Index (PeptideShaker 3.0.12 API)

A B C D E F G H I J K L M N O P Q R S T U V W Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

ABI - Enum constant in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: ABI format.
accessionExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether an accession export is needed.
ACCESSIONS_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
ACCESSIONS_TYPE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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(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.
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.
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.
ALL - Enum constant in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams
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.
Bruker - Enum constant in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Bruker format.

C

calculateSpectraDistances(Spectrum, Spectrum, String) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the spectra metrics.
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: Checks that only one variable modification is assigned per site and 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() - 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.
clearData(boolean, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Clear the data from the previous experiment.
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() - Method in class eu.isas.peptideshaker.cmd.ReportCLI: Close the PeptideShaker instance by clearing up factories and cache.
closePeptideShaker(Identification) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI: Close the PeptideShaker instance.
cmsFolder - Enum constant in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey: The folder to use for cms files.
CONFIDENT_OFFSET - Variable in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Localization score offset for modification that are confidently localized.
confident_ptms - Enum constant in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Exports the Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins
confidentOnly() - Method in class eu.isas.peptideshaker.gui.export.PtmSelectionDialog: Indicates whether only the confident modifications sites are of interest.
CONFIG_FOLDER - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
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.
CONTACT_ADDRESS - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
CONTACT_EMAIL - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
CONTACT_FIRST_NAME - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
CONTACT_LAST_NAME - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
CONTACT_URL - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
contactAddress - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
contactAddress - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The address of the contact to annotate in the mzIdentML file.
contactEmail - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
contactEmail - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The email of the contact to annotate in the mzIdentML file.
contactFirstName - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
contactFirstName - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The first name of the contact to annotate in the mzIdentML file.
contactLastName - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
contactLastName - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The last name of the contact to annotate in the mzIdentML file.
contactOrganizationAddress - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
contactOrganizationAddress - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The address of the organization of the contact to annotate in the mzIdentML file.
contactOrganizationEmail - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
contactOrganizationEmail - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The email of the organization of the contact to annotate in the mzIdentML file.
contactOrganizationName - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
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.
DEEPLC_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
deepLcExport(File, File, HashMap<String, Double>, 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.
deepLcExport(String, File, 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.Returns an ArrayList of the files exported.
DeepLcExport - Class in eu.isas.peptideshaker.followup: Export for RT prediction using DeepLC.
DeepLcExport() - Constructor for class eu.isas.peptideshaker.followup.DeepLcExport
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.
degenerated - Enum constant in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Degenerated Peptides.
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 - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The display parameters.
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.
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.
DOCUMENTATION_TYPE - Enum constant in enum eu.isas.peptideshaker.cmd.ReportCLIParams
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, SpectrumMatch, InputMap, IdentificationParameters, PeptideSpectrumAnnotator, HyperScore, WaitingHandler) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer: Scores the PSMs contained in an identification object.
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.
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.
EXPORT_FOLDER - Enum constant in enum eu.isas.peptideshaker.cmd.ReportCLIParams
EXPORT_PREFIX - Enum constant in enum eu.isas.peptideshaker.cmd.ReportCLIParams
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.
exportPeaksIntensities(FollowUpCLIInputBean, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the peaks intensities (observed).
exportPercolator(FollowUpCLIInputBean, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationParameters, 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() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Export the project as a zip file.
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.
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.
exportPSMIdentifiers(FollowUpCLIInputBean, Identification, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods
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.
exportRTValues(FollowUpCLIInputBean, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods: Exports the RT values (observed,predicted).
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.
ExportUtils - Class in eu.isas.peptideshaker.export: Utils for exports.
ExportUtils() - Constructor for class eu.isas.peptideshaker.export.ExportUtils
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

fasta - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
FASTA_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
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.
findMatchedPeaksRatio(Spectrum, int) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the ratio of matched predicted peaks.
findTerminiCoverage(ArrayList<ArrayList<Integer>>, String) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the ratio of matched predicted peaks.
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) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the contribution of validated hits of the given advocate for the entire dataset.
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.
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.
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.
getAlgorithmNameToVersionsMap() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Returns the different identification algorithm versions used in a map: algorithm name > versions.
getAlignedPeaks(Spectrum, Spectrum) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the indices of the predicted peaks and their measured matches (measuredIndex = -1 if predicted peak unmatched).
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.
getCachePercolatorFeatures() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns wether the user enabled the caching of Percolator features.
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.
getConfigFolder() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns the config folder.
getConfigFolder() - Static method in class eu.isas.peptideshaker.PeptideShaker: Returns the folder where the configuration files are stored.
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.
getCrossEntropy(Spectrum, Spectrum, double) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the cross entropy between the measured and predicted mass spectrum.
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, boolean) - 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(File, String, SpectrumExporter.ExportType) - Static method in class eu.isas.peptideshaker.followup.SpectrumExporter: Returns the destination file for the given export.
getDestinationFile(String, String, boolean) - Static method in class eu.isas.peptideshaker.followup.DeepLcExport: Returns the file where to write the 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.
getEnzymaticityFeature(PeptideAssumption, SearchParameters, SequenceProvider) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Computes the value for the enzymaticity feature.
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.
getFilteredAmbiguousModifications(Peptide, HashSet<String>) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Exports the modifications that are not confidently localized.
getFilteredConfidentModificationsSites(Peptide, HashSet<String>) - 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, 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() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails: Getter for all identification files loaded.
getIdentificationFiles(String) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Returns a list of identification files as imported from the command line option.
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.
getIntensitiesPrediction(File) - Static method in class eu.isas.peptideshaker.followup.PercolatorExport: Parses the peaks intensities prediction from MS2PIP.
getIntensityCoverageFeature(SpectrumMatch, PeptideAssumption, SearchParameters, AnnotationParameters, ModificationLocalizationParameters, SequenceProvider, SpectrumProvider) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Computes the value for the intensity coverage feature.
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() - 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.
getMeasuredAndDeltaMzFeature(SpectrumMatch, PeptideAssumption, SearchParameters, SpectrumProvider) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Computes the value for the measured and delta mass feature.
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() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the decoy series of the target decoy histogram.
getNDecoy(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the number of decoy hits found at the given score.
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() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries: Returns the target series of the target decoy histogram.
getNTarget(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the number of target hits found at the given score.
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.
getPeaksIntensitiesObsFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file where to write the peaks intensities observed values.
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(SpectrumMatch, PeptideAssumption, ArrayList<Double>, ArrayList<Spectrum>, SearchParameters, SequenceProvider, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationFactory, SpectrumProvider, ModificationParameters) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Gets the peptide data to provide to percolator.
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.
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(Peptide) - 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(PeptideMatch) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns a string with the HTML tooltip for the peptide indicating the modification details.
getPeptideModificationTooltipAsHtml(SpectrumMatch) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator: Returns a string with the HTML tooltip for the peptide indicating the modification details.
getPeptideObservedPredictedRT(SpectrumMatch, ArrayList<Double>, SpectrumProvider) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils
getPeptideRTData(SpectrumMatch, PeptideAssumption, ModificationParameters, ArrayList<Double>, SequenceProvider, SpectrumProvider, SequenceMatchingParameters, ModificationFactory) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils
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() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the number of PeptideShaker validated hits for the entire dataset.
getPeptideShakerHits(String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the number of validated hits 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.
getPeptideShakerUniqueContribution(String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Returns the contribution of unique validated hits from PeptideShaker for the given file.
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.
getPercolatorBenchmarkResultsFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file containing Percolator results for all PSMs to get confidence levels.
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.
getPhosphorylations(ModificationParameters) - Static method in class eu.isas.peptideshaker.export.ExportUtils: Returns the names of the variable modifications containing "phospho", not case sensitive.
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(double) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap: Returns the posterior error probability estimated at the given score.
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.
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.
getPSMIdentifiersFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file containing Percolator results for all PSMs to get confidence levels.
getPSMIDsPeaksExportFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file where to read the PSM ids for the peaks export.
getPsmKey(String) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns a unique key corresponding to the given PSM.
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
getRTObsPredsFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Returns the file where to write the RT observed and predicted values.
getRTValuesHeader() - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the header of the file with the RT observed and predicted values.
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.
getSequenceWithModifications(Peptide, ModificationParameters, SequenceProvider, SequenceMatchingParameters, ModificationFactory) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the sequence of the peptides with modifications encoded as required by Percolator.
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.
getSpectraCosine(Spectrum, Spectrum, ArrayList<ArrayList<Integer>>) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the cosine distance between the measured and predicted mass spectrum.
getSpectraLogDist(Spectrum, Spectrum, ArrayList<ArrayList<Integer>>, double) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Returns the log distance between the measured and predicted mass spectrum.
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(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.
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.
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
GUI - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
GZIP - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
GZIP - Enum constant in enum eu.isas.peptideshaker.cmd.ReportCLIParams

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.
IDENTIFICATION_FILES - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
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 - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
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(WaitingHandler, ArrayList<File>, SpectrumProvider, IdentificationParameters, ProjectDetails, ProcessingParameters, ExceptionHandler) - Method in class eu.isas.peptideshaker.PeptideShaker: Imports identification results from result files.
importFiles(ArrayList<File>) - Method in class eu.isas.peptideshaker.fileimport.FileImporter: Imports the identifications from the 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, SequenceProvider, SpectrumProvider, FastaMapper, ProcessingParameters, 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.
INCLUDE_PROTEIN_SEQUENCES - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
INCLUSION_LIST_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
INCLUSION_LIST_FORMAT - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
INCLUSION_LIST_PEPTIDE_FILTERS - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
INCLUSION_LIST_PROTEIN_FILTERS - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
INCLUSION_LIST_RT_WINDOW - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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.
INFERRED_OFFSET - Variable in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Localization score offset for modification that are inferred.
initiateDisplay() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Initiate the display by displaying the data in the currently selected tab.
input - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
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(File, WaitingHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Adds a spectrum file to the spectrum provider.
loadSpectrumFile(String, ArrayList<File>, WaitingHandler) - Method in class eu.isas.peptideshaker.utils.PsdbParent: Loads the spectrum file.
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.
log - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
LOG_FOLDER - Enum constant in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams
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
lowerConfidence - Enum constant in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: Group supported by low confidence peptides.
lowerEvidence - Enum constant in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: Group supported by predicted or uncertain proteins.

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.
MassLynx - Enum constant in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: MassLynx format.
matchesDirectory - Enum constant in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey: Directory where identification matches are temporarily saved to reduce the memory footprint.
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.
miscleaved - Enum constant in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Miscleaved Peptides.
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.
MS2PIP_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
MS2PIP_MODELS - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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.
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 - Class in eu.isas.peptideshaker.followup: Export training files for ms2pip.
Ms2PipExport() - Constructor for class eu.isas.peptideshaker.followup.Ms2PipExport
ms2pipExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether MS2PIP 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.
non_validated - Enum constant in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Exports accessions which cannot be mapped to a protein group.
non_validated_peptides - Enum constant in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Exports the spectra of PSMs of non-validated peptides.
non_validated_proteins - Enum constant in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Exports the spectra of PSMs of non-validated proteins.
non_validated_psms - Enum constant in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Exports the spectra of non-validated PSMs.
nonEnzymatic - Enum constant in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: Group supported by non-enzymatic shared peptide.
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.
normalizeIntensities(Spectrum, Spectrum, ArrayList<ArrayList<Integer>>) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Normalize the intensities of the observed and predicted spectra, as probability distributions for cross entropy computation.
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 - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
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.
ORGANIZATION_ADDRESS - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
ORGANIZATION_EMAIL - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
ORGANIZATION_NAME - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
ORGANIZATION_URL - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
output - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
OUTPUT_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
OUTPUT_MGF - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
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.
PEAK_INTS_OBS_PRED - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
peaksIntensitiesExport(File, File, File, Identification, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PeaksIntensitiesExport: Export the peak intensities.
peaksIntensitiesExport(File, HashMap<String, ArrayList<Spectrum>>, ArrayList<String>, Identification, ModificationParameters, SequenceProvider, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PeaksIntensitiesExport: Export the peak intensities.
PeaksIntensitiesExport - Class in eu.isas.peptideshaker.followup: Export for peak intensities.
PeaksIntensitiesExport() - Constructor for class eu.isas.peptideshaker.followup.PeaksIntensitiesExport
peaksIntensitiesObsExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether peaks intensities observed/predicted values export is needed.
PEPNOVO_TRAINING_FDR - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PEPNOVO_TRAINING_FNR - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PEPNOVO_TRAINING_FOLDER - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PEPNOVO_TRAINING_RECALIBRATION - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
peptide - Enum constant in enum eu.isas.peptideshaker.gui.JumpToPanel.JumpType
PEPTIDE - Enum constant in enum eu.isas.peptideshaker.gui.MatchValidationDialog.MatchType
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.
PEPTIDESHAKER_OUTPUT - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
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() - Constructor for class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Empty constructor for API usage via other tools.
PeptideShakerCLIInputBean(CommandLine) - Constructor for class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Construct a PeptideShakerCLIInputBean from an Apache CLI instance.
PeptideShakerCLIParams - Enum in eu.isas.peptideshaker.cmd: Enum class specifying the Command Line Parameters for PeptideShaker.
peptideShakerExports - Enum constant in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey: Folder containing the user custom exports file.
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.
peptideShakerPreferences - Enum constant in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey: Folder containing the PeptideShaker user preferences file.
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.
PERCOLATOR_BENCHMARK_RESULTS - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PERCOLATOR_CACHE - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
PERCOLATOR_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PERCOLATOR_FRAGMENTATION - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PERCOLATOR_RT - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
percolatorExport(File, File, File, File, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationParameters, 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, File, HashMap<String, ArrayList<Double>>, HashMap<String, ArrayList<Spectrum>>, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PercolatorExport: Exports a Percolator training file.
PercolatorExport - Class in eu.isas.peptideshaker.followup: Export for Percolator.
PercolatorExport() - Constructor for class eu.isas.peptideshaker.followup.PercolatorExport
percolatorExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether Percolator 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, WaitingHandler) - 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.
PROGENESIS_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PROGENESIS_TARGETED_PTMS - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PROGENESIS_TYPE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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.
PROJECT_TYPE - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
projectDetails - Variable in class eu.isas.peptideshaker.utils.PsdbParent: The project details.
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.
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, SpectrumCountingParameters, DisplayParameters) - Constructor for class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog: Creates a new PreferencesDialog with a frame as owner.
ProjectParametersDialog(Frame, Dialog, SpectrumCountingParameters, DisplayParameters) - Constructor for class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog: Creates a new PreferencesDialog with a dialog 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 - Enum constant in enum eu.isas.peptideshaker.gui.JumpToPanel.JumpType
PROTEIN - Enum constant in enum eu.isas.peptideshaker.gui.MatchValidationDialog.MatchType
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() - Constructor for class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel: Constructor which sets a new empty table.
ProteinFractionTableModel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel: Constructor which sets a new 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
PROTEOFORMS_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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.
PSDB_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PSDB_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams
PSDB_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.ReportCLIParams
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.
psm - Enum constant in enum eu.isas.peptideshaker.gui.JumpToPanel.JumpType
PSM - Enum constant in enum eu.isas.peptideshaker.gui.MatchValidationDialog.MatchType
PSM_IDENTIFIERS_EXPORT - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PSM_IDS_FOR_PEAKS_EXPORT - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
PSM_TYPE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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.
psmIdentExport(File, Identification, ModificationParameters, SequenceProvider, SequenceMatchingParameters, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PSMIdentExport: Export the PSM identifications.
PSMIdentExport - Class in eu.isas.peptideshaker.followup: Export for PSM identifications.
PSMIdentExport() - Constructor for class eu.isas.peptideshaker.followup.PSMIdentExport
PSMIdentifiersExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether PSM identifiers export is needed.
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, ProcessingParameters, IdfileReader, 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

reactive - Enum constant in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType: Reactive Peptides.
recalibrateFragmentMz(double, double[]) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation: Recalibrate an m/z array.
recalibrateSpectra() - Method in class eu.isas.peptideshaker.gui.export.FollowUpExportDialog: Lets the user select an output folder and starts the recalibration of spectra.
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.
recalibrateSpectrum(String, String, SpectrumProvider, boolean, boolean) - Method in class eu.isas.peptideshaker.recalibration.SpectrumRecalibrator: Recalibrates a spectrum.
RECALIBRATION_FOLDER - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
RECALIBRATION_MODE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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.
REFERENCE - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
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, 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.
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.
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.
REPORT_TYPE - Enum constant in enum eu.isas.peptideshaker.cmd.ReportCLIParams
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 ReportCLIInputBean 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() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Resets the advocate contribution mappings.
resetAdvocateContributions(String) - Method in class eu.isas.peptideshaker.scoring.maps.InputMap: Resets the advocate contribution mappings for the given file.
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.
RT_OBS_PRED - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
rtBinSize - Static variable in class eu.isas.peptideshaker.recalibration.RunMzDeviation: The bin size in retention time in number of MS/MS spectra.
RTValuesExport(File, File, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PercolatorExport
RTValuesExportNeeded() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean: Indicates whether RT observed/predicted values export is needed.
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.
scaleIntensities(Spectrum, Spectrum, ArrayList<ArrayList<Integer>>) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils: Scale the intensities of the observed and predicted spectra.
scorePeptidePtms(Identification, ModificationProvider, SequenceProvider, 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, PeptideMatch, IdentificationParameters, ModificationProvider, SequenceProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Scores the PTMs for a peptide match.
scorePTMs(Identification, ProteinMatch, IdentificationParameters, boolean, ModificationProvider, SequenceProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer: Scores PTMs in a protein match.
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.
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.
SEQUENCES_FILE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
SEQUENCES_TYPE - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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.
setConfigFolder(File) - Static method in class eu.isas.peptideshaker.PeptideShaker: Set the config folder.
setConfigFoler(File) - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean: Sets the config folder.
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() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the selected item based on the selected tab.
setSelectedItems(long, long, String, String) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI: Sets the keys of the selected protein, peptide and PSM.
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() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Returns whether hidden proteins should be displayed.
showHiddenProteins(boolean) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Sets 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() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Returns whether scores should be displayed.
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.
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() - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Returns whether only the validated proteins should be displayed.
showValidatedProteinsOnly(boolean) - Method in class eu.isas.peptideshaker.preferences.DisplayParameters: Sets whether only the validated proteins should be displayed.
simplerGroups - Enum constant in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: Group explained by simpler groups.
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 - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
SPECTRUM_FILES - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
SPECTRUM_FOLDER - Enum constant in enum eu.isas.peptideshaker.cmd.FollowUpCLIParams
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 - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
tempFolder - Variable in class eu.isas.peptideshaker.cmd.StirredOptionsBean: The temp folder to use for temp files.
Thermo - Enum constant in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat: Thermo format.
THREADS - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams
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 - Enum constant in enum eu.isas.peptideshaker.cmd.StirredOptions
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.
unzipFolder - Enum constant in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey: The folder to use when unzipping files.
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(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, 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(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.
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.PeptideFractionTableModel: 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.
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, 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.
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.
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() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel: 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.
updateSelection(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel: Update the selected protein and peptide.
updateSelection(boolean) - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel: Update the selected protein and peptide.
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() - 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.
updateSpectrum(long, Long) - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel: Update the spectra according to 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.
USE_LOG_FOLDER - Enum constant in enum eu.isas.peptideshaker.cmd.PathSettingsCLIParams
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

validated_all_accessions - Enum constant in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Exports all accessions of validated protein groups.
validated_main_accession - Enum constant in enum eu.isas.peptideshaker.followup.FastaExport.ExportType: Exports the main accession of validated protein groups.
validated_psms - Enum constant in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Exports the spectra of validated PSMs.
validated_psms - Enum constant in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Exports the spectra of validated PSMs.
validated_psms_peptides - Enum constant in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Exports the spectra of validated PSMs of validated peptides.
validated_psms_peptides - Enum constant in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Exports the spectra of validated PSMs of validated peptides.
validated_psms_peptides_proteins - Enum constant in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType: Exports the spectra of validated PSMs of validated peptides of validated proteins.
validated_psms_peptides_proteins - Enum constant in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType: Exports the spectra of validated PSMs of validated peptides of validated proteins.
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.
variant - Enum constant in enum eu.isas.peptideshaker.protein_inference.ProteinInference.GroupSimplificationOption: Group supported by peptide shared with protein with variant.
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.
VERSION - Enum constant in enum eu.isas.peptideshaker.cmd.MzidCLIParams

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(SimpleFileWriter) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Writes the configuration file using the provided buffered writer.
writeConfigurationToFile(File) - Static method in class eu.isas.peptideshaker.preferences.PeptideShakerPathParameters: Writes all path configurations to the given file.
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() - Method in class eu.isas.peptideshaker.export.sections.PsPsmSection: Writes the header of this section.
writeHeader(ArrayList<String>) - Method in class eu.isas.peptideshaker.export.sections.PsProteinSection: Writes the header of the protein 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(PeptideAssumptionFilter, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsInputFilterSection: 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[], int, String, boolean, boolean, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsPeptideSection: 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(Identification, IdentificationFeaturesGenerator, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, IdentificationParameters, long[], String, int, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection: Writes the desired section.
writeSection(AnnotationParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsAnnotationSection: 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.
writeSection(String, ProjectDetails, WaitingHandler) - Method in class eu.isas.peptideshaker.export.sections.PsProjectSection: 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.

Z

ZIP - Enum constant in enum eu.isas.peptideshaker.cmd.PeptideShakerCLIParams

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