Examples with ModificationLocalizationParameters com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters used on opensource projects

Example 1 with ModificationLocalizationParameters

use of com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters in project peptide-shaker by compomics.

the class ModificationLocalizationScorer method scorePTMs.

/**
 * Scores PTM locations for a desired spectrum match.
 *
 * @param identification Identification object containing the matches.
 * @param spectrumMatch The spectrum match to score.
 * @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 parameters used for identification.
 * @param waitingHandler The waiting handler to use to display progress and
 * allow canceling.
 * @param peptideSpectrumAnnotator The spectrum annotator to use.
 */
public void scorePTMs(Identification identification, SpectrumMatch spectrumMatch, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, IdentificationParameters identificationParameters, WaitingHandler waitingHandler, PeptideSpectrumAnnotator peptideSpectrumAnnotator) {
    SequenceMatchingParameters sequenceMatchingParameters = identificationParameters.getSequenceMatchingParameters();
    attachDeltaScore(identification, spectrumMatch, sequenceMatchingParameters, modificationProvider);
    ModificationLocalizationParameters scoringParameters = identificationParameters.getModificationLocalizationParameters();
    if (scoringParameters.isProbabilisticScoreCalculation()) {
        attachProbabilisticScore(spectrumMatch, sequenceProvider, spectrumProvider, modificationProvider, identificationParameters, peptideSpectrumAnnotator, identification);
    }
}

Example 2 with ModificationLocalizationParameters

use of com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters 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 ModificationLocalizationParameters

use of com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters 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 ModificationLocalizationParameters

use of com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters in project peptide-shaker by compomics.

the class StirRunnable method scoreModificationLocalization.

/**
 * Scores the modification localization for the given peptide in the given
 * spectrum match. The scores are returned in a map: modification mass to
 * modification site to modification score.
 *
 * @param spectrumMatch The spectrum match.
 * @param peptideAssumption The peptide assumption.
 *
 * @return The modification localization scores in a map.
 */
private TreeMap<Double, HashMap<Integer, Double>> scoreModificationLocalization(SpectrumMatch spectrumMatch, PeptideAssumption peptideAssumption) {
    SearchParameters searchParameters = identificationParameters.getSearchParameters();
    AnnotationParameters annotationParameters = identificationParameters.getAnnotationParameters();
    SequenceMatchingParameters sequenceMatchingParameters = identificationParameters.getSequenceMatchingParameters();
    ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
    ModificationLocalizationParameters modificationLocalizationParameters = identificationParameters.getModificationLocalizationParameters();
    SequenceMatchingParameters modificationSequenceMatchingParameters = modificationLocalizationParameters.getSequenceMatchingParameters();
    Peptide peptide = peptideAssumption.getPeptide();
    String spectrumFile = spectrumMatch.getSpectrumFile();
    String spectrumTitle = spectrumMatch.getSpectrumTitle();
    Spectrum spectrum = spectrumProvider.getSpectrum(spectrumFile, spectrumTitle);
    HashMap<Double, ArrayList<Modification>> modificationsMap = new HashMap<>(1);
    for (ModificationMatch modificationMatch : peptide.getVariableModifications()) {
        Modification refMod = modificationFactory.getModification(modificationMatch.getModification());
        double modMass = refMod.getMass();
        if (!modificationsMap.containsKey(modMass)) {
            ArrayList<Modification> modifications = modificationFactory.getSameMassNotFixedModifications(modMass, searchParameters).stream().map(modification -> modificationFactory.getModification(modification)).collect(Collectors.toCollection(ArrayList::new));
            modificationsMap.put(modMass, modifications);
        }
    }
    SpecificAnnotationParameters specificAnnotationParameters = annotationParameters.getSpecificAnnotationParameters(spectrumFile, spectrumTitle, peptideAssumption, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters, peptideSpectrumAnnotator);
    return modificationsMap.entrySet().stream().collect(Collectors.toMap(entry -> entry.getKey(), entry -> PhosphoRS.getSequenceProbabilities(peptide, entry.getValue(), modificationParameters, spectrum, sequenceProvider, annotationParameters, specificAnnotationParameters, modificationLocalizationParameters.isProbabilisticScoreNeutralLosses(), sequenceMatchingParameters, modificationSequenceMatchingParameters, peptideSpectrumAnnotator), (a, b) -> a, TreeMap::new));
}

Example 5 with ModificationLocalizationParameters

use of com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters in project peptide-shaker by compomics.

the class PeptideShaker method createProject.

/**
 * Creates a PeptideShaker project.
 *
 * @param waitingHandler the handler displaying feedback to the user
 * @param exceptionHandler handler for exceptions
 * @param identificationParameters the identification parameters
 * @param processingParameters the processing parameters
 * @param projectType the project type
 * @param spectrumCountingParameters the spectrum counting parameters
 * @param spectrumProvider the spectrum provider
 * @param setWaitingHandlerFinshedWhenDone if true, the waiting handler is
 * set to finished when the project is created
 * @param projectDetails the project details
 *
 * @throws java.lang.InterruptedException exception thrown if a thread gets
 * interrupted
 * @throws java.util.concurrent.TimeoutException exception thrown if a
 * process times out
 * @throws java.io.IOException if an exception occurs when parsing files
 */
public void createProject(IdentificationParameters identificationParameters, ProcessingParameters processingParameters, SpectrumCountingParameters spectrumCountingParameters, SpectrumProvider spectrumProvider, ProjectDetails projectDetails, ProjectType projectType, WaitingHandler waitingHandler, boolean setWaitingHandlerFinshedWhenDone, ExceptionHandler exceptionHandler) throws InterruptedException, TimeoutException, IOException {
    identification.getObjectsDB().commit();
    identificationFeaturesGenerator = new IdentificationFeaturesGenerator(identification, identificationParameters, sequenceProvider, spectrumProvider, metrics, spectrumCountingParameters);
    matchesValidator = new MatchesValidator(new TargetDecoyMap(), new TargetDecoyMap(), new TargetDecoyMap());
    if (waitingHandler.isRunCanceled()) {
        return;
    }
    PsmScoringParameters psmScoringPreferences = identificationParameters.getPsmScoringParameters();
    FastaParameters fastaParameters = identificationParameters.getFastaParameters();
    FastaSummary fastaSummary = FastaSummary.getSummary(projectDetails.getFastaFile(), fastaParameters, waitingHandler);
    // set the background species
    identificationParameters.getGeneParameters().setBackgroundSpeciesFromFastaSummary(fastaSummary);
    ArrayList<Integer> usedAlgorithms = projectDetails.getIdentificationAlgorithms();
    if (psmScoringPreferences.isScoringNeeded(usedAlgorithms)) {
        waitingHandler.appendReport("Estimating PSM scores.", true, true);
        PsmScorer psmScorer = new PsmScorer(fastaParameters, sequenceProvider, spectrumProvider);
        psmScorer.estimateIntermediateScores(identification, inputMap, processingParameters, identificationParameters, waitingHandler, exceptionHandler);
        if (psmScoringPreferences.isTargetDecoyNeededForPsmScoring(usedAlgorithms)) {
            if (fastaParameters.isTargetDecoy()) {
                waitingHandler.appendReport("Estimating intermediate scores probabilities.", true, true);
                psmScorer.estimateIntermediateScoreProbabilities(identification, inputMap, processingParameters, waitingHandler);
            } else {
                waitingHandler.appendReport("No decoy sequences found. Impossible to " + "estimate intermediate scores probabilities.", true, true);
            }
        }
        waitingHandler.appendReport("Scoring PSMs.", true, true);
        psmScorer.scorePsms(identification, inputMap, processingParameters, identificationParameters, waitingHandler);
    }
    identification.getObjectsDB().commit();
    System.gc();
    if (fastaParameters.isTargetDecoy()) {
        waitingHandler.appendReport("Computing assumptions probabilities.", true, true);
    } else {
        waitingHandler.appendReport("Importing assumptions scores.", true, true);
    }
    inputMap.estimateProbabilities(waitingHandler);
    waitingHandler.increasePrimaryProgressCounter();
    if (waitingHandler.isRunCanceled()) {
        return;
    }
    identification.getObjectsDB().commit();
    System.gc();
    waitingHandler.appendReport("Saving assumptions probabilities, selecting best match, scoring modification localization.", true, true);
    PsmProcessor psmProcessor = new PsmProcessor(identification);
    psmProcessor.processPsms(inputMap, identificationParameters, matchesValidator, modificationLocalizationScorer, sequenceProvider, spectrumProvider, modificationFactory, proteinCount, processingParameters.getnThreads(), waitingHandler, exceptionHandler);
    waitingHandler.increasePrimaryProgressCounter();
    if (waitingHandler.isRunCanceled()) {
        return;
    }
    identification.getObjectsDB().commit();
    System.gc();
    waitingHandler.appendReport("Computing PSM probabilities.", true, true);
    matchesValidator.getPsmMap().estimateProbabilities(waitingHandler);
    if (waitingHandler.isRunCanceled()) {
        return;
    }
    identification.getObjectsDB().commit();
    System.gc();
    if (projectType == ProjectType.peptide || projectType == ProjectType.protein) {
        PeptideInference peptideInference = new PeptideInference();
        ModificationLocalizationParameters modificationScoringPreferences = identificationParameters.getModificationLocalizationParameters();
        if (modificationScoringPreferences.getAlignNonConfidentModifications()) {
            waitingHandler.appendReport("Resolving peptide inference issues.", true, true);
            peptideInference.peptideInference(identification, identificationParameters, sequenceProvider, modificationFactory, waitingHandler);
            waitingHandler.increasePrimaryProgressCounter();
            if (waitingHandler.isRunCanceled()) {
                return;
            }
        }
        identification.getObjectsDB().commit();
        System.gc();
    }
    String reportTxt = "Saving probabilities";
    String waitingTitle = "Saving Probabilities.";
    ;
    switch(projectType) {
        case psm:
            reportTxt += ".";
            break;
        case peptide:
            reportTxt += ", building peptides.";
            waitingTitle += " Building Peptides.";
            break;
        default:
            reportTxt += ", building peptides and proteins.";
            waitingTitle += " Building Peptides and Proteins.";
    }
    waitingHandler.appendReport(reportTxt, true, true);
    waitingHandler.setWaitingText(waitingTitle + " Please Wait...");
    attachSpectrumProbabilitiesAndBuildPeptidesAndProteins(sequenceProvider, identificationParameters.getSequenceMatchingParameters(), projectType, fastaParameters, waitingHandler);
    waitingHandler.increasePrimaryProgressCounter();
    if (waitingHandler.isRunCanceled()) {
        return;
    }
    identification.getObjectsDB().commit();
    System.gc();
    if (projectType == ProjectType.peptide || projectType == ProjectType.protein) {
        waitingHandler.appendReport("Generating peptide map.", true, true);
        matchesValidator.fillPeptideMaps(identification, metrics, waitingHandler, identificationParameters, sequenceProvider, spectrumProvider);
        if (waitingHandler.isRunCanceled()) {
            return;
        }
        identification.getObjectsDB().commit();
        System.gc();
        waitingHandler.appendReport("Computing peptide probabilities.", true, true);
        matchesValidator.getPeptideMap().estimateProbabilities(waitingHandler);
        if (waitingHandler.isRunCanceled()) {
            return;
        }
        identification.getObjectsDB().commit();
        System.gc();
        waitingHandler.appendReport("Saving peptide probabilities.", true, true);
        matchesValidator.attachPeptideProbabilities(identification, fastaParameters, waitingHandler);
        waitingHandler.increasePrimaryProgressCounter();
        if (waitingHandler.isRunCanceled()) {
            return;
        }
        identification.getObjectsDB().commit();
        System.gc();
        if (projectType == ProjectType.protein) {
            if (identificationParameters.getProteinInferenceParameters().getSimplifyGroups()) {
                waitingHandler.appendReport("Simplifying protein groups.", true, true);
                GroupSimplification groupSimplification = new GroupSimplification();
                groupSimplification.removeRedundantGroups(identification, identificationParameters, sequenceProvider, proteinDetailsProvider, waitingHandler);
                waitingHandler.increasePrimaryProgressCounter();
                if (waitingHandler.isRunCanceled()) {
                    return;
                }
            }
            identification.getObjectsDB().commit();
            System.gc();
            ProteinInference proteinInference = new ProteinInference();
            waitingHandler.appendReport("Mapping shared peptides.", true, true);
            proteinInference.distributeSharedPeptides(identification, waitingHandler);
            waitingHandler.increasePrimaryProgressCounter();
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            identification.getObjectsDB().commit();
            System.gc();
            waitingHandler.appendReport("Generating protein map.", true, true);
            matchesValidator.fillProteinMap(identification, spectrumProvider, waitingHandler);
            waitingHandler.increasePrimaryProgressCounter();
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            identification.getObjectsDB().commit();
            System.gc();
            waitingHandler.appendReport("Selecting leading proteins, inferring peptide and protein inference status.", true, true);
            proteinInference.inferPiStatus(identification, metrics, matchesValidator.getProteinMap(), identificationParameters, sequenceProvider, proteinDetailsProvider, waitingHandler);
            waitingHandler.increasePrimaryProgressCounter();
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            identification.getObjectsDB().commit();
            System.gc();
            waitingHandler.appendReport("Computing protein probabilities.", true, true);
            matchesValidator.getProteinMap().estimateProbabilities(waitingHandler);
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            identification.getObjectsDB().commit();
            System.gc();
            waitingHandler.appendReport("Saving protein probabilities.", true, true);
            matchesValidator.attachProteinProbabilities(identification, sequenceProvider, fastaParameters, metrics, waitingHandler, identificationParameters.getFractionParameters());
            waitingHandler.increasePrimaryProgressCounter();
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            identification.getObjectsDB().commit();
            System.gc();
        }
    }
    if (fastaParameters.isTargetDecoy()) {
        IdMatchValidationParameters idMatchValidationParameters = identificationParameters.getIdValidationParameters();
        if (idMatchValidationParameters.getDefaultPsmFDR() == 1 && idMatchValidationParameters.getDefaultPeptideFDR() == 1 && idMatchValidationParameters.getDefaultProteinFDR() == 1) {
            waitingHandler.appendReport("Validating identifications at 1% FDR, quality control of matches.", true, true);
        } else {
            waitingHandler.appendReport("Validating identifications, quality control of matches.", true, true);
        }
    } else {
        waitingHandler.appendReport("Quality control of matches.", true, true);
    }
    matchesValidator.validateIdentifications(identification, metrics, inputMap, waitingHandler, exceptionHandler, identificationFeaturesGenerator, sequenceProvider, proteinDetailsProvider, spectrumProvider, geneMaps, identificationParameters, projectType, processingParameters);
    waitingHandler.increasePrimaryProgressCounter();
    if (waitingHandler.isRunCanceled()) {
        return;
    }
    identification.getObjectsDB().commit();
    System.gc();
    if (projectType == ProjectType.peptide || projectType == ProjectType.protein) {
        waitingHandler.appendReport("Scoring PTMs in peptides.", true, true);
        modificationLocalizationScorer.scorePeptidePtms(identification, modificationFactory, waitingHandler, identificationParameters);
        waitingHandler.increasePrimaryProgressCounter();
        if (waitingHandler.isRunCanceled()) {
            return;
        }
        identification.getObjectsDB().commit();
        System.gc();
        if (projectType == ProjectType.protein) {
            waitingHandler.appendReport("Estimating spectrum counting scaling values.", true, true);
            ScalingFactorsEstimators scalingFactors = new ScalingFactorsEstimators(spectrumCountingParameters);
            scalingFactors.estimateScalingFactors(identification, metrics, sequenceProvider, identificationFeaturesGenerator, waitingHandler, exceptionHandler, processingParameters);
            waitingHandler.increasePrimaryProgressCounter();
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            identification.getObjectsDB().commit();
            System.gc();
            waitingHandler.appendReport("Scoring PTMs in proteins, gathering summary metrics.", true, true);
            ProteinProcessor proteinProcessor = new ProteinProcessor(identification, identificationParameters, identificationFeaturesGenerator, sequenceProvider);
            proteinProcessor.processProteins(modificationLocalizationScorer, metrics, modificationFactory, waitingHandler, exceptionHandler, processingParameters);
            waitingHandler.increasePrimaryProgressCounter();
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            identification.getObjectsDB().commit();
            System.gc();
        }
    }
    projectCreationDuration.end();
    String report = "Identification processing completed (" + projectCreationDuration.toString() + ").";
    waitingHandler.appendReport(report, true, true);
    waitingHandler.appendReportEndLine();
    waitingHandler.appendReportEndLine();
    identification.addUrParam(new PSMaps(inputMap, matchesValidator.getPsmMap(), matchesValidator.getPeptideMap(), matchesValidator.getProteinMap()));
    if (setWaitingHandlerFinshedWhenDone) {
        waitingHandler.setRunFinished();
    }
}