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

  • Method Summary

    Modifier and Type
    Method
    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 Details

    • 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 Details

    • 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.
      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.
      geneMaps - The gene maps.
      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
      identificationFeaturesGenerator - the identification features generator
      sequenceProvider - a protein sequence provider
      spectrumProvider - The spectrum provider.
      proteinDetailsProvider - a protein details provider
      geneMaps - the gene maps
      identificationParameters - the identification parameters
      proteinMap - the protein level target/decoy scoring map
      proteinKey - the key of the protein match of interest

    • 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
      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
      targetDecoyMap - the protein level target/decoy map
      scoreThreshold - the validation score doubtfulThreshold
      nTargetLimit - the limit in number of target hits before the first decoy hit
      confidenceThreshold - the confidence doubtfulThreshold after which a match should be considered as confident
      noValidated - boolean indicating whether no validation was actually conducted
      proteinKey - the key of the protein match of interest

    • 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
      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
      peptideMap - the peptide level target/decoy scoring map
      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
      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
      psmMap - the PSM level target/decoy scoring map
      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.
      identificationParameters - the identification parameters
      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
      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
      waitingHandler - the handler displaying feedback to the user
      identificationParameters - the identification parameters
      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