Package eu.isas.peptideshaker.processing

Class PsmProcessor

java.lang.Object
eu.isas.peptideshaker.processing.PsmProcessor
public class PsmProcessor extends Object
Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    PsmProcessor(com.compomics.util.experiment.identification.Identification identification)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    processPsms(InputMap inputMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, MatchesValidator matchesValidator, ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, HashMap<String,Integer> proteinCount, int nThreads, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
    Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PsmProcessor

      public PsmProcessor(com.compomics.util.experiment.identification.Identification identification)
      Constructor.
      Parameters:
      identification - the identification

  • Method Details

    • processPsms

      public void processPsms(InputMap inputMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, MatchesValidator matchesValidator, ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, HashMap<String,Integer> proteinCount, int nThreads, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) throws InterruptedException, TimeoutException
      Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.
      Parameters:
      inputMap - The input map.
      identificationParameters - The identification parameters.
      matchesValidator - The matches validator.
      modificationLocalizationScorer - Post-translational modifications scorer.
      sequenceProvider - Protein sequence provider.
      spectrumProvider - The spectrum provider.
      modificationProvider - The modification provider to use.
      proteinCount - Map of the protein occurrence.
      nThreads - The number of threads to use.
      waitingHandler - Waiting handler to display progress and allow canceling the import.
      exceptionHandler - The handler of exceptions.
      Throws:
      InterruptedException - Exception thrown if a thread is interrupted.
      TimeoutException - Exception thrown if the process timed out.