Package eu.isas.peptideshaker.fileimport

Class PsmFirstHitRunnable

java.lang.Object
eu.isas.peptideshaker.fileimport.PsmFirstHitRunnable
All Implemented Interfaces:
Runnable
public class PsmFirstHitRunnable
extends Object
implements Runnable
This class tries to find a best hit per search engine for each spectrum match.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors 
    Constructor Description
    PsmFirstHitRunnable​(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, InputMap inputMap, HashMap<String,​Integer> proteinCount, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
    Constructor.

  • Method Summary

    Modifier and Type Method Description
    HashSet<Integer> getCharges()
    Returns the different charges found.
    double getMaxPeptideErrorDa()
    Returns the maximal peptide mass error found in Da.
    double getMaxPeptideErrorPpm()
    Returns the maximal peptide mass error found in ppm.
    double getMaxTagErrorDa()
    Returns the maximal tag mass error found in Da.
    double getMaxTagErrorPpm()
    Returns the maximal tag mass error found in ppm.
    int getMissingProteins()
    Returns the number of PSMs where a protein was missing.
    int getnRetained()
    Returns the number of PSMs retained after filtering.
    int getPeptideIssue()
    Returns the number of PSMs which did not pass the import filters due to a peptide issue.
    int getPrecursorIssue()
    Returns the number of PSMs which did not pass the import filters due to a precursor issue.
    int getProteinIssue()
    Returns the number of PSMs which did not pass the import filters due to a protein issue.
    int getPsmsRejected()
    Returns the number of PSMs which did not pass the import filters.
    void run()  

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PsmFirstHitRunnable

      public PsmFirstHitRunnable​(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, InputMap inputMap, HashMap<String,​Integer> proteinCount, 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.
      sequenceProvider - The protein sequence provider.
      spectrumProvider - The spectrum provider.
      inputMap - The input scores map.
      proteinCount - The map of protein occurrence.
      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

    • getCharges

      public HashSet<Integer> getCharges()
      Returns the different charges found.
      Returns:
      the different charges found

    • getMaxPeptideErrorPpm

      public double getMaxPeptideErrorPpm()
      Returns the maximal peptide mass error found in ppm.
      Returns:
      the maximal peptide mass error found in ppm

    • getMaxPeptideErrorDa

      public double getMaxPeptideErrorDa()
      Returns the maximal peptide mass error found in Da.
      Returns:
      the maximal peptide mass error found in Da

    • getMaxTagErrorPpm

      public double getMaxTagErrorPpm()
      Returns the maximal tag mass error found in ppm.
      Returns:
      the maximal tag mass error found in ppm

    • getMaxTagErrorDa

      public double getMaxTagErrorDa()
      Returns the maximal tag mass error found in Da.
      Returns:
      the maximal tag mass error found in Da

    • getPsmsRejected

      public int getPsmsRejected()
      Returns the number of PSMs which did not pass the import filters.
      Returns:
      the number of PSMs which did not pass the import filters

    • getProteinIssue

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

    • 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

    • getPrecursorIssue

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

    • getMissingProteins

      public int getMissingProteins()
      Returns the number of PSMs where a protein was missing.
      Returns:
      the number of PSMs where a protein was missing

    • getnRetained

      public int getnRetained()
      Returns the number of PSMs retained after filtering.
      Returns:
      the number of PSMs retained after filtering