Package eu.isas.peptideshaker.fileimport

Class PsmImportRunnable

java.lang.Object
eu.isas.peptideshaker.fileimport.PsmImportRunnable
All Implemented Interfaces:
Runnable
public class PsmImportRunnable
extends Object
implements Runnable
Runnable for the import of PSMs.
Author:
Marc Vaudel

  • Field Summary

    Fields 
    Modifier and Type Field Description
    static int BATCH_SIZE
    Size of the batches to use when adding objects to the database.

  • Constructor Summary

    Constructors 
    Constructor Description
    PsmImportRunnable​(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.identification.IdfileReader fileReader, File idFile, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
    Constructor.

  • Method Summary

    Modifier and Type Method Description
    int getModificationIssue()
    Returns the number of PSMs which did not pass the import filters due to a modification parsing issue.
    long getnPeptideAssumptionsTotal()
    Returns the total number of peptide assumptions parsed.
    long getnPSMs()
    Returns the number of PSMs processed.
    int getPeptideIssue()
    Returns the number of PSMs which did not pass the import filters due to a peptide issue.
    HashMap<String,​Integer> getProteinCount()
    Returns the occurrence of each protein.
    void run()  

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

    • PsmImportRunnable

      public PsmImportRunnable​(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.identification.IdfileReader fileReader, File idFile, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
      Constructor.
      Parameters:
      spectrumMatchQueue - the spectrum matches iterator to use
      identificationParameters - the identification parameters
      fileReader - the reader of the file which the matches are imported from
      idFile - the file which the matches are imported from
      identification - the identification object where to store the matches
      sequenceProvider - the protein sequence provider
      fastaMapper - the FASTA mapper used to map peptides to proteins
      waitingHandler - The waiting handler to display feedback to the user.
      exceptionHandler - The handler of exceptions.

  • Method Details

    • run

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

    • getnPSMs

      public long getnPSMs()
      Returns the number of PSMs processed.
      Returns:
      the number of PSMs processed

    • getnPeptideAssumptionsTotal

      public long getnPeptideAssumptionsTotal()
      Returns the total number of peptide assumptions parsed.
      Returns:
      the total number of peptide assumptions parsed

    • getPeptideIssue

      public int getPeptideIssue()
      Returns the number of PSMs which did not pass the import filters due to a peptide issue.
      Returns:
      the number of PSMs which did not pass the import filters due to a peptide issue

    • getModificationIssue

      public int getModificationIssue()
      Returns the number of PSMs which did not pass the import filters due to a modification parsing issue.
      Returns:
      the number of PSMs which did not pass the import filters due to a modification parsing issue

    • getProteinCount

      public HashMap<String,​Integer> getProteinCount()
      Returns the occurrence of each protein.
      Returns:
      the occurrence of each protein