eu.isas.peptideshaker.validation

Class MatchesValidator

java.lang.Object

eu.isas.peptideshaker.validation.MatchesValidator

public class MatchesValidator
extends Object

This class validates the quality of identification matches.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
MatchesValidator(TargetDecoyMap psmMap, TargetDecoyMap peptideMap, TargetDecoyMap proteinMap) Constructor.

Method Summary

Modifier and Type	Method and Description
void	attachPeptideProbabilities(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) Attaches the peptide posterior error probabilities to the peptide matches.
void	attachProteinProbabilities(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.parameters.identification.advanced.FractionParameters fractionParameters) Attaches the protein posterior error probability to the protein matches.
void	fillPeptideMaps(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider) Fills the peptide specific map.
void	fillProteinMap(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler) Fills the protein map.
TargetDecoyMap	getPeptideMap() Returns the peptide scoring specific map.
TargetDecoyMap	getProteinMap() Returns the protein scoring map.
TargetDecoyMap	getPsmMap() Returns the PSM scoring specific map.
static void	setDefaultMatchesQCFilters(com.compomics.util.parameters.identification.advanced.ValidationQcParameters validationQCParameters) Sets the default matches quality control filters.
void	setPeptideMap(TargetDecoyMap peptideMap) Sets the peptide scoring specific map.
void	setProteinMap(TargetDecoyMap proteinMap) Sets the protein scoring map.
void	setPsmMap(TargetDecoyMap psmMap) Sets the PSM scoring specific map.
static void	updatePeptideAssumptionValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, long spectrumMatchKey, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, boolean applyQCFilters) Updates the validation status of a peptide assumption.
static void	updatePeptideMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, TargetDecoyMap peptideMap, long peptideKey) Updates the validation status of a peptide match.
static void	updateProteinMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, TargetDecoyMap targetDecoyMap, double scoreThreshold, double nTargetLimit, double confidenceThreshold, boolean noValidated, long proteinKey) Updates the validation status of a protein match.
static void	updateProteinMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, TargetDecoyMap proteinMap, long proteinKey) Updates the validation status of a protein match.
static void	updateSpectrumMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, TargetDecoyMap psmMap, long spectrumMatchKey, boolean applyQCFilters) Updates the validation status of a spectrum match.
void	validateIdentifications(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, InputMap inputMap, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.parameters.tools.ProcessingParameters processingParameters) This method validates the identification matches of an identification object.

Methods inherited from class java.lang.Object

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

Constructor Detail

MatchesValidator

public MatchesValidator(TargetDecoyMap psmMap,
                        TargetDecoyMap peptideMap,
                        TargetDecoyMap proteinMap)

Constructor.

Parameters:

psmMap - the PSM target decoy map

peptideMap - the peptide target decoy map

proteinMap - the protein target decoy map

Method Detail

validateIdentifications

public void validateIdentifications(com.compomics.util.experiment.identification.Identification identification,
                                    com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics,
                                    InputMap inputMap,
                                    com.compomics.util.waiting.WaitingHandler waitingHandler,
                                    com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
                                    com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                    com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                    com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                    com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                                    com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                    com.compomics.util.parameters.peptide_shaker.ProjectType projectType,
                                    com.compomics.util.parameters.tools.ProcessingParameters processingParameters)
                             throws InterruptedException,
                                    TimeoutException

This method validates the identification matches of an identification object. Target Decoy thresholds must be set.

Parameters:

identification - The identification class containing the matches to validate.

metrics - If provided, metrics on fractions will be saved while iterating the matches.

geneMaps - The gene maps.

inputMap - The target decoy map of all search engine scores.

waitingHandler - The waiting handler displaying progress to the user and allowing canceling the process.

exceptionHandler - The handler for exceptions.

identificationFeaturesGenerator - The identification features generator computing information about the identification matches.

sequenceProvider - The protein sequence provider.

proteinDetailsProvider - The protein details provider.

spectrumProvider - The spectrum provider.

identificationParameters - The identification parameters.

projectType - The project type.

processingParameters - The processing parameters.

Throws:

InterruptedException - exception thrown if a thread gets interrupted

TimeoutException - exception thrown if the operation times out

updateProteinMatchValidationLevel

public static void updateProteinMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification,
                                                     com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                                     com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                                     com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                                     com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                                     com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                                                     com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                                     TargetDecoyMap proteinMap,
                                                     long proteinKey)

Updates the validation status of a protein match. If the match was manually validated nothing will be changed.

Parameters:

identification - the identification object

geneMaps - the gene maps

proteinMap - the protein level target/decoy scoring map

identificationFeaturesGenerator - the identification features generator

sequenceProvider - a protein sequence provider

spectrumProvider - The spectrum provider.

proteinDetailsProvider - a protein details provider

proteinKey - the key of the protein match of interest

identificationParameters - the identification parameters

updateProteinMatchValidationLevel

public static void updateProteinMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification,
                                                     com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                                     com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                                     com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                                     com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                                     com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                                                     com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                                     TargetDecoyMap targetDecoyMap,
                                                     double scoreThreshold,
                                                     double nTargetLimit,
                                                     double confidenceThreshold,
                                                     boolean noValidated,
                                                     long proteinKey)

Updates the validation status of a protein match. If the match was manually validated nothing will be changed.

Parameters:

identification - the identification object

targetDecoyMap - the protein level target/decoy map

sequenceProvider - a protein sequence provider

spectrumProvider - The spectrum provider.

proteinDetailsProvider - a protein details provider

geneMaps - the gene maps

scoreThreshold - the validation score doubtfulThreshold

confidenceThreshold - the confidence doubtfulThreshold after which a match should be considered as confident

noValidated - boolean indicating whether no validation was actually conducted

nTargetLimit - the limit in number of target hits before the first decoy hit

identificationFeaturesGenerator - the identification features generator

proteinKey - the key of the protein match of interest

identificationParameters - the identification parameters

updatePeptideMatchValidationLevel

public static void updatePeptideMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification,
                                                     com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                                     com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                                     com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                                     com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                                     com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                                                     com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                                     TargetDecoyMap peptideMap,
                                                     long peptideKey)

Updates the validation status of a peptide match. If the match was manually validated nothing will be changed.

Parameters:

identification - the identification object

peptideMap - the peptide level target/decoy scoring map

identificationFeaturesGenerator - the identification features generator

sequenceProvider - a protein sequence provider

proteinDetailsProvider - a protein details provider

spectrumProvider - The spectrum provider.

geneMaps - the gene maps

identificationParameters - the identification parameters

peptideKey - the key of the peptide match of interest

updateSpectrumMatchValidationLevel

public static void updateSpectrumMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification,
                                                      com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                                      com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                                      com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                                      com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                                      com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
                                                      com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                                      TargetDecoyMap psmMap,
                                                      long spectrumMatchKey,
                                                      boolean applyQCFilters)

Updates the validation status of a spectrum match. If the match was manually validated nothing will be changed.

Parameters:

identification - the identification object

geneMaps - the gene maps

psmMap - the PSM level target/decoy scoring map

identificationParameters - the identification parameters

identificationFeaturesGenerator - the identification features generator

sequenceProvider - a protein sequence provider

proteinDetailsProvider - a protein details provider

spectrumProvider - The spectrum provider.

spectrumMatchKey - the key of the spectrum match of interest

applyQCFilters - if true quality control filters will be used

updatePeptideAssumptionValidationLevel

public static void updatePeptideAssumptionValidationLevel(com.compomics.util.experiment.identification.Identification identification,
                                                          com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                                                          com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                                          com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
                                                          com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                                          com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                                          InputMap inputMap,
                                                          long spectrumMatchKey,
                                                          com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption,
                                                          boolean applyQCFilters)

Updates the validation status of a peptide assumption. If the match was manually validated nothing will be changed.

Parameters:

identification - the identification object containing the match to filter

identificationFeaturesGenerator - the identification features generator

sequenceProvider - a protein sequence provider

proteinDetailsProvider - a protein details provider

spectrumProvider - The spectrum provider.

inputMap - the target decoy map of all search engine scores

spectrumMatchKey - the key of the spectrum match having this assumption

peptideAssumption - the peptide assumption of interest

identificationParameters - the identification parameters

applyQCFilters - boolean indicating whether QC filters should be applied

fillPeptideMaps

public void fillPeptideMaps(com.compomics.util.experiment.identification.Identification identification,
                            com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics,
                            com.compomics.util.waiting.WaitingHandler waitingHandler,
                            com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                            com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                            com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)

Fills the peptide specific map.

Parameters:

identification - the identification class containing the matches to validate

metrics - if provided fraction information and found modifications will be saved while iterating the matches

identificationParameters - the identification parameters

waitingHandler - the handler displaying feedback to the user

sequenceProvider - the sequence provider

spectrumProvider - The spectrum provider.

attachPeptideProbabilities

public void attachPeptideProbabilities(com.compomics.util.experiment.identification.Identification identification,
                                       com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters,
                                       com.compomics.util.waiting.WaitingHandler waitingHandler)

Attaches the peptide posterior error probabilities to the peptide matches.

Parameters:

identification - the identification class containing the matches to validate

fastaParameters - the FASTA file parameters

waitingHandler - the handler displaying feedback to the user

fillProteinMap

public void fillProteinMap(com.compomics.util.experiment.identification.Identification identification,
                           com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                           com.compomics.util.waiting.WaitingHandler waitingHandler)

Fills the protein map.

Parameters:

identification - the identification class containing the matches to validate

spectrumProvider - The spectrum provider.

waitingHandler - the handler displaying feedback to the user

attachProteinProbabilities

public void attachProteinProbabilities(com.compomics.util.experiment.identification.Identification identification,
                                       com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                       com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters,
                                       com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics,
                                       com.compomics.util.waiting.WaitingHandler waitingHandler,
                                       com.compomics.util.parameters.identification.advanced.FractionParameters fractionParameters)

Attaches the protein posterior error probability to the protein matches.

Parameters:

identification - the identification class containing the matches to validate

sequenceProvider - the sequence provider

fastaParameters - the FASTA file parameters

metrics - if provided fraction information

waitingHandler - the handler displaying feedback to the user

fractionParameters - the fraction parameters

getPsmMap

public TargetDecoyMap getPsmMap()

Returns the PSM scoring specific map.

Returns:

the PSM scoring specific map

setPsmMap

public void setPsmMap(TargetDecoyMap psmMap)

Sets the PSM scoring specific map.

Parameters:

psmMap - the PSM scoring specific map

getPeptideMap

public TargetDecoyMap getPeptideMap()

Returns the peptide scoring specific map.

Returns:

the peptide scoring specific map

setPeptideMap

public void setPeptideMap(TargetDecoyMap peptideMap)

Sets the peptide scoring specific map.

Parameters:

peptideMap - the peptide scoring specific map

getProteinMap

public TargetDecoyMap getProteinMap()

Returns the protein scoring map.

Returns:

the protein scoring map

setProteinMap

public void setProteinMap(TargetDecoyMap proteinMap)

Sets the protein scoring map.

Parameters:

proteinMap - the protein scoring map

setDefaultMatchesQCFilters

public static void setDefaultMatchesQCFilters(com.compomics.util.parameters.identification.advanced.ValidationQcParameters validationQCParameters)

Sets the default matches quality control filters.

Parameters:

validationQCParameters - the default matches quality control filters