Package com.compomics.util.experiment.refinementparameters

Examples of com.compomics.util.experiment.refinementparameters.MascotScore

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                                        PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
                                        if (peptideAssumption.getPeptide().isSameSequenceAndModificationStatus(bestAssumption.getPeptide(), sequenceMatchingPreferences)) {
                                            if (!eValues.containsKey(se) || eValues.get(se) > eValue) {
                                                eValues.put(se, eValue);
                                                if (se == Advocate.mascot.getIndex()) {
                                                    mascotScore = ((MascotScore) assumption.getUrParam(new MascotScore(0))).getScore();
                                                } else if (se == Advocate.msAmanda.getIndex()
                                                        && peptideAssumption.getUrParam(new MsAmandaScore()) != null) {
                                                    msAmandaScore = ((MsAmandaScore) assumption.getUrParam(new MsAmandaScore())).getScore();
                                                }
                                            }
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                                        PeptideAssumption mascotAssumption = null;
                                        double bestScore = 0;
                                        for (ArrayList<SpectrumIdentificationAssumption> peptideAssumptionList : spectrumMatch.getAllAssumptions(Advocate.mascot.getIndex()).values()) {
                                            for (SpectrumIdentificationAssumption assumption : peptideAssumptionList) {
                                                PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
                                                MascotScore mascotScore = new MascotScore();
                                                mascotScore = (MascotScore) peptideAssumption.getUrParam(mascotScore);
                                                if (mascotScore.getScore() > bestScore) {
                                                    mascotAssumption = peptideAssumption;
                                                    bestScore = mascotScore.getScore();
                                                }
                                            }
                                        }
                                        if (mascotAssumption != null) {
                                            Peptide mascotPeptide = mascotAssumption.getPeptide();
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                                if (currentMinEvalue == null || eValue < currentMinEvalue) {
                                    scores.put(tempAdvocate, eValue);

                                    // save the special advocate scores
                                    if (tempAdvocate == Advocate.mascot.getIndex()) {
                                        mascotScore = ((MascotScore) peptideAssumption.getUrParam(new MascotScore(0))).getScore();
                                    } else if (tempAdvocate == Advocate.msAmanda.getIndex()
                                            && peptideAssumption.getUrParam(new MsAmandaScore()) != null) {
                                        msAmandaScore = ((MsAmandaScore) peptideAssumption.getUrParam(new MsAmandaScore())).getScore();
                                    }
                                }
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Related Classes of com.compomics.util.experiment.refinementparameters.MascotScore

  • eu.isas.peptideshaker.export.MzIdentMLExport
  • eu.isas.peptideshaker.export.OutputGenerator
  • eu.isas.peptideshaker.export.PrideXmlExport
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