Package eu.isas.peptideshaker.stirred.modules

Class StirRunnable

java.lang.Object
eu.isas.peptideshaker.stirred.modules.StirRunnable
All Implemented Interfaces:
Runnable
public class StirRunnable extends Object implements Runnable
This class scores the modification localization.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    StirRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches, com.compomics.util.experiment.io.identification.IdfileReader idfileReader, com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter writer, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.software.log.CliLogger cliLogger)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    getnModificationIssues()
    Returns the number of peptides where the modification could not be parsed.
    int
    getnPeptides()
    Returns the total number of peptides processed.
    void
    run()
     

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • StirRunnable

      public StirRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches, com.compomics.util.experiment.io.identification.IdfileReader idfileReader, com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter writer, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.software.log.CliLogger cliLogger)
      Constructor.
      Parameters:
      spectrumMatches - The spectrum matches to process.
      idfileReader - The id file reader.
      writer - The mzIdentML writer.
      identificationParameters - The identification parameters.
      fastaMapper - The sequence mapper.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      cliLogger - The logger for CLI feedback.

  • Method Details

    • run

      public void run()
      Specified by:
      run in interface Runnable

    • getnModificationIssues

      public int getnModificationIssues()
      Returns the number of peptides where the modification could not be parsed.
      Returns:
      The number of peptides where the modification could not be parsed.

    • getnPeptides

      public int getnPeptides()
      Returns the total number of peptides processed.
      Returns:
      The total number of peptides processed.