eu.isas.peptideshaker.scoring.psm_scoring

Class PsmScorer

java.lang.Object

eu.isas.peptideshaker.scoring.psm_scoring.PsmScorer

public class PsmScorer
extends Object

This class scores peptide spectrum matches.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PsmScorer(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, 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
void	estimateIntermediateScoreProbabilities(com.compomics.util.experiment.identification.Identification identification, InputMap inputMap, com.compomics.util.parameters.tools.ProcessingParameters processingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler) Estimates the probabilities associated to the intermediate PSM scores.
void	estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification, InputMap inputMap, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Scores the PSMs contained in an identification object.
ArrayList<Integer>	estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, InputMap inputMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator, com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore hyperScore, com.compomics.util.waiting.WaitingHandler waitingHandler) Scores the PSMs contained in an identification object.
void	scorePsms(com.compomics.util.experiment.identification.Identification identification, InputMap inputMap, com.compomics.util.parameters.tools.ProcessingParameters processingPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) Attaches a score to the PSMs.

Methods inherited from class java.lang.Object

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

Constructor Detail

PsmScorer

public PsmScorer(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters,
                 com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)

Constructor.

Parameters:

fastaParameters - The fasta parsing parameters.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

Method Detail

estimateIntermediateScores

public void estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification,
                                       InputMap inputMap,
                                       com.compomics.util.parameters.tools.ProcessingParameters processingParameters,
                                       com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                       com.compomics.util.waiting.WaitingHandler waitingHandler,
                                       com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
                                throws InterruptedException,
                                       TimeoutException

Scores the PSMs contained in an identification object.

Parameters:

identification - the object containing the identification matches

inputMap - the input map scores

processingParameters - the processing preferences

identificationParameters - identification parameters used

waitingHandler - the handler displaying feedback to the user

exceptionHandler - a handler for exceptions

Throws:

InterruptedException - exception thrown if a thread is interrupted

TimeoutException - exception thrown if the process times out

estimateIntermediateScores

public ArrayList<Integer> estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification,
                                                     com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
                                                     InputMap inputMap,
                                                     com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                                     com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator,
                                                     com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore hyperScore,
                                                     com.compomics.util.waiting.WaitingHandler waitingHandler)

Scores the PSMs contained in an identification object.

Parameters:

identification - the object containing the identification matches

spectrumMatch - a spectrum match containing the peptides and spectrum to score

inputMap - the input map scores

identificationParameters - identification parameters used

peptideSpectrumAnnotator - the spectrum annotator to use

hyperScore - the object to use to compute the hyperscore

waitingHandler - the handler displaying feedback to the user

Returns:

a list of advocates where no e-values could be found

estimateIntermediateScoreProbabilities

public void estimateIntermediateScoreProbabilities(com.compomics.util.experiment.identification.Identification identification,
                                                   InputMap inputMap,
                                                   com.compomics.util.parameters.tools.ProcessingParameters processingPreferences,
                                                   com.compomics.util.waiting.WaitingHandler waitingHandler)

Estimates the probabilities associated to the intermediate PSM scores.

Parameters:

identification - the object containing the identification matches

inputMap - the input map scores

processingPreferences - the processing preferences

waitingHandler - the handler displaying feedback to the user

scorePsms

public void scorePsms(com.compomics.util.experiment.identification.Identification identification,
                      InputMap inputMap,
                      com.compomics.util.parameters.tools.ProcessingParameters processingPreferences,
                      com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                      com.compomics.util.waiting.WaitingHandler waitingHandler)

Attaches a score to the PSMs.

Parameters:

identification - the object containing the identification matches

inputMap - the input map scores

processingPreferences - the processing preferences

identificationParameters - the identification parameters

waitingHandler - the handler displaying feedback to the user