Package eu.isas.peptideshaker.processing

Class ProteinProcessor

java.lang.Object
eu.isas.peptideshaker.processing.ProteinProcessor
public class ProteinProcessor extends Object
Scores modification localization on proteins, estimates spectrum counting and summary statistics values.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    ProteinProcessor(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    processProteins(ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.parameters.tools.ProcessingParameters processingParameters)
    Scores the PTMs of all protein matches contained in an identification object, estimates spectrum counting and summary statistics.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • ProteinProcessor

      public ProteinProcessor(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
      Constructor.
      Parameters:
      identification - the identification
      identificationParameters - the identification parameters
      identificationFeaturesGenerator - the identification features generator
      sequenceProvider - the sequence provider

  • Method Details

    • processProteins

      public void processProteins(ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.parameters.tools.ProcessingParameters processingParameters) throws InterruptedException, TimeoutException
      Scores the PTMs of all protein matches contained in an identification object, estimates spectrum counting and summary statistics.
      Parameters:
      modificationLocalizationScorer - The modification localization scorer to use.
      metrics - If provided, metrics on proteins will be saved while iterating the matches.
      modificationProvider - The modification provider to use.
      waitingHandler - The handler displaying feedback to the user.
      exceptionHandler - The exception handler to use.
      processingParameters - The processing parameters.
      Throws:
      InterruptedException - exception thrown if a thread gets interrupted
      TimeoutException - exception thrown if the operation times out