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 processingPreferences, 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 
    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 
    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 
    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.