com.compomics.util.experiment.identification.ptm.ptmscores

Class MDScore

java.lang.Object

com.compomics.util.experiment.identification.ptm.ptmscores.MDScore

public class MDScore
extends Object

This class estimates the MD score as described in http://www.ncbi.nlm.nih.gov/pubmed/21057138 Note: this implementation of the MD score is not restricted to phosphorylation.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
MDScore()

Method Summary

Modifier and Type	Method and Description
static Double	getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions, Peptide peptideCandidate, ArrayList<String> ptms, SequenceMatchingPreferences sequenceMatchingPreferences, Integer rounding) Returns the MD score for the given peptide in a spectrum match.

Methods inherited from class java.lang.Object

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

Constructor Detail

MDScore

public MDScore()

Method Detail

getMDScore

public static Double getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions,
                                Peptide peptideCandidate,
                                ArrayList<String> ptms,
                                SequenceMatchingPreferences sequenceMatchingPreferences,
                                Integer rounding)

Returns the MD score for the given peptide in a spectrum match. Null if not identified by Mascot. If the peptide is the not the best scoring for Mascot the score will be negative.

Parameters:

mascotAssumptions - the assumptions by Mascot

peptideCandidate - the peptide of interest

ptms - the names of the PTMs to score

sequenceMatchingPreferences - the sequence matching preferences

rounding - decimal to which the score should be rounded, ignored if null

Returns:

the MD score