Package eu.isas.peptideshaker.scoring.psm_scoring

Class BestMatchSelection

java.lang.Object
eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection
public class BestMatchSelection extends Object
This class contains the method for PSM best hit selection.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    BestMatchSelection(HashMap<String,Integer> proteinCount, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
    getBestMatch(String spectrumFile, String spectrumTitle, ArrayList<com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption> assumptions)
    Returns the best match for the given spectrum among the given peptide assumptions.
    com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
    getBestMatch(String spectrumFile, String spectrumTitle, ArrayList<com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption> assumptions, boolean silentFail)
    Returns the best match for the given spectrum among the given peptide assumptions.
    void
    selectBestHit(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, InputMap inputMap, TargetDecoyMap psmTargetDecoyMap, com.compomics.util.experiment.identification.Identification identification)
    Selects the best hit.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • BestMatchSelection

      public BestMatchSelection(HashMap<String,Integer> proteinCount, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator)
      Constructor.
      Parameters:
      proteinCount - Map of the occurrence of the protein accessions.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      identificationParameters - The identification parameters.
      peptideSpectrumAnnotator - The peptide spectrum annotator.

  • Method Details

    • selectBestHit

      public void selectBestHit(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, InputMap inputMap, TargetDecoyMap psmTargetDecoyMap, com.compomics.util.experiment.identification.Identification identification)
      Selects the best hit.
      Parameters:
      spectrumMatch - The spectrum match.
      inputMap - The input map.
      psmTargetDecoyMap - The PSM target decoy map.
      identification - The identification class.

    • getBestMatch

      public com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption getBestMatch(String spectrumFile, String spectrumTitle, ArrayList<com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption> assumptions)
      Returns the best match for the given spectrum among the given peptide assumptions.
      Parameters:
      spectrumFile - The file name of the spectrum.
      spectrumTitle - The title of the spectrum.
      assumptions - A list of peptide assumptions.
      Returns:
      The best match.

    • getBestMatch

      public com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption getBestMatch(String spectrumFile, String spectrumTitle, ArrayList<com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption> assumptions, boolean silentFail)
      Returns the best match for the given spectrum among the given peptide assumptions.
      Parameters:
      spectrumFile - The file name of the spectrum.
      spectrumTitle - The title of the spectrum.
      assumptions - A list of peptide assumptions.
      silentFail - If true, no exception will be thrown if ties cannot be broken and the first of the best hits will be returned.
      Returns:
      The best match.