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 and Description
GroupSimplification()

Method Summary

Modifier and Type	Method and 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 Detail

GroupSimplification

public GroupSimplification()

Method Detail

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