eu.isas.peptideshaker.protein_inference

Class ProteinInference

java.lang.Object

eu.isas.peptideshaker.protein_inference.ProteinInference

public class ProteinInference
extends Object

This class groups the methods for protein inference.

Author:

Marc Vaudel, Harald Barsnes

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ProteinInference.GroupSimplificationOption

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	KEYWORDS_UNCHARACTERIZED Key words used to flag uncharacterized proteins.

Constructor Summary

Constructors

Constructor and Description
ProteinInference()

Method Summary

Modifier and Type	Method and Description
void	distributeSharedPeptides(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler) Distribute the shared peptides among the protein groups.
void	inferPiStatus(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, TargetDecoyMap proteinMap, 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) Selects the leading protein of protein groups and infers PI status of peptide and proteins.
void	inferPiStatus(com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, TargetDecoyMap proteinMap, 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) Selects the leading protein of protein groups and infers PI status of peptide and proteins.

Methods inherited from class java.lang.Object

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

Field Detail

KEYWORDS_UNCHARACTERIZED

public static final String[] KEYWORDS_UNCHARACTERIZED

Key words used to flag uncharacterized proteins.

Constructor Detail

ProteinInference

public ProteinInference()

Method Detail

inferPiStatus

public void inferPiStatus(com.compomics.util.experiment.identification.Identification identification,
                          com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics,
                          TargetDecoyMap proteinMap,
                          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)

Selects the leading protein of protein groups and infers PI status of peptide and proteins.

Parameters:

identification - the identification class containing all identification matches

metrics - if provided protein metrics will be loaded while iterating the groups

proteinMap - the protein matches scoring map

identificationParameters - the identification parameters

sequenceProvider - the sequence provider

proteinDetailsProvider - the protein details provider

waitingHandler - the handler displaying feedback to the user

inferPiStatus

public void inferPiStatus(com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch,
                          com.compomics.util.experiment.identification.Identification identification,
                          com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics,
                          TargetDecoyMap proteinMap,
                          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)

Selects the leading protein of protein groups and infers PI status of peptide and proteins.

Parameters:

proteinMatch - the protein match

identification - the identification class containing all identification matches

metrics - if provided protein metrics will be loaded while iterating the groups

proteinMap - the protein matches scoring map

identificationParameters - the identification parameters

sequenceProvider - the sequence provider

proteinDetailsProvider - the protein details provider

waitingHandler - the handler displaying feedback to the user

distributeSharedPeptides

public void distributeSharedPeptides(com.compomics.util.experiment.identification.Identification identification,
                                     com.compomics.util.waiting.WaitingHandler waitingHandler)

Distribute the shared peptides among the protein groups.

Parameters:

identification - the identification class containing all identification matches

waitingHandler - the handler displaying feedback to the user