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 and 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 and 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 and Description
ReportCLI(ReportCLIInputBean reportCLIInputBean) Construct a new ReportCLI runnable from a ReportCLI Bean.