Package eu.isas.peptideshaker.fileimport

Class PsmImporter

java.lang.Object
eu.isas.peptideshaker.fileimport.PsmImporter
public class PsmImporter extends Object
This class can be used to import PSMs from search engine results.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    PsmImporter()
    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
    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
    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.
    HashMap<String,Integer>
    getProteinCount()
    Returns the occurrence of each protein.
    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
    importPsms(ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, com.compomics.util.experiment.io.identification.IdfileReader fileReader, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
    Imports PSMs.
    static void
    verifyXTandemModifications(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
    Verifies that the modifications targeted by the quick acetyl and quick pyrolidone are included in the identification parameters.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PsmImporter

      public PsmImporter()
      Constructor.

  • Method Details

    • importPsms

      public void importPsms(ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, com.compomics.util.experiment.io.identification.IdfileReader fileReader, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) throws InterruptedException, TimeoutException
      Imports PSMs.
      Parameters:
      spectrumMatches - The PSMs to import.
      identification - The identification object.
      identificationParameters - The identification parameters.
      inputMap - The input map.
      fileReader - The file reader.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      fastaMapper - The sequence mapper.
      processingParameters - The processing parameters.
      waitingHandler - The waiting handler to display progress and allow canceling the import.
      exceptionHandler - The handler of exceptions.
      Throws:
      InterruptedException - Exception thrown if a thread is interrupted.
      TimeoutException - Exception thrown if the process timed out.

    • verifyXTandemModifications

      public static void verifyXTandemModifications(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
      Verifies that the modifications targeted by the quick acetyl and quick pyrolidone are included in the identification parameters.
      Parameters:
      identificationParameters - the identification parameters

    • 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

    • 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

    • 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

    • 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

    • 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

    • getProteinCount

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