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 and 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 and 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 Detail

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 Detail

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.