Uses of Class
eu.isas.peptideshaker.preferences.ProjectDetails

Packages that use ProjectDetails

Package	Description
eu.isas.peptideshaker	PeptideShaker main calculations and jar wrapper.
eu.isas.peptideshaker.cmd	Command line usage.
eu.isas.peptideshaker.export	Exporting data from PeptideShaker.
eu.isas.peptideshaker.export.sections	Export sections.
eu.isas.peptideshaker.fileimport	Import of search results.
eu.isas.peptideshaker.gui	GUI dialogs and helper classes.
eu.isas.peptideshaker.parameters	Parameter settings.
eu.isas.peptideshaker.utils	Various utilities classes.

Uses of ProjectDetails in eu.isas.peptideshaker

Methods in eu.isas.peptideshaker with parameters of type ProjectDetails

Modifier and Type	Method	Description
void	PeptideShaker.createProject(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, ProjectDetails projectDetails, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.waiting.WaitingHandler waitingHandler, boolean setWaitingHandlerFinshedWhenDone, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Creates a PeptideShaker project.
int	PeptideShaker.importFiles(com.compomics.util.waiting.WaitingHandler waitingHandler, ArrayList<File> idFiles, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, ProjectDetails projectDetails, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Imports identification results from result files.

Uses of ProjectDetails in eu.isas.peptideshaker.cmd

Methods in eu.isas.peptideshaker.cmd with parameters of type ProjectDetails

Modifier and Type	Method	Description
static File	CLIExportMethods.exportReport(ReportCLIInputBean reportCLIInputBean, String reportType, String experiment, 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.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes an export according to the command line settings contained in the reportCLIInputBean.

Uses of ProjectDetails in eu.isas.peptideshaker.export

Methods in eu.isas.peptideshaker.export with parameters of type ProjectDetails

Modifier and Type	Method	Description
static String	PeptideShakerMethods.getSearchEnginesText(ProjectDetails projectDetails)	Returns the search engines usage details.
static void	PsdbExporter.saveAs(File destinationFile, com.compomics.util.waiting.WaitingHandler waitingHandler, 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.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters, ProjectDetails projectDetails, com.compomics.util.gui.filtering.FilterParameters filterParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache, boolean emptyCache, DisplayParameters displayParameters, File dbFolder)	Saves the given data in a psdb file.
static void	PSExportFactory.writeExport(com.compomics.util.io.export.ExportScheme exportScheme, File destinationFile, com.compomics.util.io.export.ExportFormat exportFormat, boolean gzip, String experiment, ProjectDetails projectDetails, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, long[] proteinKeys, long[] peptideKeys, long[] psmKeys, int nSurroundingAA, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes the desired export in text format.

Constructors in eu.isas.peptideshaker.export with parameters of type ProjectDetails

Modifier	Constructor	Description
	MzIdentMLExport(String peptideShakerVersion, com.compomics.util.experiment.identification.Identification identification, ProjectDetails projectDetails, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, File outputFile, boolean includeProteinSequences, com.compomics.util.waiting.WaitingHandler waitingHandler, boolean gzip)	Constructor.

Uses of ProjectDetails in eu.isas.peptideshaker.export.sections

Methods in eu.isas.peptideshaker.export.sections with parameters of type ProjectDetails

Modifier and Type	Method	Description
void	PsProjectSection.writeSection(String experiment, ProjectDetails projectDetails, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes the desired section.
void	PsSearchParametersSection.writeSection(com.compomics.util.parameters.identification.search.SearchParameters searchParameters, ProjectDetails projectDetails, com.compomics.util.waiting.WaitingHandler waitingHandler)	Writes the desired section.

Uses of ProjectDetails in eu.isas.peptideshaker.fileimport

Constructors in eu.isas.peptideshaker.fileimport with parameters of type ProjectDetails

Modifier	Constructor	Description
	FileImporter(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, ProjectDetails projectDetails, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Constructor for the importer.

Uses of ProjectDetails in eu.isas.peptideshaker.gui

Methods in eu.isas.peptideshaker.gui that return ProjectDetails

Modifier and Type	Method	Description
ProjectDetails	PeptideShakerGUI.getProjectDetails()	Returns the project details.

Methods in eu.isas.peptideshaker.gui with parameters of type ProjectDetails

Modifier and Type	Method	Description
void	PeptideShakerGUI.setProjectDetails(ProjectDetails projectDetails)	Sets the project details.

Uses of ProjectDetails in eu.isas.peptideshaker.parameters

Methods in eu.isas.peptideshaker.parameters that return ProjectDetails

Modifier and Type	Method	Description
ProjectDetails	PeptideShakerParameters.getProjectDetails()	Returns the project details.

Constructors in eu.isas.peptideshaker.parameters with parameters of type ProjectDetails

Modifier	Constructor	Description
	PeptideShakerParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, ProjectDetails projectDetails, com.compomics.util.gui.filtering.FilterParameters filterPreferences, DisplayParameters displayPreferences, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache)	Constructor for a PeptideShaker Settings class.

Uses of ProjectDetails in eu.isas.peptideshaker.utils

Fields in eu.isas.peptideshaker.utils declared as ProjectDetails

Modifier and Type	Field	Description
protected ProjectDetails	PsdbParent.projectDetails	The project details.

Methods in eu.isas.peptideshaker.utils that return ProjectDetails

Modifier and Type	Method	Description
ProjectDetails	PsdbParent.getProjectDetails()	Returns the project details.

Methods in eu.isas.peptideshaker.utils with parameters of type ProjectDetails

Modifier and Type	Method	Description
void	PsdbParent.setProjectDetails(ProjectDetails projectDetails)	Sets the project details.