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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MDScore
public MDScore()
getMDScore
public static Double getMDScore(SpectrumMatch spectrumMatch,
ArrayList<String> ptms)
- Returns the MD score for the best peptide in a spectrum match (the best
peptide has to be set before). Null if not identified by Mascot. If the
peptide is the not the best scoring for Mascot the score will be
negative.
- Parameters:
spectrumMatch
- the spectrum match of interestptms
- the names of the PTMs to score
- Returns:
- the MD score
getMDScore
public static Double getMDScore(SpectrumMatch spectrumMatch,
Peptide peptideCandidate,
ArrayList<String> ptms)
- 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:
peptideCandidate
- the peptide of interestspectrumMatch
- the spectrum match of interestptms
- the names of the PTMs to score
- Returns:
- the MD score
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