public class MatchesValidator extends Object
| Constructor and Description |
|---|
MatchesValidator(TargetDecoyMap psmMap,
TargetDecoyMap peptideMap,
TargetDecoyMap proteinMap)
Constructor.
|
| 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.
|
public MatchesValidator(TargetDecoyMap psmMap, TargetDecoyMap peptideMap, TargetDecoyMap proteinMap)
psmMap - the PSM target decoy mappeptideMap - the peptide target decoy mapproteinMap - the protein target decoy mappublic 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
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.InterruptedException - exception thrown if a thread gets
interruptedTimeoutException - exception thrown if the
operation times outpublic 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)
identification - the identification objectgeneMaps - the gene mapsproteinMap - the protein level target/decoy scoring mapidentificationFeaturesGenerator - the identification features
generatorsequenceProvider - a protein sequence providerspectrumProvider - The spectrum provider.proteinDetailsProvider - a protein details providerproteinKey - the key of the protein match of interestidentificationParameters - the identification parameterspublic 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)
identification - the identification objecttargetDecoyMap - the protein level target/decoy mapsequenceProvider - a protein sequence providerspectrumProvider - The spectrum provider.proteinDetailsProvider - a protein details providergeneMaps - the gene mapsscoreThreshold - the validation score doubtfulThresholdconfidenceThreshold - the confidence doubtfulThreshold after which a
match should be considered as confidentnoValidated - boolean indicating whether no validation was actually
conductednTargetLimit - the limit in number of target hits before the first
decoy hitidentificationFeaturesGenerator - the identification features
generatorproteinKey - the key of the protein match of interestidentificationParameters - the identification parameterspublic 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)
identification - the identification objectpeptideMap - the peptide level target/decoy scoring mapidentificationFeaturesGenerator - the identification features
generatorsequenceProvider - a protein sequence providerproteinDetailsProvider - a protein details providerspectrumProvider - The spectrum provider.geneMaps - the gene mapsidentificationParameters - the identification parameterspeptideKey - the key of the peptide match of interestpublic 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)
identification - the identification objectgeneMaps - the gene mapspsmMap - the PSM level target/decoy scoring mapidentificationParameters - the identification parametersidentificationFeaturesGenerator - the identification features
generatorsequenceProvider - a protein sequence providerproteinDetailsProvider - a protein details providerspectrumProvider - The spectrum provider.spectrumMatchKey - the key of the spectrum match of interestapplyQCFilters - if true quality control filters will be usedpublic 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)
identification - the identification object containing the match to
filteridentificationFeaturesGenerator - the identification features
generatorsequenceProvider - a protein sequence providerproteinDetailsProvider - a protein details providerspectrumProvider - The spectrum provider.inputMap - the target decoy map of all search engine scoresspectrumMatchKey - the key of the spectrum match having this
assumptionpeptideAssumption - the peptide assumption of interestidentificationParameters - the identification parametersapplyQCFilters - boolean indicating whether QC filters should be
appliedpublic 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)
identification - the identification class containing the matches to
validatemetrics - if provided fraction information and found modifications
will be saved while iterating the matchesidentificationParameters - the identification parameterswaitingHandler - the handler displaying feedback to the usersequenceProvider - the sequence providerspectrumProvider - The spectrum provider.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)
identification - the identification class containing the matches to
validatefastaParameters - the FASTA file parameterswaitingHandler - the handler displaying feedback to the userpublic void fillProteinMap(com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler)
identification - the identification class containing the matches to
validatespectrumProvider - The spectrum provider.waitingHandler - the handler displaying feedback to the userpublic 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)
identification - the identification class containing the matches to
validatesequenceProvider - the sequence providerfastaParameters - the FASTA file parametersmetrics - if provided fraction informationwaitingHandler - the handler displaying feedback to the userfractionParameters - the fraction parameterspublic TargetDecoyMap getPsmMap()
public void setPsmMap(TargetDecoyMap psmMap)
psmMap - the PSM scoring specific mappublic TargetDecoyMap getPeptideMap()
public void setPeptideMap(TargetDecoyMap peptideMap)
peptideMap - the peptide scoring specific mappublic TargetDecoyMap getProteinMap()
public void setProteinMap(TargetDecoyMap proteinMap)
proteinMap - the protein scoring mappublic static void setDefaultMatchesQCFilters(com.compomics.util.parameters.identification.advanced.ValidationQcParameters validationQCParameters)
validationQCParameters - the default matches quality control filtersCopyright © 2021. All rights reserved.