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Example 1 with PeptideAssumption

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

the class SpectrumIdentificationPanel method isBestPsmEqualForAllIdSoftware.

/**
 * Returns true if all the used id software tools agree on the top PSM
 * without accounting for modification localization, false otherwise.
 *
 * @param spectrumMatch the PSM to check
 * @param sequenceMatchingPreferences the sequence matching preferences
 * @param numberOfAdvocatesUsed the total number of advocates used for the
 * search
 *
 * @return true if all the used id software agree on the top PSM
 */
public static int isBestPsmEqualForAllIdSoftware(SpectrumMatch spectrumMatch, SequenceMatchingParameters sequenceMatchingPreferences, Integer numberOfAdvocatesUsed) {
    PeptideAssumption bestPeptideAssumption = spectrumMatch.getBestPeptideAssumption();
    HashMap<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>> peptideAssumptions = spectrumMatch.getPeptideAssumptionsMap();
    if (bestPeptideAssumption == null || peptideAssumptions == null || peptideAssumptions.isEmpty()) {
        return NO_ID;
    }
    if (peptideAssumptions.size() == 1) {
        return numberOfAdvocatesUsed == 1 ? AGREEMENT_WITH_MODS : PARTIALLY_MISSING;
    }
    int agreement = AGREEMENT_WITH_MODS;
    for (Entry<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>> entry1 : peptideAssumptions.entrySet()) {
        Entry<Double, ArrayList<PeptideAssumption>> entry2 = entry1.getValue().firstEntry();
        boolean advocateSameSequence = false, advocateSameModifications = false;
        if (entry2 != null) {
            for (PeptideAssumption peptideAssumption : entry2.getValue()) {
                if (bestPeptideAssumption.getPeptide().isSameSequenceAndModificationStatus(peptideAssumption.getPeptide(), sequenceMatchingPreferences)) {
                    advocateSameSequence = true;
                    if (bestPeptideAssumption.getPeptide().sameModificationsAs(peptideAssumption.getPeptide())) {
                        advocateSameModifications = true;
                    }
                }
                if (advocateSameSequence && advocateSameModifications) {
                    break;
                }
            }
        }
        if (!advocateSameSequence) {
            return CONFLICT;
        }
        if (!advocateSameModifications) {
            agreement = AGREEMENT;
        }
    }
    return peptideAssumptions.size() < numberOfAdvocatesUsed ? PARTIALLY_MISSING : agreement;
}
Also used : ArrayList(java.util.ArrayList) TreeMap(java.util.TreeMap) PeptideAssumption(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption)

Example 2 with PeptideAssumption

use of com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption 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);
        });
    }
}
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Example 3 with PeptideAssumption

use of com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption 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();
}
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Example 4 with PeptideAssumption

use of com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption 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);
    }
}
Also used : Modification(com.compomics.util.experiment.biology.modifications.Modification) ModificationMatch(com.compomics.util.experiment.identification.matches.ModificationMatch) ArrayList(java.util.ArrayList) TreeMap(java.util.TreeMap) ModificationScoring(com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring) ArrayList(java.util.ArrayList) List(java.util.List) PSModificationScores(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores) Peptide(com.compomics.util.experiment.biology.proteins.Peptide) PeptideAssumption(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption) PSParameter(com.compomics.util.experiment.identification.peptide_shaker.PSParameter)

Example 5 with PeptideAssumption

use of com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption 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);
    }
}
Also used : ModificationMatch(com.compomics.util.experiment.identification.matches.ModificationMatch) ModificationFactory(com.compomics.util.experiment.biology.modifications.ModificationFactory) Arrays(java.util.Arrays) ModificationType(com.compomics.util.experiment.biology.modifications.ModificationType) HashMap(java.util.HashMap) PeptideMatch(com.compomics.util.experiment.identification.matches.PeptideMatch) ModificationScoring(com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring) TreeSet(java.util.TreeSet) SpectrumMatch(com.compomics.util.experiment.identification.matches.SpectrumMatch) ArrayList(java.util.ArrayList) HashSet(java.util.HashSet) Modification(com.compomics.util.experiment.biology.modifications.Modification) WaitingHandler(com.compomics.util.waiting.WaitingHandler) ProteinMatch(com.compomics.util.experiment.identification.matches.ProteinMatch) ModificationUtils(com.compomics.util.experiment.identification.utils.ModificationUtils) SpecificAnnotationParameters(com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters) SpectrumProvider(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider) PhosphoRS(com.compomics.util.experiment.identification.modification.scores.PhosphoRS) ModificationProvider(com.compomics.util.experiment.biology.modifications.ModificationProvider) Spectrum(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum) ModificationParameters(com.compomics.util.parameters.identification.search.ModificationParameters) PSModificationScores(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores) PeptideAssumption(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption) SequenceMatchingParameters(com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters) ExperimentObject(com.compomics.util.experiment.personalization.ExperimentObject) SequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider) Set(java.util.Set) Identification(com.compomics.util.experiment.identification.Identification) Peptide(com.compomics.util.experiment.biology.proteins.Peptide) ModificationLocalizationScore(com.compomics.util.experiment.identification.modification.ModificationLocalizationScore) Collectors(java.util.stream.Collectors) AnnotationParameters(com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters) SearchParameters(com.compomics.util.parameters.identification.search.SearchParameters) PeptideSpectrumAnnotator(com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator) IdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters) List(java.util.List) Stream(java.util.stream.Stream) PSParameter(com.compomics.util.experiment.identification.peptide_shaker.PSParameter) TreeMap(java.util.TreeMap) Entry(java.util.Map.Entry) Collections(java.util.Collections) ModificationLocalizationParameters(com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters) Modification(com.compomics.util.experiment.biology.modifications.Modification) ModificationMatch(com.compomics.util.experiment.identification.matches.ModificationMatch) HashMap(java.util.HashMap) SpecificAnnotationParameters(com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters) AnnotationParameters(com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters) ArrayList(java.util.ArrayList) SpecificAnnotationParameters(com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters) Spectrum(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum) SearchParameters(com.compomics.util.parameters.identification.search.SearchParameters) ModificationScoring(com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring) Peptide(com.compomics.util.experiment.biology.proteins.Peptide) ModificationParameters(com.compomics.util.parameters.identification.search.ModificationParameters) ModificationLocalizationParameters(com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters) PSModificationScores(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores) SequenceMatchingParameters(com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters) PeptideAssumption(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption)

Aggregations

PeptideAssumption (com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption)33 ArrayList (java.util.ArrayList)26 Peptide (com.compomics.util.experiment.biology.proteins.Peptide)24 SequenceMatchingParameters (com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters)22 TreeMap (java.util.TreeMap)20 PSParameter (com.compomics.util.experiment.identification.peptide_shaker.PSParameter)19 ModificationParameters (com.compomics.util.parameters.identification.search.ModificationParameters)19 SpectrumMatch (com.compomics.util.experiment.identification.matches.SpectrumMatch)18 SequenceProvider (com.compomics.util.experiment.io.biology.protein.SequenceProvider)18 AnnotationParameters (com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters)17 SpecificAnnotationParameters (com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters)17 Spectrum (com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum)17 PeptideSpectrumAnnotator (com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator)16 IdentificationParameters (com.compomics.util.parameters.identification.IdentificationParameters)16 SpectrumProvider (com.compomics.util.experiment.mass_spectrometry.SpectrumProvider)15 HashMap (java.util.HashMap)15 HashSet (java.util.HashSet)14 TagAssumption (com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption)13 SearchParameters (com.compomics.util.parameters.identification.search.SearchParameters)12 Collectors (java.util.stream.Collectors)10