Package com.compomics.util.experiment.identification.modification.scores

Class MDScore

java.lang.Object

com.compomics.util.experiment.identification.modification.scores.MDScore

public class MDScore
extends Object

This class estimates the MD score as described in https://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	Description
MDScore()	Empty default constructor

Method Summary

Modifier and Type	Method	Description
static Double	getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions, Peptide peptideCandidate, ArrayList<String> ptms, SequenceMatchingParameters 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 Details

MDScore

public MDScore()

Empty default constructor

Method Details

getMDScore

public static Double getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions,
 Peptide peptideCandidate,
 ArrayList<String> ptms,
 SequenceMatchingParameters 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