uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide

Class PeptideScoringUseBestPSM

java.lang.Object

uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoring

uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoringUseBestPSM

public class PeptideScoringUseBestPSM
extends PeptideScoring

This class uses the PSM with the best score for scoring of a peptide.

Author:

julian

Field Summary

Fields

Modifier and Type	Field and Description
protected IntermediatePSMComparator	psmComparator the used score comparator

Fields inherited from class uk.ac.ebi.pride.utilities.pia.modeller.scores.peptide.PeptideScoring

baseScoreAccession, higherScoreBetter

Constructor Summary

Constructors

Constructor and Description
PeptideScoringUseBestPSM(String scoreAccession, boolean oboLookup)

Method Summary

Methods

Modifier and Type	Method and Description
Double	calculatePeptideScore(IntermediatePeptide intermediatePeptide) Calculates the peptide score for the intermediate peptide.

Methods inherited from class java.lang.Object

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

Field Detail

psmComparator

protected IntermediatePSMComparator psmComparator

the used score comparator

Constructor Detail

PeptideScoringUseBestPSM

public PeptideScoringUseBestPSM(String scoreAccession,
                        boolean oboLookup)

Method Detail

calculatePeptideScore

public Double calculatePeptideScore(IntermediatePeptide intermediatePeptide)

Description copied from class: PeptideScoring

Calculates the peptide score for the intermediate peptide. For the calculation, the PSMs which are retrieved from the intermediate peptide, may be only the ones passing a set filter, if the peptide was filtered before.

The scoring PSMs are set in the intermediatePeptide, as well as the final score.

Specified by:

calculatePeptideScore in class PeptideScoring