Package com.compomics.util.experiment.identification.matches

Examples of com.compomics.util.experiment.identification.matches.SpectrumMatch

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                                return DisplayPreferences.LOADING_MESSAGE;
                            }
                        }
                        return psParameter.isStarred();
                    case 2:
                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(psmKey, useDB && !isScrolling);
                        if (spectrumMatch == null) {
                            if (isScrolling()) {
                                return null;
                            } else if (!useDB) {
                                dataMissingAtRow(row);
                                return DisplayPreferences.LOADING_MESSAGE;
                            }
                        }
                        return SpectrumIdentificationPanel.isBestPsmEqualForAllIdSoftware(spectrumMatch, peptideShakerGUI.getSequenceMatchingPreferences());
                    case 3:
                        spectrumMatch = identification.getSpectrumMatch(psmKey, useDB && !isScrolling);
                        if (spectrumMatch == null) {
                            if (isScrolling()) {
                                return null;
                            } else if (!useDB) {
                                dataMissingAtRow(row);
                                return DisplayPreferences.LOADING_MESSAGE;
                            }
                        }
                        return peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(spectrumMatch, true, true, true);
                    case 4:
                        spectrumMatch = identification.getSpectrumMatch(psmKey, useDB && !isScrolling);
                        if (spectrumMatch == null) {
                            if (isScrolling()) {
                                return null;
                            } else if (!useDB) {
                                dataMissingAtRow(row);
                                return DisplayPreferences.LOADING_MESSAGE;
                            }
                        }
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            return spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value;
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            return spectrumMatch.getBestTagAssumption().getIdentificationCharge().value;
                        } else {
                            throw new IllegalArgumentException("No best assumption found for spectrum " + psmKey + ".");
                        }
                    case 5:
                        spectrumMatch = identification.getSpectrumMatch(psmKey, useDB && !isScrolling);
                        if (spectrumMatch == null) {
                            if (isScrolling()) {
                                return null;
                            } else if (!useDB) {
                                dataMissingAtRow(row);
                                return DisplayPreferences.LOADING_MESSAGE;
                            }
                        }
                        Precursor precursor = peptideShakerGUI.getPrecursor(psmKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            return Math.abs(spectrumMatch.getBestPeptideAssumption().getDeltaMass(precursor.getMz(), peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm()));
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            return Math.abs(spectrumMatch.getBestTagAssumption().getDeltaMass(precursor.getMz(), peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm()));
                        } else {
                            throw new IllegalArgumentException("No best assumption found for spectrum " + psmKey + ".");
                        }
                    case 6:
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(psmKey, new PSParameter(), useDB && !isScrolling);
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        if (psmFilter.getFileNames() != null && !psmFilter.getFileNames().contains(Spectrum.getSpectrumFile(spectrumKey))) {
            return false;
        }

        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
        if (spectrumMatch.getBestPeptideAssumption() != null) {
            return psmFilter.getAssumptionFilter().isValidated(spectrumKey, spectrumMatch.getBestPeptideAssumption(), searchParameters, annotationPreferences, peptideSpectrumAnnotator);
        } else if (spectrumMatch.getBestTagAssumption() != null) {
            //TODO: implement a tag assumption filter
            return true;
        } else {
            return true;
        }
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                HashMap<Double, ArrayList<TagAssumption>> tagAssumptions = new HashMap<Double, ArrayList<TagAssumption>>();

                PSParameter psParameter = new PSParameter();
                ArrayList<String> identifications = new ArrayList<String>();

                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);

                for (int searchEngine1 : spectrumMatch.getAdvocates()) {

                    double bestEvalue = Collections.min(spectrumMatch.getAllAssumptions(searchEngine1).keySet());

                    for (SpectrumIdentificationAssumption assumption1 : spectrumMatch.getAllAssumptions(searchEngine1).get(bestEvalue)) {

                        if (assumption1 instanceof PeptideAssumption) {

                            PeptideAssumption peptideAssumption1 = (PeptideAssumption) assumption1;
                            String id = peptideAssumption1.getPeptide().getKey();

                            if (!identifications.contains(id)) {

                                psParameter = (PSParameter) peptideAssumption1.getUrParam(psParameter);
                                double p;

                                if (multiSE && sequenceFactory.concatenatedTargetDecoy()) {
                                    p = psParameter.getSearchEngineProbability();
                                } else {
                                    p = peptideAssumption1.getScore();
                                }

                                int nSE = 1;
                                int proteinMax = 1;

                                for (String protein : peptideAssumption1.getPeptide().getParentProteins(sequenceMatchingPreferences)) {
                                    Integer tempCount = proteinCount.get(protein);
                                    if (tempCount != null && tempCount > proteinMax) {
                                        proteinMax = tempCount;
                                    }
                                }

                                for (int searchEngine2 : spectrumMatch.getAdvocates()) {

                                    if (searchEngine1 != searchEngine2) {

                                        boolean found = false;
                                        ArrayList<Double> eValues2 = new ArrayList<Double>(spectrumMatch.getAllAssumptions(searchEngine2).keySet());
                                        Collections.sort(eValues2);

                                        for (double eValue2 : eValues2) {
                                            for (SpectrumIdentificationAssumption assumption2 : spectrumMatch.getAllAssumptions(searchEngine2).get(eValue2)) {

                                                if (assumption2 instanceof PeptideAssumption) {

                                                    PeptideAssumption peptideAssumption2 = (PeptideAssumption) assumption2;

                                                    if (peptideAssumption1.getPeptide().isSameSequenceAndModificationStatus(peptideAssumption2.getPeptide(),
                                                            sequenceMatchingPreferences)) {
                                                        PSParameter psParameter2 = (PSParameter) peptideAssumption2.getUrParam(psParameter);
                                                        p = p * psParameter2.getSearchEngineProbability();
                                                        nSE++;
                                                        found = true;
                                                        break;
                                                    }
                                                }
                                            }
                                            if (found) {
                                                break;
                                            }
                                        }
                                    }
                                }

                                identifications.add(id);

                                if (!peptideAssumptions.containsKey(p)) {
                                    peptideAssumptions.put(p, new HashMap<Integer, HashMap<Integer, HashMap<Double, HashMap<Double, ArrayList<PeptideAssumption>>>>>());
                                }

                                if (!peptideAssumptions.get(p).containsKey(proteinMax)) {
                                    peptideAssumptions.get(p).put(proteinMax, new HashMap<Integer, HashMap<Double, HashMap<Double, ArrayList<PeptideAssumption>>>>());
                                }

                                if (!peptideAssumptions.get(p).get(proteinMax).containsKey(nSE)) {
                                    ArrayList<PeptideAssumption> assumptions = new ArrayList<PeptideAssumption>();
                                    assumptions.add(peptideAssumption1);
                                    peptideAssumptions.get(p).get(proteinMax).put(nSE, new HashMap<Double, HashMap<Double, ArrayList<PeptideAssumption>>>());
                                    peptideAssumptions.get(p).get(proteinMax).get(nSE).put(-1.0, new HashMap<Double, ArrayList<PeptideAssumption>>());
                                    peptideAssumptions.get(p).get(proteinMax).get(nSE).get(-1.0).put(-1.0, assumptions);
                                } else {
                                    HashMap<Ion.IonType, HashSet<Integer>> iontypes = annotationPreferences.getIonTypes();
                                    NeutralLossesMap neutralLosses = annotationPreferences.getNeutralLosses();
                                    ArrayList<Integer> charges = annotationPreferences.getValidatedCharges();
                                    MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
                                    double mzTolerance = searchParameters.getFragmentIonAccuracy();
                                    boolean isPpm = false; //@TODO change this as soon as search engine support fragment ion tolerance in ppm

                                    if (peptideAssumptions.get(p).get(proteinMax).get(nSE).containsKey(-1.0)) {
                                        ArrayList<PeptideAssumption> assumptions = peptideAssumptions.get(p).get(proteinMax).get(nSE).get(-1.0).get(-1.0);
                                        PeptideAssumption tempAssumption = assumptions.get(0);
                                        Peptide peptide = tempAssumption.getPeptide();
                                        int precursorCharge = tempAssumption.getIdentificationCharge().value;
                                        annotationPreferences.setCurrentSettings(tempAssumption, true, sequenceMatchingPreferences);
                                        double nIons = spectrumAnnotator.getCoveredAminoAcids(iontypes, neutralLosses, charges, precursorCharge,
                                                spectrum, peptide, 0, mzTolerance, isPpm, annotationPreferences.isHighResolutionAnnotation()).keySet().size();
                                        double coverage = nIons / peptide.getSequence().length();
                                        peptideAssumptions.get(p).get(proteinMax).get(nSE).put(coverage, new HashMap<Double, ArrayList<PeptideAssumption>>());
                                        peptideAssumptions.get(p).get(proteinMax).get(nSE).get(coverage).put(-1.0, assumptions);
                                        peptideAssumptions.get(p).get(proteinMax).get(nSE).remove(-1.0);
                                    }

                                    Peptide peptide = peptideAssumption1.getPeptide();
                                    int precursorCharge = peptideAssumption1.getIdentificationCharge().value;
                                    annotationPreferences.setCurrentSettings(peptideAssumption1, true, sequenceMatchingPreferences);
                                    double nIons = spectrumAnnotator.getCoveredAminoAcids(iontypes, neutralLosses, charges, precursorCharge,
                                            spectrum, peptide, 0, mzTolerance, isPpm, annotationPreferences.isHighResolutionAnnotation()).keySet().size();
                                    double coverage = nIons / peptide.getSequence().length();

                                    HashMap<Double, ArrayList<PeptideAssumption>> coverageMap = peptideAssumptions.get(p).get(proteinMax).get(nSE).get(coverage);
                                    if (coverageMap == null) {
                                        coverageMap = new HashMap<Double, ArrayList<PeptideAssumption>>();
                                        ArrayList<PeptideAssumption> assumptions = new ArrayList<PeptideAssumption>();
                                        assumptions.add(peptideAssumption1);
                                        coverageMap.put(-1.0, assumptions);
                                        peptideAssumptions.get(p).get(proteinMax).get(nSE).put(coverage, coverageMap);
                                    } else {
                                        ArrayList<PeptideAssumption> assumptions = coverageMap.get(-1.0);
                                        if (assumptions != null) {
                                            PeptideAssumption tempAssumption = assumptions.get(0);
                                            double massError = Math.abs(tempAssumption.getDeltaMass(spectrum.getPrecursor().getMz(), searchParameters.isPrecursorAccuracyTypePpm()));
                                            peptideAssumptions.get(p).get(proteinMax).get(nSE).get(coverage).put(massError, assumptions);
                                            peptideAssumptions.get(p).get(proteinMax).get(nSE).get(coverage).remove(-1.0);
                                        }

                                        double massError = Math.abs(peptideAssumption1.getDeltaMass(spectrum.getPrecursor().getMz(), searchParameters.isPrecursorAccuracyTypePpm()));
                                        assumptions = coverageMap.get(massError);

                                        if (assumptions == null) {
                                            assumptions = new ArrayList<PeptideAssumption>();
                                            coverageMap.put(massError, assumptions);
                                        }

                                        assumptions.add(peptideAssumption1);
                                    }
                                }
                            }
                        } else if (assumption1 instanceof TagAssumption) {
                            TagAssumption tagAssumption = (TagAssumption) assumption1;
                            ArrayList<TagAssumption> assumptions = tagAssumptions.get(bestEvalue);
                            if (assumptions == null) {
                                assumptions = new ArrayList<TagAssumption>();
                                tagAssumptions.put(bestEvalue, assumptions);
                            }
                            assumptions.add(tagAssumption);
                        }
                    }
                }
                if (!peptideAssumptions.isEmpty()) {

                    PeptideAssumption bestPeptideAssumption = null;
                    ArrayList<Double> ps = new ArrayList<Double>(peptideAssumptions.keySet());
                    Collections.sort(ps);
                    double retainedP = 0;

                    for (double p : ps) {

                        retainedP = p;
                        ArrayList<Integer> proteinMaxs = new ArrayList<Integer>(peptideAssumptions.get(p).keySet());
                        Collections.sort(proteinMaxs, Collections.reverseOrder());

                        for (int proteinMax : proteinMaxs) {

                            ArrayList<Integer> nSEs = new ArrayList<Integer>(peptideAssumptions.get(p).get(proteinMax).keySet());
                            Collections.sort(nSEs, Collections.reverseOrder());

                            for (int nSE : nSEs) {

                                ArrayList<Double> coverages = new ArrayList<Double>(peptideAssumptions.get(p).get(proteinMax).get(nSE).keySet());
                                Collections.sort(coverages);

                                for (double coverage : coverages) {

                                    ArrayList<Double> minErrors = new ArrayList<Double>(peptideAssumptions.get(p).get(proteinMax).get(nSE).get(coverage).keySet());
                                    Collections.sort(minErrors);

                                    for (double minError : minErrors) {
                                        for (PeptideAssumption peptideAssumption : peptideAssumptions.get(p).get(proteinMax).get(nSE).get(coverage).get(minError)) {
                                            if (idFilter.validateProteins(peptideAssumption.getPeptide(), sequenceMatchingPreferences)) {
                                                bestPeptideAssumption = peptideAssumption;
                                                break;
                                            }
                                        }
                                        if (bestPeptideAssumption != null) {
                                            break;
                                        }
                                    }
                                    if (bestPeptideAssumption != null) {
                                        break;
                                    }
                                }
                                if (bestPeptideAssumption != null) {
                                    break;
                                }
                            }
                            if (bestPeptideAssumption != null) {
                                break;
                            }
                        }
                        if (bestPeptideAssumption != null) {
                            break;
                        }
                    }
                    if (bestPeptideAssumption != null) {

                        if (multiSE) {

                            // try to find the most likely modification localization based on the search engine results
                            HashMap<PeptideAssumption, ArrayList<Double>> assumptions = new HashMap<PeptideAssumption, ArrayList<Double>>();
                            String bestAssumptionKey = bestPeptideAssumption.getPeptide().getMatchingKey(sequenceMatchingPreferences);

                            for (int searchEngine1 : spectrumMatch.getAdvocates()) {

                                boolean found = false;
                                ArrayList<Double> eValues2 = new ArrayList<Double>(spectrumMatch.getAllAssumptions(searchEngine1).keySet());
                                Collections.sort(eValues2);

                                for (double eValue : eValues2) {
                                    for (SpectrumIdentificationAssumption assumption : spectrumMatch.getAllAssumptions(searchEngine1).get(eValue)) {

                                        if (assumption instanceof PeptideAssumption) {

                                            PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;

                                            if (peptideAssumption.getPeptide().getMatchingKey(sequenceMatchingPreferences).equals(bestAssumptionKey)) {

                                                found = true;
                                                boolean found2 = false;

                                                for (PeptideAssumption assumption1 : assumptions.keySet()) {
                                                    if (assumption1.getPeptide().sameModificationsAs(peptideAssumption.getPeptide())) {
                                                        found2 = true;
                                                        psParameter = (PSParameter) assumption.getUrParam(psParameter);
                                                        assumptions.get(assumption1).add(psParameter.getSearchEngineProbability());
                                                        break;
                                                    }
                                                }

                                                if (!found2) {
                                                    assumptions.put(peptideAssumption, new ArrayList<Double>());
                                                    psParameter = (PSParameter) assumption.getUrParam(psParameter);
                                                    assumptions.get(peptideAssumption).add(psParameter.getSearchEngineProbability());
                                                }
                                            }
                                        }
                                    }

                                    if (found) {
                                        break;
                                    }
                                }
                            }

                            Double bestSeP = null;
                            int nSe = -1;

                            for (PeptideAssumption peptideAssumption : assumptions.keySet()) {

                                Double sep = Collections.min(assumptions.get(peptideAssumption));

                                if (bestSeP == null || bestSeP > sep) {
                                    bestSeP = sep;
                                    nSe = assumptions.get(peptideAssumption).size();
                                    bestPeptideAssumption = peptideAssumption;
                                } else if (assumptions.get(peptideAssumption).size() > nSe) {
                                    if (sep != null && bestSeP != null && (Math.abs(sep - bestSeP) <= 1e-10)) {
                                        nSe = assumptions.get(peptideAssumption).size();
                                        bestPeptideAssumption = peptideAssumption;
                                    }
                                }
                            }
                        }

                        // create a PeptideShaker match based on the best search engine match
                        Peptide sePeptide = bestPeptideAssumption.getPeptide();
                        ArrayList<String> psProteins = new ArrayList<String>(sePeptide.getParentProteins(sequenceMatchingPreferences));
                        ArrayList<ModificationMatch> psModificationMatches = new ArrayList<ModificationMatch>();

                        for (ModificationMatch seModMatch : sePeptide.getModificationMatches()) {
                            psModificationMatches.add(new ModificationMatch(seModMatch.getTheoreticPtm(), seModMatch.isVariable(), seModMatch.getModificationSite()));
                        }

                        Peptide psPeptide = new Peptide(sePeptide.getSequence(), psModificationMatches);
                        psPeptide.setParentProteins(psProteins);
                        PeptideAssumption psAssumption = new PeptideAssumption(psPeptide, 1, Advocate.peptideShaker.getIndex(), bestPeptideAssumption.getIdentificationCharge(), retainedP);
                        spectrumMatch.setBestPeptideAssumption(psAssumption);

                        if (orderedPsmMap != null) {
                            String peptideKey = psPeptide.getMatchingKey(sequenceMatchingPreferences);
                            ArrayList<String> spectrumKeys = keysMap.get(peptideKey);
                            if (spectrumKeys == null) {
                                spectrumKeys = new ArrayList<String>();
                                keysMap.put(peptideKey, spectrumKeys);
                            }
                            spectrumKeys.add(spectrumKey);
                        }

                        psParameter = new PSParameter();
                        psParameter.setSpectrumProbabilityScore(retainedP);

                        PSParameter matchParameter = (PSParameter) bestPeptideAssumption.getUrParam(psParameter);
                        psParameter.setSearchEngineProbability(matchParameter.getSearchEngineProbability());
                        psParameter.setAlgorithmDeltaPEP(matchParameter.getAlgorithmDeltaPEP());
                        psParameter.setDeltaPEP(matchParameter.getDeltaPEP());

                        matchesValidator.getPsmMap().addPoint(retainedP, spectrumMatch, sequenceMatchingPreferences);
                        psParameter.setSpecificMapKey(spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value + "");
                        identification.addSpectrumMatchParameter(spectrumKey, psParameter);
                        identification.updateSpectrumMatch(spectrumMatch);

                    } else {
                        throw new IllegalArgumentException("No best assumption found for spectrum " + spectrumKey + ".");
                    }
                }
                if (!tagAssumptions.isEmpty()) {
                    ArrayList<Double> evalues = new ArrayList<Double>(tagAssumptions.keySet());
                    Double bestEvalue = Collections.min(evalues);
                    TagAssumption bestAssumption = tagAssumptions.get(bestEvalue).get(0);
                    spectrumMatch.setBestTagAssumption(bestAssumption);
                    identification.updateSpectrumMatch(spectrumMatch);
                    if (spectrumMatch.getBestPeptideAssumption() == null) {
                        psParameter = new PSParameter();
                        if (!multiSE) {
                            psParameter.setSpectrumProbabilityScore(bestEvalue);
                        }
                        PSParameter matchParameter = (PSParameter) bestAssumption.getUrParam(psParameter);
                        psParameter.setSearchEngineProbability(matchParameter.getSearchEngineProbability());
                        psParameter.setAlgorithmDeltaPEP(matchParameter.getAlgorithmDeltaPEP());
                        psParameter.setDeltaPEP(matchParameter.getDeltaPEP());
                        psParameter.setSpecificMapKey(spectrumMatch.getBestTagAssumption().getIdentificationCharge().value + "");
                        identification.addSpectrumMatchParameter(spectrumKey, psParameter);
                    }
                }
                waitingHandler.increaseSecondaryProgressCounter();
                if (waitingHandler.isRunCanceled()) {
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                        if (identification.matchExists(spectrumKey)) {
                            psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);

                            if (psParameter.getMatchValidationLevel().isValidated()) {

                                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                                if (spectrumMatch.getBestPeptideAssumption() != null) {
                                    Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();

                                    if (exportType != ExportType.confident_ptms || isTargetedPeptide(peptide, targetedPTMs)) {

                                        boolean decoy = false;
                                        for (String protein : peptide.getParentProteins(sequenceMatchingPreferences)) {
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     * @throws InterruptedException
     */
    private static void writePsm(BufferedWriter writer, String spectrumKey, ArrayList<String> accessions, Identification identification, SequenceMatchingPreferences sequenceMatchingPreferences, AnnotationPreferences annotationPreferences)
            throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException, InterruptedException, MzMLUnmarshallerException {

        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
        PeptideAssumption bestAssumption = spectrumMatch.getBestPeptideAssumption();
        Peptide peptide = bestAssumption.getPeptide();
        MSnSpectrum spectrum = (MSnSpectrum) SpectrumFactory.getInstance().getSpectrum(spectrumKey);

        if (accessions == null) {
            accessions = peptide.getParentProteins(sequenceMatchingPreferences);
        }
        PTMFactory ptmFactory = PTMFactory.getInstance();
        PtmToPrideMap ptmToPrideMap = null;
        // get the psi-mod mappings
        try {
            PrideObjectsFactory prideObjectsFactory = PrideObjectsFactory.getInstance();
            ptmToPrideMap = prideObjectsFactory.getPtmToPrideMap();
        } catch (Exception e) {
            e.printStackTrace();
        }

        for (String accession : accessions) {

            PeptideSpectrumAnnotator spectrumAnnotator = new PeptideSpectrumAnnotator();

            ArrayList<IonMatch> annotations = spectrumAnnotator.getSpectrumAnnotation(
                    annotationPreferences.getIonTypes(),
                    annotationPreferences.getNeutralLosses(),
                    annotationPreferences.getValidatedCharges(),
                    spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value,
                    spectrum,
                    spectrumMatch.getBestPeptideAssumption().getPeptide(),
                    spectrum.getIntensityLimit(annotationPreferences.getAnnotationIntensityLimit()),
                    annotationPreferences.getFragmentIonAccuracy(), false,
                    annotationPreferences.isHighResolutionAnnotation());

            for (IonMatch ionMatch : annotations) {
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            for (String spectrumKey : identification.getSpectrumIdentification(spectrumFileName)) {

                waitingHandler.increaseSecondaryProgressCounter();

                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);

                HashMap<Double, ArrayList<PSParameter>> pepToParameterMap = new HashMap<Double, ArrayList<PSParameter>>();

                for (int searchEngine : spectrumMatch.getAdvocates()) {

                    ArrayList<Double> eValues = new ArrayList<Double>(spectrumMatch.getAllAssumptions(searchEngine).keySet());
                    Collections.sort(eValues);
                    double previousP = 0;
                    ArrayList<PSParameter> previousAssumptionsParameters = new ArrayList<PSParameter>();
                    SpectrumIdentificationAssumption previousAssumption = null;

                    for (double eValue : eValues) {

                        for (SpectrumIdentificationAssumption assumption : spectrumMatch.getAllAssumptions(searchEngine).get(eValue)) {
                            PSParameter psParameter = new PSParameter();
                            psParameter = (PSParameter) assumption.getUrParam(psParameter);
                            if (psParameter == null) {
                                psParameter = new PSParameter();
                            }
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                                    ArrayList<Double> retentionTimes = new ArrayList<Double>();
                                    for (String spectrumKey : validatedPsms) {
                                        retentionTimes.add(spectrumFactory.getPrecursor(spectrumKey).getRt());
                                    }
                                    for (String spectrumKey : validatedPsms) {
                                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                                            String line = getInclusionListLine(spectrumMatch, retentionTimes, rtWindow, exportFormat, searchParameters);
                                            b.write(line);
                                            b.newLine();
                                        }
                                    }
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                        double confidenceLevel = getHighConfidenceThreshold(psmTargetDecoyMap, charge, spectrumFile, fdrThreshold);
                        if (psParameter.getPsmConfidence() >= confidenceLevel) {
                            if (spectrum == null) {
                                spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
                            }
                            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                            if (spectrumMatch.getBestPeptideAssumption() != null) {
                                String sequence = spectrumMatch.getBestPeptideAssumption().getPeptide().getSequence();
                                HashMap<String, String> tags = new HashMap<String, String>();
                                tags.put("SEQ", sequence);
                                spectrum.writeMgf(writerGood, tags);
                            }
                        }
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        waitingHandler.setSecondaryProgressCounterIndeterminate(false);
        waitingHandler.setMaxSecondaryProgressCounter(max);

        PSParameter psParameter = new PSParameter();
        for (String spectrumKey : inspectedSpectra) {
            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
            if (spectrumMatch.getBestPeptideAssumption() != null) {
                psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                scorePTMs(identification, spectrumMatch, searchParameters, annotationPreferences, ptmScoringPreferences, sequenceMatchingPreferences, waitingHandler);
            }
        }
View Full Code Here
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            HashMap<Double, ArrayList<Integer>> confidentSites = new HashMap<Double, ArrayList<Integer>>();

            // Map confident sites
            for (String spectrumKey : bestKeys) {
                psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                PSPtmScores psmScores = (PSPtmScores) spectrumMatch.getUrParam(new PSPtmScores());

                for (String ptmName : psmScores.getScoredPTMs()) {
                    PtmScoring psmScoring = psmScores.getPtmScoring(ptmName);
                    PtmScoring peptideScoring = peptideScores.getPtmScoring(ptmName);
                    if (peptideScoring == null) {
                        peptideScoring = new PtmScoring(ptmName);
                        peptideScores.addPtmScoring(ptmName, peptideScoring);
                    }
                    for (int site : psmScoring.getAllPtmLocations()) {
                        double psmDScore = psmScoring.getDeltaScore(site);
                        double peptideDScore = peptideScoring.getDeltaScore(site);
                        if (peptideDScore < psmDScore) {
                            peptideScoring.setDeltaScore(site, psmDScore);
                        }
                        double psmPScore = psmScoring.getProbabilisticScore(site);
                        double peptidePScore = peptideScoring.getProbabilisticScore(site);
                        if (peptidePScore < psmPScore) {
                            peptideScoring.setProbabilisticScore(site, psmPScore);
                        }
                        int psmValidationLevel = psmScoring.getLocalizationConfidence(site);
                        int peptideValidationLevel = peptideScoring.getLocalizationConfidence(site);
                        if (peptideValidationLevel < psmValidationLevel) {
                            peptideScoring.setSiteConfidence(site, psmValidationLevel);
                        }
                    }
                }

                for (Integer confidentSite : psmScores.getConfidentSites()) {
                    for (String ptmName : psmScores.getConfidentModificationsAt(confidentSite)) {
                        PTM ptm = ptmFactory.getPTM(ptmName);
                        Double ptmMass = ptm.getMass();
                        ArrayList<Integer> ptmConfidentSites = confidentSites.get(ptmMass);
                        if (ptmConfidentSites == null) {
                            ptmConfidentSites = new ArrayList<Integer>();
                            confidentSites.put(ptmMass, ptmConfidentSites);
                        }
                        if (!ptmConfidentSites.contains(confidentSite)) {
                            ptmConfidentSites.add(confidentSite);
                            peptideScores.addConfidentModificationSite(ptmName, confidentSite);
                            ModificationMatch newMatch = new ModificationMatch(ptmName, true, confidentSite);
                            newMatch.setConfident(true);
                            ArrayList<ModificationMatch> newPtmMatches = newMatches.get(ptmMass);
                            if (newPtmMatches == null) {
                                newPtmMatches = new ArrayList<ModificationMatch>();
                                newMatches.put(ptmMass, newPtmMatches);
                            }
                            newPtmMatches.add(newMatch);
                            if (newPtmMatches.size() > variableModifications.get(ptmMass)) {
                                throw new IllegalArgumentException("More sites than PTMs on peptide " + peptideMatch.getKey() + " for PTM of mass " + ptmMass + ".");
                            }
                            ArrayList<Integer> ptmInferredSites = inferredSites.get(ptmMass);
                            if (ptmInferredSites != null) {
                                ptmInferredSites.remove(confidentSite);
                                if (ptmInferredSites.isEmpty()) {
                                    inferredSites.remove(ptmMass);
                                }
                            }
                        }
                    }
                }
            }

            boolean enoughSites = true;
            for (double ptmMass : variableModifications.keySet()) {
                int nPtms = variableModifications.get(ptmMass);
                int nConfident = 0;
                ArrayList<Integer> ptmConfidentSites = confidentSites.get(ptmMass);
                if (ptmConfidentSites != null) {
                    nConfident = ptmConfidentSites.size();
                }
                if (nConfident < nPtms) {
                    enoughSites = false;
                    break;
                }
            }
            if (!enoughSites) {

                HashMap<Double, HashMap<Double, HashMap<Double, HashMap<Integer, ArrayList<String>>>>> ambiguousSites = new HashMap<Double, HashMap<Double, HashMap<Double, HashMap<Integer, ArrayList<String>>>>>();

                for (String spectrumKey : bestKeys) {

                    psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                    PSPtmScores psmScores = (PSPtmScores) spectrumMatch.getUrParam(new PSPtmScores());

                    for (int representativeSite : psmScores.getRepresentativeSites()) {
                        HashMap<Integer, ArrayList<String>> ambiguousMappingAtSite = psmScores.getAmbiguousPtmsAtRepresentativeSite(representativeSite);
                        int mappingSize = ambiguousMappingAtSite.size();
                        for (int site : ambiguousMappingAtSite.keySet()) {
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TOP

Related Classes of com.compomics.util.experiment.identification.matches.SpectrumMatch

  • eu.isas.peptideshaker.export.OutputGenerator
  • eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection
  • eu.isas.peptideshaker.export.sections.PsPsmSection
  • eu.isas.peptideshaker.fileimport.PsmImporter
  • eu.isas.peptideshaker.filtering.PsmFilter
  • eu.isas.peptideshaker.followup.InclusionListExport
  • eu.isas.peptideshaker.followup.ProgenesisExcelExport
  • eu.isas.peptideshaker.followup.ProgenesisExport
  • eu.isas.peptideshaker.followup.SpectrumExporter
  • eu.isas.peptideshaker.followup.SwathExport
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