Package eu.isas.peptideshaker.scoring.psm_scoring

Class TieBreaker

java.lang.Object
eu.isas.peptideshaker.scoring.psm_scoring.TieBreaker
public class TieBreaker extends Object
This class breaks ties between equally scoring peptides.
Author:
Marc Vaudel

  • Constructor Summary

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

  • Method Summary

    Modifier and Type
    Method
    Description
    com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
    getBestPeptideAssumption(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption1, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption2, boolean silentFail)
    Returns the best assumption between the two given possibilities for the given spectrum.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • TieBreaker

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

  • Method Details

    • getBestPeptideAssumption

      public com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption getBestPeptideAssumption(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption1, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption2, boolean silentFail)
      Returns the best assumption between the two given possibilities for the given spectrum.
      Parameters:
      spectrumFile - The spectrum file name.
      spectrumTitle - The spectrum title.
      peptideAssumption1 - The first possible peptide.
      peptideAssumption2 - The second possible peptide.
      silentFail - If false an exception will be thrown if tie could not be broken.
      Returns:
      The best assumption between the two given possibilities for the given spectrum.