Examples of eu.isas.peptideshaker.ptm.PtmScorer.scorePTMs()

Class eu.isas.peptideshaker.ptm.PtmScorer

Examples of eu.isas.peptideshaker.ptm.PtmScorer.scorePTMs()

eu.isas.peptideshaker.ptm.PtmScorer.scorePTMs()
Scores PTM locations for a desired spectrumMatch. @param identification identification object containing the identificationmatches @param spectrumMatch The spectrum match of interest @param searchParameters the search preferences containing the m/ztolerances @param annotationPreferences the spectrum annotation preferences @param scoringPreferences the PTM scoring preferences @param sequenceMatchingPreferences the sequence matching preferences @param waitingHandler waiting handler to display progress and allowcancelling @throws Exception exception thrown whenever an error occurred whilereading/writing the an identification match

            psMaps = (PSMaps) getIdentification().getUrParam(psMaps);
            PsmPTMMap psmPTMMap = psMaps.getPsmPTMMap();
            PtmScorer ptmScorer = new PtmScorer(psmPTMMap);
            Identification identification = getIdentification();
            ProteinMatch proteinMatch = identification.getProteinMatch(selectedProteinKey);
            ptmScorer.scorePTMs(identification, proteinMatch, getSearchParameters(), getAnnotationPreferences(), false, getPtmScoringPreferences(), getSequenceMatchingPreferences());
        } catch (Exception e) {
            catchException(e);
        }


        overviewPanel.updateProteinTable();

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                    }
                    if (candidate) {
                        ProteinMatch proteinMatch = peptideShakerGUI.getIdentification().getProteinMatch(proteinKey);
                        if (proteins.contains(proteinMatch.getMainMatch())) {
                            try {
                                ptmScorer.scorePTMs(identification, proteinMatch, peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getAnnotationPreferences(), false, peptideShakerGUI.getPtmScoringPreferences(), peptideShakerGUI.getSequenceMatchingPreferences());
                            } catch (Exception e) {
                                peptideShakerGUI.catchException(e);
                            }
                        }
                    }

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