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

Class AAIntensityRankScore

java.lang.Object

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

public class AAIntensityRankScore
extends Object

The intensity rank sub-score as adapted from the DirecTag paper where the minimal value per amino-scid is retained (http://www.ncbi.nlm.nih.gov/pubmed/18630943).

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static int	nBins The number of bins for the spectrum intensities.

Constructor Summary

Constructors

Constructor and Description
AAIntensityRankScore()

Method Summary

Methods

Modifier and Type	Method and Description
static double	getScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int identificationCharge, double mzTolerance) Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks.
static double	getScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int identificationCharge, double mzTolerance, 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

Field Detail

nBins

public static final int nBins

The number of bins for the spectrum intensities.

See Also:

Constant Field Values

Constructor Detail

AAIntensityRankScore

public AAIntensityRankScore()

Method Detail

getScore

public static double getScore(Peptide peptide,
              MSnSpectrum spectrum,
              HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
              NeutralLossesMap neutralLosses,
              ArrayList<Integer> charges,
              int identificationCharge,
              double mzTolerance)

Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks. For every amino-acid, the rank of the most intense peak is taken and the average value over the sequence is returned.

Parameters:

peptide - the peptide of interest

spectrum - the spectrum of interest

iontypes - the fragment ions to annotate

neutralLosses - the neutral losses to annotate

charges - the fragment charges to look for

identificationCharge - the precursor charge

mzTolerance - the ms2 m/z tolerance

Returns:

the score of the match

getScore

public static double getScore(Peptide peptide,
              MSnSpectrum spectrum,
              HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
              NeutralLossesMap neutralLosses,
              ArrayList<Integer> charges,
              int identificationCharge,
              double mzTolerance,
              PeptideSpectrumAnnotator peptideSpectrumAnnotator)

Scores the match between the given peptide and spectrum using the intensity rank of the matched peaks. For every amino-acid, the rank of the most intense peak is taken and the average value over the sequence is returned.

Parameters:

peptide - the peptide of interest

spectrum - the spectrum of interest

iontypes - the fragment ions to annotate

neutralLosses - the neutral losses to annotate

charges - the fragment charges to look for

identificationCharge - the precursor charge

mzTolerance - the ms2 m/z tolerance

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

Returns:

the score of the match