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

Example 1 with SpecificAnnotationParameters

use of com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters 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 2 with SpecificAnnotationParameters

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

the class ModificationLocalizationScorer method attachProbabilisticScore.

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

Example 3 with SpecificAnnotationParameters

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

the class TieBreaker method nCoveredAminoAcids.

/**
 * Returns the number of amino acids covered by the fragment ions.
 *
 * @param spectrumFile The spectrum file name.
 * @param spectrumTitle The spectrum title.
 * @param peptideAssumption The peptide assumption.
 * @param spectrum The spectrum.
 * @param spectrum If true lower intensities are filtered out.
 *
 * @return The number of amino acids covered by the fragment ions.
 */
private int nCoveredAminoAcids(String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Spectrum spectrum, boolean intensityLimit) {
    SpecificAnnotationParameters specificAnnotationPreferences = annotationParameters.getSpecificAnnotationParameters(spectrumFile, spectrumTitle, peptideAssumption, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters, peptideSpectrumAnnotator);
    Map<Integer, ArrayList<IonMatch>> coveredAminoAcids = peptideSpectrumAnnotator.getCoveredAminoAcids(annotationParameters, specificAnnotationPreferences, spectrumFile, spectrumTitle, spectrum, peptideAssumption.getPeptide(), modificationParameters, sequenceProvider, modificationSequenceMatchingParameters, intensityLimit);
    return coveredAminoAcids.size();
}

Example 4 with SpecificAnnotationParameters

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

the class OverviewPanel method updateBubblePlot.

/**
 * Updated the bubble plot with the current PSMs.
 */
public void updateBubblePlot() {
    if (peptideTable.getSelectedRow() != -1 && displaySpectrum) {
        ArrayList<String> selectedIndexes = new ArrayList<>();
        // get the currenly selected rows in the psm table
        int[] selectedPsmRows = psmTable.getSelectedRows();
        SelfUpdatingTableModel psmTableModel = (SelfUpdatingTableModel) psmTable.getModel();
        ArrayList<IonMatch[]> allAnnotations = new ArrayList<>();
        ArrayList<Spectrum> allSpectra = new ArrayList<>();
        SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
        IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
        ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
        SequenceMatchingParameters modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
        AnnotationParameters annotationParameters = identificationParameters.getAnnotationParameters();
        DisplayParameters displayParameters = peptideShakerGUI.getDisplayParameters();
        ArrayList<Peptide> peptides = new ArrayList<>();
        SpectrumProvider spectrumProvider = peptideShakerGUI.getSpectrumProvider();
        PeptideSpectrumAnnotator spectrumAnnotator = new PeptideSpectrumAnnotator();
        SpecificAnnotationParameters specificAnnotationParameters = null;
        int maxCharge = 1;
        HashSet<String> allModifications = new HashSet<>();
        // iterate the selected psms rows
        for (int row : selectedPsmRows) {
            int psmIndex = psmTableModel.getViewIndex(row);
            long spectrumMatchKey = psmKeys[psmIndex];
            SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumMatchKey);
            selectedIndexes.add((psmIndex + 1) + " " + Charge.toString(spectrumMatch.getBestPeptideAssumption().getIdentificationCharge()));
            String spectrumFile = spectrumMatch.getSpectrumFile();
            String spectrumTitle = spectrumMatch.getSpectrumTitle();
            Spectrum currentSpectrum = spectrumProvider.getSpectrum(spectrumFile, spectrumTitle);
            if (currentSpectrum != null) {
                PeptideAssumption peptideAssumption = spectrumMatch.getBestPeptideAssumption();
                Peptide peptide = peptideAssumption.getPeptide();
                specificAnnotationParameters = peptideShakerGUI.getSpecificAnnotationParameters(spectrumFile, spectrumTitle, peptideAssumption);
                peptides.add(peptide);
                IonMatch[] annotations = spectrumAnnotator.getSpectrumAnnotation(annotationParameters, specificAnnotationParameters, spectrumFile, spectrumTitle, currentSpectrum, peptide, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                allAnnotations.add(annotations);
                allSpectra.add(currentSpectrum);
                int currentCharge = spectrumMatch.getBestPeptideAssumption().getIdentificationCharge();
                if (currentCharge > maxCharge) {
                    maxCharge = currentCharge;
                }
                allModifications.addAll(ModificationUtils.getAllModifications(peptide, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters));
                currentSpectrumMatchKey = spectrumMatch.getKey();
            }
        }
        double bubbleScale = annotationParameters.getFragmentIonAccuracy() * 10 * peptideShakerGUI.getBubbleScale();
        massErrorBubblePlot = new MassErrorBubblePlot(selectedIndexes, allAnnotations, allSpectra, annotationParameters.getFragmentIonAccuracy(), bubbleScale, selectedIndexes.size() == 1, displayParameters.showBars(), identificationParameters.getSearchParameters().getFragmentAccuracyType() == 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);
        bubbleJPanel.removeAll();
        bubbleJPanel.add(massErrorBubblePlot);
        bubbleJPanel.revalidate();
        bubbleJPanel.repaint();
        if (allSpectra.size() == 2) {
            for (int i = 0; i < allSpectra.size(); i++) {
                if (i == 0) {
                    Spectrum spectrum = allSpectra.get(i);
                    spectrumPanel = new SpectrumPanel(spectrum.mz, ArrayUtil.scaleToMax(spectrum.intensity), 500, "2", "", 40, false, false, false, 2, false);
                    // @TODO: implement ties resolution in the spectrum panel
                    spectrumPanel.setAnnotateHighestPeak(annotationParameters.getTiesResolution() == SpectrumAnnotator.TiesResolution.mostIntense);
                    // @TODO: the selection of the peak to annotate should be done outside the spectrum panel
                    spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(allAnnotations.get(i)), annotationParameters.getTiesResolution() == SpectrumAnnotator.TiesResolution.mostIntense);
                    SpectrumPanel.setKnownMassDeltas(peptideShakerGUI.getCurrentMassDeltas());
                    spectrumPanel.setDeltaMassWindow(peptideShakerGUI.getIdentificationParameters().getAnnotationParameters().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());
                    spectrumPanel.showAnnotatedPeaksOnly(!annotationParameters.showAllPeaks());
                    spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationParameters.yAxisZoomExcludesBackgroundPeaks());
                    Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
                    Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);
                    spectrumPanel.addAutomaticDeNovoSequencing(peptides.get(i), allAnnotations.get(i), forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), false, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                } else {
                    Spectrum spectrum = allSpectra.get(i);
                    spectrumPanel.addMirroredSpectrum(spectrum.mz, ArrayUtil.scaleToMax(spectrum.intensity), 500, "2", "", false, peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedMirroredPeakColor(), peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedMirroredPeakColor());
                    // @TODO: implement ties resolution in the spectrum panel
                    spectrumPanel.setAnnotateHighestPeak(annotationParameters.getTiesResolution() == SpectrumAnnotator.TiesResolution.mostIntense);
                    spectrumPanel.setAnnotationsMirrored(SpectrumAnnotator.getSpectrumAnnotation(allAnnotations.get(i)));
                    Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
                    Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);
                    spectrumPanel.addAutomaticDeNovoSequencing(peptides.get(i), allAnnotations.get(i), forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), true, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                }
            }
            spectrumPanel.rescale(0.0, spectrumPanel.getMaxXAxisValue());
            spectrumSplitPane.setDividerLocation(0);
            spectrumContainerJPanel.revalidate();
            spectrumContainerJPanel.repaint();
            spectrumJPanel.removeAll();
            spectrumJPanel.add(spectrumPanel);
            spectrumJPanel.revalidate();
            spectrumJPanel.repaint();
        } else {
            spectrumSplitPane.setDividerLocation(spectrumSubPlotDividerLocation);
            spectrumContainerJPanel.revalidate();
            spectrumContainerJPanel.repaint();
        }
        peptideShakerGUI.updateAnnotationMenus(specificAnnotationParameters, maxCharge, allModifications);
    }
}

Example 5 with SpecificAnnotationParameters

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

the class OverviewPanel method updateSpectrum.

/**
 * Update the spectrum to the currently selected PSM.
 *
 * @param row the row index of the PSM
 * @param resetMzRange if true the mz range is reset, if false the current
 * zoom range is kept
 */
private void updateSpectrum(int row, boolean resetMzRange) {
    if (row != -1) {
        this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
        SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) psmTable.getModel();
        int psmIndex = tableModel.getViewIndex(row);
        long spectrumMatchKey = psmKeys[psmIndex];
        if (displaySpectrum) {
            SpectrumProvider spectrumProvider = peptideShakerGUI.getSpectrumProvider();
            SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumMatchKey);
            String spectrumFile = spectrumMatch.getSpectrumFile();
            String spectrumTitle = spectrumMatch.getSpectrumTitle();
            Spectrum currentSpectrum = spectrumProvider.getSpectrum(spectrumFile, spectrumTitle);
            if (currentSpectrum != null && currentSpectrum.getNPeaks() > 0) {
                boolean newMax = false;
                if (resetMzRange) {
                    lastMzMaximum = 0;
                }
                if (peptideShakerGUI.getSelectedPeptideKey() != NO_KEY) {
                    double newMaximum = currentSpectrum.getMaxMz();
                    if (lastMzMaximum < newMaximum) {
                        lastMzMaximum = newMaximum;
                        newMax = true;
                    }
                }
                double lowerMzZoomRange = 0;
                double upperMzZoomRange = lastMzMaximum;
                if (spectrumPanel != null && spectrumPanel.getXAxisZoomRangeLowerValue() != 0 && !newMax) {
                    // @TODO: sometimes the range is reset when is should not be...
                    lowerMzZoomRange = spectrumPanel.getXAxisZoomRangeLowerValue();
                    upperMzZoomRange = spectrumPanel.getXAxisZoomRangeUpperValue();
                }
                // add the data to the spectrum panel
                Precursor precursor = currentSpectrum.getPrecursor();
                spectrumPanel = new SpectrumPanel(currentSpectrum.mz, currentSpectrum.intensity, precursor.mz, Charge.toString(spectrumMatch.getBestPeptideAssumption().getIdentificationCharge()), "", 40, false, false, false, 2, false);
                spectrumPanel.setKnownMassDeltas(peptideShakerGUI.getCurrentMassDeltas());
                spectrumPanel.setDeltaMassWindow(peptideShakerGUI.getIdentificationParameters().getAnnotationParameters().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());
                // get the spectrum annotations
                PeptideAssumption peptideAssumption = spectrumMatch.getBestPeptideAssumption();
                Peptide currentPeptide = peptideAssumption.getPeptide();
                PeptideSpectrumAnnotator spectrumAnnotator = new PeptideSpectrumAnnotator();
                AnnotationParameters annotationParameters = peptideShakerGUI.getIdentificationParameters().getAnnotationParameters();
                SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
                IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
                ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
                SequenceMatchingParameters modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
                SpecificAnnotationParameters specificAnnotationParameters = peptideShakerGUI.getSpecificAnnotationParameters(spectrumFile, spectrumTitle, peptideAssumption);
                IonMatch[] annotations = spectrumAnnotator.getSpectrumAnnotation(annotationParameters, specificAnnotationParameters, spectrumFile, spectrumTitle, currentSpectrum, currentPeptide, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                // @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);
                spectrumPanel.rescale(lowerMzZoomRange, upperMzZoomRange);
                // show all or just the annotated peaks
                spectrumPanel.showAnnotatedPeaksOnly(!annotationParameters.showAllPeaks());
                spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationParameters.yAxisZoomExcludesBackgroundPeaks());
                Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
                Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);
                // add de novo sequencing
                spectrumPanel.addAutomaticDeNovoSequencing(currentPeptide, annotations, forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), false, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                // add the spectrum panel to the frame
                spectrumJPanel.removeAll();
                spectrumJPanel.add(spectrumPanel);
                spectrumJPanel.revalidate();
                spectrumJPanel.repaint();
                // create and display the fragment ion table
                ArrayList<IonMatch[]> allAnnotations = getAnnotationsForAllSelectedSpectra();
                DisplayParameters displayParameters = peptideShakerGUI.getDisplayParameters();
                if (!displayParameters.useIntensityIonTable()) {
                    fragmentIonsJScrollPane.setViewportView(new FragmentIonTable(currentPeptide, allAnnotations, specificAnnotationParameters.getFragmentIonTypes(), specificAnnotationParameters.getNeutralLossesMap(), specificAnnotationParameters.getSelectedCharges().contains(1), specificAnnotationParameters.getSelectedCharges().contains(2), modificationParameters, sequenceProvider, modificationSequenceMatchingParameters));
                } else {
                    ArrayList<Spectrum> spectra = Arrays.stream(getSelectedPsmKeys()).mapToObj(key -> peptideShakerGUI.getIdentification().getSpectrumMatch(key)).map(selectedMatch -> spectrumProvider.getSpectrum(selectedMatch.getSpectrumFile(), selectedMatch.getSpectrumTitle())).collect(Collectors.toCollection(ArrayList::new));
                    fragmentIonsJScrollPane.setViewportView(new FragmentIonTable(currentPeptide, allAnnotations, spectra, specificAnnotationParameters.getFragmentIonTypes(), specificAnnotationParameters.getNeutralLossesMap(), specificAnnotationParameters.getSelectedCharges().contains(1), specificAnnotationParameters.getSelectedCharges().contains(2), modificationParameters, sequenceProvider, modificationSequenceMatchingParameters));
                }
                // create the sequence fragment ion view
                secondarySpectrumPlotsJPanel.removeAll();
                sequenceFragmentationPanel = new SequenceFragmentationPanel(peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(spectrumMatch, false, false, true), annotations, true, peptideShakerGUI.getIdentificationParameters().getSearchParameters().getModificationParameters(), forwardIon, rewindIon);
                sequenceFragmentationPanel.setMinimumSize(new Dimension(sequenceFragmentationPanel.getPreferredSize().width, sequenceFragmentationPanel.getHeight()));
                sequenceFragmentationPanel.setOpaque(true);
                sequenceFragmentationPanel.setBackground(Color.WHITE);
                secondarySpectrumPlotsJPanel.add(sequenceFragmentationPanel);
                // create the intensity histograms
                intensityHistogram = new IntensityHistogram(annotations, currentSpectrum, annotationParameters.getAnnotationIntensityLimit());
                secondarySpectrumPlotsJPanel.add(intensityHistogram);
                // create the miniature mass error plot
                massErrorPlot = new MassErrorPlot(annotations, currentSpectrum, specificAnnotationParameters.getFragmentIonAccuracy(), peptideShakerGUI.getIdentificationParameters().getSearchParameters().getFragmentAccuracyType() == SearchParameters.MassAccuracyType.PPM);
                if (massErrorPlot.getNumberOfDataPointsInPlot() > 0) {
                    secondarySpectrumPlotsJPanel.add(massErrorPlot);
                }
                // update the UI
                secondarySpectrumPlotsJPanel.revalidate();
                secondarySpectrumPlotsJPanel.repaint();
                // update the bubble plot
                updateBubblePlot();
                // disable the spectrum tab if more than two psms are selected
                spectrumJTabbedPane.setEnabledAt(2, psmTable.getSelectedRowCount() <= 2);
                peptideShakerGUI.enableSpectrumExport(psmTable.getSelectedRowCount() <= 2);
                // move to the bubble plot tab if more than two psms are selected and the spectrum tab was selected
                if (psmTable.getSelectedRowCount() > 2 && spectrumJTabbedPane.getSelectedIndex() == 2) {
                    spectrumJTabbedPane.setSelectedIndex(1);
                }
                if (psmTable.getSelectedRowCount() > 2) {
                    spectrumJTabbedPane.setToolTipTextAt(2, "Available for single or double spectrum selection only");
                } else {
                    spectrumJTabbedPane.setToolTipTextAt(2, null);
                }
                // update the panel border title
                updateSpectrumPanelBorderTitle(currentSpectrum);
                spectrumMainPanel.revalidate();
                spectrumMainPanel.repaint();
            }
        }
        this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
    } else {
        // nothing to display, empty previous results
        spectrumJPanel.removeAll();
        spectrumJPanel.revalidate();
        spectrumJPanel.repaint();
        secondarySpectrumPlotsJPanel.removeAll();
        secondarySpectrumPlotsJPanel.revalidate();
        secondarySpectrumPlotsJPanel.repaint();
        fragmentIonsJScrollPane.setViewportView(null);
        fragmentIonsJScrollPane.revalidate();
        fragmentIonsJScrollPane.repaint();
        bubbleJPanel.removeAll();
        bubbleJPanel.revalidate();
        bubbleJPanel.repaint();
        ((TitledBorder) spectrumMainPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
        spectrumMainPanel.repaint();
    }
}