Examples with ModificationScoring com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring used on opensource projects

Example 1 with ModificationScoring

use of com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring in project peptide-shaker by compomics.

the class ModificationLocalizationScorer method attachDeltaScore.

/**
 * Scores the modification locations using the delta score.
 *
 * @param identification Identification object containing the matches.
 * @param spectrumMatch The spectrum match of interest.
 * @param sequenceMatchingParameters The sequence matching preferences.
 * @param modificationProvider The modification provider to use.
 */
public void attachDeltaScore(Identification identification, SpectrumMatch spectrumMatch, SequenceMatchingParameters sequenceMatchingParameters, ModificationProvider modificationProvider) {
    PSModificationScores modificationScores = (PSModificationScores) spectrumMatch.getUrParam(PSModificationScores.dummy);
    if (modificationScores == null) {
        modificationScores = new PSModificationScores();
        spectrumMatch.addUrParam(modificationScores);
    }
    Peptide psPeptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
    HashMap<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>> assumptions = spectrumMatch.getPeptideAssumptionsMap();
    String mainSequence = psPeptide.getSequence();
    HashMap<String, List<Integer>> modificationParameters = Arrays.stream(psPeptide.getVariableModifications()).collect(Collectors.groupingBy(ModificationMatch::getModification, HashMap::new, Collectors.mapping(ModificationMatch::getSite, Collectors.toList())));
    for (Entry<String, List<Integer>> entry : modificationParameters.entrySet()) {
        String modName = entry.getKey();
        List<Integer> sites = entry.getValue();
        Modification modification1 = modificationProvider.getModification(modName);
        for (int modSite : sites) {
            double refP = 1, secondaryP = 1;
            for (TreeMap<Double, ArrayList<PeptideAssumption>> algorithmAssumptions : assumptions.values()) {
                for (ArrayList<PeptideAssumption> assumptionsAtScore : algorithmAssumptions.values()) {
                    for (PeptideAssumption peptideAssumption : assumptionsAtScore) {
                        if (peptideAssumption.getPeptide().getSequence().equals(mainSequence)) {
                            boolean modificationAtSite = false, modificationFound = false;
                            Peptide peptide = peptideAssumption.getPeptide();
                            for (ModificationMatch modMatch : peptide.getVariableModifications()) {
                                Modification modification2 = modificationProvider.getModification(modMatch.getModification());
                                if (modification1.getMass() == modification2.getMass()) {
                                    modificationFound = true;
                                    PSParameter psParameter = (PSParameter) peptideAssumption.getUrParam(PSParameter.dummy);
                                    double p = psParameter.getProbability();
                                    if (modMatch.getSite() == modSite) {
                                        modificationAtSite = true;
                                        if (p < refP) {
                                            refP = p;
                                        }
                                    }
                                }
                            }
                            if (!modificationAtSite && modificationFound) {
                                PSParameter psParameter = (PSParameter) peptideAssumption.getUrParam(PSParameter.dummy);
                                double p = psParameter.getProbability();
                                if (p < secondaryP) {
                                    secondaryP = p;
                                }
                            }
                        }
                    }
                }
            }
            ModificationScoring modificationScoring = modificationScores.getModificationScoring(modName);
            if (modificationScoring == null) {
                modificationScoring = new ModificationScoring(modName);
                modificationScores.addModificationScoring(modName, modificationScoring);
            }
            if (secondaryP < refP) {
                secondaryP = refP;
            }
            double deltaScore = (secondaryP - refP) * 100;
            modificationScoring.setDeltaScore(modSite, deltaScore);
        }
        identification.updateObject(spectrumMatch.getKey(), spectrumMatch);
    }
}

Example 2 with ModificationScoring

use of com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring in project peptide-shaker by compomics.

the class ModificationLocalizationScorer method attachProbabilisticScore.

/**
 * Attaches the selected probabilistic modification score.
 *
 * @param spectrumMatch The spectrum match studied, the score will be
 * calculated for the best assumption only.
 * @param sequenceProvider The protein sequence provider to use.
 * @param spectrumProvider The spectrum provider to use.
 * @param modificationProvider The modification provider to use.
 * @param identificationParameters The identification parameters.
 * @param peptideSpectrumAnnotator The peptide spectrum annotator to use.
 * @param identification The identification object containing the matches.
 */
private void attachProbabilisticScore(SpectrumMatch spectrumMatch, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, IdentificationParameters identificationParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, Identification identification) {
    SearchParameters searchParameters = identificationParameters.getSearchParameters();
    AnnotationParameters annotationParameters = identificationParameters.getAnnotationParameters();
    ModificationLocalizationParameters scoringParameters = identificationParameters.getModificationLocalizationParameters();
    SequenceMatchingParameters sequenceMatchingParameters = identificationParameters.getSequenceMatchingParameters();
    SequenceMatchingParameters modificationSequenceMatchingParameters = scoringParameters.getSequenceMatchingParameters();
    ModificationParameters modificationParameters = searchParameters.getModificationParameters();
    PSModificationScores modificationScores = (PSModificationScores) spectrumMatch.getUrParam(PSModificationScores.dummy);
    if (modificationScores != null) {
        modificationScores = new PSModificationScores();
        spectrumMatch.addUrParam(modificationScores);
    }
    HashMap<Double, ArrayList<Modification>> modificationsMap = new HashMap<>(1);
    HashMap<Double, Integer> nMod = new HashMap<>(1);
    PeptideAssumption bestPeptideAssumption = spectrumMatch.getBestPeptideAssumption();
    Peptide peptide = bestPeptideAssumption.getPeptide();
    for (ModificationMatch modificationMatch : peptide.getVariableModifications()) {
        Modification refMod = modificationProvider.getModification(modificationMatch.getModification());
        double modMass = refMod.getMass();
        if (!modificationsMap.containsKey(modMass)) {
            ArrayList<Modification> modifications = modificationFactory.getSameMassNotFixedModifications(modMass, searchParameters).stream().map(modification -> modificationProvider.getModification(modification)).collect(Collectors.toCollection(ArrayList::new));
            modificationsMap.put(modMass, modifications);
            nMod.put(modMass, 1);
        } else {
            nMod.put(modMass, nMod.get(modMass) + 1);
        }
    }
    if (!modificationsMap.isEmpty()) {
        String spectrumFile = spectrumMatch.getSpectrumFile();
        String spectrumTitle = spectrumMatch.getSpectrumTitle();
        Spectrum spectrum = spectrumProvider.getSpectrum(spectrumFile, spectrumTitle);
        SpecificAnnotationParameters specificAnnotationParameters = annotationParameters.getSpecificAnnotationParameters(spectrumFile, spectrumTitle, bestPeptideAssumption, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters, peptideSpectrumAnnotator);
        for (double modMass : modificationsMap.keySet()) {
            HashMap<Integer, Double> scores = null;
            if (scoringParameters.getSelectedProbabilisticScore() == ModificationLocalizationScore.PhosphoRS) {
                scores = PhosphoRS.getSequenceProbabilities(peptide, modificationsMap.get(modMass), modificationParameters, spectrum, sequenceProvider, annotationParameters, specificAnnotationParameters, scoringParameters.isProbabilisticScoreNeutralLosses(), sequenceMatchingParameters, modificationSequenceMatchingParameters, peptideSpectrumAnnotator);
                if (scores == null) {
                    throw new IllegalArgumentException("An error occurred while scoring spectrum " + spectrumTitle + " of file " + spectrumFile + " with PhosphoRS.");
                // Most likely a compatibility issue with utilities
                }
            }
            if (scores != null) {
                // remap to searched modifications
                Modification mappedModification = null;
                String peptideSequence = peptide.getSequence();
                for (int site : scores.keySet()) {
                    if (site == 0) {
                        // N-term mod
                        for (Modification modification : modificationsMap.get(modMass)) {
                            if (modification.getModificationType().isNTerm()) {
                                mappedModification = modification;
                                break;
                            }
                        }
                        if (mappedModification == null) {
                            throw new IllegalArgumentException("Could not map the PTM of mass " + modMass + " on the N-terminus of the peptide " + peptideSequence + ".");
                        }
                    } else if (site == peptideSequence.length() + 1) {
                        // C-term mod
                        for (Modification modification : modificationsMap.get(modMass)) {
                            if (modification.getModificationType().isCTerm()) {
                                mappedModification = modification;
                                break;
                            }
                        }
                        if (mappedModification == null) {
                            throw new IllegalArgumentException("Could not map the PTM of mass " + modMass + " on the C-terminus of the peptide " + peptideSequence + ".");
                        }
                    } else {
                        for (Modification modification : modificationsMap.get(modMass)) {
                            mappedModification = modification;
                            break;
                        }
                        if (mappedModification == null) {
                            throw new IllegalArgumentException("Could not map the PTM of mass " + modMass + " at site " + site + " in peptide " + peptide.getSequence() + ".");
                        }
                    }
                    String modName = mappedModification.getName();
                    ModificationScoring modificationScoring = modificationScores.getModificationScoring(modName);
                    if (modificationScoring == null) {
                        modificationScoring = new ModificationScoring(modName);
                        modificationScores.addModificationScoring(modName, modificationScoring);
                    }
                    modificationScoring.setProbabilisticScore(site, scores.get(site));
                }
            }
        }
        identification.updateObject(spectrumMatch.getKey(), spectrumMatch);
    }
}

Example 3 with ModificationScoring

use of com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring in project peptide-shaker by compomics.

the class ModificationLocalizationScorer method modificationSiteInference.

/**
 * Infers the modification site of the best peptide assumption of the given
 * spectrum match.
 *
 * @param spectrumMatch The spectrum match.
 * @param sequenceProvider The sequence provider to use.
 * @param modificationProvider The modification provider to use.
 * @param identificationParameters The identification parameters.
 */
public void modificationSiteInference(SpectrumMatch spectrumMatch, SequenceProvider sequenceProvider, ModificationProvider modificationProvider, IdentificationParameters identificationParameters) {
    Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
    int nVariableModifications = peptide.getNVariableModifications();
    if (nVariableModifications > 0) {
        SearchParameters searchParameters = identificationParameters.getSearchParameters();
        PSModificationScores modificationScores = (PSModificationScores) spectrumMatch.getUrParam(PSModificationScores.dummy);
        HashMap<Double, ArrayList<ModificationMatch>> modMatchesMap = new HashMap<>(nVariableModifications);
        HashMap<Double, HashMap<Integer, String>> possiblePositions = new HashMap<>(nVariableModifications);
        HashMap<Double, HashMap<Integer, ArrayList<String>>> confidentSites = new HashMap<>(nVariableModifications);
        for (ModificationMatch modificationMatch : peptide.getVariableModifications()) {
            String modName = modificationMatch.getModification();
            Modification modification = modificationProvider.getModification(modName);
            double modMass = modification.getMass();
            ArrayList<ModificationMatch> modOccurence = modMatchesMap.get(modMass);
            if (modOccurence == null) {
                modOccurence = new ArrayList<>(1);
                modMatchesMap.put(modMass, modOccurence);
            }
            HashMap<Integer, String> modPossibleSites = possiblePositions.get(modMass);
            if (modPossibleSites == null) {
                modPossibleSites = new HashMap<>(1);
                possiblePositions.put(modMass, modPossibleSites);
            }
            boolean maybeNotTerminal = modification.getModificationType() == ModificationType.modaa;
            if (!maybeNotTerminal) {
                ArrayList<String> expectedModifications = modificationFactory.getExpectedVariableModifications(searchParameters);
                for (String otherModName : expectedModifications) {
                    if (!otherModName.equals(modName)) {
                        Modification otherModification = modificationProvider.getModification(otherModName);
                        if (otherModification.getMass() == modMass && modification.getModificationType() != otherModification.getModificationType()) {
                            maybeNotTerminal = true;
                            break;
                        }
                    }
                }
            }
            if (maybeNotTerminal) {
                modOccurence.add(modificationMatch);
                for (String similarModName : modificationFactory.getSameMassNotFixedModifications(modMass, searchParameters)) {
                    Modification similarModification = modificationProvider.getModification(similarModName);
                    if (modification.getMass() == modMass) {
                        int[] possibleSites = ModificationUtils.getPossibleModificationSites(peptide, similarModification, sequenceProvider, identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters());
                        for (int pos : possibleSites) {
                            modPossibleSites.put(pos, similarModName);
                        }
                    }
                }
            } else {
                ModificationScoring modificationScoring = modificationScores.getModificationScoring(modName);
                if (modificationScoring == null) {
                    modificationScoring = new ModificationScoring(modName);
                    modificationScores.addModificationScoring(modName, modificationScoring);
                }
                modificationScoring.setSiteConfidence(modificationMatch.getSite(), ModificationScoring.VERY_CONFIDENT);
                modificationMatch.setConfident(true);
                HashMap<Integer, ArrayList<String>> modificationSites = confidentSites.get(modification.getMass());
                if (modificationSites == null) {
                    modificationSites = new HashMap<>(1);
                    confidentSites.put(modMass, modificationSites);
                }
                int site = modificationMatch.getSite();
                ArrayList<String> modNames = modificationSites.get(site);
                if (modNames == null) {
                    modNames = new ArrayList<>(1);
                    modificationSites.put(site, modNames);
                }
                modNames.add(modName);
            }
        }
        ModificationLocalizationParameters modificationScoringParameters = identificationParameters.getModificationLocalizationParameters();
        Set<Double> modMasses = modMatchesMap.keySet();
        // p score -> d-score -> Map mod mass -> site -> list of modifications
        TreeMap<Double, TreeMap<Double, TreeMap<Double, HashMap<Integer, HashSet<String>>>>> ambiguousScoreToSiteMap = new TreeMap<>();
        HashMap<Double, Integer> nRepresentativesMap = new HashMap<>(modMasses.size());
        ArrayList<ModificationMatch> assignedModifications = new ArrayList<>(peptide.getNVariableModifications());
        // p-score -> d-score -> mod mass -> list of posssible sites
        TreeMap<Double, TreeMap<Double, TreeMap<Double, TreeSet<Integer>>>> scoreToSiteMap = new TreeMap<>();
        for (double modMass : modMasses) {
            ArrayList<ModificationMatch> modificationMatches = modMatchesMap.get(modMass);
            int nMods = modificationMatches.size();
            HashMap<Integer, String> modificationPossibleSites = possiblePositions.get(modMass);
            int nPossibleSites = modificationPossibleSites.size();
            HashMap<Integer, ArrayList<String>> modificationConfidentSites = confidentSites.get(modMass);
            if (modificationConfidentSites == null) {
                modificationConfidentSites = new HashMap<>(1);
                confidentSites.put(modMass, modificationConfidentSites);
            }
            if (nPossibleSites < nMods) {
                throw new IllegalArgumentException("The occurence of modification of mass " + modMass + " (" + modificationMatches.size() + ") is higher than the number of possible sites (" + modificationPossibleSites.size() + ") on sequence " + peptide.getSequence() + " in spectrum " + spectrumMatch.getKey() + ".");
            } else if (modificationPossibleSites.size() == modificationMatches.size()) {
                for (ModificationMatch modMatch : modificationMatches) {
                    String modName = modMatch.getModification();
                    int site = modMatch.getSite();
                    ModificationScoring modificationScoring = modificationScores.getModificationScoring(modName);
                    if (modificationScoring == null) {
                        modificationScoring = new ModificationScoring(modName);
                        modificationScores.addModificationScoring(modName, modificationScoring);
                    }
                    modificationScoring.setSiteConfidence(site, ModificationScoring.VERY_CONFIDENT);
                    modMatch.setConfident(true);
                    ArrayList<String> modificationsAtAA = modificationConfidentSites.get(site);
                    if (modificationsAtAA == null) {
                        modificationsAtAA = new ArrayList<>(1);
                        modificationConfidentSites.put(site, modificationsAtAA);
                    }
                    modificationsAtAA.add(modName);
                    assignedModifications.add(modMatch);
                }
            } else if (!modificationScoringParameters.isProbabilisticScoreCalculation()) {
                // no probabilistic score in that case
                double pScore = 0;
                for (ModificationMatch modificationMatch : modificationMatches) {
                    String modName = modificationMatch.getModification();
                    ModificationScoring modificationScoring = modificationScores.getModificationScoring(modName);
                    int site = modificationMatch.getSite();
                    Double dScore = modificationScoring.getDeltaScore(site);
                    if (dScore == 0.0) {
                        modificationScoring.setSiteConfidence(site, ModificationScoring.RANDOM);
                        modificationMatch.setConfident(false);
                    } else if (dScore <= 95) {
                        modificationScoring.setSiteConfidence(site, ModificationScoring.DOUBTFUL);
                        modificationMatch.setConfident(false);
                    } else {
                        modificationScoring.setSiteConfidence(site, ModificationScoring.CONFIDENT);
                        modificationMatch.setConfident(true);
                        ArrayList<String> modificationsAtAA = modificationConfidentSites.get(site);
                        if (modificationsAtAA == null) {
                            modificationsAtAA = new ArrayList<>(1);
                            modificationConfidentSites.put(site, modificationsAtAA);
                        }
                        modificationsAtAA.add(modName);
                    }
                    if (!modificationMatch.getConfident()) {
                        TreeMap<Double, TreeMap<Double, HashMap<Integer, HashSet<String>>>> pScoreAmbiguousMap = ambiguousScoreToSiteMap.get(pScore);
                        if (pScoreAmbiguousMap == null) {
                            pScoreAmbiguousMap = new TreeMap<>();
                            ambiguousScoreToSiteMap.put(pScore, pScoreAmbiguousMap);
                        }
                        TreeMap<Double, HashMap<Integer, HashSet<String>>> dScoreAmbiguousMap = pScoreAmbiguousMap.get(dScore);
                        if (dScoreAmbiguousMap == null) {
                            dScoreAmbiguousMap = new TreeMap<>();
                            pScoreAmbiguousMap.put(dScore, dScoreAmbiguousMap);
                        }
                        HashMap<Integer, HashSet<String>> massAmbiguousMap = dScoreAmbiguousMap.get(modMass);
                        if (massAmbiguousMap == null) {
                            massAmbiguousMap = new HashMap<>(nPossibleSites);
                            dScoreAmbiguousMap.put(modMass, massAmbiguousMap);
                        }
                        HashSet<String> modifications = massAmbiguousMap.get(site);
                        if (modifications == null) {
                            modifications = new HashSet<>(1);
                            massAmbiguousMap.put(site, modifications);
                        }
                        modifications.add(modName);
                    }
                    assignedModifications.add(modificationMatch);
                }
            } else {
                for (int site : modificationPossibleSites.keySet()) {
                    String modName = modificationPossibleSites.get(site);
                    ModificationScoring modificationScoring = modificationScores.getModificationScoring(modName);
                    double pScore = 0;
                    double dScore = 0;
                    if (modificationScoring != null) {
                        pScore = modificationScoring.getProbabilisticScore(site);
                        dScore = modificationScoring.getDeltaScore(site);
                    }
                    TreeMap<Double, TreeMap<Double, TreeSet<Integer>>> pScoreMap = scoreToSiteMap.get(pScore);
                    if (pScoreMap == null) {
                        pScoreMap = new TreeMap<>();
                        scoreToSiteMap.put(pScore, pScoreMap);
                    }
                    TreeMap<Double, TreeSet<Integer>> dScoreMap = pScoreMap.get(dScore);
                    if (dScoreMap == null) {
                        dScoreMap = new TreeMap<>();
                        pScoreMap.put(dScore, dScoreMap);
                    }
                    TreeSet<Integer> dScoreSites = dScoreMap.get(modMass);
                    if (dScoreSites == null) {
                        dScoreSites = new TreeSet<>();
                        dScoreMap.put(modMass, dScoreSites);
                    }
                    dScoreSites.add(site);
                }
            }
        }
        // Assign modifications to the sites passing the threshold.
        if (!scoreToSiteMap.isEmpty()) {
            HashMap<Double, Integer> processedSitesMap = new HashMap<>(modMasses.size());
            for (Entry<Double, TreeMap<Double, TreeMap<Double, TreeSet<Integer>>>> entry1 : scoreToSiteMap.descendingMap().entrySet()) {
                double pScore = entry1.getKey();
                TreeMap<Double, TreeMap<Double, TreeSet<Integer>>> pScoreMap = entry1.getValue();
                for (Entry<Double, TreeMap<Double, TreeSet<Integer>>> entry2 : pScoreMap.descendingMap().entrySet()) {
                    double dScore = entry2.getKey();
                    TreeMap<Double, TreeSet<Integer>> dScoreMap = entry2.getValue();
                    for (Entry<Double, TreeSet<Integer>> entry : dScoreMap.entrySet()) {
                        double modificationMass = entry.getKey();
                        ArrayList<ModificationMatch> modificationMatches = modMatchesMap.get(modificationMass);
                        HashMap<Integer, String> modificationPossibleSites = possiblePositions.get(modificationMass);
                        HashMap<Integer, ArrayList<String>> modificationConfidentSites = confidentSites.get(modificationMass);
                        int nMods = modificationMatches.size();
                        int nPossibleSites = modificationPossibleSites.size();
                        double randomScoreThreshold = modificationScoringParameters.getSelectedProbabilisticScore().getRandomThreshold(nMods, nPossibleSites);
                        double confidenceThreshold = modificationScoringParameters.getProbabilisticScoreThreshold();
                        TreeSet<Integer> sites = dScoreMap.get(modificationMass);
                        Integer nAssignedSites = processedSitesMap.get(modificationMass);
                        if (nAssignedSites == null) {
                            nAssignedSites = 0;
                        }
                        for (int site : sites) {
                            String modName = modificationPossibleSites.get(site);
                            ModificationScoring modificationScoring = modificationScores.getModificationScoring(modName);
                            if (modificationScoring == null) {
                                modificationScoring = new ModificationScoring(modName);
                                modificationScores.addModificationScoring(modName, modificationScoring);
                            }
                            ModificationMatch modificationMatch = null;
                            if (nAssignedSites < nMods) {
                                boolean alreadyOccupied = false;
                                for (ModificationMatch assignedMatch : assignedModifications) {
                                    if (assignedMatch.getSite() == site) {
                                        alreadyOccupied = true;
                                        break;
                                    }
                                }
                                if (!alreadyOccupied) {
                                    if (pScore >= confidenceThreshold) {
                                        modificationMatch = modificationMatches.get(nAssignedSites);
                                        modificationMatch.setSite(site);
                                        modificationMatch.setModification(modName);
                                        assignedModifications.add(modificationMatch);
                                        modificationScoring.setSiteConfidence(site, ModificationScoring.VERY_CONFIDENT);
                                        modificationMatch.setConfident(true);
                                        ArrayList<String> modificationsAtAA = modificationConfidentSites.get(site);
                                        if (modificationsAtAA == null) {
                                            modificationsAtAA = new ArrayList<>(1);
                                            modificationConfidentSites.put(site, modificationsAtAA);
                                        }
                                        modificationsAtAA.add(modName);
                                        nAssignedSites++;
                                        processedSitesMap.put(modificationMass, nAssignedSites);
                                    } else if (pScore > randomScoreThreshold) {
                                        modificationScoring.setSiteConfidence(site, ModificationScoring.DOUBTFUL);
                                    } else {
                                        modificationScoring.setSiteConfidence(site, ModificationScoring.RANDOM);
                                    }
                                }
                            }
                            if (modificationMatch == null) {
                                TreeMap<Double, TreeMap<Double, HashMap<Integer, HashSet<String>>>> pScoreAmbiguousMap = ambiguousScoreToSiteMap.get(pScore);
                                if (pScoreAmbiguousMap == null) {
                                    pScoreAmbiguousMap = new TreeMap<>();
                                    ambiguousScoreToSiteMap.put(pScore, pScoreAmbiguousMap);
                                }
                                TreeMap<Double, HashMap<Integer, HashSet<String>>> dScoreAmbiguousMap = pScoreAmbiguousMap.get(dScore);
                                if (dScoreAmbiguousMap == null) {
                                    dScoreAmbiguousMap = new TreeMap<>();
                                    pScoreAmbiguousMap.put(dScore, dScoreAmbiguousMap);
                                }
                                HashMap<Integer, HashSet<String>> massAmbiguousMap = dScoreAmbiguousMap.get(modificationMass);
                                if (massAmbiguousMap == null) {
                                    massAmbiguousMap = new HashMap<>(nPossibleSites);
                                    dScoreAmbiguousMap.put(modificationMass, massAmbiguousMap);
                                }
                                HashSet<String> modifications = massAmbiguousMap.get(site);
                                if (modifications == null) {
                                    modifications = new HashSet<>(1);
                                    massAmbiguousMap.put(site, modifications);
                                }
                                modifications.add(modName);
                            }
                        }
                    }
                }
            }
        }
        // See whether there are sites that are not confidently assigned.
        for (double modMass : confidentSites.keySet()) {
            HashMap<Integer, ArrayList<String>> modConfidentSitesMap = confidentSites.get(modMass);
            ArrayList<Integer> modConfidentSites = new ArrayList<>(modConfidentSitesMap.keySet());
            int nConfident = 0;
            for (int site : modConfidentSites) {
                ArrayList<String> modifications = modConfidentSitesMap.get(site);
                for (String modName : modifications) {
                    modificationScores.addConfidentModificationSite(modName, site);
                }
                nConfident += modifications.size();
            }
            modConfidentSites.size();
            ArrayList<ModificationMatch> modificationMatches = modMatchesMap.get(modMass);
            int nMods = modificationMatches.size();
            if (nConfident < nMods) {
                int nRepresentatives = nMods - nConfident;
                if (nRepresentatives > 0) {
                    nRepresentativesMap.put(modMass, nRepresentatives);
                }
            }
        }
        // Create ambiguous site groups and assign the remaining modifications to the best scoring sites.
        if (!nRepresentativesMap.isEmpty()) {
            HashMap<Double, HashMap<Integer, HashMap<Integer, HashSet<String>>>> representativeToSecondaryMap = getRepresentativeToSecondaryMap(ambiguousScoreToSiteMap, nRepresentativesMap);
            for (Entry<Double, HashMap<Integer, HashMap<Integer, HashSet<String>>>> entry1 : representativeToSecondaryMap.entrySet()) {
                double modMass = entry1.getKey();
                HashMap<Integer, HashMap<Integer, HashSet<String>>> massMap = entry1.getValue();
                ArrayList<ModificationMatch> modificationMatches = modMatchesMap.get(modMass);
                int nMods = modificationMatches.size();
                int nRepresentativeSites = nRepresentativesMap.get(modMass);
                if (nRepresentativeSites != massMap.size()) {
                    throw new IllegalArgumentException("Unexpected number of representative sites.");
                }
                int nConfident = nMods - nRepresentativeSites;
                int modMatchIndex = nConfident;
                for (Entry<Integer, HashMap<Integer, HashSet<String>>> entry : massMap.entrySet()) {
                    int representativeSite = entry.getKey();
                    HashMap<Integer, HashSet<String>> sites = entry.getValue();
                    modificationScores.addAmbiguousModificationSites(representativeSite, sites);
                    ModificationMatch modificationMatch = modificationMatches.get(modMatchIndex);
                    String modName = null;
                    for (String possibleModName : sites.get(representativeSite)) {
                        Modification possibleModification = modificationProvider.getModification(possibleModName);
                        if (possibleModification.getMass() == modMass) {
                            modName = possibleModName;
                            break;
                        }
                    }
                    if (modName == null) {
                        throw new IllegalArgumentException("No candidate modification of mass " + modMass + " found at site " + representativeSite + " on peptide " + peptide.getSequence() + ".");
                    }
                    modificationMatch.setModification(modName);
                    modificationMatch.setSite(representativeSite);
                    modificationMatch.setConfident(false);
                    modMatchIndex++;
                }
            }
        }
    }
}

Example 4 with ModificationScoring

use of com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring in project peptide-shaker by compomics.

the class PsPeptideSection method getfeature.

/**
 * Returns the component of the section corresponding to the given feature.
 *
 * @param identification the identification of the project
 * @param identificationFeaturesGenerator the identification features
 * generator of the project
 * @param sequenceProvider a provider for the protein sequences
 * @param proteinDetailsProvider a provider for protein details
 * @param identificationParameters the identification parameters
 * @param nSurroundingAA the number of surrounding amino acids to export
 * @param linePrefix the line prefix to use.
 * @param peptideMatch the peptide match
 * @param peptideFeature the peptide feature to export
 * @param validatedOnly whether only validated matches should be exported
 * @param decoys whether decoy matches should be exported as well
 * @param waitingHandler the waiting handler
 *
 * @return the component of the section corresponding to the given feature
 */
public static String getfeature(Identification identification, IdentificationFeaturesGenerator identificationFeaturesGenerator, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, IdentificationParameters identificationParameters, int nSurroundingAA, String linePrefix, PeptideMatch peptideMatch, PsPeptideFeature peptideFeature, boolean validatedOnly, boolean decoys, WaitingHandler waitingHandler) {
    switch(peptideFeature) {
        case accessions:
            TreeMap<String, int[]> proteinMapping = peptideMatch.getPeptide().getProteinMapping();
            return proteinMapping.navigableKeySet().stream().collect(Collectors.joining(","));
        case protein_description:
            proteinMapping = peptideMatch.getPeptide().getProteinMapping();
            return proteinMapping.navigableKeySet().stream().map(accession -> proteinDetailsProvider.getDescription(accession)).collect(Collectors.joining(","));
        case protein_groups:
            TreeSet<Long> proteinGroups = identification.getProteinMatches(peptideMatch.getKey());
            return proteinGroups.stream().map(proteinGroupKey -> getProteinGroupText(proteinGroupKey, identification)).collect(Collectors.joining(";"));
        case best_protein_group_validation:
            MatchValidationLevel bestProteinValidationLevel = MatchValidationLevel.none;
            proteinGroups = identification.getProteinMatches(peptideMatch.getKey());
            for (long proteinGroup : proteinGroups) {
                if (identification.getProteinIdentification().contains(proteinGroup)) {
                    PSParameter psParameter = (PSParameter) (identification.getProteinMatch(proteinGroup)).getUrParam(PSParameter.dummy);
                    if (psParameter.getMatchValidationLevel().getIndex() > bestProteinValidationLevel.getIndex()) {
                        bestProteinValidationLevel = psParameter.getMatchValidationLevel();
                    }
                }
            }
            return bestProteinValidationLevel.getName();
        case confidence:
            PSParameter psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            return Double.toString(psParameter.getConfidence());
        case decoy:
            return PeptideUtils.isDecoy(peptideMatch.getPeptide(), sequenceProvider) ? "1" : "0";
        case hidden:
            psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            return psParameter.getHidden() ? "1" : "0";
        case localization_confidence:
            return getPeptideModificationLocationConfidence(peptideMatch, identificationParameters.getSearchParameters().getModificationParameters());
        case pi:
            psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            return psParameter.getProteinInferenceClassAsString();
        case position:
            proteinMapping = peptideMatch.getPeptide().getProteinMapping();
            return proteinMapping.entrySet().stream().map(entry -> getPeptideLocalizationText(entry.getKey(), entry.getValue())).collect(Collectors.joining(";"));
        case psms:
            return Integer.toString(peptideMatch.getSpectrumCount());
        case variable_ptms:
            return PeptideUtils.getVariableModificationsAsString(peptideMatch.getPeptide());
        case fixed_ptms:
            ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
            SequenceMatchingParameters modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
            return PeptideUtils.getFixedModificationsAsString(peptideMatch.getPeptide(), modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
        case score:
            psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            return Double.toString(psParameter.getTransformedScore());
        case raw_score:
            psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            return Double.toString(psParameter.getScore());
        case sequence:
            return peptideMatch.getPeptide().getSequence();
        case missed_cleavages:
            int nMissedCleavages = peptideMatch.getPeptide().getNMissedCleavages(identificationParameters.getSearchParameters().getDigestionParameters());
            return Integer.toString(nMissedCleavages);
        case modified_sequence:
            modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
            modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
            return peptideMatch.getPeptide().getTaggedModifiedSequence(modificationParameters, sequenceProvider, modificationSequenceMatchingParameters, false, false, true, null);
        case starred:
            psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            return psParameter.getStarred() ? "1" : "0";
        case aaBefore:
            TreeMap<String, String[]> aaMap = PeptideUtils.getAaBefore(peptideMatch.getPeptide(), nSurroundingAA, sequenceProvider);
            return aaMap.values().stream().map(aas -> Arrays.stream(aas).collect(Collectors.joining(","))).collect(Collectors.joining(";"));
        case aaAfter:
            aaMap = PeptideUtils.getAaAfter(peptideMatch.getPeptide(), nSurroundingAA, sequenceProvider);
            return aaMap.values().stream().map(aas -> Arrays.stream(aas).collect(Collectors.joining(","))).collect(Collectors.joining(";"));
        case nValidatedProteinGroups:
            return Integer.toString(identificationFeaturesGenerator.getNValidatedProteinGroups(peptideMatch.getKey(), waitingHandler));
        case unique_group:
            return identification.getProteinMatches(peptideMatch.getKey()).size() == 1 ? "1" : "0";
        case validated:
            psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            return psParameter.getMatchValidationLevel().toString();
        case validated_psms:
            return Integer.toString(identificationFeaturesGenerator.getNValidatedSpectraForPeptide(peptideMatch.getKey()));
        case probabilistic_score:
            PSModificationScores ptmScores = (PSModificationScores) peptideMatch.getUrParam(PSModificationScores.dummy);
            if (ptmScores != null) {
                StringBuilder result = new StringBuilder();
                TreeSet<String> modList = new TreeSet<>(ptmScores.getScoredModifications());
                for (String mod : modList) {
                    ModificationScoring ptmScoring = ptmScores.getModificationScoring(mod);
                    TreeSet<Integer> sites = new TreeSet<>(ptmScoring.getProbabilisticSites());
                    if (!sites.isEmpty()) {
                        if (result.length() > 0) {
                            result.append(", ");
                        }
                        result.append(mod).append(" (");
                        boolean firstSite = true;
                        for (int site : sites) {
                            if (firstSite) {
                                firstSite = false;
                            } else {
                                result.append(", ");
                            }
                            result.append(site).append(": ").append(ptmScoring.getProbabilisticScore(site));
                        }
                        result.append(")");
                    }
                }
                return result.toString();
            }
            return "";
        case d_score:
            StringBuilder result = new StringBuilder();
            ptmScores = (PSModificationScores) peptideMatch.getUrParam(PSModificationScores.dummy);
            if (ptmScores != null) {
                TreeSet<String> modList = new TreeSet<>(ptmScores.getScoredModifications());
                for (String mod : modList) {
                    ModificationScoring ptmScoring = ptmScores.getModificationScoring(mod);
                    TreeSet<Integer> sites = new TreeSet<>(ptmScoring.getDSites());
                    if (!sites.isEmpty()) {
                        if (result.length() > 0) {
                            result.append(", ");
                        }
                        result.append(mod).append(" (");
                        boolean firstSite = true;
                        for (int site : sites) {
                            if (firstSite) {
                                firstSite = false;
                            } else {
                                result.append(", ");
                            }
                            result.append(site).append(": ").append(ptmScoring.getDeltaScore(site));
                        }
                        result.append(")");
                    }
                }
                return result.toString();
            }
            return "";
        case confident_modification_sites:
            String sequence = peptideMatch.getPeptide().getSequence();
            return identificationFeaturesGenerator.getConfidentModificationSites(peptideMatch, sequence);
        case confident_modification_sites_number:
            return identificationFeaturesGenerator.getConfidentModificationSitesNumber(peptideMatch);
        case ambiguous_modification_sites:
            sequence = peptideMatch.getPeptide().getSequence();
            return identificationFeaturesGenerator.getAmbiguousModificationSites(peptideMatch, sequence);
        case ambiguous_modification_sites_number:
            return identificationFeaturesGenerator.getAmbiguousModificationSiteNumber(peptideMatch);
        case confident_phosphosites:
            ArrayList<String> modifications = new ArrayList<>(3);
            for (String ptm : identificationParameters.getSearchParameters().getModificationParameters().getAllNotFixedModifications()) {
                if (ptm.contains("Phospho")) {
                    modifications.add(ptm);
                }
            }
            return identificationFeaturesGenerator.getConfidentModificationSites(peptideMatch, peptideMatch.getPeptide().getSequence(), modifications);
        case confident_phosphosites_number:
            modifications = new ArrayList<>(3);
            for (String ptm : identificationParameters.getSearchParameters().getModificationParameters().getAllNotFixedModifications()) {
                if (ptm.contains("Phospho")) {
                    modifications.add(ptm);
                }
            }
            return identificationFeaturesGenerator.getConfidentModificationSitesNumber(peptideMatch, modifications);
        case ambiguous_phosphosites:
            modifications = new ArrayList<>(3);
            for (String ptm : identificationParameters.getSearchParameters().getModificationParameters().getAllNotFixedModifications()) {
                if (ptm.contains("Phospho")) {
                    modifications.add(ptm);
                }
            }
            return identificationFeaturesGenerator.getAmbiguousModificationSites(peptideMatch, peptideMatch.getPeptide().getSequence(), modifications);
        case ambiguous_phosphosites_number:
            modifications = new ArrayList<>(3);
            for (String ptm : identificationParameters.getSearchParameters().getModificationParameters().getAllNotFixedModifications()) {
                if (ptm.contains("Phospho")) {
                    modifications.add(ptm);
                }
            }
            return identificationFeaturesGenerator.getAmbiguousModificationSiteNumber(peptideMatch, modifications);
        default:
            return "Not implemented";
    }
}

Example 5 with ModificationScoring

use of com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring in project peptide-shaker by compomics.

the class PsPsmSection method getPeptideModificationLocationConfidence.

/**
 * Returns the peptide modification location confidence as a string.
 *
 * @param spectrumMatch the spectrum match
 * @param modificationParameters the PTM profile
 *
 * @return the peptide modification location confidence as a string
 */
public static String getPeptideModificationLocationConfidence(SpectrumMatch spectrumMatch, ModificationParameters modificationParameters) {
    PSModificationScores psPtmScores = (PSModificationScores) spectrumMatch.getUrParam(PSModificationScores.dummy);
    if (psPtmScores != null) {
        TreeSet<String> modList = new TreeSet<>(psPtmScores.getScoredModifications());
        StringBuilder result = new StringBuilder();
        for (String mod : modList) {
            if (result.length() > 0) {
                result.append(", ");
            }
            result.append(mod).append(" (");
            ModificationScoring ptmScoring = psPtmScores.getModificationScoring(mod);
            boolean firstSite = true;
            for (int site : ptmScoring.getOrderedPtmLocations()) {
                if (firstSite) {
                    firstSite = false;
                } else {
                    result.append(", ");
                }
                int ptmConfidence = ptmScoring.getLocalizationConfidence(site);
                switch(ptmConfidence) {
                    case ModificationScoring.NOT_FOUND:
                        result.append(site).append(": Not Scored");
                        break;
                    case ModificationScoring.RANDOM:
                        result.append(site).append(": Random");
                        break;
                    case ModificationScoring.DOUBTFUL:
                        result.append(site).append(": Doubtfull");
                        break;
                    case ModificationScoring.CONFIDENT:
                        result.append(site).append(": Confident");
                        break;
                    case ModificationScoring.VERY_CONFIDENT:
                        result.append(site).append(": Very Confident");
                        break;
                    default:
                        break;
                }
            }
            result.append(")");
        }
        return result.toString();
    }
    return "";
}