Class SnrScore
java.lang.Object
com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
public class SnrScore extends Object
This score uses the intensity distribution of the peaks to evaluate an SNR
score.
- Author:
- Marc Vaudel
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Constructor Summary
Constructors Constructor Description SnrScore()
Constructor. -
Method Summary
Modifier and Type Method Description double
getScore(Peptide peptide, Spectrum spectrum, ArrayList<IonMatch> ionMatchesList)
Returns the score.double
getScore(Peptide peptide, Spectrum spectrum, HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.double
getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the score.
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Constructor Details
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SnrScore
public SnrScore()Constructor.
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Method Details
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getScore
public double getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)Returns the score.- Parameters:
peptide
- the peptide of interestspectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumspectrum
- the spectrum of interestannotationSettings
- the general spectrum annotation settingsspecificAnnotationSettings
- the annotation settings specific to this PSMpeptideSpectrumAnnotator
- the spectrum annotator to usemodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mapping- Returns:
- the score of the match
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getScore
Returns the score.- Parameters:
peptide
- the peptide of interestspectrum
- the spectrum of interestionMatchesList
- the ion matches obtained from spectrum annotation- Returns:
- the score of the match
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getScore
public double getScore(Peptide peptide, Spectrum spectrum, HashMap<Double,ArrayList<IonMatch>> ionMatches)Returns the score.- Parameters:
peptide
- the peptide of interestspectrum
- the spectrum of interestionMatches
- the ion matches obtained from spectrum annotation indexed by mz- Returns:
- the score of the match
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