Index

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|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

call() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLI

Calling this method will run the configured PeptideShaker process.

call() - Method in class eu.isas.peptideshaker.cmd.MzidCLI

Calling this method will run the configured PeptideShaker process.

call() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLI

call() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI

call() - Method in class eu.isas.peptideshaker.cmd.ReportCLI

Calling this method will run the configured PeptideShaker process.

catchException(Exception) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Method called whenever an exception is caught.

catchException(Exception) - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel

catchException(Exception) - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel

catchException(Exception) - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel

checkFastaFile() - Method in class eu.isas.peptideshaker.gui.NewDialog

Checks whether the FASTA file loaded contains mainly UniProt concatenated target decoy.

checkForNewSearchGUIVersion(String) - Method in class eu.isas.peptideshaker.gui.WelcomeDialog

Check for new version.

checkForNewVersion() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Check for new version.

checkNewsFeed() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Displays a news feed at the bottom of the GUI.

checkPeptide(Peptide, SequenceProvider, SequenceMatchingParameters) - Static method in class eu.isas.peptideshaker.protein_inference.PeptideChecker

Corrects the protein mapping based on the confident or inferred variable modifications when located at the protein termini or targeting amino acid patterns.

clean(double) - Method in class eu.isas.peptideshaker.scoring.maps.specific.ModificationSpecificMap

clean(double) - Method in class eu.isas.peptideshaker.scoring.maps.specific.SimpleSpecificMap

clean(double) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap

Handles sparse maps.

cleanProviders() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters

Cleans the SequenceProvider and ProteinDetailsProvider, please use only temporary or if you know what you do

cleanUp() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

Removes empty points and clears dependent metrics if needed.

clearData() - 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_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.

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, 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, Identification, ModificationParameters, SequenceMatchingParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.DeepLcExport

Exports DeepLC training files for each of the spectrum files.

DeepLcExport - 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.

exportPercolator(FollowUpCLIInputBean, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods

Exports the files needed by Percolator.

exportProgenesis(FollowUpCLIInputBean, Identification, WaitingHandler, SequenceProvider, ProteinDetailsProvider, SequenceMatchingParameters) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods

Exports the identification in a Progenesis compatible format.

exportProjectAsZip() - 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.

exportReport(ReportCLIInputBean, String, String, ProjectDetails, Identification, GeneMaps, IdentificationFeaturesGenerator, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, int, SpectrumCountingParameters, WaitingHandler) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods

Writes an export according to the command line settings contained in the reportCLIInputBean.

exportSelectedSpectraAsMgf() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Export the current spectrum as an mgf.

exportSequenceFragmentationAsFigure() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Export the current sequence fragmentation as a figure.

exportSpectra(FollowUpCLIInputBean, Identification, SpectrumProvider, WaitingHandler, SequenceMatchingParameters) - Static method in class eu.isas.peptideshaker.cmd.CLIExportMethods

Exports the spectra as specified in the follow-up input bean.

exportSpectra(File, WaitingHandler, SpectrumExporter.ExportType, SequenceMatchingParameters) - Method in class eu.isas.peptideshaker.followup.SpectrumExporter

Exports the spectra from different categories of PSMs according to the export type.

exportSpectrumAsFigure() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Export the current spectrum as a figure.

extension - Variable in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat

The extension of the file.

extractAndUpdatePathOptions(String[]) - Static method in class eu.isas.peptideshaker.cmd.PathSettingsCLI

If the arguments contains changes to the paths these arguments will be extracted and the paths updated, before the remaining non-path options are returned for further processing.

F

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.

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.

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.

getContactAddress() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean

Returns the contact address.

getContactAddress() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the address of the contact for the mzIdentML dataset.

getContactEmail() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean

Returns the contact email.

getContactEmail() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the e-mail of the contact for the mzIdentML dataset.

getContactFirstName() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean

Returns the contact first name.

getContactFirstName() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the first name of the contact for the mzIdentML dataset.

getContactLastName() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean

Returns the contact last name.

getContactLastName() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the last name of the contact for the mzIdentML dataset.

getContactUrl() - Method in class eu.isas.peptideshaker.cmd.MzidCLIInputBean

Returns the contact URL.

getContactUrl() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the URL of the contact for the mzIdentML dataset.

getCorrectedCharge(int) - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap

For grouped files, returns the reference category of the group.

getCreationDate() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Getter for the creation date of the project.

getCurrentMassDeltas() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Get the current delta masses for use when annotating the spectra.

getCurrentPxAccession() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI

Returns the current PX accession number.

getCurrentSpeciesList() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI

Returns the list of species for the currently selected assay or project.

getDatabaseLink(String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Transforms the protein accession number into an HTML link to the corresponding database.

getDatabaseLink(String, boolean, boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Transforms the protein accession number into an HTML link to the corresponding database.

getDatabaseLinks(String[]) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Transforms the protein accession number into an HTML link to the corresponding database.

getDatabaseLinks(String[], boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Transforms the protein accession number into an HTML link to the corresponding database.

getDatabaseText(FastaParameters, FastaSummary) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods

Returns the database usage details.

getDbFolder() - Method in class eu.isas.peptideshaker.utils.PsdbParent

Returns the folder where the database is stored.

getDecoyType() - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods

Returns the decoy sequences creation details.

getDeepLcStem() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

Returns the stem to use for the path to DeepLC files.

getDefaultDocumentation(String) - Static method in class eu.isas.peptideshaker.export.PSExportFactory

Returns the default file name for the export of the documentation of the given report export type.

getDefaultExportScheme(String) - Static method in class eu.isas.peptideshaker.export.PSExportFactory

Returns the desired default export scheme.

getDefaultExportSchemesNames() - Static method in class eu.isas.peptideshaker.export.PSExportFactory

Returns a list of the default export schemes.

getDefaultPeptideSelection(long) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the default peptide, i.e., the "best" peptide for the given protein.

getDefaultPsmSelection(long) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the default PSM, i.e., the "best" PSM for the given peptide.

getDefaultReportName(String, String) - Static method in class eu.isas.peptideshaker.export.PSExportFactory

Returns the default file name for the export of a report based on the project details

getDescription() - Method in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey

getDestinationFile(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.

getFilteredAmbiguousModificationsRepresentativeSites(PSModificationScores, HashSet<String>, int) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Exports the ambiguously localized modification representative sites in a map: site > mapped modifications.

getFilteredAmbiguousModificationsSecondarySites(PSModificationScores, HashSet<String>, int) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Exports the ambiguously localized modification secondary sites in a map: site > mapped modifications.

getFilteredConfidentModificationsSites(PSModificationScores, HashSet<String>, int) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Exports the confidently localized modification sites in a map: site > mapped modifications.

getFilterParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Return the filter parameters to use.

getFilterParameters() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters

Returns the GUI display parameters.

getFilterParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent

Returns the filter preferences.

getFNR() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries

Returns the probabilistic FNR series.

getFnrLimit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults

Returns the FNR limit.

getFNRResults(TargetDecoyResults) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries

Completes the results at the desired FNR threshold.

getFollowUpCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean

Returns the follow-up options required.

getFragmentMzError(double, double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation

Returns the fragment error at the given retention time and fragment m/z.

getFragmentMZList(double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation

Returns the list for fragment ion m/z bins at a given retention time point.

getGeneAnnotation() - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods

Returns the gene annotation method usage details.

getGeneMaps() - Method in class eu.isas.peptideshaker.fileimport.FileImporter

Returns the gene maps.

getGeneMaps() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the gene maps.

getGeneMaps() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters

Returns the gene maps.

getGeneMaps() - Method in class eu.isas.peptideshaker.PeptideShaker

Returns the gene maps.

getGeneMaps() - Method in class eu.isas.peptideshaker.utils.PsdbParent

Returns the gene maps.

getGoAccessionLink(String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Returns the GO accession number as a web link to the given GO term at QuickGO.

getGOPanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the GO Panel.

getGroupedCategories() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap

Returns a list of grouped categories from grouped files.

getHeader(SearchParameters, Boolean) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils

Returns the header of the Percolator training file.

getHeaderHeight() - Method in class eu.isas.peptideshaker.export.PsExportStyle

getHeaderStyle() - Method in class eu.isas.peptideshaker.export.PsExportStyle

getHeaderStyle(int) - Method in class eu.isas.peptideshaker.export.PsExportStyle

getId() - Method in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey

getIdentification() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the identification displayed.

getIdentification() - Method in class eu.isas.peptideshaker.PeptideShaker

Returns the identification object.

getIdentification() - Method in class eu.isas.peptideshaker.utils.PsdbParent

Returns the identification object.

getIdentificationAlgorithms() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns a list of identification algorithms used based on the identification files of the project.

getIdentificationAlgorithmsForFile(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the identification algorithms used to create the id file in map: algorithm name > algorithm version.

getIdentificationFeaturesCache() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters

Returns the identification features cache used by the identification features generator before saving the file.

getIdentificationFeaturesGenerator() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the identification features generator.

getIdentificationFeaturesGenerator() - Method in class eu.isas.peptideshaker.PeptideShaker

Returns the identification features generator used when loading the files.

getIdentificationFeaturesGenerator() - Method in class eu.isas.peptideshaker.utils.PsdbParent

Returns the identification features generator object.

getIdentificationFiles() - 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.

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() - Method in class eu.isas.peptideshaker.cmd.IdentificationParametersCLI

Returns the path to the jar file.

getJarFilePath() - Static method in class eu.isas.peptideshaker.PeptideShaker

Retrieves the path to the jar file.

getJsonFile() - Static method in class eu.isas.peptideshaker.export.PSExportFactory

Returns the file where to save the implemented export schemes.

getJsonFolder() - Static method in class eu.isas.peptideshaker.export.PSExportFactory

Returns the folder where to save the implemented export schemes.

getKeyFromId(String) - Static method in enum eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.PeptideShakerPathKey

Returns the key from its id.

getLastSelectedFolder() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the last selected folder.

getLastSelectedFolder(LastSelectedFolder) - Method in class eu.isas.peptideshaker.gui.pride.DatabaseHelpDialog

Returns the last selected folder.

getLogFileMessage() - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLI

Returns the "see the log file" message.

getLogFolder() - Method in class eu.isas.peptideshaker.cmd.PathSettingsCLIInputBean

Returns the folder where to save the log files.

getLogScoreLimit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults

Returns the score limit obtained with the current validation settings.

getMainTitleRowHeight() - Method in class eu.isas.peptideshaker.export.PsExportStyle

getMainTitleStyle() - Method in class eu.isas.peptideshaker.export.PsExportStyle

getMap() - Method in class eu.isas.peptideshaker.scoring.maps.InputMap

Returns the first target/decoy map of the input map in case a single algorithm was used.

getMapSize() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

Returns the size of the map.

getMapsSize() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap

Returns the overall number of points across all maps.

getMassErrorPlot() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Returns the mass error plot panel.

getMatchesDirectoryParent() - Static method in class eu.isas.peptideshaker.PeptideShaker

Returns the matches directory parent.

getMatchesDirectoryParentFile() - Static method in class eu.isas.peptideshaker.PeptideShaker

Returns the matches directory parent.

getMatchesDirectorySubPath() - Static method in class eu.isas.peptideshaker.PeptideShaker

Returns the directory used to store the identification matches.

getMatchesFolder() - Static method in class eu.isas.peptideshaker.PeptideShaker

Returns the path to the matches folder according to the user path settings.

getMaxPeptideErrorDa() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable

Returns the maximal peptide mass error found in Da.

getMaxPeptideErrorDa() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter

Returns the maximal peptide mass error found in Da.

getMaxPeptideErrorPpm() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable

Returns the maximal peptide mass error found in ppm.

getMaxPeptideErrorPpm() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter

Returns the maximal peptide mass error found in ppm.

getMaxTagErrorDa() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable

Returns the maximal tag mass error found in Da.

getMaxTagErrorDa() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter

Returns the maximal tag mass error found in Da.

getMaxTagErrorPpm() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable

Returns the maximal tag mass error found in ppm.

getMaxTagErrorPpm() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter

Returns the maximal tag mass error found in ppm.

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.

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, Boolean, ArrayList<Double>, SearchParameters, SequenceProvider, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, ModificationFactory, SpectrumProvider) - Static method in class eu.isas.peptideshaker.utils.PercolatorUtils

Gets the peptide data to provide to percolator.

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.

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.

getPercolatorFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

Returns the file where to write the training file for Percolator.

getPercolatorFragmentationFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

Returns the file with fragmentation values for Percolator.

getPercolatorRtFile() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

Returns the file with retention time values for Percolator.

getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.FastaExport.ExportType

Returns all possibilities descriptions in an array of string.

getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat

Returns all possibilities descriptions in an array of string.

getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.InclusionListExport.PeptideFilterType

Returns all possibilities descriptions in an array of string.

getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.ProgenesisExport.ExportType

Returns all possibilities descriptions in an array of string.

getPossibilities() - Static method in enum eu.isas.peptideshaker.followup.SpectrumExporter.ExportType

Returns all possibilities descriptions in an array of string.

getPossibilitiesDescriptions() - Method in class eu.isas.peptideshaker.gui.JumpToPanel

Returns a list of descriptions corresponding to every item matching the search.

getPossibleCategories() - Method in class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap

Returns the categories found in the map

getPrecursorIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable

Returns the number of PSMs which did not pass the import filters due to a precursor issue.

getPrecursorIssue() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter

Returns the number of PSMs which did not pass the import filters due to a precursor issue.

getPrecursorMzCorrection(double, double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation

Returns an interpolation of the median error in the bins surrounding the given precursor m/z when recalibrating with m/z only.

getPrecursorRTList() - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation

Returns the list of precursor retention time bins.

getPreferredAccessionColumnWidth(JTable, int, int, Integer) - Static method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel

Gets the preferred width of the column specified by colIndex.

getPreferredColumnWidth(JTable, int, int) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Gets the preferred width of the column specified by colIndex.

getPrideAccessionLink(String) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Returns the project accession number as a web link to the given project in PRIDE.

getPrideAssayArchiveLink(String, String) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Returns the assay accession number as a web link to the given assay in the PRIDE archive.

getPrideContactGroup() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE contact group.

getPrideExperimentDescription() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE experiment project description.

getPrideExperimentLabel() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE experiment label.

getPrideExperimentProjectTitle() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE experiment project title.

getPrideExperimentTitle() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE experiment title.

getPrideFile() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean

Returns the pride file.

getPrideInstrument() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE instrument.

getPrideOutputFolder() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE output folder.

getPrideProjectArchiveLink(String) - Static method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Returns the project accession number as a web link to the given project in the PRIDE archive.

getPrideProtocol() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE protocol.

getPrideReferenceGroup() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE reference group.

getPrideSample() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the PRIDE sample.

getProbability(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.

getPsmMap() - Method in class eu.isas.peptideshaker.scoring.PSMaps

Returns the target decoy map at the psm level.

getPsmMap() - Method in class eu.isas.peptideshaker.validation.MatchesValidator

Returns the PSM scoring specific map.

getPsmsRejected() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable

Returns the number of PSMs which did not pass the import filters.

getPsmsRejected() - Method in class eu.isas.peptideshaker.fileimport.PsmImporter

Returns the number of PSMs which did not pass the import filters.

getPtmScoring(ModificationLocalizationParameters) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods

Returns the PTM scoring methods used.

getRecalibratedFileName(String) - Static method in class eu.isas.peptideshaker.followup.RecalibrationExporter

Returns the name of the recalibrated file.

getRecalibrationFolder() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

The folder where to export recalibrated spectra.

getRecalibrationMode() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

The recalibration mode.

getRecentProjects() - Method in class eu.isas.peptideshaker.preferences.UserParameters

Returns the paths of the recent projects.

getReport() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the report created during the loading of the project.

getReportCLIInputBean() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean

Returns the report export options required.

getReportNamePrefix() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean

Returns the report name prefix.

getReportOutputFolder() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean

Returns the report output folder.

getReportStyle(ExcelWriter) - Static method in class eu.isas.peptideshaker.export.PsExportStyle

Returns the style attached to that writer or create a new one if none found.

getReportTypes() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean

Returns the types of output required by the user.

getReshakeableFiles() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI

Returns the list of reshakable file types.

getResidueAnnotation(long, SequenceMatchingParameters, IdentificationFeaturesGenerator, Metrics, Identification, boolean, SearchParameters, boolean) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Returns the residue annotation for a given protein in a map for enzymatic or not enzymatic peptides only.

getResolution() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

Returns the minimal detectable PEP variation in percent.

getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel

getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel

getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel

getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel

getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel

getRowCount() - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel

getRunMzDeviations(String) - Method in class eu.isas.peptideshaker.recalibration.SpectrumRecalibrator

Returns the mz deviation statistics class for the spectrum file of interest.

getScoreAndConfidenceDecimalFormat() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the decimal format used for the score and confidence columns.

getScoreLimit() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults

Returns the score limit obtained with the current validation settings.

getScores() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

Returns the sorted scores implemented in this map.

getScores() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries

Returns the score series.

getScoresLog() - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries

Returns the log score series.

getSearchEnginesText(ProjectDetails) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods

Returns the search engines usage details.

getSearchGUIText() - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods

Returns the SearchGUI usage details.

getSearchSettingsFiles() - Method in class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI

Returns the list of files that search settings can be extracted from.

getSelectedIdentificationAssumptions() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption

getSelectedIdentificationAssumptions() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption

getSelectedIdentificationAssumptions() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel

Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption

getSelectedModification() - Method in class eu.isas.peptideshaker.gui.ModificationDialog

Returns the selected modification.

getSelectedModification() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

Returns the selected modification name.

getSelectedPeptideKey() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the key of the selected peptide.

getSelectedProteinKey() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the key of the selected protein.

getSelectedPsmKeys() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Returns the keys of the selected spectra in the PSM table.

getSelectedPsmsKeys() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

Returns the keys of the selected PSMs.

getSelectedSpectrumFile() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the currently selected spectrum file.

getSelectedSpectrumTabIndex() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Returns the current selected tab in the spectrum and fragment ions tabbed pane.

getSelectedSpectrumTitle() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the currently selected spectrum title.

getSelectedSpectrumTitle() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel

Returns the title of the currently selected spectrum.

getSelectedSpectrumTitles() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

Returns the titles of the selected spectra in the PSM table in a map by file name.

getSelectedSpectrumTitles() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Returns the titles of the selected spectra in the PSM table in a map by file name.

getSelectedSpectrumTitles() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel

Returns the titles of the selected spectra in the PSM table in a map by file name.

getSelectedTab() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the selected tab as indexed by the static fields.

getSequenceFragmentationPlot() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Returns the sequence fragmentation plot panel.

getSequencePlot(ProteinSequencePanelParent, JSparklinesDataset, HashMap<Integer, ArrayList<ResidueAnnotation>>, boolean, boolean) - Method in class eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel

Returns a sequence plot as a ChartPanel.

getSequenceProvider() - Method in class eu.isas.peptideshaker.fileimport.FileImporter

Returns the sequence provider.

getSequenceProvider() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the sequence provider.

getSequenceProvider() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters

Returns the sequence provider saved when loading the files.

getSequenceProvider() - Method in class eu.isas.peptideshaker.PeptideShaker

Returns the sequence provider.

getSequenceProvider() - Method in class eu.isas.peptideshaker.utils.PsdbParent

Returns the sequence provider.

getSlope(double) - Method in class eu.isas.peptideshaker.recalibration.RunMzDeviation

Returns the precursor m/z deviation slope at a given retention time point.

getSparklineColor() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Get the sparklines color.

getSparklineColorNonValidated() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Get the non-validated sparklines color.

getSparklineColorNotFound() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Get the not found sparklines color.

getSparklineColorPossible() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Get the possible sparklines color.

getSparkLineDataSeriesCoverage(double[], int[], HashMap<Integer, Color>) - Static method in class eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel

Returns an array list with the coverage.

getSpecificAnnotationParameters(String, String, SpectrumIdentificationAssumption) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the specific annotation parameters corresponding to the given spectrum, hit, and the menu selections.

getSpectrum() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

Returns the spectrum panel.

getSpectrum() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Returns the spectrum panel.

getSpectrum() - Method in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel

Returns the spectrum panel.

getSpectrumAndPlots() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Returns the extended spectrum panel.

getSpectrumCounting(SpectrumCountingParameters) - Static method in class eu.isas.peptideshaker.export.PeptideShakerMethods

Returns the spectrum counting method usage details.

getSpectrumCountingParameters() - Method in class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog

Returns the spectrum counting preferences.

getSpectrumCountingParameters() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the spectrum counting parameters.

getSpectrumCountingParameters() - Method in class eu.isas.peptideshaker.utils.PsdbParent

Returns the spectrum counting preferences.

getSpectrumCountingPreferences() - Method in class eu.isas.peptideshaker.gui.parameters.SpectrumCountingSettingsDialog

Returns the spectrum counting preferences as set by the user.

getSpectrumCountingPreferences() - Method in class eu.isas.peptideshaker.parameters.PeptideShakerParameters

Returns the spectrum counting preferences of the project.

getSpectrumExportFolder() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

Returns the folder where to export the spectrum files.

getSpectrumExportTypeIndex() - Method in class eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

Returns the type of export needed for the spectra.

getSpectrumFileNames() - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the name of the input spectrum files as a set.

getSpectrumFilePath(String) - Method in class eu.isas.peptideshaker.preferences.ProjectDetails

Returns the path to the file corresponding to the given name.

getSpectrumFiles() - Method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean

Returns the spectrum files.

getSpectrumFiles(String) - Static method in class eu.isas.peptideshaker.cmd.PeptideShakerCLIInputBean

Returns a list of spectrum files as imported from the command line option.

getSpectrumIdentificationPanel() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the SpectrumIdentificationPanel.

getSpectrumProvider() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the spectrum provider.

getSpectrumProvider() - Method in class eu.isas.peptideshaker.utils.PsdbParent

Returns the spectrum provider.

getSrsAccessionLink(String, String) - Method in class eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

Returns the protein accession number as a web link to the given protein at https://srs.ebi.ac.uk.

getStandardHeight() - Method in class eu.isas.peptideshaker.export.PsExportStyle

getStandardStyle() - Method in class eu.isas.peptideshaker.export.PsExportStyle

getStandardStyle(int) - Method in class eu.isas.peptideshaker.export.PsExportStyle

getStarHider() - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Returns the object responsible for starring/hiding matches.

getSuffix(SpectrumExporter.ExportType) - Static method in class eu.isas.peptideshaker.followup.SpectrumExporter

Returns the suffix for a spectrum file name.

getTagAssumptionFeature(Identification, IdentificationFeaturesGenerator, SpectrumProvider, IdentificationParameters, String, TagAssumption, String, String, PSParameter, PsIdentificationAlgorithmMatchesFeature, WaitingHandler) - Static method in class eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection

Writes the feature associated to the match of the given tag assumption.

getTaggedPeptideSequence(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, File, 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.

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 DeepLC export is needed.

Ms2PipUtils - Class in eu.isas.peptideshaker.utils

Utils for the export and import of ms2pip results.

Ms2PipUtils() - Constructor for class eu.isas.peptideshaker.utils.Ms2PipUtils

msFileHandler - Variable in class eu.isas.peptideshaker.utils.PsdbParent

The mass spectrometry file handler.

mzBinSize - Static variable in class eu.isas.peptideshaker.recalibration.RunMzDeviation

The bin size in m/z in number of MS/MS spectra.

MzidCLI - Class in eu.isas.peptideshaker.cmd

Command line interface to export mzid files from psdb files.

MzidCLI(MzidCLIInputBean) - Constructor for class eu.isas.peptideshaker.cmd.MzidCLI

Construct a new MzidCLI runnable from a MzidCLI input bean.

MzidCLIInputBean - Class in eu.isas.peptideshaker.cmd

This class is a simple bean wrapping the CLI parameters provided in an Options instance.

MzidCLIInputBean(CommandLine) - Constructor for class eu.isas.peptideshaker.cmd.MzidCLIInputBean

Parses a MzidCLI command line and stores the input in the attributes.

MzidCLIParams - Enum in eu.isas.peptideshaker.cmd

Enum class specifying the Command Line Parameters for mzid export.

MzIdentMLExport - Class in eu.isas.peptideshaker.export

The class that takes care of converting the data to mzIdentML.

MzIdentMLExport(String, Identification, ProjectDetails, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumProvider, ModificationProvider, FastaSummary, IdentificationFeaturesGenerator, File, boolean, WaitingHandler, boolean) - Constructor for class eu.isas.peptideshaker.export.MzIdentMLExport

Constructor.

MzIdentMLExportDialog - Class in eu.isas.peptideshaker.gui.export

A dialog where the user can export the project to mzIdentML.

MzIdentMLExportDialog(PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.export.MzIdentMLExportDialog

Create a new MzIdentMLExportDialog.

N

nDecoy - Variable in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint

The number of decoy hits at this point.

NewDialog - Class in eu.isas.peptideshaker.gui

A dialog for selecting the files to load.

NewDialog(PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.NewDialog

Creates a new open dialog.

NewDialog(WelcomeDialog, PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.NewDialog

Creates a new open dialog.

newItemSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

Provides to the PeptideShakerGUI instance the currently selected peptide and PSM.

newItemSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.

newItemSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel

Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.

newItemSelection() - Method in class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel

Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.

NO_ID - Static variable in class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel

Static index for the ID software agreement: no psm found.

NO_MODIFICATION - Static variable in class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

The modification name for no modification.

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.

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.

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_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, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PercolatorExport

Exports a Percolator training file for each of the spectrum files.

percolatorExport(File, HashMap<String, ArrayList<Double>>, HashMap<String, ArrayList<Spectrum>>, Identification, SearchParameters, SequenceMatchingParameters, AnnotationParameters, ModificationLocalizationParameters, SequenceProvider, SpectrumProvider, WaitingHandler) - Static method in class eu.isas.peptideshaker.followup.PercolatorExport

Exports a Percolator training file.

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 DeepLC export is needed.

PercolatorUtils - Class in eu.isas.peptideshaker.utils

Utils for the export and import of Percolator results.

PercolatorUtils() - Constructor for class eu.isas.peptideshaker.utils.PercolatorUtils

PrideDataTypeSelectionDialog - Class in eu.isas.peptideshaker.gui.pride

A dialog for selecting if public or private data is to be loaded.

PrideDataTypeSelectionDialog(JFrame, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideDataTypeSelectionDialog

Creates a new PrideDataTypeSelectionDialog.

PrideFreeTextSearchDialog - Class in eu.isas.peptideshaker.gui.pride

A dialog for using PRIDE free text search via https://www.ebi.ac.uk/pride/archive/simpleSearch.

PrideFreeTextSearchDialog(JDialog, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideFreeTextSearchDialog

Creates a new PrideFreeTextSearchDialog.

PridePrivateDataDialog - Class in eu.isas.peptideshaker.gui.pride

A dialog for getting the PRIDE private project access information from the user.

PridePrivateDataDialog(Frame, boolean, String) - Constructor for class eu.isas.peptideshaker.gui.pride.PridePrivateDataDialog

Creates a new PridePrivateDataDialog.

PrideReshakeGUI - Class in eu.isas.peptideshaker.gui.pride

Frame for talking to the PRIDE Archive web service to select projects for reshaking.

PrideReshakeGUI(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI

Creates a new PrideReShakeGUI frame.

PrideReshakeGUI(PeptideShakerGUI, String, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI

Creates a new PrideReShakeGUI frame.

PrideReshakeSetupDialog - Class in eu.isas.peptideshaker.gui.pride

Dialog for setting up the PRIDE Reshake.

PrideReshakeSetupDialog(PrideReshakeGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideReshakeSetupDialog

Creates a new PrideReshakeSetupDialog.

PrideSearchParametersDialog - Class in eu.isas.peptideshaker.gui.pride

Display the extracted search settings to the user.

PrideSearchParametersDialog(PrideReshakeGUI, File, String, ArrayList<File>, ArrayList<File>, File, String, String, String, boolean) - Constructor for class eu.isas.peptideshaker.gui.pride.PrideSearchParametersDialog

Creates a new PrideSearchParametersDialog.

process(File, File, File, FMIndex, FastaSummary, MsFileHandler, IdentificationParameters, 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_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.

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, File, Identification, SequenceProvider, FastaMapper, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.fileimport.PsmImportRunnable

Constructor.

PsmProcessor - Class in eu.isas.peptideshaker.processing

Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.

PsmProcessor(Identification) - Constructor for class eu.isas.peptideshaker.processing.PsmProcessor

Constructor.

PsmProcessorRunnable - Class in eu.isas.peptideshaker.processing

This class processes PSMs.

PsmProcessorRunnable(ConcurrentLinkedQueue<Long>, Identification, IdentificationParameters, InputMap, MatchesValidator, ModificationLocalizationScorer, SequenceProvider, SpectrumProvider, ModificationProvider, HashMap<String, Integer>, WaitingHandler, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.processing.PsmProcessorRunnable

Constructor.

PsmScorer - Class in eu.isas.peptideshaker.scoring.psm_scoring

This class scores peptide spectrum matches.

PsmScorer(FastaParameters, SequenceProvider, SpectrumProvider) - Constructor for class eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer

Constructor.

PsmTableModel - Class in eu.isas.peptideshaker.gui.tablemodels

Table model for a set of peptide to spectrum matches.

PsmTableModel() - Constructor for class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel

Constructor for an empty table.

PsmTableModel(Identification, DisplayFeaturesGenerator, SpectrumProvider, IdentificationParameters, long[], boolean, ExceptionHandler) - Constructor for class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel

Constructor which sets a new table.

PsPeptideSection - Class in eu.isas.peptideshaker.export.sections

This class outputs the peptide related export features.

PsPeptideSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsPeptideSection

Constructor.

PsProjectSection - Class in eu.isas.peptideshaker.export.sections

This class outputs the project related export features.

PsProjectSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsProjectSection

Constructor

PsProteinSection - Class in eu.isas.peptideshaker.export.sections

This class outputs the protein related export features.

PsProteinSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsProteinSection

Constructor.

PsPsmSection - Class in eu.isas.peptideshaker.export.sections

This class outputs the PSM level export features.

PsPsmSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsPsmSection

Constructor.

PsPtmScoringSection - Class in eu.isas.peptideshaker.export.sections

This class outputs the project related export features.

PsPtmScoringSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsPtmScoringSection

Constructor.

PsSearchParametersSection - Class in eu.isas.peptideshaker.export.sections

This class outputs the search parameters related export features.

PsSearchParametersSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsSearchParametersSection

Constructor.

PsSpectrumCountingSection - Class in eu.isas.peptideshaker.export.sections

This class outputs the spectrum counting related export features.

PsSpectrumCountingSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsSpectrumCountingSection

Constructor.

PsValidationSection - Class in eu.isas.peptideshaker.export.sections

This class outputs the validation related export features.

PsValidationSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.peptideshaker.export.sections.PsValidationSection

Constructor.

PsZipUtils - Class in eu.isas.peptideshaker.utils

This class contains information and methods to zip and unzip files from PeptideShaker.

PsZipUtils() - Constructor for class eu.isas.peptideshaker.utils.PsZipUtils

PtmSelectionDialog - Class in eu.isas.peptideshaker.gui.export

PTM location dialog for the Progenesis export.

PtmSelectionDialog(Frame, ArrayList<String>) - Constructor for class eu.isas.peptideshaker.gui.export.PtmSelectionDialog

Creates a new PtmSelectionDialog.

put(double, boolean) - Method in class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

Puts a new point in the target/decoy map at the given score.

Q

QC_PLOTS_TAB_INDEX - Static variable in class eu.isas.peptideshaker.gui.PeptideShakerGUI

The QC Plots tab index.

QCPanel - Class in eu.isas.peptideshaker.gui.tabpanels

This panel will display QC statistics for the current project.

QCPanel(PeptideShakerGUI) - Constructor for class eu.isas.peptideshaker.gui.tabpanels.QCPanel

Creates a new QCPanel.

QuickGoTerm() - Constructor for class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel.QuickGoTerm

R

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 FollowUpCLIInputBean from an Apache CLI instance.

ReportCLIParams - Enum in eu.isas.peptideshaker.cmd

This class provides the available reports as command line parameters.

reportExportNeeded() - Method in class eu.isas.peptideshaker.cmd.ReportCLIInputBean

Indicates whether a report export is required by the user.

reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel

Reset the peptide keys.

reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel

Resets the peptide keys.

reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel

Reset the protein keys.

reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel

Reset the protein keys.

reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel

Reset the protein keys.

reset() - Method in class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel

Resets the peptide keys.

resetAdvocateContributions() - 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.

rtBinSize - Static variable in class eu.isas.peptideshaker.recalibration.RunMzDeviation

The bin size in retention time in number of MS/MS spectra.

run() - Method in class eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable

run() - Method in class eu.isas.peptideshaker.fileimport.PsmImportRunnable

run() - Method in class eu.isas.peptideshaker.processing.PsmProcessorRunnable

run() - Method in class eu.isas.peptideshaker.stirred.modules.StirRunnable

run() - Method in class eu.isas.peptideshaker.stirred.Stirred

Runs the stirred process.

RunMzDeviation - Class in eu.isas.peptideshaker.recalibration

This class computes the mz deviations for a a given run (i.e.

RunMzDeviation(String, Identification, SequenceProvider, SpectrumProvider, IdentificationParameters, WaitingHandler) - Constructor for class eu.isas.peptideshaker.recalibration.RunMzDeviation

Creates a map of m/z deviations for a given run.

S

saveAs(File, WaitingHandler, Identification, IdentificationParameters, SequenceProvider, ProteinDetailsProvider, SpectrumCountingParameters, ProjectDetails, FilterParameters, Metrics, GeneMaps, ProjectType, IdentificationFeaturesCache, boolean, DisplayParameters, File) - Static method in class eu.isas.peptideshaker.export.PsdbExporter

Saves the given data in a psdb file.

SaveDialog - Class in eu.isas.peptideshaker.gui

A dialog for displaying the various save/export options.

SaveDialog(PeptideShakerGUI, boolean) - Constructor for class eu.isas.peptideshaker.gui.SaveDialog

Create a new SaveDialog.

saveFactory(PSExportFactory) - Static method in class eu.isas.peptideshaker.export.PSExportFactory

Saves the factory in the user folder.

saveProject(boolean, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Saves the modifications made to the project.

saveProject(WaitingHandler, boolean) - Method in class eu.isas.peptideshaker.utils.PsdbParent

Saves the project in the psdb file.

saveProjectAs(boolean, boolean) - Method in class eu.isas.peptideshaker.gui.PeptideShakerGUI

Save the project to a new location.

saveUserParameters() - Method in class eu.isas.peptideshaker.preferences.UserPreferencesParent

Saves the user preferences.

scorePeptidePtms(Identification, ModificationProvider, WaitingHandler, IdentificationParameters) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer

Scores the PTMs of all peptide matches contained in an identification object.

scorePsms(Identification, InputMap, ProcessingParameters, IdentificationParameters, WaitingHandler) - Method in class eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer

Attaches a score to the PSMs.

scorePTMs(Identification, PeptideMatch, IdentificationParameters, ModificationProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer

Scores the PTMs for a peptide match.

scorePTMs(Identification, ProteinMatch, IdentificationParameters, boolean, ModificationProvider, WaitingHandler) - Method in class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer

Scores PTMs in a protein match.

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.

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

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