Uses of Class
eu.isas.reporter.preferences.DisplayPreferences

Packages that use DisplayPreferences

Package	Description
eu.isas.reporter.calculation.clustering	Package containing classes used for the clustering.
eu.isas.reporter.gui	Package containing the GUI classes used for the generation of exports.
eu.isas.reporter.gui.tablemodels	Package containing table models.
eu.isas.reporter.io	Package containing classes used for saving and opening projects.

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

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

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 DisplayPreferences in eu.isas.reporter.gui

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

Modifier and Type	Method	Description
DisplayPreferences	ReporterGUI.getDisplayParameters()	Returns the display parameters.

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

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 DisplayPreferences in eu.isas.reporter.gui.tablemodels

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

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 DisplayPreferences

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.

Uses of DisplayPreferences in eu.isas.reporter.io

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

Modifier and Type	Method	Description
DisplayPreferences	ProjectImporter.getDisplayPreferences()	Returns the display preferences.

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

Modifier and Type	Method	Description
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.