Package com.compomics.util.experiment.identification.psm_scoring.psm_scores

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

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SnrScore

public SnrScore()

Constructor.

Method Details

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 interest

spectrumFile - the file of the spectrum

spectrumTitle - the title of the spectrum

spectrum - the spectrum of interest

annotationSettings - the general spectrum annotation settings

specificAnnotationSettings - the annotation settings specific to this PSM

peptideSpectrumAnnotator - the spectrum annotator to use

modificationParameters - the modification parameters

sequenceProvider - a provider for the protein sequences

modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping

Returns:

the score of the match

getScore

public double getScore(Peptide peptide,
 Spectrum spectrum,
 ArrayList<IonMatch> ionMatchesList)

Returns the score.

Parameters:

peptide - the peptide of interest

spectrum - the spectrum of interest

ionMatchesList - the ion matches obtained from spectrum annotation

Returns:

the score of the match

getScore

public double getScore(Peptide peptide,
 Spectrum spectrum,
 HashMap<Double,ArrayList<IonMatch>> ionMatches)

Returns the score.

Parameters:

peptide - the peptide of interest

spectrum - the spectrum of interest

ionMatches - the ion matches obtained from spectrum annotation indexed by mz

Returns:

the score of the match