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 and 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 and 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 Detail

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 Detail

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.