Package 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
    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
    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.
    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
    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.
    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 Details

    • 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 Details

    • 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