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

Example 6 with SequenceMatchingParameters

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

the class PsmProcessorRunnable method attachAssumptionsProbabilities.

/**
 * Attaches the spectrum posterior error probabilities to the peptide
 * assumptions.
 *
 * @param inputMap map of the input scores
 * @param fastaParameters the FASTA parsing parameters
 * @param sequenceMatchingPreferences the sequence matching preferences
 * @param waitingHandler the handler displaying feedback to the user
 */
private void attachAssumptionsProbabilities(SpectrumMatch spectrumMatch) {
    FastaParameters fastaParameters = identificationParameters.getFastaParameters();
    SequenceMatchingParameters sequenceMatchingParameters = identificationParameters.getSequenceMatchingParameters();
    // Peptides
    HashMap<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>> peptideAssumptionsMap = spectrumMatch.getPeptideAssumptionsMap();
    TreeMap<Double, ArrayList<PSParameter>> pepToParameterMap = new TreeMap<>();
    for (Map.Entry<Integer, TreeMap<Double, ArrayList<PeptideAssumption>>> entry : peptideAssumptionsMap.entrySet()) {
        int searchEngine = entry.getKey();
        TreeMap<Double, ArrayList<PeptideAssumption>> seMapping = entry.getValue();
        double previousP = 0.0;
        ArrayList<PSParameter> previousAssumptionsParameters = new ArrayList<>(2);
        PeptideAssumption previousAssumption = null;
        for (Map.Entry<Double, ArrayList<PeptideAssumption>> entry2 : seMapping.entrySet()) {
            double eValue = entry2.getKey();
            ArrayList<PeptideAssumption> peptideAssumptions = entry2.getValue();
            for (PeptideAssumption assumption : peptideAssumptions) {
                PSParameter psParameter = (PSParameter) assumption.getUrParam(PSParameter.dummy);
                if (psParameter == null) {
                    psParameter = new PSParameter();
                }
                if (fastaParameters.isTargetDecoy()) {
                    double newP = inputMap.getProbability(searchEngine, eValue);
                    double pep = previousP;
                    if (newP > previousP) {
                        pep = newP;
                        previousP = newP;
                    }
                    psParameter.setProbability(pep);
                    ArrayList<PSParameter> pSParameters = pepToParameterMap.get(pep);
                    if (pSParameters == null) {
                        pSParameters = new ArrayList<>(1);
                        pepToParameterMap.put(pep, pSParameters);
                    }
                    pSParameters.add(psParameter);
                    if (previousAssumption != null) {
                        Peptide newPeptide = assumption.getPeptide();
                        Peptide previousPeptide = previousAssumption.getPeptide();
                        if (!newPeptide.isSameSequenceAndModificationStatus(previousPeptide, sequenceMatchingParameters)) {
                            for (PSParameter previousParameter : previousAssumptionsParameters) {
                                double deltaPEP = pep - previousParameter.getProbability();
                                previousParameter.setAlgorithmDeltaPEP(deltaPEP);
                            }
                            previousAssumptionsParameters.clear();
                        }
                    }
                    previousAssumption = assumption;
                    previousAssumptionsParameters.add(psParameter);
                } else {
                    psParameter.setProbability(1.0);
                }
                assumption.addUrParam(psParameter);
            }
        }
        for (PSParameter previousParameter : previousAssumptionsParameters) {
            double deltaPEP = 1 - previousParameter.getProbability();
            previousParameter.setAlgorithmDeltaPEP(deltaPEP);
        }
    }
    // Compute the delta pep score accross all search engines
    double previousPEP = Double.NaN;
    ArrayList<PSParameter> previousParameters = new ArrayList<>();
    for (Map.Entry<Double, ArrayList<PSParameter>> entry : pepToParameterMap.entrySet()) {
        double pep = entry.getKey();
        if (!Double.isNaN(previousPEP)) {
            for (PSParameter previousParameter : previousParameters) {
                double delta = pep - previousPEP;
                previousParameter.setDeltaPEP(delta);
            }
        }
        previousParameters = entry.getValue();
        previousPEP = pep;
    }
    for (PSParameter previousParameter : previousParameters) {
        double delta = 1 - previousParameter.getProbability();
        previousParameter.setDeltaPEP(delta);
    }
    if (waitingHandler.isRunCanceled()) {
        return;
    }
    // Assumptions
    HashMap<Integer, TreeMap<Double, ArrayList<TagAssumption>>> tagAssumptionsMap = spectrumMatch.getTagAssumptionsMap();
    for (Map.Entry<Integer, TreeMap<Double, ArrayList<TagAssumption>>> entry : tagAssumptionsMap.entrySet()) {
        int algorithm = entry.getKey();
        TreeMap<Double, ArrayList<TagAssumption>> seMapping = entry.getValue();
        double previousP = 0;
        ArrayList<PSParameter> previousAssumptionsParameters = new ArrayList<>();
        TagAssumption previousAssumption = null;
        for (Map.Entry<Double, ArrayList<TagAssumption>> entry2 : seMapping.entrySet()) {
            double score = entry2.getKey();
            for (TagAssumption assumption : entry2.getValue()) {
                PSParameter psParameter = (PSParameter) assumption.getUrParam(PSParameter.dummy);
                if (psParameter == null) {
                    psParameter = new PSParameter();
                }
                if (fastaParameters.isTargetDecoy()) {
                    double newP = inputMap.getProbability(algorithm, score);
                    double pep = previousP;
                    if (newP > previousP) {
                        pep = newP;
                        previousP = newP;
                    }
                    psParameter.setProbability(pep);
                    ArrayList<PSParameter> pSParameters = pepToParameterMap.get(pep);
                    if (pSParameters == null) {
                        pSParameters = new ArrayList<>(1);
                        pepToParameterMap.put(pep, pSParameters);
                    }
                    pSParameters.add(psParameter);
                    if (previousAssumption != null) {
                        boolean same = false;
                        Tag newTag = ((TagAssumption) assumption).getTag();
                        Tag previousTag = previousAssumption.getTag();
                        if (newTag.isSameSequenceAndModificationStatusAs(previousTag, sequenceMatchingParameters)) {
                            same = true;
                        }
                        if (!same) {
                            for (PSParameter previousParameter : previousAssumptionsParameters) {
                                double deltaPEP = pep - previousParameter.getProbability();
                                previousParameter.setAlgorithmDeltaPEP(deltaPEP);
                            }
                            previousAssumptionsParameters.clear();
                        }
                    }
                    previousAssumption = assumption;
                    previousAssumptionsParameters.add(psParameter);
                } else {
                    psParameter.setProbability(1.0);
                }
                assumption.addUrParam(psParameter);
            }
        }
        for (PSParameter previousParameter : previousAssumptionsParameters) {
            double deltaPEP = 1 - previousParameter.getProbability();
            previousParameter.setAlgorithmDeltaPEP(deltaPEP);
        }
    }
}

Example 7 with SequenceMatchingParameters

use of com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters 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 8 with SequenceMatchingParameters

use of com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters 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();
    }
}

Example 9 with SequenceMatchingParameters

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

the class OverviewPanel method getAnnotationsForAllSelectedSpectra.

/**
 * Returns an arraylist of the spectrum annotations for all the selected
 * PSMs.
 *
 * @return an arraylist of the spectrum annotations
 */
private ArrayList<IonMatch[]> getAnnotationsForAllSelectedSpectra() {
    ArrayList<IonMatch[]> allAnnotations = new ArrayList<>();
    int[] selectedRows = psmTable.getSelectedRows();
    IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
    AnnotationParameters annotationParameters = identificationParameters.getAnnotationParameters();
    SpectrumProvider spectrumProvider = peptideShakerGUI.getSpectrumProvider();
    PeptideSpectrumAnnotator spectrumAnnotator = new PeptideSpectrumAnnotator();
    SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
    ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
    SequenceMatchingParameters modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
    for (int row : selectedRows) {
        SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) psmTable.getModel();
        int psmIndex = tableModel.getViewIndex(row);
        long spectrumMatchKey = psmKeys[psmIndex];
        SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumMatchKey);
        String spectrumFile = spectrumMatch.getSpectrumFile();
        String spectrumTitle = spectrumMatch.getSpectrumTitle();
        Spectrum currentSpectrum = spectrumProvider.getSpectrum(spectrumFile, spectrumTitle);
        if (currentSpectrum != null && peptideTable.getSelectedRow() != -1) {
            // get the spectrum annotations
            PeptideAssumption peptideAssumption = spectrumMatch.getBestPeptideAssumption();
            Peptide peptide = peptideAssumption.getPeptide();
            SpecificAnnotationParameters specificAnnotationParameters = peptideShakerGUI.getSpecificAnnotationParameters(spectrumFile, spectrumTitle, peptideAssumption);
            IonMatch[] annotations = spectrumAnnotator.getSpectrumAnnotation(annotationParameters, specificAnnotationParameters, spectrumFile, spectrumTitle, currentSpectrum, peptide, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
            allAnnotations.add(annotations);
            currentSpectrumMatchKey = spectrumMatchKey;
        }
    }
    return allAnnotations;
}

Example 10 with SequenceMatchingParameters

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

the class StirRunnable method scoreModificationLocalization.

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