Package eu.isas.reporter.cli

Class ReporterCLI

java.lang.Object
eu.isas.peptideshaker.preferences.UserPreferencesParent
eu.isas.peptideshaker.utils.PsdbParent
eu.isas.reporter.cli.ReporterCLI
All Implemented Interfaces:
AutoCloseable, Callable
public class ReporterCLI extends eu.isas.peptideshaker.utils.PsdbParent implements Callable
Command line interface for reporter.
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

  • Method Summary

    Modifier and Type
    Method
    Description
    Object
    call()
     
    static void
    close(com.compomics.util.experiment.identification.Identification identification)
    Close the Reporter instance.
    static boolean
    isValidCommandLine(org.apache.commons.cli.CommandLine aLine)
    Indicates whether the command line is valid.
    static void
    main(String[] args)
    Starts the launcher by calling the launch method.
    static void
    redirectErrorStream(File logFolder)
    Redirects the error stream to the Reporter.log file in the given folder.

    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, toString, wait, wait, wait

  • Method Details

    • isValidCommandLine

      public static boolean isValidCommandLine(org.apache.commons.cli.CommandLine aLine)
      Indicates whether the command line is valid.
      Parameters:
      aLine - the command line
      Returns:
      a boolean indicating whether the command line is valid

    • call

      public Object call() throws IOException, ClassNotFoundException
      Specified by:
      call in interface Callable
      Throws:
      IOException
      ClassNotFoundException

    • close

      public static void close(com.compomics.util.experiment.identification.Identification identification) throws IOException, SQLException
      Close the Reporter instance. Closes file connections and deletes temporary files.
      Parameters:
      identification - the identification
      Throws:
      IOException - thrown of IOException occurs
      SQLException - thrown if SQLException occurs

    • 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

    • redirectErrorStream

      public static void redirectErrorStream(File logFolder)
      Redirects the error stream to the Reporter.log file in the given folder.
      Parameters:
      logFolder - the folder where to save the log