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,
Integer peptideCharge,
MSnSpectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
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, Integer peptideCharge, MSnSpectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex) throws InterruptedException, org.apache.commons.math.MathException
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrum
- the spectrum of interestidentificationParameters
- the identification parametersspecificAnnotationPreferences
- the annotation preferences specific
to this PSMpeptideSpectrumAnnotator
- the spectrum annotator to usescoreIndex
- the index of the score to useInterruptedException
- exception thrown if the thread is
interruptedorg.apache.commons.math.MathException
- exception thrown if a math exception occurred when estimating the noise levelpublic double getScore(Peptide peptide, Integer peptideCharge, MSnSpectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex) throws InterruptedException, org.apache.commons.math.MathException
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrum
- the spectrum of interestidentificationParameters
- the identification parametersspecificAnnotationPreferences
- the annotation preferences specific
to this PSMpeptideSpectrumAnnotator
- the spectrum annotator to usescoreIndex
- the index of the score to useInterruptedException
- exception thrown if the thread is
interruptedorg.apache.commons.math.MathException
- exception thrown if a math exception occurred when estimating the noise levelpublic double getScore(Peptide peptide, Integer peptideCharge, MSnSpectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator, PsmScore psmScore) throws InterruptedException, org.apache.commons.math.MathException
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrum
- the spectrum of interestidentificationParameters
- the identification parametersspecificAnnotationPreferences
- the annotation preferences specific
to this psmpeptideSpectrumAnnotator
- the spectrum annotator to usepsmScore
- the score to useInterruptedException
- exception thrown if the thread is
interruptedorg.apache.commons.math.MathException
- exception thrown if a math exception occurred when estimating the noise levelCopyright © 2019. All rights reserved.