionsBean(CommandLine) - Constructor for class eu.isas.peptideshaker.cmd.StirredOptionsBean: Parses all the arguments from a command line.
StirRunnable - Class in eu.isas.peptideshaker.stirred.modules: This class scores the modification localization.
StirRunnable(ConcurrentLinkedQueue<SpectrumMatch>, IdfileReader, SimpleMzIdentMLExporter, IdentificationParameters, FastaMapper, SequenceProvider, SpectrumProvider, CliLogger) - Constructor for class eu.isas.peptideshaker.stirred.modules.StirRunnable: Constructor.
STRUCTURES_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The Structures tab index.
SUFFIX - Static variable in class eu.isas.peptideshaker.followup.RecalibrationExporter: Suffix for the mgf file containing all recalibrated spectra.
suspiciousInput(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns a boolean indicating if a suspicious input was detected.

T

TagMapper - Class in eu.isas.peptideshaker.protein_inference: This class can be used to map tags to proteins.
TagMapper(IdentificationParameters, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.protein_inference.TagMapper: Constructor.
TargetDecoyMap - Class in eu.isas.peptideshaker.scoring.targetdecoy: This map contains the information of a target/decoy strategy.
TargetDecoyMap() - Constructor for class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Constructor.
TargetDecoyMap(Integer) - Constructor for class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Constructor.
TargetDecoyPoint - Class in eu.isas.peptideshaker.scoring.targetdecoy: This class represents a target/decoy hit in its simplest form.
TargetDecoyPoint() - Constructor for class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint: Constructor.
TargetDecoyResults - Class in eu.isas.peptideshaker.scoring.targetdecoy: This class will compile Target/decoy results of a certain target/decoy map according to user's validation criteria
TargetDecoyResults() - Constructor for class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults: Constructor.
TargetDecoySeries - Class in eu.isas.peptideshaker.scoring.targetdecoy: This class will contain the PEP, FDR and FNR values of a target decoy map directly available for plotting.
TargetDecoySeries(HashMap<Double, TargetDecoyPoint>) - Constructor for class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Constructor.
TEMP_FOLDER_NAME - Static variable in class eu.isas.peptideshaker.utils.PsZipUtils: Suffix for folders where the content of zip files should be extracted.
tempFolder - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The temp folder to use for temp files.
thresholdUpdated() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Returns true of the data has been reloaded with the currently selected threshold.
TieBreaker - Class in eu.isas.peptideshaker.scoring.psm_scoring: This class breaks ties between equally scoring peptides.
TieBreaker(HashMap<String, Integer>, IdentificationParameters, PeptideSpectrumAnnotator, SequenceProvider, SpectrumProvider) - Constructor for class eu.isas.peptideshaker.scoring.psm_scoring.TieBreaker: Constructor.
TIMEOUT_DAYS - Static variable in class eu.isas.peptideshaker.PeptideShaker: Default time out in days.
timeOutDays - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The timeout time in days.
Tips - Class in eu.isas.peptideshaker.utils: This class provides the tips of the day.
TITLED_BORDER_HORIZONTAL_PADDING - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The horizontal padding used before and after the text in the titled borders.
TITLED_BORDER_HORIZONTAL_PADDING_HTML - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The horizontal padding used before and after the text in the titled borders.
toString() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLI
toString() - Method in class eu.isas.peptideshaker.cmd.MzidCLI
toString() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLI
toString() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI
toString() - Method in class eu.isas.peptideshaker.cmd.ReportCLI

U

unHidePeptide(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Unhides a peptide match.
unHideProtein(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Unhides a protein match.
unHidePsm(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Unhides a psm match.
UnipeptExport - Class in eu.isas.peptideshaker.export: Export peptide sequences to the Unipept web interface.
UnipeptExport() - Constructor for class eu.isas.peptideshaker.export.UnipeptExport
unStarPeptide(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Unstars a peptide match.
unStarProtein(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Unstars a protein match.
unStarPsm(long) - Method in class eu.isas.peptideshaker.utils.StarHider: Unstars a PSM match.
UNZIP_SUB_FOLDER - Static variable in class eu.isas.peptideshaker.utils.PsZipUtils: The sub folder where the unzipped files should be stored.
updateAnnotationMenu() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Updates the ions used for fragment annotation.
updateAnnotationMenuBarVisableOptions(boolean, boolean, boolean, boolean, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Updates the visible menu items on the settings menu of the annotation menu bar.
updateAnnotationMenus(SpecificAnnotationParameters, int, HashSet<String>) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the annotation menu bar with the current annotation preferences.
updateBasicProteinAnnotation(String) - Method in class eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel: Updates the basic protein annotation information.
updateBubblePlot() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Updated the bubble plot with the current PSMs.
updateDataModel(ArrayList<Long>) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel: Update the data in the table model without having to reset the whole table model.
updateDataModel(Identification, IdentificationFeaturesGenerator, DisplayFeaturesGenerator, String, long[]) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel: Update the data in the table model without having to reset the whole table model.
updateDataModel(PeptideShakerGUI) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel: Update the data in the table model without having to reset the whole table model.
updateDataModel(ArrayList<Long>) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel: Update the data in the table model without having to reset the whole table model.
updateDataModel(Identification, IdentificationFeaturesGenerator, ProteinDetailsProvider, SequenceProvider, GeneMaps, DisplayFeaturesGenerator, long[]) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel: Update the data in the table model without having to reset the whole table model.
updateDataModel(Identification, DisplayFeaturesGenerator, IdentificationParameters, long[]) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel: Update the data in the table model without having to reset the whole table model.
updateFilterSettingsField(String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the filter settings field.
updateFrameTitle() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Add the experiment title to the frame title.
updateGraphics(ProgressDialogX) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Updates the graphics components.
updateMainMatch(String, int) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the protein match in the different tabs.
updateMainMatch(String, int) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Update the main match for the given row in the protein table.
updateMappings() - Method in class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel: Update the GO mappings.
updateModelType() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Updates the model type if the Jmol structure is currently visible.
updateModificationColorCoding() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the modification color coding in all tabs.
updateModificationColors() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Update the modification color coding.
updateModificationColors() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Update the PTM color coding.
updateModificationColors() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Update the PTM color coding.
updateModificationColors() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Update the PTM color coding.
updateModificationProfiles(ProgressDialogX) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Redraws the modification profiles.
updateNotesNotificationCounter() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the notification counter for the notes.
updatePeptideAssumptionValidationLevel(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, IdentificationParameters, InputMap, long, PeptideAssumption, boolean) - Static method in class eu.isas.peptideshaker.validation.MatchesValidator: Updates the validation status of a peptide assumption.
updatePeptideMatchValidationLevel(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, GeneMaps, IdentificationParameters, TargetDecoyMap, long) - Static method in class eu.isas.peptideshaker.validation.MatchesValidator: Updates the validation status of a peptide match.
updatePeptidePanelTitle() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Updates the peptide panel title with the number of validated/confident proteins.
updatePeptideProteinInference(int) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Update the protein inference type for the currently selected peptide.
updatePeptideProteinInference(int) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Update the protein inference type for the currently selected peptide.
updatePeptideTable(ProgressDialogX) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Updates the peptide table.
updatePlotSizes() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Update the plot sizes.
updateProjectTableSelection() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI: Updates the project table selection.
updateProteinMatchValidationLevel(Identification, IdentificationFeaturesGenerator, SequenceProvider, SpectrumProvider, ProteinDetailsProvider, GeneMaps, IdentificationParameters, TargetDecoyMap, long) - Static method in class eu.isas.peptideshaker.validation.MatchesValidator: Updates the validation status of a protein match.
updateProteinMatchValidationLevel(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, GeneMaps, IdentificationParameters, TargetDecoyMap, double, double, double, boolean, long) - Static method in class eu.isas.peptideshaker.validation.MatchesValidator: Updates the validation status of a protein match.
updateProteinPanelTitle() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Updates the protein panel title with the number of validated/confident proteins.
updateProteinTable() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Updates the results in the protein table and reselect the desired protein.
updatePsmOrder() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Update the PSM order in the PSM table.
updatePsmPanelTitle() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Updates the PSM panel title with the number of validated/confident
updateRecentProjectsList() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Add the list of recently used files to the file menu.
updateRelatedPeptidesTable(ProgressDialogX) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Updates the related peptides table.
updateScores() - Method in class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel: Hides or displays the score column in the protein table.
updateScores() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Hides or displays the score columns in the protein and peptide tables.
updateScores() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Hides or displays the score column in the protein table.
updateScores() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Hides or displays the score columns in the protein and peptide tables.
updateScores() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Hides or displays the search engine scores in the spectrum identifications table.
updateSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Tries to find the last selected peptide.
updateSelection(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Update the selected protein and peptide.
updateSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: Update the selected protein and peptide.
updateSelection(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Update the selected protein and peptide.
updateSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Updates the spectrum selected according to the user's last selection.
updateSelectionInCurrentTab() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Updates the selected items in the currently opened tab.
updateSelectionInTab() - Method in class eu.isas.peptideshaker.gui.JumpToPanel: Updates the item selection in the selected tab.
updateSeparators() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Method called whenever the component is resized to maintain the look of the GUI.
updateSeparators() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Method called whenever the component is resized to maintain the look of the GUI.
updateSeparators() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Method called whenever the component is resized to maintain the look of the GUI.
updateSeparators() - Method in class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Update the separators if the frame size changes.
updateSpectrum(long, Long) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Update the spectra according to the currently selected PSM.
updateSpectrum() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Updates the spectrum annotation.
updateSpectrum() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel: Update the spectrum based on the currently selected PSM.
updateSpectrumAnnotations() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Updates the annotations in the selected tab.
updateSpectrumMatchValidationLevel(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, GeneMaps, IdentificationParameters, TargetDecoyMap, long, boolean) - Static method in class eu.isas.peptideshaker.validation.MatchesValidator: Updates the validation status of a spectrum match.
updateSurroundingAminoAcids() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the number of surrounding amino acids displayed.
updateSurroundingAminoAcids() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Update the number of surrounding amino acids displayed.
updateTabbedPanes() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the tabbed panes.
updateTables() - Method in class eu.isas.peptideshaker.gui.filtering.FiltersDialog: Updates the tables with the filters.
updateTipsNotificationCounter() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Update the notification counter for the tips.
useIntensityIonTable() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: If true, the ion table is shown as an intensity version, false displays the standard Mascot version.
useLogFile() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLIInputBean: Return true if a log file is to be used.
UserParameters - Class in eu.isas.peptideshaker.preferences: In this class are stored the user preferences for PeptideShaker.
UserParameters() - Constructor for class eu.isas.peptideshaker.preferences.UserParameters: Constructor.
userPreferences - Variable in class eu.isas.peptideshaker.preferences.UserPreferencesParent: The user preferences.
UserPreferencesParent - Class in eu.isas.peptideshaker.preferences: Implementing this class will give you access to the saved user preferences.
UserPreferencesParent() - Constructor for class eu.isas.peptideshaker.preferences.UserPreferencesParent

V

validatedDecoyValues - Variable in class eu.isas.peptideshaker.gui.tabpanels.QCPanel: Values of the validated decoy hits.
validatedDoubtfulValues - Variable in class eu.isas.peptideshaker.gui.tabpanels.QCPanel: Values of the doubtful validated target hits.
validatedValues - Variable in class eu.isas.peptideshaker.gui.tabpanels.QCPanel: Values of the validated target hits.
validateIdentifications(Identification, Metrics, InputMap, WaitingHandler, ExceptionHandler, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, GeneMaps, IdentificationParameters, ProjectType, ProcessingParameters) - Method in class eu.isas.peptideshaker.validation.MatchesValidator: This method validates the identification matches of an identification object.
validateInput() - Method in class eu.isas.peptideshaker.gui.parameters.DisplayPreferencesDialog: Validates the user input.
validateInput() - Method in class eu.isas.peptideshaker.gui.parameters.SpectrumCountingSettingsDialog: Validates the user input.
validateInput(boolean) - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeSetupDialog: Inspects the parameters validity.
validateParametersInput(boolean) - Method in class eu.isas.peptideshaker.gui.pride.DatabaseHelpDialog: Inspects the parameters validity.
VALIDATION_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI: The Validation tab index.
ValidationPanel - Class in eu.isas.peptideshaker.gui.tabpanels: This panel displays statistical information about the dataset.
ValidationPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel: Create a new StatsPanel.
valueOf(String) - Static method in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.cmd.MzidCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.cmd.StirredOptions: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.gui.JumpToPanel.JumpType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.gui.MatchValidationDialog.MatchType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: Returns the enum constant of this type with the specified name.
values() - Static method in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.cmd.MzidCLIParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.cmd.ReportCLIParams: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.cmd.StirredOptions: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.gui.JumpToPanel.JumpType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.gui.MatchValidationDialog.MatchType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: Returns an array containing the constants of this enum type, in the order they are declared.
verifyFileExtension(File, InclusionListExport.ExportFormat) - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Verifies that the file extension is chosen according to the manufacturers specification and adds the extension if missing.
verifyXTandemModifications(IdentificationParameters) - Static method in class eu.isas.peptideshaker.fileimport.PsmImporter: Verifies that the modifications targeted by the quick acetyl and quick pyrolidone are included in the identification parameters.

W

WelcomeDialog - Class in eu.isas.peptideshaker.gui: A simple welcome dialog with the option to open an existing project or create a new one.
WelcomeDialog(PeptideShakerGUI, boolean, boolean, boolean) - Constructor for class eu.isas.peptideshaker.gui.WelcomeDialog: Create a new WelcomeDialog.
writeConfigFile(File, String, SearchParameters) - Static method in class eu.isas.peptideshaker.followup.Ms2PipExport: Writes a config file for a given model.
writeConfigurationToFile(File) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Writes all path configurations to the given file.
writeConfigurationToFile(SimpleFileWriter) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Writes the configuration file using the provided buffered writer.
writeDocumentation(ExportScheme, ExportFormat, File) - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Writes the documentation related to a report.
writeExport(ExportScheme, File, ExportFormat, boolean, String, ProjectDetails, Identification, IdentificationFeaturesGenerator, GeneMaps, long[], long[], long[], int, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, SpectrumCountingParameters, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.PSExportFactory: Writes the desired export in text format.
writeHeader() - Method in class eu.isas.peptideshaker.export.sections.PsFragmentSection: Writes the header of this section.
writeHeader() - Method in class eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection: Writes the header of this section.
writeHeader() - Method in class eu.isas.peptideshaker.export.sections.PsPeptideSection: Writes the title of the section.
writeHeader(ArrayList<String>) - Method in class eu.isas.peptideshaker.export.sections.PsProteinSection: Writes the header of the protein section.
writeHeader() - Method in class eu.isas.peptideshaker.export.sections.PsPsmSection: Writes the header of this section.
writePathToFile(SimpleFileWriter, PeptideShakerPathParameters.PeptideShakerPathKey) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Writes the path of interest using the provided buffered writer.
writePepXmlFile(Identification, IdentificationParameters, SpectrumProvider, File, String, WaitingHandler, ExceptionHandler) - Method in class eu.isas.peptideshaker.followup.PepXmlExport: Writes the PSM results to the given file in the PepXML format.
writeProgenesisExport(File, SequenceProvider, ProteinDetailsProvider, Identification, ProgenesisExport.ExportType, WaitingHandler, HashSet<String>, SequenceMatchingParameters) - Static method in class eu.isas.peptideshaker.followup.ProgenesisExport: Writes a file containing the PSMs in a Progenesis compatible format.
writeProteoforms(File, Identification, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.ProteoformExport: Writes an export with all the possible proteoforms of the validated proteins.
writeRecalibratedSpectra(boolean, boolean, File, Identification, SequenceProvider, SpectrumProvider, IdentificationParameters, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.RecalibrationExporter: Writes the recalibrated spectra in files named according to getRecalibratedFileName in the given folder.
writeSection(AnnotationParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsAnnotationSection: Writes the desired section.
writeSection(String, String, SpectrumIdentificationAssumption, SequenceProvider, SpectrumProvider, IdentificationParameters, String, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsFragmentSection: Writes the desired section.
writeSection(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, IdentificationParameters, long[], String, int, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection: Writes the desired section.
writeSection(PeptideAssumptionFilter, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsInputFilterSection: Writes the desired section.
writeSection(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, IdentificationParameters, long[], int, String, boolean, boolean, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsPeptideSection: Writes the desired section.
writeSection(String, ProjectDetails, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsProjectSection: Writes the desired section.
writeSection(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, GeneMaps, IdentificationParameters, long[], int, boolean, boolean, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsProteinSection: Writes the desired section.
writeSection(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, IdentificationParameters, long[], String, int, boolean, boolean, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsPsmSection: Writes the desired section.
writeSection(ModificationLocalizationParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsPtmScoringSection: Writes the desired section.
writeSection(SearchParameters, ProjectDetails, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsSearchParametersSection: Writes the desired section.
writeSection(SpectrumCountingParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsSpectrumCountingSection: Writes the desired section.
writeSection(PSMaps, IdentificationParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsValidationSection: Writes the desired section.

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