Index

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

A

addExcludingPtm(String) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Adds an excluding PTM.

addExportScheme(ExportScheme) - Method in class eu.isas.reporter.export.report.ReporterExportFactory

addPeptideClass(String) - Method in class eu.isas.reporter.settings.ClusteringSettings

Adds a class to the selected classes.

addPeptideMatchQuantificationDetails(int, Long, PeptideQuantificationDetails) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Adds peptide quantification details ratio to the cache.

addProteinClass(String) - Method in class eu.isas.reporter.settings.ClusteringSettings

Adds a class to the selected classes.

addProteinMatchQuantificationDetails(int, long, ProteinQuantificationDetails) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Adds protein quantification details to the cache.

addPsmClass(String) - Method in class eu.isas.reporter.settings.ClusteringSettings

Adds a class to the selected classes.

addPSMQuantificationDetails(String, String, PsmQuantificationDetails) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Adds PSM quantification details ratio to the cache.

addPtmQuantificationDetails(String, long, int, ProteinPtmQuantificationDetails) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Adds protein level PTM quantification details to the cache.

addSpectrumQuantificationDetails(String, String, SpectrumQuantificationDetails) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Adds spectrum quantification details ratio to the cache.

AGREEMENT - Static variable in class eu.isas.reporter.gui.resultpanels.OverviewPanel

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.reporter.gui.resultpanels.OverviewPanel

Static index for the ID software agreement: the ID softwares all have the same top ranking peptide.

all - Enum constant in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

ALL - Enum constant in enum eu.isas.reporter.cli.PathSettingsCLIParams

autoResizeComponents() - Method in class eu.isas.reporter.gui.resultpanels.OverviewPanel

Set the optimal size of the components.

C

call() - Method in class eu.isas.reporter.cli.PathSettingsCLI

Sets the path settings and returns null.

call() - Method in class eu.isas.reporter.cli.ReportCLI

Calling this method will run the configured Reporter process.

call() - Method in class eu.isas.reporter.cli.ReporterCLI

catchException(Exception) - Method in class eu.isas.reporter.gui.ReporterGUI

Method called whenever an exception is caught.

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

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

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

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

Check for new version.

checkForNewVersion() - Method in class eu.isas.reporter.gui.ReporterGUI

Check for new version.

clearData(boolean) - Method in class eu.isas.reporter.gui.ReporterGUI

Clear the data from the previous experiment.

clearPeptideClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Clears the peptide classes.

clearProteinClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Clears the protein classes.

clearPsmClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Clears the peptide classes.

CLIExportMethods - Class in eu.isas.reporter.cli

This class groups standard methods used by the different command line interfaces.

CLIExportMethods() - Constructor for class eu.isas.reporter.cli.CLIExportMethods

clone() - Method in class eu.isas.reporter.settings.NormalizationSettings

clone() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

clone() - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

clone() - Method in class eu.isas.reporter.settings.ReporterPreferences

clone() - Method in class eu.isas.reporter.settings.ReporterSettings

close(Identification) - Static method in class eu.isas.reporter.cli.ReporterCLI

Close the Reporter instance.

closePeptideShaker() - Method in class eu.isas.reporter.cli.ReportCLI

Close the Reporter instance by clearing up factories and cache.

closeReporter() - Method in class eu.isas.reporter.gui.ReporterGUI

Closes Reporter.

ClusterBuilder - Class in eu.isas.reporter.calculation.clustering

Methods for building clusters based on a reporter project.

ClusterBuilder() - Constructor for class eu.isas.reporter.calculation.clustering.ClusterBuilder

Constructor.

ClusterClassKey - Interface in eu.isas.reporter.calculation.clustering

Key for a cluster class.

ClusteringSettings - Class in eu.isas.reporter.settings

Settings for the clustering.

ClusteringSettings() - Constructor for class eu.isas.reporter.settings.ClusteringSettings

Constructor.

ClusteringSettingsDialog - Class in eu.isas.reporter.gui.settings.display

Clustering settings dialog.

ClusteringSettingsDialog(JFrame, ClusteringSettings, boolean) - Constructor for class eu.isas.reporter.gui.settings.display.ClusteringSettingsDialog

Constructor.

clusterProfiles(Identification, IdentificationParameters, SequenceProvider, SpectrumProvider, Metrics, ReporterIonQuantification, QuantificationFeaturesGenerator, DisplayPreferences, boolean, WaitingHandler) - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Clusters the profiles according to the given parameters.

CONFIG_FOLDER - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

CONFLICT - Static variable in class eu.isas.reporter.gui.resultpanels.OverviewPanel

Static index for the ID software agreement: the ID software have different top ranking peptides.

CONTAMINANTS - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

CorrectionMatrix - Class in eu.isas.reporter.calculation

A correction matrix contains the deisotoping coefficients as well as the labels to be corrected.

CorrectionMatrix(double[][], HashMap<Integer, String>, double) - Constructor for class eu.isas.reporter.calculation.CorrectionMatrix

Constructor.

createNewProject(PsdbParent, ReporterSettings, ReporterIonQuantification, ProcessingParameters, DisplayPreferences) - Method in class eu.isas.reporter.gui.ReporterGUI

Closes the currently opened project, open the new project dialog and loads the new project on the interface

createOptionsCLI(Options) - Method in class eu.isas.reporter.cli.IdentificationParametersCLI

createOptionsCLI(Options) - Static method in enum eu.isas.reporter.cli.PathSettingsCLIParams

Creates the options for the command line interface based on the possible values.

createOptionsCLI(Options) - Static method in enum eu.isas.reporter.cli.ReportCLIParams

Creates the options for the command line interface based on the possible values.

createOptionsCLI(Options) - Static method in enum eu.isas.reporter.cli.ReporterCLIParameters

Creates the options for the command line interface based on the possible values.

D

deactivateSelfUpdatingTableModels() - Method in class eu.isas.reporter.gui.resultpanels.OverviewPanel

Deactivates the self updating tables.

DEFAULT_REPORTER_ION_TOLERANCE_ITRAQ - Static variable in class eu.isas.reporter.io.ProjectImporter

The default reporter ion tolerance for TMT data.

DEFAULT_REPORTER_ION_TOLERANCE_TMT - Static variable in class eu.isas.reporter.io.ProjectImporter

The default reporter ion tolerance for TMT data.

deisotope(HashMap<String, IonMatch>, Spectrum, double, boolean) - Method in class eu.isas.reporter.calculation.Deisotoper

This method returns deisotoped intensities.

Deisotoper - Class in eu.isas.reporter.calculation

This class takes care of the deisotoping of reporter ion intensities.

Deisotoper(ReporterMethod, double) - Constructor for class eu.isas.reporter.calculation.Deisotoper

Constructor.

description - Variable in enum eu.isas.reporter.cli.PathSettingsCLIParams

The description of the command line option.

description - Variable in enum eu.isas.reporter.cli.ReportCLIParams

Explanation for the CLI parameter.

description - Variable in enum eu.isas.reporter.cli.ReporterCLIParameters

Explanation for the CLI parameter.

description - Variable in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

Description of the ratio type.

DisplayPreferences - Class in eu.isas.reporter.preferences

Reporter display preferences.

DisplayPreferences() - Constructor for class eu.isas.reporter.preferences.DisplayPreferences

Constructor.

DOCUMENTATION_TYPE - Enum constant in enum eu.isas.reporter.cli.ReportCLIParams

documentationExportNeeded() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Indicates whether a documentation export is required by the user.

downloadSearchGUI() - Method in class eu.isas.reporter.gui.WelcomeDialog

Download SearchGUI.

E

emptyPTMList() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Empty the list of ignored PTMs.

estimatePeptideMatchQuantificationDetails(Identification, SpectrumProvider, QuantificationFeaturesGenerator, RatioEstimationSettings, ReporterIonQuantification, PeptideMatch, WaitingHandler) - Static method in class eu.isas.reporter.Reporter

Returns the quantification details of a peptide match.

estimateProteinMatchQuantificationDetails(Identification, SpectrumProvider, IdentificationFeaturesGenerator, QuantificationFeaturesGenerator, RatioEstimationSettings, ReporterIonQuantification, SearchParameters, ProteinMatch, WaitingHandler) - Static method in class eu.isas.reporter.Reporter

Returns the quantification details of a protein match.

estimatePSMQuantificationDetails(Identification, SpectrumProvider, QuantificationFeaturesGenerator, ReporterIonSelectionSettings, RatioEstimationSettings, ReporterIonQuantification, Long) - Static method in class eu.isas.reporter.Reporter

Returns the quantification details of a PSM.

estimatePTMQuantificationDetails(Identification, SpectrumProvider, QuantificationFeaturesGenerator, RatioEstimationSettings, ReporterIonQuantification, SearchParameters, SequenceMatchingParameters, String, long, int, WaitingHandler) - Static method in class eu.isas.reporter.Reporter

Returns the quantification details of a PTM on a protein.//@TODO: discriminate peptides according to the neighboring sites?

estimateRatios(RatioEstimationSettings, ArrayList<Double>) - Static method in class eu.isas.reporter.calculation.RatioEstimator

Estimate the ratio resulting from the compilation of several ratios.

estimateSpectrumQuantificationDetails(Identification, SpectrumProvider, QuantificationFeaturesGenerator, ReporterIonQuantification, ReporterIonSelectionSettings, SpectrumMatch) - Static method in class eu.isas.reporter.Reporter

Returns the quantification details of a spectrum.

eu.isas.reporter - package eu.isas.reporter

Main package.

eu.isas.reporter.calculation - package eu.isas.reporter.calculation

Package containing classes used for the calculation.

eu.isas.reporter.calculation.clustering - package eu.isas.reporter.calculation.clustering

Package containing classes used for the clustering.

eu.isas.reporter.calculation.clustering.keys - package eu.isas.reporter.calculation.clustering.keys

Package containing classes used to index cluster classes.

eu.isas.reporter.calculation.normalization - package eu.isas.reporter.calculation.normalization

Package containing classes used for the quantification.

eu.isas.reporter.cli - package eu.isas.reporter.cli

Package containing the CLI classes.

eu.isas.reporter.export.report - package eu.isas.reporter.export.report

Package containing classes used for the generation of reports.

eu.isas.reporter.export.report.sections - package eu.isas.reporter.export.report.sections

Package containing classes used for the generation of export sections.

eu.isas.reporter.gui - package eu.isas.reporter.gui

Package containing the GUI classes used for the generation of exports.

eu.isas.reporter.gui.export - package eu.isas.reporter.gui.export

Package containing GUI classes used for the generation of exports.

eu.isas.reporter.gui.resultpanels - package eu.isas.reporter.gui.resultpanels

Package containing GUI classes used for the display of results.

eu.isas.reporter.gui.settings - package eu.isas.reporter.gui.settings

Package containing GUI classes used for the edition of settings.

eu.isas.reporter.gui.settings.display - package eu.isas.reporter.gui.settings.display

Package containing GUI classes used for the edition of the display settings.

eu.isas.reporter.gui.settings.quantification - package eu.isas.reporter.gui.settings.quantification

Package containing GUI classes used for the edition of the quantification settings.

eu.isas.reporter.gui.tablemodels - package eu.isas.reporter.gui.tablemodels

Package containing table models.

eu.isas.reporter.io - package eu.isas.reporter.io

Package containing classes used for saving and opening projects.

eu.isas.reporter.preferences - package eu.isas.reporter.preferences

Package containing the different preferences.

eu.isas.reporter.quantificationdetails - package eu.isas.reporter.quantificationdetails

Package containing the quantification objects at the different levels.

eu.isas.reporter.settings - package eu.isas.reporter.settings

Package containing the different settings.

eu.isas.reporter.utils - package eu.isas.reporter.utils

Package containing util classes.

EXPORT_FOLDER - Enum constant in enum eu.isas.reporter.cli.ReportCLIParams

EXPORT_PREFIX - Enum constant in enum eu.isas.reporter.cli.ReportCLIParams

exportDocumentation(ReportCLIInputBean, String, WaitingHandler) - Static method in class eu.isas.reporter.cli.CLIExportMethods

Writes the documentation corresponding to an export given the command line arguments.

exportNeeded() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Indicates whether a report export is needed.

exportReport(ReportCLIInputBean, String, String, ProjectDetails, Identification, GeneMaps, IdentificationFeaturesGenerator, SequenceProvider, SpectrumProvider, ProteinDetailsProvider, QuantificationFeaturesGenerator, ReporterIonQuantification, ReporterSettings, IdentificationParameters, int, SpectrumCountingParameters, WaitingHandler) - Static method in class eu.isas.reporter.cli.CLIExportMethods

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

extractAndUpdatePathOptions(String[]) - Static method in class eu.isas.reporter.cli.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.

G

geneMaps - Variable in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

The gene maps.

getAnnotationParameters() - Method in class eu.isas.reporter.settings.ReporterSettings

Returns the spectrum annotation parameters.

getBestReporterIonMatch(ReporterIon, int, Spectrum, double, boolean) - Static method in class eu.isas.reporter.Reporter

Returns the best reporter ion match based on mass accuracy.

getClassesColors() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the classes color coding.

getClusterBuilder() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the cluster builder.

getClusteringSettings() - Method in class eu.isas.reporter.gui.settings.display.ClusteringSettingsDialog

Returns the clustering settings as set by the user.

getClusteringSettings() - Method in class eu.isas.reporter.preferences.DisplayPreferences

Returns the clustering settings.

getColor(String) - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the color corresponding to a cluster class.

getColumnClass(int) - Method in class eu.isas.reporter.gui.tablemodels.PeptideTableModel

getColumnClass(int) - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

getColumnClass(int) - Method in class eu.isas.reporter.gui.tablemodels.PsmTableModel

getColumnCount() - Method in class eu.isas.reporter.gui.tablemodels.PeptideTableModel

getColumnCount() - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

getColumnCount() - Method in class eu.isas.reporter.gui.tablemodels.PsmTableModel

getColumnName(int) - Method in class eu.isas.reporter.gui.tablemodels.PeptideTableModel

getColumnName(int) - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

getColumnName(int) - Method in class eu.isas.reporter.gui.tablemodels.PsmTableModel

getCommandLineDescription() - Static method in enum eu.isas.reporter.calculation.normalization.NormalizationType

Returns the different options as command line description.

getCommandLineDescription() - Static method in enum eu.isas.reporter.settings.ReporterIonsLocationType

Returns the different options as command line description.

getCommandLineOptions() - Method in class eu.isas.reporter.export.report.ReporterExportFactory

Returns the list of implemented reports as command line option.

getConfigFolder() - Static method in class eu.isas.reporter.Reporter

Returns the folder where the configuration files are stored.

getContaminants() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the file containing the contaminants.

getContaminants(SearchParameters, FastaParameters, PeptideVariantsParameters, WaitingHandler) - Method in class eu.isas.reporter.settings.NormalizationSettings

Returns the accessions of the contaminants as a set taken from the contaminantsFastaFile.

getContaminantsFastaFile() - Method in class eu.isas.reporter.settings.NormalizationSettings

Returns the FASTA file containing the contaminant proteins.

getDefaultClusterMetrics(IdentificationParameters, Identification) - Static method in class eu.isas.reporter.io.ProjectImporter

Returns the cluster metrics for a given project.

getDefaultContaminantFile() - Static method in class eu.isas.reporter.settings.NormalizationSettings

Returns the default contaminants file.

getDefaultDocumentation(String) - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

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

getDefaultExportSchemesNames() - Method in class eu.isas.reporter.export.report.ReporterExportFactory

Returns a list of the default export schemes.

getDefaultReporterIonQuantification(IdentificationParameters) - Static method in class eu.isas.reporter.io.ProjectImporter

Returns the default reporter ion quantification based on the identification parameters.

getDefaultReporterSettings(ReporterMethod, IdentificationParameters) - Static method in class eu.isas.reporter.io.ProjectImporter

Returns the default reporter settings as inferred from the identification parameters.

getDefaultReporterSettings(ReporterMethod, IdentificationParameters, ReporterSettings) - Static method in class eu.isas.reporter.io.ProjectImporter

Returns the default reporter settings as inferred from the identification parameters.

getDefaultReportName(String, String) - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

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

getDefaultSettings() - Method in class eu.isas.reporter.settings.ReporterPreferences

Returns the default settings.

getDeisotopedIntensity(String) - Method in class eu.isas.reporter.quantificationdetails.SpectrumQuantificationDetails

Returns the intensity of the given sample.

getDeisotoper(ReporterMethod, double) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Returns the deisotoper corresponding to the given method.

getDescription() - Method in interface eu.isas.reporter.calculation.clustering.ClusterClassKey

Returns the description of the cluster class.

getDescription() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

getDescription() - Method in class eu.isas.reporter.calculation.clustering.keys.ProteinClusterClassKey

getDescription() - Method in class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

getDescription() - Method in enum eu.isas.reporter.preferences.ReporterPathPreferences.ReporterPathKey

getDimension() - Method in class eu.isas.reporter.calculation.CorrectionMatrix

Returns the dimension of the correction matrix.

getDisplayFeaturesGenerator() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the display features generator.

getDisplayParameters() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the display parameters.

getDisplayPreferences() - Method in class eu.isas.reporter.io.ProjectImporter

Returns the display preferences.

getDocumentationTypes() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Returns the type of documentation required by the user.

getEnzymesFile() - Static method in class eu.isas.reporter.Reporter

Returns the enzymes file.

getErrorKeys(String) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Returns a list containing the keys of the paths where the tool is not able to write.

getExceptionHandler() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the exception handler.

getExcludingPtms() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Returns the list of PTMs to ignore.

getExportFeatures(String, boolean) - Method in class eu.isas.reporter.export.report.ReporterExportFactory

getExportScheme(String) - Method in class eu.isas.reporter.export.report.ReporterExportFactory

getExportTypeFromCommandLineOption(int) - Method in class eu.isas.reporter.export.report.ReporterExportFactory

Returns the export type based on the number used in command line.

getFeature(Identification, SpectrumProvider, QuantificationFeaturesGenerator, ReporterIonQuantification, ReporterSettings, long, ReporterPsmFeatures, String) - Static method in class eu.isas.reporter.export.report.sections.ReporterPsmSection

Returns the report component corresponding to a feature at a given channel.

getFeature(SpectrumProvider, QuantificationFeaturesGenerator, ReporterIonQuantification, long, ReporterProteinFeatures, String, WaitingHandler) - Static method in class eu.isas.reporter.export.report.sections.ReporterProteinSection

Returns the report component corresponding to a feature at a given channel.

getFeature(SpectrumProvider, QuantificationFeaturesGenerator, ReporterIonQuantification, PeptideMatch, ReporterPeptideFeature, String, WaitingHandler) - Static method in class eu.isas.reporter.export.report.sections.ReporterPeptideSection

Returns the report component corresponding to a feature at a given channel.

getFile() - Method in class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

Returns the spectrum file.

getFilteredPeptides() - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the peptide keys retained after filtering.

getFilteredProteins() - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the protein keys retained after filtering.

getFilteredPsms() - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the PSM keys retained after filtering.

getFilterParameters() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the filter parameters.

getForbiddenPtms() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Returns the PTMs not carried by the peptide.

getForbiddenPtmsAsSet() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Returns the forbidden PTMs as a set.

getGeneMaps() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the gene maps of the loaded project.

getHeaderHeight() - Method in class eu.isas.reporter.export.report.ReporterReportStyle

getHeaderStyle() - Method in class eu.isas.reporter.export.report.ReporterReportStyle

getHeaderStyle(int) - Method in class eu.isas.reporter.export.report.ReporterReportStyle

getId() - Method in enum eu.isas.reporter.preferences.ReporterPathPreferences.ReporterPathKey

getIdentification() - Method in class eu.isas.reporter.gui.NewDialog

Returns the identification displayed.

getIdentification() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the identification of the psdb file.

getIdentificationDisplayPreferences() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the identification display preferences.

getIdentificationFeaturesGenerator() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the identification features generator.

getIdentificationParameters() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the identification parameters.

getIdentificationParameters() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the identification parameters.

getIdentificationParametersFile() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the identification parameters file.

getIgnoredPtms() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the list of PTMs to ignore.

getIgnoreMc() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns a boolean indicating whether peptides presenting missed cleavages should be ignored.

getIgnoreNull() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns a boolean indicating whether peptides presenting null intensities should be ignored.

getImplementedSections() - Method in class eu.isas.reporter.export.report.ReporterExportFactory

getIndexOfSelectedItem() - Method in class eu.isas.reporter.gui.JumpToPanel

Returns the index of the selected item.

getInstance() - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

Static method to get the instance of the factory.

getIsotopesFile() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the isotope correction file, null if not set.

getJarFilePath() - Method in class eu.isas.reporter.cli.PathSettingsCLI

Returns the path to the jar file.

getJarFilePath() - Static method in class eu.isas.reporter.Reporter

Returns the path to the jar file.

getJsonFile() - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

Returns the file where to save the implemented export schemes.

getJsonFolder() - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

Returns the folder where to save the implemented export schemes.

getKeyFromId(String) - Static method in enum eu.isas.reporter.preferences.ReporterPathPreferences.ReporterPathKey

Returns the key from its id.

getKMeansClusteringSettings() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the k-means clustering settings.

getkMeansClutering() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the k-means clustering results.

getLastSelectedFolder() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the last selected folder.

getLogFolder() - Method in class eu.isas.reporter.cli.PathSettingsCLIInputBean

Returns the folder where to save the log files.

getMainTitleRowHeight() - Method in class eu.isas.reporter.export.report.ReporterReportStyle

getMainTitleStyle() - Method in class eu.isas.reporter.export.report.ReporterReportStyle

getMatchesFolder() - Static method in class eu.isas.reporter.Reporter

Returns the file containing the database.

getMaxRatio() - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the maximal ratio included in the clusters.

getMethodsFile() - Method in class eu.isas.reporter.gui.NewDialog

Returns the current methods file.

getMethodsFile() - Static method in class eu.isas.reporter.Reporter

Returns the default methods file.

getMetrics() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the metrics saved while loading the files.

getMinRatio() - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the minimal ratio included in the clusters.

getMinUnique() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the minimum number of unique peptides to consider only those for a protein group ratio estimation.

getMinUnique() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Returns the minimal number of unique peptides required for a protein, ignored if negative.

getMostAccurate() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Indicates whether the most accurate reporter ion should be used.

getName() - Method in interface eu.isas.reporter.calculation.clustering.ClusterClassKey

Returns the name of the cluster class.

getName() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

getName() - Method in class eu.isas.reporter.calculation.clustering.keys.ProteinClusterClassKey

getName() - Method in class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

getNonSelectedColor(String) - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the color for a non-selected line of this class.

getNormalizationSettings() - Method in class eu.isas.reporter.gui.settings.quantification.NormalizationSettingsDialog

Returns the settings as set by the user.

getNormalizationSettings() - Method in class eu.isas.reporter.settings.ReporterSettings

Returns the normalization settings.

getNormalizationType(int) - Static method in enum eu.isas.reporter.calculation.normalization.NormalizationType

Returns the normalization type corresponding to the given index.

getNormalizationType(String) - Static method in enum eu.isas.reporter.calculation.normalization.NormalizationType

Returns the normalization type corresponding to the given name.

getnThreads() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the number of threads to use.

getOptionIDs() - Static method in enum eu.isas.reporter.cli.PathSettingsCLIParams

Returns the list of supported command line options.

getOptionsAsString() - Method in class eu.isas.reporter.cli.IdentificationParametersCLI

getOptionsAsString() - Static method in enum eu.isas.reporter.cli.PathSettingsCLIParams

Returns the options as a string.

getOptionsAsString() - Static method in enum eu.isas.reporter.cli.ReportCLIParams

Returns the options as a string.

getOptionsAsString() - Static method in enum eu.isas.reporter.cli.ReporterCLIParameters

Returns the options as a string.

getOutputFile() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the output file where to save the project, null if not set.

getOutputOptionsAsString() - Static method in enum eu.isas.reporter.cli.ReportCLIParams

Returns the output options as a string.

getPathPreference(ReporterPathPreferences.ReporterPathKey, String) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Returns the path according to the given key and path.

getPaths() - Method in class eu.isas.reporter.cli.PathSettingsCLIInputBean

Returns the specific paths provided by the user in a map: Path id > path.

getPathSettingsCLIInputBean() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Returns the path settings provided by the user.

getPathSettingsCLIInputBean() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the path settings provided by the user.

getPeptideClasses(Long) - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the cluster classes corresponding to a peptide match.

getPeptideClassKey(String) - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the class key corresponding to the given name.

getPeptideIndex(Long) - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the index of the cluster of the given peptide key.

getPeptideKeysMap() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns a map of the possible keys indexed by their toString() representation.

getPeptideMatchQuantificationDetails(int, Long) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Returns peptide quantification details, null if not in cache.

getPeptideMatchQuantificationDetails(SpectrumProvider, PeptideMatch, WaitingHandler) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Returns the quantification details of a peptide match.

getPeptideNormalization() - Method in class eu.isas.reporter.settings.NormalizationSettings

Returns the type of normalization used to normalize the peptides.

getPeptideNormalizationType() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the peptide normalization.

getPeptideShakerFile() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the PeptideShaker file.

getPeptideValidationLevel() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Indicates the validation level to require for peptide quantification.

getPercentile() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the percentile for ratio window estimation.

getPercentile() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Returns the share in percent of ratios considered to set the width of the maximum likelihood estimators.

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

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

getPossiblePeptideClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the possible peptide classes names.

getPossibleProteinClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the possible protein classes names.

getPossiblePsmClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the possible PSM classes names.

getPossiblePtms() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Returns the PTMs possibly carried by the peptides.

getPossiblePtmsAsSet() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Returns the possible PTMs as a set.

getPrecMzTolerance() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the m/z tolerance to use for the precursor ion window.

getPrecMzTolerancePpm() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Indicates whether the precursor ion window m/z tolerance is in ppm.

getPrecRtTolerance() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the RT tolerance to use for the precursor ion window in seconds.

getPrecursorMzTolerance() - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Returns the precursor m/Z tolerance used to match quantification spectra to identification spectra.

getPrecursorRTTolerance() - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Returns the precursor RT tolerance used to match quantification spectra to identification spectra.

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

Gets the preferred width of the column specified by colIndex.

getProjectDetails() - Method in class eu.isas.reporter.gui.NewDialog

Returns the project details.

getProjectDetails() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the project details.

getProjectDetails() - Method in class eu.isas.reporter.settings.ReporterSettings

Returns the project details.

getProjectParameters() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the project parameters.

getProteinClasses(Long) - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the cluster classes corresponding to a protein match.

getProteinClassKey(String) - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the class key corresponding to the given name.

getProteinDetailsProvider() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the protein details provider.

getProteinIndex(Long) - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the index of the cluster of the given protein key.

getProteinKeysMap() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns a map of the possible keys indexed by their toString() representation.

getProteinMatchQuantificationDetails(int, long) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Returns protein quantification details, null if not in cache.

getProteinMatchQuantificationDetails(SpectrumProvider, long, WaitingHandler) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Returns the quantification details of a protein match.

getProteinNormalization() - Method in class eu.isas.reporter.settings.NormalizationSettings

Returns the type of normalization used to normalize the proteins.

getProteinNormalizationType() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the protein normalization.

getProteinRatioType() - Method in class eu.isas.reporter.preferences.DisplayPreferences

Returns the index of the selected protein ratio type to display.

getProteinRatioType(int) - Static method in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

Returns the ratio type corresponding to the given index.

getProteinValidationLevel() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Indicates the validation level to require for protein quantification.

getPsdbBean() - Method in class eu.isas.reporter.gui.NewDialog

Returns the psdb parent object providing all information contained in the psdb file

getPsdbFile() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Returns the psdb file from which the information can be obtained.

getPsmClasses(Long) - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the cluster classes corresponding to a PSM.

getPsmClassKey(String) - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the class key corresponding to the given name.

getPsmIndex(Long) - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the index of the cluster of the given PSM key.

getPsmKeysMap() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns a map of the possible keys indexed by their toString() representation.

getPsmNormalization() - Method in class eu.isas.reporter.settings.NormalizationSettings

Returns the type of normalization used to normalize the PSMs.

getPsmNormalizationType() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the PSM normalization.

getPSMQuantificationDetails(SpectrumProvider, Long) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Returns the quantification details of a PSM.

getPSMQuantificationDetails(String, String) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Returns PSM quantification details, null if not in cache.

getPsmValidationLevel() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Indicates the validation level to require for PSM quantification.

getPtmQuantificationDetails(String, long, int) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Returns protein level PTM quantification details, null if not in cache.

getPTMQuantificationDetails(SpectrumProvider, String, long, int, WaitingHandler) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Returns the quantification details of a PTM.

getQuantificationFeaturesCache() - Method in class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Returns the quantification features cache.

getQuantificationFeaturesGenerator() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the quantification features generator.

getRatio(String) - Method in class eu.isas.reporter.quantificationdetails.ProteinPtmQuantificationDetails

Returns the ratio of a given sample.

getRatio(String) - Method in class eu.isas.reporter.quantificationdetails.SpectrumQuantificationDetails

Returns the ratio of a given sample.

getRatio(String, NormalizationFactors) - Method in class eu.isas.reporter.quantificationdetails.PeptideQuantificationDetails

Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors.

getRatio(String, NormalizationFactors) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors.

getRatio(String, NormalizationFactors) - Method in class eu.isas.reporter.quantificationdetails.PsmQuantificationDetails

Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors.

getRatioAmplitude() - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Returns the maximal value between the absolute value of the min and max ratios.

getRatioEstimationSettings() - Method in class eu.isas.reporter.gui.settings.quantification.RatioEstimationSettingsDialog

Returns the settings as set by the user.

getRatioEstimationSettings() - Method in class eu.isas.reporter.settings.ReporterSettings

Returns the ratio estimation settings.

getRatioResolution() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Returns the ratio resolution.

getRawRatio(String) - Method in class eu.isas.reporter.quantificationdetails.PeptideQuantificationDetails

Returns the raw (not normalized) ratio of a given sample.

getRawRatio(String) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Returns the raw (not normalized) ratio of a given sample.

getRawRatio(String) - Method in class eu.isas.reporter.quantificationdetails.PsmQuantificationDetails

Returns the raw (not normalized) ratio of a given sample.

getReagentMass(int) - Method in class eu.isas.reporter.calculation.CorrectionMatrix

Returns the mass affected by the given column of the matrix.

getReagentOrder() - Method in class eu.isas.reporter.gui.ReagentOrderDialog

Returns the new reagents order.

getReagents() - Method in class eu.isas.reporter.gui.NewDialog

Returns the reagents.

getReagents() - Method in class eu.isas.reporter.preferences.DisplayPreferences

Returns the reagents in the user defined order.

getReagentsNames() - Method in class eu.isas.reporter.calculation.CorrectionMatrix

Returns the names of the reagents involved in the deisotoping by this matrix indexed by their isotopic number.

getReferenceSamples() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the list of reference samples indexed by ordered reagent mass, 1 is the first reagent.

getReportCLIInputBean() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the report export options required.

getReporterGui() - Method in class eu.isas.reporter.gui.NewDialog

getReporterIonQuantification() - Method in class eu.isas.reporter.gui.NewDialog

Returns the reporter ion quantification.

getReporterIonQuantification() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the reporter ion quantification.

getReporterIonQuantification() - Method in class eu.isas.reporter.io.ProjectImporter

Returns the reporter ion quantification object loaded from the file.

getReporterIonSelectionSettings() - Method in class eu.isas.reporter.gui.settings.quantification.ReporterIonSelectionSettingsDialog

Returns the settings as set by the user.

getReporterIonSelectionSettings() - Method in class eu.isas.reporter.settings.ReporterSettings

Returns the reporter ion selection settings.

getReporterIonsLocation() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Indicates whether the quantification peaks are in the same spectra as the identification peaks.

getReporterIonsLocation() - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Returns the reporter ions location.

getReporterIonsLocationType(int) - Static method in enum eu.isas.reporter.settings.ReporterIonsLocationType

Returns the reporter ions location type corresponding to the given index.

getReporterIonsLocationType(String) - Static method in enum eu.isas.reporter.settings.ReporterIonsLocationType

Returns the reporter ions location type corresponding to the given name.

getReporterIonsMzTolerance() - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Returns the tolerance used to match reporter ions.

getReporterIonTolerance() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the tolerance used for the reporter ion matching in the spectrum.

getReporterMethod() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the name of the reporter methods provided by the user.

getReporterSettings() - Method in class eu.isas.reporter.gui.NewDialog

Returns the reporter settings.

getReporterSettings() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the reporter settings.

getReporterSettings() - Method in class eu.isas.reporter.gui.settings.ReporterSettingsDialog

Returns the reporter settings as set by the user.

getReporterSettings() - Method in class eu.isas.reporter.io.ProjectImporter

Returns the reporter settings loaded from the file.

getReportNamePrefix() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Returns the report name prefix.

getReportOutputFolder() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Returns the report output folder.

getReportStyle(ExcelWriter) - Static method in class eu.isas.reporter.export.report.ReporterReportStyle

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

getReportTypes() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Returns the types of output required by the user.

getRepoterMatch(String) - Method in class eu.isas.reporter.quantificationdetails.SpectrumQuantificationDetails

Returns the reporter ion match of the given sample.

getResolution() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the resolution for ratio estimation.

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

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

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

getScoreAndConfidenceDecimalFormat() - Method in class eu.isas.reporter.gui.ReporterGUI

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

getSearchParameters() - Method in class eu.isas.reporter.gui.NewDialog

Returns the search parameters.

getSelectedMethod() - Method in class eu.isas.reporter.gui.NewDialog

Returns the selected method.

getSelectedPeptideClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the selected peptide cluster classes represented by their toString() method.

getSelectedPeptides() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the list of selected peptides.

getSelectedProteinClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the selected protein cluster classes represented by their toString() method.

getSelectedProteins() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the list of selected proteins.

getSelectedPsmClasses() - Method in class eu.isas.reporter.settings.ClusteringSettings

Returns the selected PSM cluster classes represented by their toString() method.

getSelectedPsms() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the list of selected PSMs.

getSequenceProvider() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the sequence provider.

getSharedRatio(String, NormalizationFactors) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors.

getSharedRawRatio(String) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Returns the shared raw (not normalized) ratio of a given sample.

getSparklineColor() - Method in class eu.isas.reporter.gui.ReporterGUI

Get the sparklines color.

getSparklineColorDoubtful() - Method in class eu.isas.reporter.gui.ReporterGUI

Get the not doubtful sparklines color.

getSparklineColorNonValidated() - Method in class eu.isas.reporter.gui.ReporterGUI

Get the non-validated sparklines color.

getSparklineColorNotFound() - Method in class eu.isas.reporter.gui.ReporterGUI

Get the not found sparklines color.

getSpectrumCountingParameters() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the spectrum counting parameters.

getSpectrumProvider() - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the spectrum provider.

getSpectrumProvider() - Method in class eu.isas.reporter.io.ProjectImporter

Returns the spectrum provider.

getSpectrumQuantificationDetails(SpectrumProvider, ReporterIonQuantification, ReporterIonSelectionSettings, SpectrumMatch) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Returns the quantification details of a spectrum.

getSpectrumQuantificationDetails(String, String) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Returns spectrum quantification details, null if not in cache.

getStableProteins() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the file containing the stable proteins.

getStableProteins(SearchParameters, FastaParameters, PeptideVariantsParameters, WaitingHandler) - Method in class eu.isas.reporter.settings.NormalizationSettings

Returns the accessions of the stable proteins as a set taken from the stableProteinsFastaFile.

getStableProteinsFastaFile() - Method in class eu.isas.reporter.settings.NormalizationSettings

Returns the FASTA file containing the stable proteins.

getStandardHeight() - Method in class eu.isas.reporter.export.report.ReporterReportStyle

getStandardStyle() - Method in class eu.isas.reporter.export.report.ReporterReportStyle

getStandardStyle(int) - Method in class eu.isas.reporter.export.report.ReporterReportStyle

getTempFolder() - Method in class eu.isas.reporter.cli.PathSettingsCLIInputBean

Returns the temp folder, an empty string if not set.

getTempFolderPath(File) - Static method in class eu.isas.reporter.Reporter

Returns the folder to use for temporary files.

getUniqueRatio(String, NormalizationFactors) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors.

getUniqueRawRatio(String) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Returns the unique raw (not normalized) ratio of a given sample.

getUserPreferences() - Static method in class eu.isas.reporter.settings.ReporterPreferences

Loads the quantification user preferences.

getUserPreferencesFile() - Static method in class eu.isas.reporter.settings.ReporterPreferences

Returns the file used to save the user preferences.

getUserPreferencesFolder() - Static method in class eu.isas.reporter.settings.ReporterPreferences

Returns the folder used to save the user preferences.

getUserSchemesNames() - Method in class eu.isas.reporter.export.report.ReporterExportFactory

Returns a list of the name of the available user schemes.

getUserSelectedFile(String, String, String, String, boolean) - Method in class eu.isas.reporter.gui.ReporterGUI

Returns the file selected by the user, or null if no file was selected.

getUtilitiesUserParameters() - Method in class eu.isas.reporter.gui.ReporterGUI

getValidationPeptide() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the validation level to use for peptides.

getValidationProtein() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the validation level to use for proteins.

getValidationPsm() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the validation level to use for PSMs.

getValueAt(int, int) - Method in class eu.isas.reporter.calculation.CorrectionMatrix

Returns the value of the matrix at row i and column j.

getValueAt(int, int) - Method in class eu.isas.reporter.gui.tablemodels.PeptideTableModel

getValueAt(int, int) - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

getValueAt(int, int) - Method in class eu.isas.reporter.gui.tablemodels.PsmTableModel

getVersion() - Method in class eu.isas.reporter.utils.Properties

Retrieves the version number set in the pom file.

getZipExport() - Method in class eu.isas.reporter.cli.ReporterCLIInputBean

Returns the file where to export the project as zip file.

H

hasArg - Variable in enum eu.isas.reporter.cli.ReportCLIParams

Boolean indicating whether the parameter has arguments.

hasInput() - Method in class eu.isas.reporter.cli.PathSettingsCLIInputBean

Indicates whether the user gave some path configuration input.

I

id - Variable in enum eu.isas.reporter.cli.PathSettingsCLIParams

The id of the command line option.

id - Variable in enum eu.isas.reporter.cli.ReportCLIParams

Short Id for the CLI parameter.

id - Variable in enum eu.isas.reporter.cli.ReporterCLIParameters

Short Id for the CLI parameter.

ID - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

IdentificationParametersCLI - Class in eu.isas.reporter.cli

The SearchParametersCLI allows creating search parameters files using command line arguments.

IdentificationParametersCLI(String[]) - Constructor for class eu.isas.reporter.cli.IdentificationParametersCLI

Construct a new SearchParametersCLI runnable from a list of arguments.

IGNORE_MC - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

IGNORE_NULL - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

IGNORE_PTMS - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

importPeptideShakerProject(PsdbParent, ArrayList<File>, WaitingHandler) - Method in class eu.isas.reporter.io.ProjectImporter

Imports the identification results from a PeptideShaker file.

importReporterProject(PsdbParent, WaitingHandler) - Method in class eu.isas.reporter.io.ProjectImporter

Loads the Reporter project.

index - Variable in enum eu.isas.reporter.calculation.normalization.NormalizationType

The index of the normalization type.

index - Variable in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

Index of the ratio type.

index - Variable in enum eu.isas.reporter.settings.ReporterIonsLocationType

The index of the reporter ions location type.

ION_TOL - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

isCanceled() - Method in class eu.isas.reporter.gui.settings.display.ClusteringSettingsDialog

Indicates whether the user clicked the cancel button.

isCanceled() - Method in class eu.isas.reporter.gui.settings.quantification.NormalizationSettingsDialog

Indicates whether the user canceled the editing.

isCanceled() - Method in class eu.isas.reporter.gui.settings.quantification.RatioEstimationSettingsDialog

Indicates whether the user canceled the editing.

isCanceled() - Method in class eu.isas.reporter.gui.settings.quantification.ReporterIonSelectionSettingsDialog

Indicates whether the user canceled the editing.

isCanceled() - Method in class eu.isas.reporter.gui.settings.ReporterSettingsDialog

Indicates whether the user canceled the editing.

isCancelled() - Method in class eu.isas.reporter.gui.NewDialog

Indicates whether the user canceled the project creation.

isCancelled() - Method in class eu.isas.reporter.gui.ReagentOrderDialog

Indicates whether the user canceled the dialog.

isCellEditable(int, int) - Method in class eu.isas.reporter.gui.tablemodels.PeptideTableModel

isCellEditable(int, int) - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

isCellEditable(int, int) - Method in class eu.isas.reporter.gui.tablemodels.PsmTableModel

isCTerm() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Indicates whether the peptide is C-term.

isEmpty() - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Indicates whether the cache is empty

isIgnoreMissedCleavages() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Returns a boolean indicating whether miscleaved peptides should be ignored.

isIgnoreNullIntensities() - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Returns a boolean indicating whether null intensities should be ignored.

isInstantiated() - Method in class eu.isas.reporter.gui.tablemodels.PeptideTableModel

Indicates whether the table content was instantiated.

isInstantiated() - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

Indicates whether the table content was instantiated.

isInstantiated() - Method in class eu.isas.reporter.gui.tablemodels.PsmTableModel

Indicates whether the table content was instantiated.

isMostAccurate() - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Returns a boolean indicating whether the most accurate ion should be retained for quantification.

isNotModified() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Indicates whether the peptides must be not modified.

isNTerm() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Indicates whether the peptide is N-term.

ISOTOPES - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

isPeptideValid(RatioEstimationSettings, Identification, SearchParameters, PeptideMatch) - Static method in class eu.isas.reporter.calculation.QuantificationFilter

Filters the peptide to be used for quantification according to the user quantification preferences.

isPrecursorMzPpm() - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Indicates whether the precursor matching tolerance is in ppm or in m/z

isProteinValid(RatioEstimationSettings, Identification, long) - Static method in class eu.isas.reporter.calculation.QuantificationFilter

Filters the protein to be used for quantification according to the user quantification preferences.

isPsmValid(RatioEstimationSettings, Identification, long) - Static method in class eu.isas.reporter.calculation.QuantificationFilter

Filters the PSMs to be used for quantification according to the user quantification preferences.

isRatioValid(RatioEstimationSettings, Double) - Static method in class eu.isas.reporter.calculation.QuantificationFilter

Filters out NaN and 0 ratios.

isSameAs(NormalizationSettings) - Method in class eu.isas.reporter.settings.NormalizationSettings

Indicates whether another setting is the same as this one.

isSameAs(RatioEstimationSettings) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Indicates whether another setting is the same as this one.

isSameAs(ReporterIonSelectionSettings) - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Indicates whether another setting is the same as this one.

isSameAs(ReporterPreferences) - Method in class eu.isas.reporter.settings.ReporterPreferences

Indicates whether another setting is the same as this one.

isSameAs(ReporterSettings) - Method in class eu.isas.reporter.settings.ReporterSettings

Indicates whether another setting is the same as this one.

isStarred() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Indicates whether the peptides must be starred.

isStarred() - Method in class eu.isas.reporter.calculation.clustering.keys.ProteinClusterClassKey

Indicates whether the proteins must be starred.

isStarred() - Method in class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

Indicates whether the PSMs must be starred.

isValidCommandLine(CommandLine) - Static method in class eu.isas.reporter.cli.ReporterCLI

Indicates whether the command line is valid.

J

JumpToPanel - Class in eu.isas.reporter.gui

A Jump To panel for use in the menu bar in the main frame.

JumpToPanel(ReporterGUI) - Constructor for class eu.isas.reporter.gui.JumpToPanel

Creates a new JumpToPanel.

JumpToPanel.JumpType - Enum in eu.isas.reporter.gui

Enum of the types of data to jump to.

L

LabellingEfficiencyDialog - Class in eu.isas.reporter.gui

Labeling efficiency dialog.

LabellingEfficiencyDialog(Dialog, JFrame, Image, Image, LastSelectedFolder) - Constructor for class eu.isas.reporter.gui.LabellingEfficiencyDialog

Constructor with a dialog as owner.

LINE_WIDTH - Static variable in class eu.isas.reporter.gui.resultpanels.OverviewPanel

The default line width for the line plots.

loadData(Identification, IdentificationParameters, SequenceProvider, SpectrumProvider, Metrics, DisplayPreferences, ReporterIonQuantification, QuantificationFeaturesGenerator, WaitingHandler) - Method in class eu.isas.reporter.calculation.clustering.ClusterBuilder

Filters the proteins and indexes them according to the clustering settings and stores the result in the attribute maps.

loadDataForRows(ArrayList<Integer>, WaitingHandler) - Method in class eu.isas.reporter.gui.tablemodels.PeptideTableModel

loadDataForRows(ArrayList<Integer>, WaitingHandler) - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

loadDataForRows(ArrayList<Integer>, WaitingHandler) - Method in class eu.isas.reporter.gui.tablemodels.PsmTableModel

loadFromFile(File) - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

Loads an export factory from a file.

LOADING_MESSAGE - Static variable in class eu.isas.reporter.preferences.DisplayPreferences

The text displayed in the cell of a table in case the data is not loaded.

loadPathParametersFromFile(File) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Loads the path preferences from a text file.

loadPathParametersFromLine(String) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Loads a path to be set from a line.

LOG_FOLDER - Enum constant in enum eu.isas.reporter.cli.PathSettingsCLIParams

M

main(String[]) - Static method in class eu.isas.reporter.cli.IdentificationParametersCLI

Starts the launcher by calling the launch method.

main(String[]) - Static method in class eu.isas.reporter.cli.PathSettingsCLI

Starts the launcher by calling the launch method.

main(String[]) - Static method in class eu.isas.reporter.cli.ReportCLI

Starts the launcher by calling the launch method.

main(String[]) - Static method in class eu.isas.reporter.cli.ReporterCLI

Starts the launcher by calling the launch method.

main(String[]) - Static method in class eu.isas.reporter.gui.ReporterGUI

main(String[]) - Static method in class eu.isas.reporter.ReporterWrapper

Starts the launcher by calling the launch method.

main(String[]) - Static method in class eu.isas.reporter.ReporterZipFileChecker

Start ReporterZipFileChecker.

main(String[]) - Static method in class eu.isas.reporter.utils.ReporterMerger

mandatory - Variable in enum eu.isas.reporter.cli.ReportCLIParams

Boolean indicating whether the parameter is mandatory.

mandatory - Variable in enum eu.isas.reporter.cli.ReporterCLIParameters

Boolean indicating whether the parameter is mandatory.

mean - Enum constant in enum eu.isas.reporter.calculation.normalization.NormalizationType

median - Enum constant in enum eu.isas.reporter.calculation.normalization.NormalizationType

memoryCheck() - Method in class eu.isas.reporter.calculation.QuantificationFeaturesCache

Indicates whether the memory used by the application is lower than a given share of the heap size.

mEstimate(RatioEstimationSettings, double[]) - Static method in class eu.isas.reporter.calculation.RatioEstimator

Returns the compilation of various ratios using a redescending M-estimator.

METHOD - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

MethodSettingsDialog - Class in eu.isas.reporter.gui

Dialog for setting the reporter method details.

MethodSettingsDialog(NewDialog, boolean) - Constructor for class eu.isas.reporter.gui.MethodSettingsDialog

Creates a new MethodSettingsDialog.

MIN_UNIQUE - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

minimizeChart() - Method in class eu.isas.reporter.gui.ReporterGUI

If a chart is maximized, then minimize it.

minimizeChart() - Method in class eu.isas.reporter.gui.resultpanels.OverviewPanel

If a chart is maximized, then minimize it.

mode - Enum constant in enum eu.isas.reporter.calculation.normalization.NormalizationType

MOST_ACCURATE - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

ms2Spectra - Enum constant in enum eu.isas.reporter.settings.ReporterIonsLocationType

The reporter ions are in the same MS2 spectrum.

ms3Spectra - Enum constant in enum eu.isas.reporter.settings.ReporterIonsLocationType

The reporter ions are in the related MS3 spectrum.

N

name - Variable in enum eu.isas.reporter.calculation.normalization.NormalizationType

The name of the normalization type.

name - Variable in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

Name of the ratio type.

name - Variable in enum eu.isas.reporter.settings.ReporterIonsLocationType

The name of the reporter ions location type.

names() - Static method in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

Returns an array of names of the different options.

NewDialog - Class in eu.isas.reporter.gui

This panel will be used to load the necessary files and settings to start the analysis.

NewDialog(ReporterGUI, boolean) - Constructor for class eu.isas.reporter.gui.NewDialog

Constructor.

NewDialog(WelcomeDialog, ReporterGUI, boolean) - Constructor for class eu.isas.reporter.gui.NewDialog

Constructor.

NO_ID - Static variable in class eu.isas.reporter.gui.resultpanels.OverviewPanel

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

none - Enum constant in enum eu.isas.reporter.calculation.normalization.NormalizationType

NORMALIZATION_PEPTIDE - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

NORMALIZATION_PROTEIN - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

NORMALIZATION_PSM - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

NormalizationSettings - Class in eu.isas.reporter.settings

Settings used for the normalization.

NormalizationSettings() - Constructor for class eu.isas.reporter.settings.NormalizationSettings

Constructor.

NormalizationSettingsDialog - Class in eu.isas.reporter.gui.settings.quantification

The preferences dialog.

NormalizationSettingsDialog(JDialog, NormalizationSettings, boolean) - Constructor for class eu.isas.reporter.gui.settings.quantification.NormalizationSettingsDialog

Creates a new NormalizationSettingsDialog.

NormalizationType - Enum in eu.isas.reporter.calculation.normalization

Enum for the different normalization types supported.

Normalizer - Class in eu.isas.reporter.calculation.normalization

Normalizes the ratios according to the NormalizationSettings.

Normalizer() - Constructor for class eu.isas.reporter.calculation.normalization.Normalizer

O

OUT - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

OverviewPanel - Class in eu.isas.reporter.gui.resultpanels

The Overview tab.

OverviewPanel(ReporterGUI) - Constructor for class eu.isas.reporter.gui.resultpanels.OverviewPanel

Creates a new OverviewPanel.

P

PARTIALLY_MISSING - Static variable in class eu.isas.reporter.gui.resultpanels.OverviewPanel

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.reporter.cli

Allows the user to set the path settings in command line.

PathSettingsCLI(PathSettingsCLIInputBean) - Constructor for class eu.isas.reporter.cli.PathSettingsCLI

Constructor.

PathSettingsCLIInputBean - Class in eu.isas.reporter.cli

Parses the command line and retrieves the user input.

PathSettingsCLIInputBean(CommandLine) - Constructor for class eu.isas.reporter.cli.PathSettingsCLIInputBean

Construct a FollowUpCLIInputBean from an Apache CLI instance.

PathSettingsCLIParams - Enum in eu.isas.reporter.cli

Parameters for the path settings command line.

PeptideClusterClassKey - Class in eu.isas.reporter.calculation.clustering.keys

Key for the class of a peptide cluster.

PeptideClusterClassKey() - Constructor for class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Constructor.

PeptideQuantificationDetails - Class in eu.isas.reporter.quantificationdetails

This class contains the quantitative information at the peptide level.

PeptideQuantificationDetails() - Constructor for class eu.isas.reporter.quantificationdetails.PeptideQuantificationDetails

PeptideTableModel - Class in eu.isas.reporter.gui.tablemodels

Model for the peptide table.

PeptideTableModel() - Constructor for class eu.isas.reporter.gui.tablemodels.PeptideTableModel

Constructor which sets a new empty table.

PeptideTableModel(Identification, SpectrumProvider, IdentificationFeaturesGenerator, ReporterIonQuantification, QuantificationFeaturesGenerator, DisplayFeaturesGenerator, DisplayPreferences, IdentificationParameters, String, long[], boolean, ExceptionHandler) - Constructor for class eu.isas.reporter.gui.tablemodels.PeptideTableModel

Constructor which sets a new table.

PERCENTILE - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

PREC_WINDOW_MZ_TOL - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

PREC_WINDOW_MZ_TOL_PPM - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

PREC_WINDOW_RT_TOL - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

precursorMatching - Enum constant in enum eu.isas.reporter.settings.ReporterIonsLocationType

The reporter ions are found by matching on mass and retention time.

ProjectDetails - Class in eu.isas.reporter.preferences

This class contains the reporter details on the project.

ProjectDetails() - Constructor for class eu.isas.reporter.preferences.ProjectDetails

ProjectImporter - Class in eu.isas.reporter.io

Imports a project from a psdb file.

ProjectImporter() - Constructor for class eu.isas.reporter.io.ProjectImporter

Constructor.

ProjectImporter(Dialog) - Constructor for class eu.isas.reporter.io.ProjectImporter

Constructor.

ProjectSaver - Class in eu.isas.reporter.io

This class can be used to save the Reporter projects in a psdb file.

ProjectSaver() - Constructor for class eu.isas.reporter.io.ProjectSaver

Properties - Class in eu.isas.reporter.utils

This class contains many of the properties that are used during the use of the tool, but that are not stored in the UserProperties.prop file between each run of the program.

Properties() - Constructor for class eu.isas.reporter.utils.Properties

Creates a new empty Properties object.

proteinAndPeptides - Enum constant in enum eu.isas.reporter.gui.JumpToPanel.JumpType

ProteinClusterClassKey - Class in eu.isas.reporter.calculation.clustering.keys

Key for the class of a protein cluster.

ProteinClusterClassKey() - Constructor for class eu.isas.reporter.calculation.clustering.keys.ProteinClusterClassKey

Constructor.

ProteinPtmQuantificationDetails - Class in eu.isas.reporter.quantificationdetails

This class contains the quantitative information at the GO level.

ProteinPtmQuantificationDetails() - Constructor for class eu.isas.reporter.quantificationdetails.ProteinPtmQuantificationDetails

ProteinQuantificationDetails - Class in eu.isas.reporter.quantificationdetails

This class contains the quantitative information at the protein level.

ProteinQuantificationDetails() - Constructor for class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

ProteinRatioType - Enum in eu.isas.reporter.quantificationdetails

Enum for the protein ratio types.

ProteinTableModel - Class in eu.isas.reporter.gui.tablemodels

Model for the protein table.

ProteinTableModel() - Constructor for class eu.isas.reporter.gui.tablemodels.ProteinTableModel

Constructor for an empty table.

ProteinTableModel(Identification, IdentificationFeaturesGenerator, ProteinDetailsProvider, SequenceProvider, GeneMaps, ReporterIonQuantification, QuantificationFeaturesGenerator, DisplayFeaturesGenerator, DisplayPreferences, ExceptionHandler, long[]) - Constructor for class eu.isas.reporter.gui.tablemodels.ProteinTableModel

Constructor.

PSDB_FILE - Enum constant in enum eu.isas.reporter.cli.ReportCLIParams

PsmClusterClassKey - Class in eu.isas.reporter.calculation.clustering.keys

Key for the class of a PSM cluster.

PsmClusterClassKey() - Constructor for class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

Constructor.

PsmQuantificationDetails - Class in eu.isas.reporter.quantificationdetails

This class contains the quantitative information at the PSM level.

PsmQuantificationDetails() - Constructor for class eu.isas.reporter.quantificationdetails.PsmQuantificationDetails

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

Model for the PSM table.

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

Constructor which sets a new empty table.

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

Constructor which sets a new table.

Q

QuantificationFeaturesCache - Class in eu.isas.reporter.calculation

The quantification features cache stores quantification features.

QuantificationFeaturesCache() - Constructor for class eu.isas.reporter.calculation.QuantificationFeaturesCache

Constructor.

QuantificationFeaturesGenerator - Class in eu.isas.reporter.calculation

The quantification features generator provides various quantification features.

QuantificationFeaturesGenerator(QuantificationFeaturesCache, Identification, IdentificationFeaturesGenerator, ReporterSettings, ReporterIonQuantification, SearchParameters, SequenceMatchingParameters) - Constructor for class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Constructor.

QuantificationFilter - Class in eu.isas.reporter.calculation

This class indicates whether identification features or ratios are valid according to the user settings.

QuantificationFilter() - Constructor for class eu.isas.reporter.calculation.QuantificationFilter

R

RatioEstimationSettings - Class in eu.isas.reporter.settings

Settings for the estimation of a peptide or protein ratio.

RatioEstimationSettings() - Constructor for class eu.isas.reporter.settings.RatioEstimationSettings

Constructor.

RatioEstimationSettingsDialog - Class in eu.isas.reporter.gui.settings.quantification

The preferences dialog.

RatioEstimationSettingsDialog(JDialog, RatioEstimationSettings, ModificationParameters, boolean) - Constructor for class eu.isas.reporter.gui.settings.quantification.RatioEstimationSettingsDialog

Creates a new RatioEstimationSettingsDialog.

RatioEstimator - Class in eu.isas.reporter.calculation

This class estimates ratios at the peptide and protein level.

RatioEstimator() - Constructor for class eu.isas.reporter.calculation.RatioEstimator

ReagentOrderDialog - Class in eu.isas.reporter.gui

Dialog for altering the reagent order.

ReagentOrderDialog(ReporterGUI, boolean, ArrayList<String>, ReporterMethod, ReporterIonQuantification, ArrayList<String>) - Constructor for class eu.isas.reporter.gui.ReagentOrderDialog

Creates a new ReagetOrderDialog.

recluster(int, boolean) - Method in class eu.isas.reporter.gui.ReporterGUI

Set the number of clusters and recluster.

redirectErrorStream(File) - Static method in class eu.isas.reporter.cli.ReporterCLI

Redirects the error stream to the Reporter.log file in the given folder.

REFERENCE - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

removeExportScheme(String) - Method in class eu.isas.reporter.export.report.ReporterExportFactory

REPORT_TYPE - Enum constant in enum eu.isas.reporter.cli.ReportCLIParams

ReportCLI - Class in eu.isas.reporter.cli

This class performs the command line export of reports in command line.

ReportCLI(ReportCLIInputBean) - Constructor for class eu.isas.reporter.cli.ReportCLI

Construct a new ReportCLI runnable from a ReportCLI Bean.

ReportCLIInputBean - Class in eu.isas.reporter.cli

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

ReportCLIInputBean(CommandLine) - Constructor for class eu.isas.reporter.cli.ReportCLIInputBean

Construct a ReportCLIInputBean from an Apache CLI instance.

ReportCLIParams - Enum in eu.isas.reporter.cli

This class provides the available reports as command line parameters.

ReportDialog - Class in eu.isas.reporter.gui.export

This dialog allows the user to select, add and edit reports.

ReportDialog(ReporterGUI) - Constructor for class eu.isas.reporter.gui.export.ReportDialog

Constructor.

Reporter - Class in eu.isas.reporter

Reporter performs reporter ion based quantification on MS2/MS3 spectra.

Reporter() - Constructor for class eu.isas.reporter.Reporter

Empty constructor for instantiation purposes.

REPORTER_IONS_LOCATION - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

REPORTER_SETTINGS_TABLE_NAME - Static variable in class eu.isas.reporter.io.ProjectSaver

Name for the reporter settings table.

ReporterCLI - Class in eu.isas.reporter.cli

Command line interface for reporter.

ReporterCLIInputBean - Class in eu.isas.reporter.cli

This class is used to verify that a command line is valid and parse its parameters.

ReporterCLIInputBean(CommandLine) - Constructor for class eu.isas.reporter.cli.ReporterCLIInputBean

Parses the arguments of a command line.

ReporterCLIParameters - Enum in eu.isas.reporter.cli

Command line option parameters for ReporterCLI.

ReporterExportFactory - Class in eu.isas.reporter.export.report

The reporter export factory manages the reports available from Reporter.

reporterExports - Enum constant in enum eu.isas.reporter.preferences.ReporterPathPreferences.ReporterPathKey

Folder containing the user custom exports file.

ReporterGUI - Class in eu.isas.reporter.gui

The main Reporter GUI.

ReporterGUI() - Constructor for class eu.isas.reporter.gui.ReporterGUI

Creates a new ReporterGUI.

ReporterIonSelectionSettings - Class in eu.isas.reporter.settings

Preferences for the reporter ions selection in spectra.

ReporterIonSelectionSettings() - Constructor for class eu.isas.reporter.settings.ReporterIonSelectionSettings

Constructor.

ReporterIonSelectionSettingsDialog - Class in eu.isas.reporter.gui.settings.quantification

The preferences dialog.

ReporterIonSelectionSettingsDialog(JDialog, ReporterIonSelectionSettings, boolean) - Constructor for class eu.isas.reporter.gui.settings.quantification.ReporterIonSelectionSettingsDialog

Creates a new ReporterIonSelectionSettingsDialog.

ReporterIonSelectionSettingsDialog(JDialog, ReporterIonSelectionSettings, ReporterMethod, boolean) - Constructor for class eu.isas.reporter.gui.settings.quantification.ReporterIonSelectionSettingsDialog

Creates a new ReporterIonSelectionSettingsDialog.

ReporterIonsLocationType - Enum in eu.isas.reporter.settings

Enum of the possible spectrum reporter ions locations.

ReporterMerger - Class in eu.isas.reporter.utils

Merging Reporter protein reports.

ReporterMerger() - Constructor for class eu.isas.reporter.utils.ReporterMerger

ReporterPathPreferences - Class in eu.isas.reporter.preferences

This class sets the path preferences for the files to read/write.

ReporterPathPreferences() - Constructor for class eu.isas.reporter.preferences.ReporterPathPreferences

ReporterPathPreferences.ReporterPathKey - Enum in eu.isas.reporter.preferences

Enum of the paths which can be set in Reporter.

ReporterPeptideSection - Class in eu.isas.reporter.export.report.sections

This class outputs the peptide related quantification export features.

ReporterPeptideSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.reporter.export.report.sections.ReporterPeptideSection

Constructor.

ReporterPreferences - Class in eu.isas.reporter.settings

This class contains the quantification options set by the user.

ReporterProteinSection - Class in eu.isas.reporter.export.report.sections

This class outputs the protein related export features.

ReporterProteinSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.reporter.export.report.sections.ReporterProteinSection

Constructor.

ReporterPsmSection - Class in eu.isas.reporter.export.report.sections

This class outputs the PSM level quantification export features.

ReporterPsmSection(ArrayList<ExportFeature>, boolean, boolean, ExportWriter) - Constructor for class eu.isas.reporter.export.report.sections.ReporterPsmSection

Constructor.

ReporterReportStyle - Class in eu.isas.reporter.export.report

This class contains the style for a Reporter Excel export.

ReporterSettings - Class in eu.isas.reporter.settings

This class contains the reporter settings for this project.

ReporterSettings() - Constructor for class eu.isas.reporter.settings.ReporterSettings

Constructor.

ReporterSettingsDialog - Class in eu.isas.reporter.gui.settings

The preferences dialog.

ReporterSettingsDialog(JDialog, ReporterSettings, ModificationParameters, ReporterMethod, boolean) - Constructor for class eu.isas.reporter.gui.settings.ReporterSettingsDialog

Creates a new PreferencesDialog.

ReporterWrapper - Class in eu.isas.reporter

A wrapper class used to start the jar file with parameters.

ReporterWrapper(String[]) - Constructor for class eu.isas.reporter.ReporterWrapper

Starts the launcher by calling the launch method.

ReporterZipFileChecker - Class in eu.isas.reporter

A wrapper class used to check if the jar file is attempted started from within an unzipped zip file.

ReporterZipFileChecker(String[]) - Constructor for class eu.isas.reporter.ReporterZipFileChecker

Checks if the jar file is started from within an unzipped zip file.

reportExportNeeded() - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Indicates whether a report export is required by the user.

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

Resets the peptide keys.

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

Reset the protein keys.

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

Resets the peptide keys.

resetSelection() - Method in class eu.isas.reporter.gui.resultpanels.OverviewPanel

Reselect the proteins, peptides and PSMs.

RESOLUTION - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

restart() - Method in class eu.isas.reporter.gui.ReporterGUI

Closes and restarts Reporter.

S

saveFactory(ReporterExportFactory) - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

Saves the factory in the user folder.

saveProject(ReporterSettings, ReporterIonQuantification, DisplayPreferences, PsdbParent, WaitingHandler) - Static method in class eu.isas.reporter.io.ProjectSaver

Saves the Reporter project information in the given database.

saveProjectAs(boolean, boolean) - Method in class eu.isas.reporter.gui.ReporterGUI

Save the project to the currentPSFile location.

saveUserPreferences() - Method in class eu.isas.reporter.gui.ReporterGUI

Saves the user parameters.

saveUserPreferences(ReporterPreferences) - Static method in class eu.isas.reporter.settings.ReporterPreferences

Convenience method saving the user preferences.

selectTextField() - Method in class eu.isas.reporter.gui.JumpToPanel

Move the focus to the Jump To text field and select all the content.

setAllPathsIn(String) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Sets all the paths inside a given folder.

setAnnotationParameters(AnnotationParameters) - Method in class eu.isas.reporter.settings.ReporterSettings

Sets the spectrum annotation parameters.

setClassesColors(HashMap<String, Color>) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the classes color coding.

setClusteringSettings(ClusteringSettings) - Method in class eu.isas.reporter.preferences.DisplayPreferences

Sets the clustering settings.

setColor(Color) - Method in class eu.isas.reporter.gui.JumpToPanel

Set the color for the hits.

setColor(String, Color) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the cluster class color.

setContaminantsFastaFile(File) - Method in class eu.isas.reporter.settings.NormalizationSettings

Sets the FASTA file containing the contaminant proteins.

setcTerm(Boolean) - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Sets whether the peptide is C-term.

setDefaultSettings(ReporterSettings) - Method in class eu.isas.reporter.settings.ReporterPreferences

Sets the default settings.

setDeisotopedIntensity(String, double) - Method in class eu.isas.reporter.quantificationdetails.SpectrumQuantificationDetails

Sets the value of a deisotoped intensity.

setEnabled(boolean) - Method in class eu.isas.reporter.gui.JumpToPanel

setFile(String) - Method in class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

Sets the spectrum file.

setForbiddenPtms(ArrayList<String>) - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Sets the PTMs not carried by the peptide.

setIconImage(Image) - Method in class eu.isas.reporter.gui.WelcomeDialog

setIgnoreMissedCleavages(boolean) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Sets whether miscleaved peptides should be ignored.

setIgnoreNullIntensities(boolean) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Sets whether null intensities should be ignored.

setJsonFolder(String) - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

Sets the folder where to save the implemented export schemes.

setKMeansClusteringSettings(KMeansClusteringSettings) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the k-means clustering settings.

setLastSelectedFolder(LastSelectedFolder) - Method in class eu.isas.reporter.gui.ReporterGUI

Set the last selected folder.

setMethodsFile(File) - Method in class eu.isas.reporter.gui.NewDialog

Set the current method file.

setMinUnique(int) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Sets the minimal number of unique peptides required for a protein, ignored if negative.

setMostAccurate(boolean) - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Sets whether the most accurate ion should be retained for quantification.

setNormalizationSettings(NormalizationSettings) - Method in class eu.isas.reporter.settings.ReporterSettings

Sets the normalization settings.

setNotModified(boolean) - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Sets whether the peptides must be not modified.

setnTerm(Boolean) - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Sets whether the peptide is N-term.

setPathConfiguration() - Static method in class eu.isas.reporter.Reporter

Sets the path configuration.

setPathPreference(ReporterPathPreferences.ReporterPathKey, String) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Sets the path according to the given key and path.

setPathSettings() - Method in class eu.isas.reporter.cli.PathSettingsCLI

Sets the path settings according to the pathSettingsCLIInputBean.

setPeptideClassKeys(ArrayList<PeptideClusterClassKey>) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the cluster class keys.

setPeptideNormalization(NormalizationType) - Method in class eu.isas.reporter.settings.NormalizationSettings

Sets the type of normalization used to normalize the peptides.

setPeptideNormalizationFactors(ReporterIonQuantification, RatioEstimationSettings, NormalizationSettings, SequenceMatchingParameters, Identification, SpectrumProvider, QuantificationFeaturesGenerator, ProcessingParameters, SearchParameters, FastaParameters, PeptideVariantsParameters, ExceptionHandler, WaitingHandler) - Method in class eu.isas.reporter.calculation.normalization.Normalizer

Sets the peptide normalization factors in the ReporterIonQuantification object.

setPeptideValidationLevel(MatchValidationLevel) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Sets the validation level to require for quantification.

setPercentile(double) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Sets the share in percent of ratios considered to set the width of the maximum likelihood estimators.

setPossiblePtms(ArrayList<String>) - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Sets the PTMs possibly carried by the peptides.

setPrecursorMzPpm(boolean) - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Sets whether the precursor matching tolerance is in ppm or in m/z

setPrecursorMzTolerance(double) - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Sets the precursor m/z tolerance used to match quantification spectra to identification spectra.

setPrecursorRTTolerance(double) - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Sets the precursor RT tolerance used to match quantification spectra to identification spectra.

setProjectDetails(ProjectDetails) - Method in class eu.isas.reporter.settings.ReporterSettings

Sets the project details.

setProteinClassKeys(ArrayList<ProteinClusterClassKey>) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the cluster class keys.

setProteinKeys(ArrayList<Long>) - Method in class eu.isas.reporter.gui.JumpToPanel

Set the current protein keys to search in.

setProteinNormalization(NormalizationType) - Method in class eu.isas.reporter.settings.NormalizationSettings

Sets the type of normalization used to normalize the proteins.

setProteinNormalizationFactors(ReporterIonQuantification, RatioEstimationSettings, NormalizationSettings, Identification, SpectrumProvider, Metrics, QuantificationFeaturesGenerator, ProcessingParameters, SearchParameters, FastaParameters, PeptideVariantsParameters, ExceptionHandler, WaitingHandler) - Method in class eu.isas.reporter.calculation.normalization.Normalizer

Sets the protein normalization factors in the ReporterIonQuantification object.

setProteinRatioType(int) - Method in class eu.isas.reporter.preferences.DisplayPreferences

Sets the index of the selected protein ratio type to display.

setProteinTableProperties(JTable, Color, Color, Color, Color, DecimalFormat, Class, Integer, Double) - Static method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

Set up the properties of the protein table.

setProteinValidationLevel(MatchValidationLevel) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Sets the validation level to require for quantification.

setPsmClassKeys(ArrayList<PsmClusterClassKey>) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the cluster class keys.

setPsmNormalization(NormalizationType) - Method in class eu.isas.reporter.settings.NormalizationSettings

Sets the type of normalization used to normalize the PSMs.

setPsmNormalizationFactors(ReporterIonQuantification, RatioEstimationSettings, NormalizationSettings, SequenceMatchingParameters, Identification, SpectrumProvider, QuantificationFeaturesGenerator, ProcessingParameters, SearchParameters, FastaParameters, PeptideVariantsParameters, ExceptionHandler, WaitingHandler) - Method in class eu.isas.reporter.calculation.normalization.Normalizer

Sets the PSM normalization factors in the ReporterIonQuantification object.

setPsmValidationLevel(MatchValidationLevel) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Sets the validation level to require for quantification.

setQuantificationFeaturesCache(QuantificationFeaturesCache) - Method in class eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Sets the quantification features cache.

setRatio(String, double) - Method in class eu.isas.reporter.quantificationdetails.ProteinPtmQuantificationDetails

Sets a ratio.

setRatio(String, double) - Method in class eu.isas.reporter.quantificationdetails.SpectrumQuantificationDetails

Sets a ratio.

setRatioEstimationSettings(RatioEstimationSettings) - Method in class eu.isas.reporter.settings.ReporterSettings

Sets the ratio estimation settings.

setRatioResolution(double) - Method in class eu.isas.reporter.settings.RatioEstimationSettings

Sets the ratio resolution.

setRawRatio(String, double) - Method in class eu.isas.reporter.quantificationdetails.PeptideQuantificationDetails

Sets a raw (not normalized) normalized ratio.

setRawRatio(String, double) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Sets a raw (not normalized) normalized ratio.

setRawRatio(String, double) - Method in class eu.isas.reporter.quantificationdetails.PsmQuantificationDetails

Sets a raw (not normalized) normalized ratio.

setReagents(ArrayList<String>) - Method in class eu.isas.reporter.gui.NewDialog

Set the reagents.

setReagents(ArrayList<String>) - Method in class eu.isas.reporter.preferences.DisplayPreferences

Set the regents.

setReporterIonSelectionSettings(ReporterIonSelectionSettings) - Method in class eu.isas.reporter.settings.ReporterSettings

Sets the reporter ion selection settings.

setReporterIonsLocation(ReporterIonsLocationType) - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Set the reporter ions location.

setReporterIonsMzTolerance(double) - Method in class eu.isas.reporter.settings.ReporterIonSelectionSettings

Sets the tolerance used to match reporter ions.

setReporterMatch(String, IonMatch) - Method in class eu.isas.reporter.quantificationdetails.SpectrumQuantificationDetails

Sets the value of a reporter ion match.

setReportNamePrefix(String) - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Set the report name prefix.

setReportOutputFolder(File) - Method in class eu.isas.reporter.cli.ReportCLIInputBean

Set the report output folder.

setSelectedItem(int) - Method in class eu.isas.reporter.gui.JumpToPanel

Sets the index of the selected item.

setSelectedMethod(ReporterMethod) - Method in class eu.isas.reporter.gui.NewDialog

Set the selected method.

setSelectedPeptideClasses(ArrayList<String>) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the selected peptide cluster classes represented by their toString() method.

setSelectedPeptides(ArrayList<Long>, boolean, boolean) - Method in class eu.isas.reporter.gui.ReporterGUI

Set the list of selected peptides.

setSelectedProteinClasses(ArrayList<String>) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the selected protein cluster classes represented by their toString() method.

setSelectedProteins(ArrayList<Long>, boolean, boolean) - Method in class eu.isas.reporter.gui.ReporterGUI

Set the list of selected proteins.

setSelectedPsmClasses(ArrayList<String>) - Method in class eu.isas.reporter.settings.ClusteringSettings

Sets the selected PSM cluster classes represented by their toString() method.

setSelectedPsms(ArrayList<Long>, boolean, boolean) - Method in class eu.isas.reporter.gui.ReporterGUI

Set the list of selected PSMs.

setSharedRawRatio(String, double) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Sets a shared raw (not normalized) normalized ratio.

setStableProteinsFastaFile(File) - Method in class eu.isas.reporter.settings.NormalizationSettings

Sets the FASTA file containing the stable proteins.

setStarred(Boolean) - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Sets whether the peptides must be starred.

setStarred(Boolean) - Method in class eu.isas.reporter.calculation.clustering.keys.ProteinClusterClassKey

Sets whether the proteins must be starred.

setStarred(Boolean) - Method in class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

Sets whether the PSMs must be starred.

setTempFolderPath(String) - Static method in class eu.isas.reporter.Reporter

Sets the folder to use for temporary files.

setType(JumpToPanel.JumpType) - Method in class eu.isas.reporter.gui.JumpToPanel

Changes the type of jumpToPanel.

setUniqueRawRatio(String, double) - Method in class eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails

Sets a unique raw (not normalized) normalized ratio.

setUserPreferencesFolder(String) - Static method in class eu.isas.reporter.settings.ReporterPreferences

Sets the folder used to save the user preferences.

setVisible(boolean) - Method in class eu.isas.reporter.gui.WelcomeDialog

Make sure that the dummy frame is hidden when the dialog is not visible.

shared - Enum constant in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

showScores(boolean) - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

Sets whether the scores should be displayed.

SpectrumMerger - Class in eu.isas.reporter.utils

Merging of MS2 and MS3 data from Fusion instruments to merge the reporters from HCD MS3 with the identification from CID MS2.

SpectrumMerger() - Constructor for class eu.isas.reporter.utils.SpectrumMerger

SpectrumQuantificationDetails - Class in eu.isas.reporter.quantificationdetails

This class contains the quantitative information at the spectrum level.

SpectrumQuantificationDetails() - Constructor for class eu.isas.reporter.quantificationdetails.SpectrumQuantificationDetails

STABLE_PROTEINS - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

sum - Enum constant in enum eu.isas.reporter.calculation.normalization.NormalizationType

T

testReporterGrouping() - Method in class eu.isas.reporter.utils.ReporterMerger

Test reporter grouping.

THREADS - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

TITLED_BORDER_HORIZONTAL_PADDING - Static variable in class eu.isas.reporter.gui.ReporterGUI

The horizontal padding used before and after the text in the titled borders.

toString() - Method in class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

toString() - Method in class eu.isas.reporter.calculation.clustering.keys.ProteinClusterClassKey

toString() - Method in class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

toString() - Method in class eu.isas.reporter.cli.PathSettingsCLI

toString() - Method in class eu.isas.reporter.cli.ReportCLI

U

unique - Enum constant in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

updateDataModel(Identification, IdentificationFeaturesGenerator, ProteinDetailsProvider, SequenceProvider, SpectrumProvider, GeneMaps, ReporterIonQuantification, QuantificationFeaturesGenerator, DisplayFeaturesGenerator, DisplayPreferences, long[]) - Method in class eu.isas.reporter.gui.tablemodels.ProteinTableModel

Update the data in the table model without having to reset the whole table model.This keeps the sorting order of the table.

updateDataModel(Identification, IdentificationFeaturesGenerator, ReporterIonQuantification, QuantificationFeaturesGenerator, DisplayFeaturesGenerator, DisplayPreferences, IdentificationParameters, String, long[], boolean) - Method in class eu.isas.reporter.gui.tablemodels.PeptideTableModel

Update the data in the table model without having to reset the whole table model.

updateDataModel(Identification, SpectrumProvider, DisplayFeaturesGenerator, DisplayPreferences, IdentificationParameters, ReporterIonQuantification, QuantificationFeaturesGenerator, long[], boolean) - Method in class eu.isas.reporter.gui.tablemodels.PsmTableModel

Update the data in the table model without having to reset the whole table model.

updateDisplay() - Method in class eu.isas.reporter.gui.resultpanels.OverviewPanel

Updates the display with the underlying data.

updateReagentNames() - Method in class eu.isas.reporter.gui.NewDialog

Update the reagent names in the sample assignment table.

updateSelection(boolean) - Method in class eu.isas.reporter.gui.resultpanels.OverviewPanel

Update the selection.

updateSelectionInTab() - Method in class eu.isas.reporter.gui.JumpToPanel

Updates the item selection in the selected tab.

USE_LOG_FOLDER - Enum constant in enum eu.isas.reporter.cli.PathSettingsCLIParams

useLogFile() - Method in class eu.isas.reporter.cli.PathSettingsCLIInputBean

Return true if a log file is to be used.

V

VALIDATION_PEPTIDE - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

VALIDATION_PROTEIN - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

VALIDATION_PSM - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

valueOf(String) - Static method in enum eu.isas.reporter.calculation.normalization.NormalizationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum eu.isas.reporter.cli.PathSettingsCLIParams

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum eu.isas.reporter.cli.ReportCLIParams

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum eu.isas.reporter.cli.ReporterCLIParameters

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum eu.isas.reporter.gui.JumpToPanel.JumpType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum eu.isas.reporter.preferences.ReporterPathPreferences.ReporterPathKey

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum eu.isas.reporter.settings.ReporterIonsLocationType

Returns the enum constant of this type with the specified name.

values() - Static method in enum eu.isas.reporter.calculation.normalization.NormalizationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum eu.isas.reporter.cli.PathSettingsCLIParams

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum eu.isas.reporter.cli.ReportCLIParams

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum eu.isas.reporter.cli.ReporterCLIParameters

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum eu.isas.reporter.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.reporter.preferences.ReporterPathPreferences.ReporterPathKey

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum eu.isas.reporter.quantificationdetails.ProteinRatioType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum eu.isas.reporter.settings.ReporterIonsLocationType

Returns an array containing the constants of this enum type, in the order they are declared.

W

WelcomeDialog - Class in eu.isas.reporter.gui

A simple welcome dialog with the option to open an existing project or create a new one.

WelcomeDialog(ReporterGUI, boolean, boolean, boolean) - Constructor for class eu.isas.reporter.gui.WelcomeDialog

Create a new WelcomeDialog.

writeConfigurationToFile(SimpleFileWriter) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Writes the configuration file using the provided buffered writer.

writeConfigurationToFile(File) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Writes all path configurations to the given file.

writeDocumentation(ExportScheme, ExportFormat, File) - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

Writes the documentation related to a report.

writeExport(ExportScheme, File, ExportFormat, String, ProjectDetails, Identification, IdentificationFeaturesGenerator, SequenceProvider, SpectrumProvider, ProteinDetailsProvider, GeneMaps, QuantificationFeaturesGenerator, ReporterIonQuantification, ReporterSettings, IdentificationParameters, ArrayList<String>, long[], long[], String, int, SpectrumCountingParameters, WaitingHandler) - Static method in class eu.isas.reporter.export.report.ReporterExportFactory

Writes the desired export in text format.If an argument is not needed, provide null (at your own risks).

writeHeader(ReporterIonQuantification) - Method in class eu.isas.reporter.export.report.sections.ReporterPeptideSection

Writes the title of the section.

writeHeader(ReporterIonQuantification) - Method in class eu.isas.reporter.export.report.sections.ReporterProteinSection

Writes the header of the protein section.

writeHeader(ReporterIonQuantification) - Method in class eu.isas.reporter.export.report.sections.ReporterPsmSection

Writes the header of this section.

writePathToFile(SimpleFileWriter, ReporterPathPreferences.ReporterPathKey) - Static method in class eu.isas.reporter.preferences.ReporterPathPreferences

Writes the path of interest using the provided buffered writer.

writeSection(Identification, IdentificationFeaturesGenerator, SequenceProvider, SpectrumProvider, ProteinDetailsProvider, GeneMaps, QuantificationFeaturesGenerator, ReporterIonQuantification, ReporterSettings, IdentificationParameters, long[], int, boolean, boolean, WaitingHandler) - Method in class eu.isas.reporter.export.report.sections.ReporterProteinSection

Writes the desired section.

writeSection(Identification, IdentificationFeaturesGenerator, SequenceProvider, SpectrumProvider, ProteinDetailsProvider, QuantificationFeaturesGenerator, ReporterIonQuantification, ReporterSettings, IdentificationParameters, long[], int, String, boolean, boolean, WaitingHandler) - Method in class eu.isas.reporter.export.report.sections.ReporterPeptideSection

Writes the desired section.

writeSection(Identification, IdentificationFeaturesGenerator, SequenceProvider, SpectrumProvider, ProteinDetailsProvider, QuantificationFeaturesGenerator, ReporterIonQuantification, ReporterSettings, IdentificationParameters, long[], String, int, boolean, boolean, WaitingHandler) - Method in class eu.isas.reporter.export.report.sections.ReporterPsmSection

Writes the desired section.

Z

ZIP - Enum constant in enum eu.isas.reporter.cli.ReporterCLIParameters

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