Uses of Class
eu.isas.reporter.settings.ReporterSettings

Packages that use ReporterSettings

Package	Description
eu.isas.reporter.calculation	Package containing classes used for the calculation.
eu.isas.reporter.cli	Package containing the CLI classes.
eu.isas.reporter.export.report	Package containing classes used for the generation of reports.
eu.isas.reporter.export.report.sections	Package containing classes used for the generation of export sections.
eu.isas.reporter.gui	Package containing the GUI classes used for the generation of exports.
eu.isas.reporter.gui.settings	Package containing GUI classes used for the edition of settings.
eu.isas.reporter.io	Package containing classes used for saving and opening projects.
eu.isas.reporter.settings	Package containing the different settings.

Uses of ReporterSettings in eu.isas.reporter.calculation

Constructors in eu.isas.reporter.calculation with parameters of type ReporterSettings

Modifier	Constructor	Description
	QuantificationFeaturesGenerator(QuantificationFeaturesCache quantificationFeaturesCache, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, ReporterSettings reporterSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters)	Constructor.

Uses of ReporterSettings in eu.isas.reporter.cli

Methods in eu.isas.reporter.cli with parameters of type ReporterSettings

Modifier and Type	Method	Description
static void	CLIExportMethods.exportReport(ReportCLIInputBean reportCLIInputBean, String reportType, String experiment, eu.isas.peptideshaker.preferences.ProjectDetails projectDetails, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes an export according to the command line settings contained in the reportCLIInputBean.

Uses of ReporterSettings in eu.isas.reporter.export.report

Methods in eu.isas.reporter.export.report with parameters of type ReporterSettings

Modifier and Type	Method	Description
static void	ReporterExportFactory.writeExport(com.compomics.util.io.export.ExportScheme exportScheme, File destinationFile, com.compomics.util.io.export.ExportFormat exportFormat, String experiment, eu.isas.peptideshaker.preferences.ProjectDetails projectDetails, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, ArrayList<String> proteinKeys, long[] peptideKeys, long[] psmKeys, String proteinMatchKey, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes the desired export in text format.If an argument is not needed, provide null (at your own risks).

Uses of ReporterSettings in eu.isas.reporter.export.report.sections

Methods in eu.isas.reporter.export.report.sections with parameters of type ReporterSettings

Modifier and Type	Method	Description
static String	ReporterPsmSection.getFeature(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, long matchKey, com.compomics.util.io.export.features.reporter.ReporterPsmFeatures psmFeatures, String sampleIndex)	Returns the report component corresponding to a feature at a given channel.
void	ReporterPeptideSection.writeSection(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, int nSurroundingAA, String linePrefix, boolean validatedOnly, boolean decoys, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes the desired section.
void	ReporterProteinSection.writeSection(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, int nSurroundingAas, boolean validatedOnly, boolean decoys, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes the desired section.
void	ReporterPsmSection.writeSection(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, long[] keys, String linePrefix, int nSurroundingAA, boolean validatedOnly, boolean decoys, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes the desired section.

Uses of ReporterSettings in eu.isas.reporter.gui

Methods in eu.isas.reporter.gui that return ReporterSettings

Modifier and Type	Method	Description
ReporterSettings	NewDialog.getReporterSettings()	Returns the reporter settings.
ReporterSettings	ReporterGUI.getReporterSettings()	Returns the reporter settings.

Methods in eu.isas.reporter.gui with parameters of type ReporterSettings

Modifier and Type	Method	Description
void	ReporterGUI.createNewProject(eu.isas.peptideshaker.utils.PsdbParent psdbParent, ReporterSettings reporterSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, DisplayPreferences displayPreferences)	Closes the currently opened project, open the new project dialog and loads the new project on the interface

Uses of ReporterSettings in eu.isas.reporter.gui.settings

Methods in eu.isas.reporter.gui.settings that return ReporterSettings

Modifier and Type	Method	Description
ReporterSettings	ReporterSettingsDialog.getReporterSettings()	Returns the reporter settings as set by the user.

Constructors in eu.isas.reporter.gui.settings with parameters of type ReporterSettings

Modifier	Constructor	Description
	ReporterSettingsDialog(JDialog parentDialog, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, boolean editable)	Creates a new PreferencesDialog.

Uses of ReporterSettings in eu.isas.reporter.io

Methods in eu.isas.reporter.io that return ReporterSettings

Modifier and Type	Method	Description
static ReporterSettings	ProjectImporter.getDefaultReporterSettings(com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)	Returns the default reporter settings as inferred from the identification parameters.
static ReporterSettings	ProjectImporter.getDefaultReporterSettings(com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, ReporterSettings reporterSettings)	Returns the default reporter settings as inferred from the identification parameters.
ReporterSettings	ProjectImporter.getReporterSettings()	Returns the reporter settings loaded from the file.

Methods in eu.isas.reporter.io with parameters of type ReporterSettings

Modifier and Type	Method	Description
static ReporterSettings	ProjectImporter.getDefaultReporterSettings(com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, ReporterSettings reporterSettings)	Returns the default reporter settings as inferred from the identification parameters.
static void	ProjectSaver.saveProject(ReporterSettings reporterSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, DisplayPreferences displayPreferences, eu.isas.peptideshaker.utils.PsdbParent psdbParent, com.compomics.util.waiting.WaitingHandler waitingHandler)	Saves the Reporter project information in the given database.

Uses of ReporterSettings in eu.isas.reporter.settings

Methods in eu.isas.reporter.settings that return ReporterSettings

Modifier and Type	Method	Description
ReporterSettings	ReporterSettings.clone()
ReporterSettings	ReporterPreferences.getDefaultSettings()	Returns the default settings.

Methods in eu.isas.reporter.settings with parameters of type ReporterSettings

Modifier and Type	Method	Description
boolean	ReporterSettings.isSameAs(ReporterSettings anotherSetting)	Indicates whether another setting is the same as this one.
void	ReporterPreferences.setDefaultSettings(ReporterSettings defaultSettings)	Sets the default settings.