Examples of PsmPTMMap

     */
    public void updateMainMatch(String mainMatch, int proteinInferenceType) {
        try {
            PSMaps psMaps = new PSMaps();
            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) {

Examples of eu.isas.peptideshaker.scoring.PsmPTMMap


                // update protein level PTM scoring
                ArrayList<String> proteins = peptideMatch.getTheoreticPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences());
                PSMaps psMaps = new PSMaps();
                psMaps = (PSMaps) identification.getUrParam(psMaps);
                PsmPTMMap psmPTMMap = psMaps.getPsmPTMMap();
                PtmScorer ptmScorer = new PtmScorer(psmPTMMap);


                for (String proteinKey : peptideShakerGUI.getIdentification().getProteinIdentification()) {
                    boolean candidate = false;
                    for (String protein : proteins) {

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