public class SnrScore extends Object
Constructor and Description |
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SnrScore()
Constructor.
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Modifier and Type | Method and Description |
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double |
getScore(Peptide peptide,
Spectrum spectrum,
ArrayList<IonMatch> ionMatchesList)
Returns the score.
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double |
getScore(Peptide peptide,
Spectrum spectrum,
HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.
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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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public double getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
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 mappingpublic double getScore(Peptide peptide, Spectrum spectrum, ArrayList<IonMatch> ionMatchesList)
peptide
- the peptide of interestspectrum
- the spectrum of interestionMatchesList
- the ion matches obtained from spectrum annotationpublic double getScore(Peptide peptide, Spectrum spectrum, HashMap<Double,ArrayList<IonMatch>> ionMatches)
peptide
- the peptide of interestspectrum
- the spectrum of interestionMatches
- the ion matches obtained from spectrum annotation
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