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

Class IntensityRankScore

java.lang.Object

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

public class IntensityRankScore
extends Object

The intensity rank sub-score as adapted from the DirecTag manuscript (http://www.ncbi.nlm.nih.gov/pubmed/18630943).

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
IntensityRankScore()

Method Summary

Modifier and Type	Method and Description
static double	getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences) Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.
static double	getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator) Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.

Methods inherited from class java.lang.Object

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

Constructor Detail

IntensityRankScore

public IntensityRankScore()

Method Detail

getScore

public static double getScore(Peptide peptide,
                              MSnSpectrum spectrum,
                              AnnotationSettings annotationPreferences,
                              SpecificAnnotationSettings specificAnnotationPreferences)

Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks. The score goes from the most intense peaks to the lowest and returns the intensity rank at which more than 1% of the total number of peaks is not annotated.

Parameters:

peptide - the peptide of interest

spectrum - the spectrum of interest

annotationPreferences - the general spectrum annotation preferences

specificAnnotationPreferences - the annotation preferences specific to this psm

Returns:

the score of the match

getScore

public static double getScore(Peptide peptide,
                              MSnSpectrum spectrum,
                              AnnotationSettings annotationPreferences,
                              SpecificAnnotationSettings specificAnnotationPreferences,
                              PeptideSpectrumAnnotator peptideSpectrumAnnotator)

Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks. The score goes from the most intense peaks to the lowest and returns the intensity rank at which more than 1% of the total number of peaks is not annotated.

Parameters:

peptide - the peptide of interest

spectrum - the spectrum of interest

annotationPreferences - the general spectrum annotation preferences

specificAnnotationPreferences - the annotation preferences specific to this psm

peptideSpectrumAnnotator - an external annotator (if null an internal will be used)

Returns:

the score of the match