Package eu.isas.reporter.cli

Class ReportCLI

java.lang.Object
eu.isas.peptideshaker.preferences.UserPreferencesParent
eu.isas.peptideshaker.utils.PsdbParent
eu.isas.reporter.cli.ReportCLI
All Implemented Interfaces:
AutoCloseable
public class ReportCLI extends eu.isas.peptideshaker.utils.PsdbParent
This class performs the command line export of reports in command line.
Author:
Marc Vaudel, Harald Barsnes

  • Field Summary

    Fields inherited from class eu.isas.peptideshaker.utils.PsdbParent

    dbFolder, displayParameters, filterParameters, geneMaps, identification, identificationFeaturesGenerator, identificationParameters, metrics, msFileHandler, projectDetails, projectParameters, projectType, proteinDetailsProvider, psdbFile, sequenceProvider, spectrumCountingParameters

    Fields inherited from class eu.isas.peptideshaker.preferences.UserPreferencesParent

    userPreferences

  • Constructor Summary

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

  • Method Summary

    Modifier and Type
    Method
    Description
    Object
    call()
    Calling this method will run the configured Reporter process.
    void
    closePeptideShaker()
    Close the Reporter instance by clearing up factories and cache.
    static void
    main(String[] args)
    Starts the launcher by calling the launch method.
    String
    toString()
     

    Methods inherited from class eu.isas.peptideshaker.utils.PsdbParent

    close, getDbFolder, getDisplayParameters, getExtendedProjectReport, getFilterParameters, getGeneMaps, getIdentification, getIdentificationFeaturesGenerator, getIdentificationParameters, getMetrics, getProjectDetails, getProjectParameters, getProjectType, getProteinDetailsProvider, getPsdbFile, getPsdbImportFromZip, getSequenceProvider, getSpectrumCountingParameters, getSpectrumProvider, getUserParameters, loadFastaFile, loadPsdbFile, loadPsdbFromZipFile, loadSpectrumFile, loadSpectrumFile, loadSpectrumFiles, loadSpectrumFiles, resetIdentificationFeaturesGenerator, saveProject, setDbFolder, setDefaultParameters, setDisplayParameters, setFilterParameters, setGeneMaps, setIdentification, setIdentificationFeaturesGenerator, setIdentificationParameters, setMetrics, setMsFileHandler, setProject, setProjectDetails, setProjectType, setProteinDetailsProvider, setPsdbFile, setPsdbImportFromZip, setSequenceProvider, setSpectrumCountingParameters

    Methods inherited from class eu.isas.peptideshaker.preferences.UserPreferencesParent

    loadUserParameters, saveUserParameters

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • ReportCLI

      public ReportCLI(ReportCLIInputBean reportCLIInputBean)
      Construct a new ReportCLI runnable from a ReportCLI Bean. When initialization is successful, calling "run" will open the PeptideShaker project and write the desired output files.
      Parameters:
      reportCLIInputBean - the input bean

  • Method Details

    • call

      public Object call()
      Calling this method will run the configured Reporter process.
      Returns:
      returns 1 if the process was canceled

    • main

      public static void main(String[] args)
      Starts the launcher by calling the launch method. Use this as the main class in the jar file.
      Parameters:
      args - the command line arguments

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • closePeptideShaker

      public void closePeptideShaker() throws IOException, SQLException, InterruptedException
      Close the Reporter instance by clearing up factories and cache.
      Throws:
      IOException - thrown if an exception occurred when closing the connection to a file
      SQLException - thrown if an exception occurred when closing the connection to the back-end database
      InterruptedException - thrown if a threading error occurred