Examples of PtmScorer

eu.isas.peptideshaker.ptm.PtmScorer
This class scores the PSM PTMs using the scores implemented in compomics utilities. @author Marc Vaudel

Examples of eu.isas.peptideshaker.ptm.PtmScorer

    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) {
            catchException(e);
        }


        overviewPanel.updateProteinTable();

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Examples of eu.isas.peptideshaker.ptm.PtmScorer

                // 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) {
                        if (proteinKey.contains(protein)) {
                            candidate = true;
                        }
                    }
                    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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Examples of eu.isas.peptideshaker.ptm.PtmScorer

        PsmSpecificMap psmMap = new PsmSpecificMap();
        PeptideSpecificMap peptideMap = new PeptideSpecificMap();
        ProteinMap proteinMap = new ProteinMap();
        matchesValidator = new MatchesValidator(psmMap, peptideMap, proteinMap);
        PsmPTMMap psmPTMMap = new PsmPTMMap();
        ptmScorer = new PtmScorer(psmPTMMap);
    }

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Examples of eu.isas.peptideshaker.ptm.PtmScorer

    public PeptideShaker(MsExperiment experiment, Sample sample, int replicateNumber, PSMaps psMaps) {
        this.experiment = experiment;
        this.sample = sample;
        this.replicateNumber = replicateNumber;
        matchesValidator = new MatchesValidator(psMaps.getPsmSpecificMap(), psMaps.getPeptideSpecificMap(), psMaps.getProteinMap());
        ptmScorer = new PtmScorer(psMaps.getPsmPTMMap());
    }

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