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

Class ComplementarityScore

java.lang.Object

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

public class ComplementarityScore
extends Object

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

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
ComplementarityScore()

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 complementarity 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 complementarity of the matched peaks.

Methods inherited from class java.lang.Object

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

Constructor Detail

ComplementarityScore

public ComplementarityScore()

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 complementarity of the matched peaks. For every residue, a list of matched peaks is established and if any is found, the score per residue is the log of the number of matched ions. The peptide score is the average of the residue scores.

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 complementarity of the matched peaks. For every residue, a list of matched peaks is established and if any is found, the score per residue is the log of the number of matched ions. The peptide score is the average of the residue scores.

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