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

Example 1 with Identification

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

the class ProteinStructurePanel method updateSelection.

/**
 * Update the selected protein and peptide.
 *
 * @param scrollToVisible if true the table also scrolls to make the
 * selected row visible
 */
public void updateSelection(boolean scrollToVisible) {
    int proteinRow = 0;
    long proteinKey = peptideShakerGUI.getSelectedProteinKey();
    long peptideKey = peptideShakerGUI.getSelectedPeptideKey();
    String spectrumFile = peptideShakerGUI.getSelectedSpectrumFile();
    String spectrumTitle = peptideShakerGUI.getSelectedSpectrumTitle();
    Identification identification = peptideShakerGUI.getIdentification();
    if (proteinKey == NO_KEY && peptideKey == NO_KEY && spectrumFile != null && spectrumTitle != null) {
        long psmKey = SpectrumMatch.getKey(spectrumFile, spectrumTitle);
        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(psmKey);
        if (spectrumMatch != null && spectrumMatch.getBestPeptideAssumption() != null) {
            Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
            peptideKey = peptide.getMatchingKey(peptideShakerGUI.getIdentificationParameters().getSequenceMatchingParameters());
        }
    }
    if (proteinKey == NO_KEY && peptideKey != NO_KEY) {
        final long peptideKeyFinal = peptideKey;
        ProteinMatch tempProteinMatch = identification.getProteinIdentification().parallelStream().map(key -> identification.getProteinMatch(key)).filter(proteinMatch -> Arrays.stream(proteinMatch.getPeptideMatchesKeys()).anyMatch(key -> key == peptideKeyFinal)).findAny().orElse(null);
        if (tempProteinMatch != null) {
            proteinKey = tempProteinMatch.getKey();
            peptideShakerGUI.setSelectedItems(proteinKey, peptideKey, spectrumFile, spectrumTitle);
        }
        if (proteinKey != NO_KEY) {
            proteinRow = getProteinRow(proteinKey);
        }
        if (proteinKeys.length == 0) {
            clearData();
            return;
        }
        if (proteinRow == -1) {
            peptideShakerGUI.resetSelectedItems();
            proteinTableMouseReleased(null);
        } else if (proteinTable.getSelectedRow() != proteinRow) {
            proteinTable.setRowSelectionInterval(proteinRow, proteinRow);
            if (scrollToVisible) {
                proteinTable.scrollRectToVisible(proteinTable.getCellRect(proteinRow, 0, false));
            }
            proteinTableMouseReleased(null);
        }
        int peptideRow = 0;
        if (peptideKey != NO_KEY) {
            peptideRow = getPeptideRow(peptideKey);
        }
        if (peptideTable.getSelectedRow() != peptideRow && peptideRow != -1) {
            peptideTable.setRowSelectionInterval(peptideRow, peptideRow);
            if (scrollToVisible) {
                peptideTable.scrollRectToVisible(peptideTable.getCellRect(peptideRow, 0, false));
            }
            peptideTableMouseReleased(null);
        }
        if (spectrumFile != null && spectrumTitle != null) {
            peptideShakerGUI.setSelectedItems(peptideShakerGUI.getSelectedProteinKey(), peptideShakerGUI.getSelectedPeptideKey(), spectrumFile, spectrumTitle);
        }
    }
}

Example 2 with Identification

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

the class ModificationLocalizationScorer method scorePTMs.

/**
 * Scores PTMs in a protein match.
 *
 * @param identification The identification object containing the matches.
 * @param proteinMatch The protein match.
 * @param identificationParameters The identification parameters.
 * @param scorePeptides If true, peptides will be scored as well.
 * @param modificationProvider The modification provider to use.
 * @param waitingHandler The waiting handler to sue, ignored if null.
 */
public void scorePTMs(Identification identification, ProteinMatch proteinMatch, IdentificationParameters identificationParameters, boolean scorePeptides, ModificationProvider modificationProvider, WaitingHandler waitingHandler) {
    HashMap<Integer, ArrayList<String>> confidentSites = new HashMap<>();
    HashMap<Integer, HashMap<Integer, HashSet<String>>> ambiguousSites = new HashMap<>();
    for (long peptideKey : proteinMatch.getPeptideMatchesKeys()) {
        PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
        Peptide peptide = peptideMatch.getPeptide();
        PSParameter psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
        if (psParameter.getMatchValidationLevel().isValidated() && peptide.getNVariableModifications() > 0) {
            PSModificationScores peptideScores = (PSModificationScores) peptideMatch.getUrParam(PSModificationScores.dummy);
            if (peptideScores == null || scorePeptides) {
                scorePTMs(identification, peptideMatch, identificationParameters, modificationProvider, waitingHandler);
                peptideScores = (PSModificationScores) peptideMatch.getUrParam(PSModificationScores.dummy);
            }
            if (peptideScores != null) {
                int[] peptideStart = peptide.getProteinMapping().get(proteinMatch.getLeadingAccession());
                for (int confidentSite : peptideScores.getConfidentSites()) {
                    for (int peptideTempStart : peptideStart) {
                        int siteOnProtein = peptideTempStart + confidentSite - 1;
                        ArrayList<String> modificationsAtSite = confidentSites.get(siteOnProtein);
                        if (modificationsAtSite == null) {
                            modificationsAtSite = new ArrayList<>();
                            confidentSites.put(siteOnProtein, modificationsAtSite);
                        }
                        for (String modName : peptideScores.getConfidentModificationsAt(confidentSite)) {
                            if (!modificationsAtSite.contains(modName)) {
                                modificationsAtSite.add(modName);
                            }
                        }
                    }
                }
                for (int representativeSite : peptideScores.getRepresentativeSites()) {
                    HashMap<Integer, HashSet<String>> peptideAmbiguousSites = peptideScores.getAmbiguousModificationsAtRepresentativeSite(representativeSite);
                    for (int peptideTempStart : peptideStart) {
                        int proteinRepresentativeSite = peptideTempStart + representativeSite - 1;
                        HashMap<Integer, HashSet<String>> proteinAmbiguousSites = ambiguousSites.get(proteinRepresentativeSite);
                        if (proteinAmbiguousSites == null) {
                            proteinAmbiguousSites = new HashMap<>(peptideAmbiguousSites.size());
                            ambiguousSites.put(proteinRepresentativeSite, proteinAmbiguousSites);
                        }
                        for (int peptideSite : peptideAmbiguousSites.keySet()) {
                            int siteOnProtein = peptideTempStart + peptideSite - 1;
                            proteinAmbiguousSites.put(siteOnProtein, peptideAmbiguousSites.get(peptideSite));
                        }
                    }
                }
            }
        }
    }
    // remove ambiguous sites where a confident was found and merge overlapping groups
    PSModificationScores proteinScores = new PSModificationScores();
    ArrayList<Integer> representativeSites = new ArrayList<>(ambiguousSites.keySet());
    Collections.sort(representativeSites);
    for (Integer representativeSite : representativeSites) {
        HashMap<Integer, HashSet<String>> secondarySitesMap = ambiguousSites.get(representativeSite);
        ArrayList<Integer> secondarySites = new ArrayList<>(secondarySitesMap.keySet());
        for (int secondarySite : secondarySites) {
            ArrayList<String> confidentModifications = confidentSites.get(secondarySite);
            if (confidentModifications != null) {
                boolean sameModification = confidentModifications.stream().map(modName -> modificationProvider.getModification(modName)).anyMatch(confidentModification -> secondarySitesMap.get(secondarySite).stream().map(modName -> modificationProvider.getModification(modName)).anyMatch(secondaryModification -> secondaryModification.getMass() == confidentModification.getMass()));
                if (sameModification) {
                    ambiguousSites.remove(representativeSite);
                    break;
                }
            }
            if (secondarySite != representativeSite) {
                ArrayList<Integer> tempRepresentativeSites = new ArrayList<>(ambiguousSites.keySet());
                Collections.sort(tempRepresentativeSites);
                for (Integer previousSite : tempRepresentativeSites) {
                    if (previousSite >= representativeSite) {
                        break;
                    }
                    if (previousSite == secondarySite) {
                        HashMap<Integer, HashSet<String>> previousSites = ambiguousSites.get(previousSite);
                        HashSet<String> previousModifications = previousSites.get(previousSite);
                        boolean sameModification = previousModifications.stream().map(modName -> modificationProvider.getModification(modName)).anyMatch(previousModification -> secondarySitesMap.get(secondarySite).stream().map(modName -> modificationProvider.getModification(modName)).anyMatch(secondaryModification -> secondaryModification.getMass() == previousModification.getMass()));
                        if (sameModification) {
                            for (int tempSecondarySite : secondarySitesMap.keySet()) {
                                if (!previousSites.containsKey(secondarySite)) {
                                    previousSites.put(tempSecondarySite, secondarySitesMap.get(tempSecondarySite));
                                }
                            }
                            ambiguousSites.remove(representativeSite);
                        }
                    }
                }
            }
        }
    }
    for (int confidentSite : confidentSites.keySet()) {
        for (String modName : confidentSites.get(confidentSite)) {
            proteinScores.addConfidentModificationSite(modName, confidentSite);
        }
    }
    for (int representativeSite : ambiguousSites.keySet()) {
        proteinScores.addAmbiguousModificationSites(representativeSite, ambiguousSites.get(representativeSite));
    }
    proteinMatch.addUrParam(proteinScores);
}

Example 3 with Identification

use of com.compomics.util.experiment.identification.Identification 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 4 with Identification

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

the class QCPanel method getPeptideModificationEnrichmentSpecificityDataset.

/**
 * Returns the dataset for the peptide modification rate QC plot.
 *
 * @return the dataset for the peptide modification rate QC plot
 */
private DefaultCategoryDataset getPeptideModificationEnrichmentSpecificityDataset() {
    ModificationFactory modificationFactory = ModificationFactory.getInstance();
    Identification identification = peptideShakerGUI.getIdentification();
    SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
    IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
    ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
    SequenceMatchingParameters modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
    ArrayList<String> modNames = modificationParameters.getAllNotFixedModifications();
    HashMap<String, Integer> modifiedPeptidesMap = new HashMap<>(modNames.size());
    HashMap<String, Integer> possiblyModifiedPeptidesMap = new HashMap<>(modNames.size());
    progressDialog.setPrimaryProgressCounterIndeterminate(false);
    progressDialog.setMaxPrimaryProgressCounter(identification.getPeptideIdentification().size());
    progressDialog.setValue(0);
    PeptideMatchesIterator peptideMatchesIterator = identification.getPeptideMatchesIterator(progressDialog);
    PeptideMatch peptideMatch;
    while ((peptideMatch = peptideMatchesIterator.next()) != null) {
        PSParameter psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
        if (psParameter.getMatchValidationLevel().isValidated()) {
            Peptide peptide = peptideMatch.getPeptide();
            for (String modName : modificationParameters.getAllNotFixedModifications()) {
                Modification modification = modificationFactory.getModification(modName);
                int[] possibleSites = ModificationUtils.getPossibleModificationSites(peptide, modification, sequenceProvider, modificationSequenceMatchingParameters);
                if (possibleSites.length != 0) {
                    Integer nPossiblePeptides = possiblyModifiedPeptidesMap.get(modName);
                    if (nPossiblePeptides == null) {
                        possiblyModifiedPeptidesMap.put(modName, 1);
                    } else {
                        possiblyModifiedPeptidesMap.put(modName, nPossiblePeptides + 1);
                    }
                    boolean modified = false;
                    for (ModificationMatch modificationMatch : peptide.getVariableModifications()) {
                        if (modificationMatch.getModification().equals(modName)) {
                            modified = true;
                            break;
                        }
                    }
                    if (modified) {
                        Integer nModifiedPeptides = modifiedPeptidesMap.get(modName);
                        if (nModifiedPeptides == null) {
                            modifiedPeptidesMap.put(modName, 1);
                        } else {
                            modifiedPeptidesMap.put(modName, nModifiedPeptides + 1);
                        }
                    }
                }
            }
        }
        if (progressDialog.isRunCanceled()) {
            break;
        }
        progressDialog.increaseSecondaryProgressCounter();
    }
    DefaultCategoryDataset dataset = new DefaultCategoryDataset();
    for (String modName : modificationParameters.getAllNotFixedModifications()) {
        Integer nFound = modifiedPeptidesMap.get(modName);
        if (nFound == null) {
            nFound = 0;
        }
        Integer nPossible = possiblyModifiedPeptidesMap.get(modName);
        Double rate = 0.0;
        if (nPossible != null) {
            rate = (100.0 * nFound) / nPossible;
        }
        dataset.addValue(rate, "Modified", modName);
        double rest = 0.0;
        if (nPossible != null) {
            rest = 100 - rate;
        }
        dataset.addValue(rest, "Not Modified", modName);
    }
    return dataset;
}

Example 5 with Identification

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

the class QCPanel method getPeptideModificationEfficiencyDataset.

/**
 * Returns the dataset for the peptide modification efficiency QC plot.
 *
 * @return the dataset for the peptide modification efficiency QC plot
 */
private DefaultCategoryDataset getPeptideModificationEfficiencyDataset() {
    ModificationFactory modificationFactory = ModificationFactory.getInstance();
    Identification identification = peptideShakerGUI.getIdentification();
    SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
    IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
    ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
    SequenceMatchingParameters modificationSequenceMatchingPreferences = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
    ArrayList<String> modNames = modificationParameters.getAllNotFixedModifications();
    HashMap<String, Integer> modifiedSitesMap = new HashMap<>(modNames.size());
    HashMap<String, Integer> possibleSitesMap = new HashMap<>(modNames.size());
    PSParameter psParameter = new PSParameter();
    progressDialog.setPrimaryProgressCounterIndeterminate(false);
    progressDialog.setMaxPrimaryProgressCounter(identification.getPeptideIdentification().size());
    progressDialog.setValue(0);
    PeptideMatchesIterator peptideMatchesIterator = identification.getPeptideMatchesIterator(progressDialog);
    PeptideMatch peptideMatch;
    while ((peptideMatch = peptideMatchesIterator.next()) != null) {
        psParameter = (PSParameter) peptideMatch.getUrParam(psParameter);
        if (psParameter.getMatchValidationLevel().isValidated()) {
            Peptide peptide = peptideMatch.getPeptide();
            HashMap<String, Integer> peptideModificationsMap = new HashMap<>(peptide.getVariableModifications().length);
            for (ModificationMatch modificationMatch : peptide.getVariableModifications()) {
                String modName = modificationMatch.getModification();
                Integer occurrence = peptideModificationsMap.get(modName);
                if (occurrence == null) {
                    peptideModificationsMap.put(modName, 1);
                } else {
                    peptideModificationsMap.put(modName, occurrence + 1);
                }
            }
            for (String modName : modificationParameters.getAllNotFixedModifications()) {
                Modification modification = modificationFactory.getModification(modName);
                int[] possibleSites = ModificationUtils.getPossibleModificationSites(peptide, modification, sequenceProvider, modificationSequenceMatchingPreferences);
                if (possibleSites.length != 0) {
                    Integer occurrencePeptide = peptideModificationsMap.get(modName);
                    if (occurrencePeptide != null) {
                        Integer occurrenceDataset = modifiedSitesMap.get(modName);
                        if (occurrenceDataset == null) {
                            modifiedSitesMap.put(modName, occurrencePeptide);
                        } else {
                            modifiedSitesMap.put(modName, occurrenceDataset + occurrencePeptide);
                        }
                    }
                    Integer possibleSitesDataset = possibleSitesMap.get(modName);
                    if (possibleSitesDataset == null) {
                        possibleSitesMap.put(modName, possibleSites.length);
                    } else {
                        possibleSitesMap.put(modName, possibleSitesDataset + possibleSites.length);
                    }
                }
            }
        }
        if (progressDialog.isRunCanceled()) {
            break;
        }
        progressDialog.increaseSecondaryProgressCounter();
    }
    DefaultCategoryDataset dataset = new DefaultCategoryDataset();
    for (String modName : modificationParameters.getAllNotFixedModifications()) {
        Integer nFound = modifiedSitesMap.get(modName);
        if (nFound == null) {
            nFound = 0;
        }
        Integer nPossible = possibleSitesMap.get(modName);
        Double rate = 0.0;
        if (nPossible != null) {
            rate = (100.0 * nFound) / nPossible;
        }
        dataset.addValue(rate, "Modified", modName);
        double rest = 100 - rate;
        dataset.addValue(rest, "Not Modified", modName);
    }
    return dataset;
}