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.
-
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 MascotpeptideCandidate
- the peptide of interestptms
- the names of the PTMs to scoresequenceMatchingPreferences
- the sequence matching preferencesrounding
- decimal to which the score should be rounded, ignored if null- Returns:
- the MD score
-