Package eu.isas.reporter.cli

Class CLIExportMethods

java.lang.Object
eu.isas.reporter.cli.CLIExportMethods
public class CLIExportMethods extends Object
This class groups standard methods used by the different command line interfaces.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    CLIExportMethods()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Writes the documentation corresponding to an export given the command line arguments.
    static void
    exportReport(ReportCLIInputBean reportCLIInputBean, String reportType, String experiment, eu.isas.peptideshaker.preferences.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.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Writes an export according to the command line settings contained in the reportCLIInputBean.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • CLIExportMethods

      public CLIExportMethods()

  • Method Details

    • exportReport

      public static void exportReport(ReportCLIInputBean reportCLIInputBean, String reportType, String experiment, eu.isas.peptideshaker.preferences.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.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, ReporterSettings reporterSettings, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, org.apache.commons.math.MathException
      Writes an export according to the command line settings contained in the reportCLIInputBean.
      Parameters:
      reportCLIInputBean - the command line settings
      reportType - the report type
      experiment - the experiment of the project
      projectDetails - the project details of the project
      identification - the identification of the project
      geneMaps - the gene maps
      identificationFeaturesGenerator - the identification features generator
      sequenceProvider - the sequence provider
      spectrumProvider - the spectrum provider
      proteinDetailsProvider - the protein details provider
      quantificationFeaturesGenerator - the object generating the quantification features
      reporterIonQuantification - the reporter ion quantification object containing the quantification configuration
      reporterSettings - the reporter settings
      identificationParameters - the identification parameters used
      nSurroundingAA - the number of amino acids to export on the side of peptide sequences
      spectrumCountingParameters - the spectrum counting parameters
      waitingHandler - waiting handler displaying feedback to the user
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file
      InterruptedException - exception thrown whenever a threading issue occurred while interacting with the database
      SQLException - exception thrown whenever an SQL exception occurred while interacting with the database
      ClassNotFoundException - exception thrown whenever an exception occurred while deserializing an object
      org.apache.commons.math.MathException - exception thrown whenever an exception occurred while estimating the theoretical coverage of a protein
      IllegalArgumentException

    • exportDocumentation

      public static void exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Writes the documentation corresponding to an export given the command line arguments.
      Parameters:
      reportCLIInputBean - the command line arguments
      reportType - the type of report of interest
      waitingHandler - waiting handler displaying feedback to the user
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file