Package eu.isas.peptideshaker.protein_inference

Class GroupSimplification

java.lang.Object
eu.isas.peptideshaker.protein_inference.GroupSimplification
public class GroupSimplification extends Object
This class handles the simplification of redundant groups based on the protein inference settings.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    GroupSimplification()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static boolean
    isLowerEvidence(String accession, String[] otherAccessions, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
    Returns a boolean indicating whether the protein is considered as uncharacterized compared to the others.
    void
    removeRedundantGroups(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.identification.matches.ProteinMatch proteinSharedGroup, HashMap<Long,long[]> processedKeys, HashSet<Long> toDelete, com.compomics.util.threading.SimpleSemaphore mutex, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Removes the redundant groups for the given protein shared group.
    void
    removeRedundantGroups(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Remove groups that can be explained by a simpler group.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • GroupSimplification

      public GroupSimplification()

  • Method Details

    • removeRedundantGroups

      public void removeRedundantGroups(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Remove groups that can be explained by a simpler group.
      Parameters:
      identification - the identification class containing all identification matches
      identificationParameters - the identification parameters
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider
      waitingHandler - the handler displaying feedback to the user

    • removeRedundantGroups

      public void removeRedundantGroups(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.identification.matches.ProteinMatch proteinSharedGroup, HashMap<Long,long[]> processedKeys, HashSet<Long> toDelete, com.compomics.util.threading.SimpleSemaphore mutex, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Removes the redundant groups for the given protein shared group.
      Parameters:
      identification - The identification object containing the identification matches.
      identificationParameters - The identification parameters.
      sequenceProvider - The protein sequence provider.
      proteinDetailsProvider - The protein details provider.
      proteinSharedGroup - The protein shared group investigated.
      processedKeys - Map of the already processed keys.
      toDelete - Set of the keys to delete.
      mutex - Mutex to synchronize the different threads.
      waitingHandler - Waiting handler to show progress and interrupt processes.

    • isLowerEvidence

      public static boolean isLowerEvidence(String accession, String[] otherAccessions, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
      Returns a boolean indicating whether the protein is considered as uncharacterized compared to the others.
      Parameters:
      accession - the accession of the protein
      otherAccessions - the accessions of the other protein
      proteinDetailsProvider - the protein details provider
      Returns:
      a boolean indicating whether the protein is considered as uncharacterized