Uses of Class
eu.isas.peptideshaker.cmd.ReportCLIInputBean

Packages that use ReportCLIInputBean 
Package Description
eu.isas.peptideshaker.cmd
Command line usage.

  • Uses of ReportCLIInputBean in eu.isas.peptideshaker.cmd

    Methods in eu.isas.peptideshaker.cmd that return ReportCLIInputBean 
    Modifier and Type Method Description
    ReportCLIInputBean PeptideShakerCLIInputBean.getReportCLIInputBean()
    Returns the report export options required.
    Methods in eu.isas.peptideshaker.cmd with parameters of type ReportCLIInputBean 
    Modifier and Type Method Description
    static void CLIExportMethods.exportDocumentation​(ReportCLIInputBean reportCLIInputBean, String reportType, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Writes the documentation corresponding to an export given the command line arguments.
    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.
    Constructors in eu.isas.peptideshaker.cmd with parameters of type ReportCLIInputBean 
    Constructor Description
    ReportCLI​(ReportCLIInputBean reportCLIInputBean)
    Construct a new ReportCLI runnable from a ReportCLI Bean.