Examples with Peptide com.compomics.util.experiment.biology.proteins.Peptide used on opensource projects

Example 1 with Peptide

use of com.compomics.util.experiment.biology.proteins.Peptide in project peptide-shaker by compomics.

the class SpectrumIdentificationPanel method populateIdResultsTable.

/**
 * Populates the assumptions table with assumptions from the selected
 * spectrum match.
 *
 * @param spectrumMatchKey the key of the selected spectrum match
 */
private void populateIdResultsTable(long spectrumMatchKey) {
    currentAssumptionsList = new ArrayList<>(8);
    searchResultsTablePeptideTooltips = new ArrayList<>(8);
    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumMatchKey);
    if (spectrumMatch != null) {
        // sort peptides by pep, tool, and sequence
        HashMap<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>> peptideAssumptions = spectrumMatch.getPeptideAssumptionsMap();
        TreeMap<Double, TreeMap<Integer, TreeMap<String, ArrayList<PeptideAssumption>>>> peptideAssumptionsByPep = new TreeMap<>();
        for (Entry<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>> entry1 : peptideAssumptions.entrySet()) {
            int tool = entry1.getKey();
            for (Entry<Double, ArrayList<PeptideAssumption>> entry2 : entry1.getValue().entrySet()) {
                ArrayList<PeptideAssumption> assumptions = entry2.getValue();
                for (PeptideAssumption peptideAssumption : assumptions) {
                    PSParameter psParameter = (PSParameter) peptideAssumption.getUrParam(PSParameter.dummy);
                    double pep = psParameter.getProbability();
                    TreeMap<Integer, TreeMap<String, ArrayList<PeptideAssumption>>> mapAtPep = peptideAssumptionsByPep.get(pep);
                    if (mapAtPep == null) {
                        mapAtPep = new TreeMap<>();
                        peptideAssumptionsByPep.put(pep, mapAtPep);
                    }
                    TreeMap<String, ArrayList<PeptideAssumption>> toolMap = mapAtPep.get(tool);
                    if (toolMap == null) {
                        toolMap = new TreeMap<>();
                        mapAtPep.put(tool, toolMap);
                    }
                    String sequence = peptideAssumption.getPeptide().getSequence();
                    ArrayList<PeptideAssumption> sequenceAssumptions = toolMap.get(sequence);
                    if (sequenceAssumptions == null) {
                        sequenceAssumptions = new ArrayList<>(1);
                        toolMap.put(sequence, sequenceAssumptions);
                    }
                    sequenceAssumptions.add(peptideAssumption);
                }
            }
        }
        // Add peptides to the list to display
        peptideAssumptionsByPep.values().stream().flatMap(subMap -> subMap.values().stream()).flatMap(subMap -> subMap.values().stream()).flatMap(assumptionList -> assumptionList.stream()).forEach(peptideAssumption -> {
            Peptide peptide = peptideAssumption.getPeptide();
            if (peptideShakerGUI.getIdentificationParameters().getPeptideAssumptionFilter().validatePeptide(peptide, peptideShakerGUI.getIdentificationParameters().getSequenceMatchingParameters(), peptideShakerGUI.getIdentificationParameters().getSearchParameters().getDigestionParameters())) {
                if (vallidatedPsmsCheckBox.isSelected()) {
                    PSParameter psParameter = (PSParameter) peptideAssumption.getUrParam(PSParameter.dummy);
                    if (psParameter.getMatchValidationLevel().isValidated()) {
                        currentAssumptionsList.add(peptideAssumption);
                        searchResultsTablePeptideTooltips.add(peptideShakerGUI.getDisplayFeaturesGenerator().getPeptideModificationTooltipAsHtml(peptide));
                    }
                } else {
                    currentAssumptionsList.add(peptideAssumption);
                    searchResultsTablePeptideTooltips.add(peptideShakerGUI.getDisplayFeaturesGenerator().getPeptideModificationTooltipAsHtml(peptide));
                }
            }
        });
        // Add tags to the list to display. Scores cannot be compared between algorithms so keep sorting by tool.
        spectrumMatch.getTagAssumptionsMap().values().stream().flatMap(subMap -> subMap.values().stream()).flatMap(array -> array.stream()).forEach(tagAssumption -> {
            // @TODO: filter the tags as well? and respect the vallidatedPsmsCheckBox value!
            currentAssumptionsList.add(tagAssumption);
            String toolTip = peptideShakerGUI.getDisplayFeaturesGenerator().getTagModificationTooltipAsHtml(tagAssumption.getTag());
            searchResultsTablePeptideTooltips.add(toolTip);
        });
    }
}

Example 2 with Peptide

use of com.compomics.util.experiment.biology.proteins.Peptide in project peptide-shaker by compomics.

the class SpectrumIdentificationPanel method updateSpectrum.

/**
 * Update the spectrum based on the currently selected PSM.
 */
public void updateSpectrum() {
    if (spectrumTable.getSelectedRow() != -1) {
        spectrumChartPanel.removeAll();
        String spectrumTitle = getSelectedSpectrumTitle();
        Spectrum currentSpectrum = peptideShakerGUI.getSpectrumProvider().getSpectrum(fileSelected, spectrumTitle);
        AnnotationParameters annotationParameters = peptideShakerGUI.getIdentificationParameters().getAnnotationParameters();
        long spectrumMatchKey = SpectrumMatch.getKey(fileSelected, spectrumTitle);
        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumMatchKey);
        // get the selected spectrum
        if (currentSpectrum != null && currentSpectrum.getNPeaks() > 0) {
            Precursor precursor = currentSpectrum.getPrecursor();
            String chargeAsString = "";
            if (spectrumMatch != null) {
                if (spectrumMatch.getBestPeptideAssumption() != null) {
                    chargeAsString = Charge.toString(spectrumMatch.getBestPeptideAssumption().getIdentificationCharge());
                } else if (spectrumMatch.getBestTagAssumption() != null) {
                    chargeAsString = Charge.toString(spectrumMatch.getBestTagAssumption().getIdentificationCharge());
                }
            } else {
                chargeAsString = precursor.getPossibleChargesAsString();
            }
            double[] intensitiesAsArray = searchResultsTable.getSelectedRowCount() == 1 ? currentSpectrum.intensity : ArrayUtil.scaleToMax(currentSpectrum.intensity);
            spectrumPanel = new SpectrumPanel(currentSpectrum.mz, intensitiesAsArray, precursor.mz, chargeAsString, "", 40, false, false, false, 2, false);
            spectrumPanel.setKnownMassDeltas(peptideShakerGUI.getCurrentMassDeltas());
            spectrumPanel.setDeltaMassWindow(annotationParameters.getFragmentIonAccuracy());
            spectrumPanel.setBorder(null);
            spectrumPanel.setDataPointAndLineColor(peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedPeakColor(), 0);
            spectrumPanel.setPeakWaterMarkColor(peptideShakerGUI.getUtilitiesUserParameters().getSpectrumBackgroundPeakColor());
            spectrumPanel.setPeakWidth(peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedPeakWidth());
            spectrumPanel.setBackgroundPeakWidth(peptideShakerGUI.getUtilitiesUserParameters().getSpectrumBackgroundPeakWidth());
            // add the mirrored spectrum
            if (searchResultsTable.getSelectedRowCount() == 2) {
                spectrumPanel.addMirroredSpectrum(currentSpectrum.mz, ArrayUtil.scaleToMax(currentSpectrum.intensity), precursor.mz, chargeAsString, "", false, peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedMirroredPeakColor(), peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedMirroredPeakColor());
            }
        }
        // add spectrum annotations
        if (spectrumMatch != null) {
            SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
            IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
            ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
            SequenceMatchingParameters modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
            SearchParameters searchParameters = identificationParameters.getSearchParameters();
            DisplayParameters displayParameters = peptideShakerGUI.getDisplayParameters();
            int forwardIon = searchParameters.getForwardIons().get(0);
            int rewindIon = searchParameters.getRewindIons().get(0);
            if (currentSpectrum != null && spectrumPanel != null) {
                if (currentSpectrum.getNPeaks() > 0) {
                    int maxPrecursorCharge = 1;
                    String modifiedSequence = "";
                    HashSet<String> allModifications = new HashSet<>();
                    ArrayList<IonMatch[]> allAnnotations = new ArrayList<>();
                    ArrayList<Spectrum> allSpectra = new ArrayList<>();
                    ArrayList<String> selectedIndexes = new ArrayList<>();
                    SpecificAnnotationParameters specificAnnotationParameters = null;
                    for (int i = 0; i < searchResultsTable.getSelectedRowCount(); i++) {
                        SpectrumIdentificationAssumption currentAssumption = currentAssumptionsList.get(searchResultsTable.getSelectedRows()[i]);
                        if (currentAssumption != null) {
                            selectedIndexes.add((i + 1) + " " + Charge.toString(currentAssumption.getIdentificationCharge()));
                            if (currentAssumption instanceof PeptideAssumption) {
                                PeptideAssumption currentPeptideAssumption = (PeptideAssumption) currentAssumption;
                                Peptide peptide = currentPeptideAssumption.getPeptide();
                                PeptideSpectrumAnnotator peptideSpectrumAnnotator = new PeptideSpectrumAnnotator();
                                specificAnnotationParameters = peptideShakerGUI.getSpecificAnnotationParameters(fileSelected, spectrumTitle, currentPeptideAssumption);
                                IonMatch[] annotations = peptideSpectrumAnnotator.getSpectrumAnnotation(annotationParameters, specificAnnotationParameters, fileSelected, spectrumTitle, currentSpectrum, peptide, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                                allAnnotations.add(annotations);
                                allSpectra.add(currentSpectrum);
                                // add the spectrum annotations
                                if (i == 0) {
                                    // @TODO: the selection of the peak to annotate should be done outside the spectrum panel
                                    spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), annotationParameters.getTiesResolution() == SpectrumAnnotator.TiesResolution.mostIntense);
                                    // add de novo sequencing
                                    spectrumPanel.addAutomaticDeNovoSequencing(peptide, annotations, forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), false, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                                } else {
                                    spectrumPanel.setAnnotationsMirrored(SpectrumAnnotator.getSpectrumAnnotation(annotations));
                                    // add de novo sequencing
                                    spectrumPanel.addAutomaticDeNovoSequencing(peptide, annotations, forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), true, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                                }
                                if (currentPeptideAssumption.getIdentificationCharge() > maxPrecursorCharge) {
                                    maxPrecursorCharge = currentPeptideAssumption.getIdentificationCharge();
                                }
                                if (!modifiedSequence.isEmpty()) {
                                    modifiedSequence += " vs. ";
                                }
                                modifiedSequence += peptide.getTaggedModifiedSequence(modificationParameters, sequenceProvider, modificationSequenceMatchingParameters, false, false, true, displayParameters.getDisplayedModifications());
                                allModifications.addAll(ModificationUtils.getAllModifications(peptide, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters));
                            } else if (currentAssumption instanceof TagAssumption) {
                                TagAssumption tagAssumption = (TagAssumption) currentAssumption;
                                TagSpectrumAnnotator spectrumAnnotator = new TagSpectrumAnnotator();
                                specificAnnotationParameters = peptideShakerGUI.getSpecificAnnotationParameters(fileSelected, spectrumTitle, tagAssumption);
                                IonMatch[] annotations = spectrumAnnotator.getSpectrumAnnotation(annotationParameters, modificationParameters, modificationSequenceMatchingParameters, specificAnnotationParameters, fileSelected, spectrumTitle, currentSpectrum, tagAssumption.getTag());
                                // add the spectrum annotations
                                // @TODO: the selection of the peak to annotate should be done outside the spectrum panel
                                spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), annotationParameters.getTiesResolution() == SpectrumAnnotator.TiesResolution.mostIntense);
                                // add de novo sequencing
                                spectrumPanel.addAutomaticDeNovoSequencing(tagAssumption.getTag(), annotations, forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), false);
                                // get the modifications for the tag
                                allModifications.addAll(ModificationUtils.getAllModifications(tagAssumption.getTag(), modificationParameters, modificationSequenceMatchingParameters));
                                if (tagAssumption.getIdentificationCharge() > maxPrecursorCharge) {
                                    maxPrecursorCharge = tagAssumption.getIdentificationCharge();
                                }
                                if (!modifiedSequence.isEmpty()) {
                                    modifiedSequence += " vs. ";
                                }
                                modifiedSequence += tagAssumption.getTag().getTaggedModifiedSequence(modificationParameters, false, false, true, false, modificationSequenceMatchingParameters, displayParameters.getDisplayedModifications());
                            } else {
                                throw new UnsupportedOperationException("Spectrum annotation not implemented for identification assumption of type " + currentAssumption.getClass() + ".");
                            }
                        }
                    }
                    spectrumPanel.showAnnotatedPeaksOnly(!annotationParameters.showAllPeaks());
                    spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationParameters.yAxisZoomExcludesBackgroundPeaks());
                    peptideShakerGUI.updateAnnotationMenus(specificAnnotationParameters, maxPrecursorCharge, allModifications);
                    // update the spectrum title
                    if (searchResultsTable.getSelectedRowCount() == 1) {
                        ((TitledBorder) spectrumPanelPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + modifiedSequence + "   " + maxPrecursorCharge + "   " + Util.roundDouble(currentSpectrum.getPrecursor().mz, 2) + " m/z)" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    } else if (searchResultsTable.getSelectedRowCount() == 2) {
                        ((TitledBorder) spectrumPanelPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + modifiedSequence + ")" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    } else if (searchResultsTable.getSelectedRowCount() > 2) {
                        ((TitledBorder) spectrumPanelPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + searchResultsTable.getSelectedRowCount() + " PSMs)" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    }
                    spectrumPanelPanel.repaint();
                    if (searchResultsTable.getSelectedRowCount() > 2) {
                        SearchParameters.MassAccuracyType fragmentAccuracyType = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getFragmentAccuracyType();
                        double bubbleScale = annotationParameters.getFragmentIonAccuracy() * 10 * peptideShakerGUI.getBubbleScale();
                        DisplayParameters displayPreferences = peptideShakerGUI.getDisplayParameters();
                        MassErrorBubblePlot massErrorBubblePlot = new MassErrorBubblePlot(selectedIndexes, allAnnotations, allSpectra, annotationParameters.getFragmentIonAccuracy(), bubbleScale, selectedIndexes.size() == 1, displayPreferences.showBars(), fragmentAccuracyType == SearchParameters.MassAccuracyType.PPM);
                        // hide the legend if selecting more than 20 spectra // @TODO: 20 should not be hardcoded here..
                        if (selectedIndexes.size() > 20) {
                            massErrorBubblePlot.getChartPanel().getChart().getLegend().setVisible(false);
                        }
                        // hide the outline
                        massErrorBubblePlot.getChartPanel().getChart().getPlot().setOutlineVisible(false);
                        spectrumChartPanel.add(massErrorBubblePlot);
                    }
                }
            }
            if (searchResultsTable.getSelectedRowCount() <= 2) {
                spectrumChartPanel.add(spectrumPanel);
            }
        } else {
            // update the spectrum title
            ((TitledBorder) spectrumPanelPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + Util.roundDouble(currentSpectrum.getPrecursor().mz, 2) + " m/z)" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
            if (currentSpectrum.getNPeaks() > 0) {
                spectrumChartPanel.add(spectrumPanel);
            }
            spectrumPanelPanel.repaint();
        }
    }
    spectrumChartPanel.revalidate();
    spectrumChartPanel.repaint();
}

Example 3 with Peptide

use of com.compomics.util.experiment.biology.proteins.Peptide 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 4 with Peptide

use of com.compomics.util.experiment.biology.proteins.Peptide 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 5 with Peptide

use of com.compomics.util.experiment.biology.proteins.Peptide 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);
}