Uses of Class
eu.isas.reporter.calculation.QuantificationFeaturesGenerator

Packages that use QuantificationFeaturesGenerator

Package	Description
eu.isas.reporter	Main package.
eu.isas.reporter.calculation.clustering	Package containing classes used for the clustering.
eu.isas.reporter.calculation.normalization	Package containing classes used for the quantification.
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.tablemodels	Package containing table models.

Uses of QuantificationFeaturesGenerator in eu.isas.reporter

Methods in eu.isas.reporter with parameters of type QuantificationFeaturesGenerator

Modifier and Type	Method	Description
static PeptideQuantificationDetails	Reporter.estimatePeptideMatchQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)	Returns the quantification details of a peptide match.
static ProteinQuantificationDetails	Reporter.estimateProteinMatchQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)	Returns the quantification details of a protein match.
static PsmQuantificationDetails	Reporter.estimatePSMQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, ReporterIonSelectionSettings reporterIonSelectionSettings, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, Long matchKey)	Returns the quantification details of a PSM.
static ProteinPtmQuantificationDetails	Reporter.estimatePTMQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, String ptmName, long matchKey, int site, com.compomics.util.waiting.WaitingHandler waitingHandler)	Returns the quantification details of a PTM on a protein.//@TODO: discriminate peptides according to the neighboring sites?
static SpectrumQuantificationDetails	Reporter.estimateSpectrumQuantificationDetails(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, ReporterIonSelectionSettings reporterIonSelectionSettings, com.compomics.util.experiment.identification.matches.SpectrumMatch aSpectrumMatch)	Returns the quantification details of a spectrum.

Uses of QuantificationFeaturesGenerator in eu.isas.reporter.calculation.clustering

Methods in eu.isas.reporter.calculation.clustering with parameters of type QuantificationFeaturesGenerator

Modifier and Type	Method	Description
com.compomics.util.math.clustering.KMeansClustering	ClusterBuilder.clusterProfiles(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, DisplayPreferences displayPreferences, boolean loadData, com.compomics.util.waiting.WaitingHandler waitingHandler)	Clusters the profiles according to the given parameters.
void	ClusterBuilder.loadData(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, DisplayPreferences displayPreferences, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.waiting.WaitingHandler waitingHandler)	Filters the proteins and indexes them according to the clustering settings and stores the result in the attribute maps.

Uses of QuantificationFeaturesGenerator in eu.isas.reporter.calculation.normalization

Methods in eu.isas.reporter.calculation.normalization with parameters of type QuantificationFeaturesGenerator

Modifier and Type	Method	Description
void	Normalizer.setPeptideNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)	Sets the peptide normalization factors in the ReporterIonQuantification object.
void	Normalizer.setProteinNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)	Sets the protein normalization factors in the ReporterIonQuantification object.
void	Normalizer.setPsmNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)	Sets the PSM normalization factors in the ReporterIonQuantification object.

Uses of QuantificationFeaturesGenerator in eu.isas.reporter.cli

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

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 QuantificationFeaturesGenerator in eu.isas.reporter.export.report

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

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 QuantificationFeaturesGenerator in eu.isas.reporter.export.report.sections

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

Modifier and Type	Method	Description
static String	ReporterPeptideSection.getFeature(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, com.compomics.util.io.export.features.reporter.ReporterPeptideFeature peptideFeatures, String sampleIndex, com.compomics.util.waiting.WaitingHandler waitingHandler)	Returns the report component corresponding to a feature at a given channel.
static String	ReporterProteinSection.getFeature(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, long proteinKey, com.compomics.util.io.export.features.reporter.ReporterProteinFeatures proteinFeatures, String sampleIndex, com.compomics.util.waiting.WaitingHandler waitingHandler)	Returns the report component corresponding to a feature at a given channel.
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 QuantificationFeaturesGenerator in eu.isas.reporter.gui

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

Modifier and Type	Method	Description
QuantificationFeaturesGenerator	ReporterGUI.getQuantificationFeaturesGenerator()	Returns the quantification features generator.

Uses of QuantificationFeaturesGenerator in eu.isas.reporter.gui.tablemodels

Methods in eu.isas.reporter.gui.tablemodels with parameters of type QuantificationFeaturesGenerator

Modifier and Type	Method	Description
void	PeptideTableModel.updateDataModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator, DisplayPreferences displayPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, String proteinAccession, long[] peptideKeys, boolean showScores)	Update the data in the table model without having to reset the whole table model.
void	ProteinTableModel.updateDataModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator, DisplayPreferences displayPreferences, long[] proteinKeys)	Update the data in the table model without having to reset the whole table model.This keeps the sorting order of the table.
void	PsmTableModel.updateDataModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator, DisplayPreferences displayPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, long[] psmKeys, boolean displayScores)	Update the data in the table model without having to reset the whole table model.

Constructors in eu.isas.reporter.gui.tablemodels with parameters of type QuantificationFeaturesGenerator

Modifier	Constructor	Description
	PeptideTableModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator, DisplayPreferences displayPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, String proteinAccession, long[] peptideKeys, boolean displayScores, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Constructor which sets a new table.
	ProteinTableModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator, DisplayPreferences displayPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, long[] proteinKeys)	Constructor.
	PsmTableModel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator, DisplayPreferences displayPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, QuantificationFeaturesGenerator quantificationFeaturesGenerator, long[] psmKeys, boolean displayScores, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Constructor which sets a new table.