Package eu.isas.peptideshaker.stirred.modules

Class IdImporter

java.lang.Object
eu.isas.peptideshaker.stirred.modules.IdImporter
public class IdImporter extends Object
This class imports the ids from a file.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    IdImporter(File searchEngineResultsFile, com.compomics.software.log.CliLogger cliLogger)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    com.compomics.util.experiment.io.identification.IdfileReader
    getIdFileReader()
    Returns the identification file reader used.
    ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch>
    loadSpectrumMatches(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Parses the spectrum matches and returns them in an ArrayList.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • IdImporter

      public IdImporter(File searchEngineResultsFile, com.compomics.software.log.CliLogger cliLogger)
      Constructor.
      Parameters:
      searchEngineResultsFile - The search engine results file.
      cliLogger - The logger to use for CLI report.

  • Method Details

    • loadSpectrumMatches

      public ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch> loadSpectrumMatches(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Parses the spectrum matches and returns them in an ArrayList.
      Parameters:
      identificationParameters - The identification parameters to use.
      spectrumProvider - The spectrum provider to use.
      waitingHandler - The waiting handler to use.
      Returns:
      The spectrum matches in an ArrayList.

    • getIdFileReader

      public com.compomics.util.experiment.io.identification.IdfileReader getIdFileReader()
      Returns the identification file reader used.
      Returns:
      The identification file reader.