Class PsmScoresEstimator
java.lang.Object
com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
public class PsmScoresEstimator extends Object
This class can be used to estimate PSM scores.
- Author:
- Marc Vaudel
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Constructor Summary
Constructors Constructor Description PsmScoresEstimator()
Constructor using a uniform fragmentation.PsmScoresEstimator(PeptideFragmentationModel peptideFragmentationModel)
Constructor. -
Method Summary
Modifier and Type Method Description double
getDecreasingScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)
Scores the match between the given peptide and spectrum using the given score.double
getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)
Scores the match between the given peptide and spectrum using the given score.double
getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, PsmScore psmScore)
Scores the match between the given peptide and spectrum using the given score.
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Constructor Details
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PsmScoresEstimator
Constructor.- Parameters:
peptideFragmentationModel
- the peptide fragmentation model to use
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PsmScoresEstimator
public PsmScoresEstimator()Constructor using a uniform fragmentation.
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Method Details
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getDecreasingScore
public double getDecreasingScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)Scores the match between the given peptide and spectrum using the given score. The score is forced to decrease with the quality of the match by taking the opposite value when relevant.- Parameters:
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumspectrum
- the spectrum of interestidentificationParameters
- the identification parametersspecificAnnotationParameters
- the annotation preferences specific to this PSMmodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mappingpeptideSpectrumAnnotator
- the spectrum annotator to usescoreIndex
- the index of the score to use- Returns:
- the score of the match
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getScore
public double getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)Scores the match between the given peptide and spectrum using the given score.- Parameters:
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumspectrum
- the spectrum of interestidentificationParameters
- the identification parametersspecificAnnotationParameters
- the annotation preferences specific to this PSMmodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mappingpeptideSpectrumAnnotator
- the spectrum annotator to usescoreIndex
- the index of the score to use- Returns:
- the score of the match
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getScore
public double getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, PsmScore psmScore)Scores the match between the given peptide and spectrum using the given score.- Parameters:
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrum
- the spectrum of interestspectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumidentificationParameters
- the identification parametersspecificAnnotationParameters
- the annotation preferences specific to this psmmodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mappingpeptideSpectrumAnnotator
- the spectrum annotator to usepsmScore
- the score to use- Returns:
- the score of the match
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