public class PsmScoresEstimator extends Object
Constructor and Description |
---|
PsmScoresEstimator()
Constructor using a uniform fragmentation.
|
PsmScoresEstimator(PeptideFragmentationModel peptideFragmentationModel)
Constructor.
|
Modifier and Type | Method and 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.
|
public PsmScoresEstimator(PeptideFragmentationModel peptideFragmentationModel)
peptideFragmentationModel
- the peptide fragmentation model to usepublic PsmScoresEstimator()
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)
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 usepublic 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)
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 usepublic 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)
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 useCopyright © 2021. All rights reserved.