Examples with ChartChangeListener org.jfree.chart.event.ChartChangeListener used on opensource projects

Example 1 with ChartChangeListener

use of org.jfree.chart.event.ChartChangeListener in project peptide-shaker by compomics.

the class OverviewPanel method updateSequenceCoverage.

/**
 * Updates the sequence coverage panel.
 *
 * @param proteinAccession the protein accession
 * @param updateProtein if true, force a complete recreation of the plot
 */
private void updateSequenceCoverage(long proteinKey, String proteinAccession, boolean updateProtein) {
    // @TODO: should be in a separate thread that is possible to cancel if the selection changes
    try {
        // only need to redo this if the protein changes
        if (updateProtein || !proteinAccession.equalsIgnoreCase(currentProteinAccession) || coverage == null) {
            updateProteinSequenceCoveragePanelTitle(proteinAccession);
            updatePtmCoveragePlot(proteinAccession);
            updatePeptideVariationsCoveragePlot(proteinAccession);
        }
        currentProteinAccession = proteinAccession;
        SearchParameters searchParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters();
        ArrayList<Integer> selectedPeptideStart = new ArrayList<>();
        int selectionLength = 0;
        if (peptideTable.getSelectedRow() != -1) {
            SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) peptideTable.getModel();
            int peptideIndex = tableModel.getViewIndex(peptideTable.getSelectedRow());
            long peptideKey = peptideKeys[peptideIndex];
            PeptideMatch peptideMatch = peptideShakerGUI.getIdentification().getPeptideMatch(peptideKey);
            String peptideSequence = peptideMatch.getPeptide().getSequence();
            selectionLength = peptideSequence.length();
            try {
                for (int startIndex : peptideMatch.getPeptide().getProteinMapping().get(currentProteinAccession)) {
                    selectedPeptideStart.add(startIndex);
                }
            } catch (Exception e) {
            // ignore errors due to the user switching too quickly between rows. seems to solve themselves anyway
            }
        }
        IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();
        int[] validationCoverage;
        if (coverageShowAllPeptidesJRadioButtonMenuItem.isSelected()) {
            validationCoverage = identificationFeaturesGenerator.getAACoverage(proteinKey);
        } else {
            validationCoverage = identificationFeaturesGenerator.estimateAACoverage(proteinKey, coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem.isSelected());
        }
        double minHeight = 0.2, maxHeight = 1;
        NonSymmetricalNormalDistribution peptideLengthDistribution = peptideShakerGUI.getMetrics().getPeptideLengthDistribution();
        if (peptideLengthDistribution != null) {
            double medianLength = peptideLengthDistribution.getMean();
            maxHeight = (1 - minHeight) * peptideLengthDistribution.getProbabilityAt(medianLength);
        }
        double[] coverageLikelihood = identificationFeaturesGenerator.getCoverableAA(proteinKey);
        double[] coverageHeight = new double[coverageLikelihood.length];
        for (int i = 0; i < coverageLikelihood.length; i++) {
            double p = coverageLikelihood[i];
            coverageHeight[i] = minHeight + p / maxHeight;
        }
        HashMap<Integer, Color> colors = new HashMap<>();
        colors.put(MatchValidationLevel.confident.getIndex(), peptideShakerGUI.getSparklineColor());
        colors.put(MatchValidationLevel.doubtful.getIndex(), peptideShakerGUI.getUtilitiesUserParameters().getSparklineColorDoubtful());
        colors.put(MatchValidationLevel.not_validated.getIndex(), peptideShakerGUI.getSparklineColorNonValidated());
        colors.put(MatchValidationLevel.none.getIndex(), peptideShakerGUI.getSparklineColorNotFound());
        int userSelectionIndex = 0;
        while (colors.containsKey(userSelectionIndex)) {
            userSelectionIndex++;
        }
        // @TODO: use non hard coded value
        colors.put(userSelectionIndex, Color.blue);
        int[] coverageColor = validationCoverage.clone();
        for (int aaStart : selectedPeptideStart) {
            for (int aa = aaStart; aa < aaStart + selectionLength; aa++) {
                coverageColor[aa] = userSelectionIndex;
            }
        }
        // Dirty fix until the width of the sparkline can change
        int transparentIndex = userSelectionIndex + 1;
        colors.put(userSelectionIndex + 1, new Color(0, 0, 0, 0));
        for (int aa = 0; aa < coverageHeight.length; aa++) {
            if (coverageColor[aa] == MatchValidationLevel.none.getIndex()) {
                if (coverageLikelihood[aa] < 0.01 || !coverageShowPossiblePeptidesJCheckBoxMenuItem.isSelected()) {
                    // NOTE: if the fix is removed, make sure that this line is kept!!!
                    coverageColor[aa] = transparentIndex;
                }
            }
        }
        // create the coverage plot
        ArrayList<JSparklinesDataSeries> sparkLineDataSeriesCoverage = ProteinSequencePanel.getSparkLineDataSeriesCoverage(coverageHeight, coverageColor, colors);
        HashMap<Integer, ArrayList<ResidueAnnotation>> proteinTooltips = peptideShakerGUI.getDisplayFeaturesGenerator().getResidueAnnotation(proteinKey, peptideShakerGUI.getIdentificationParameters().getSequenceMatchingParameters(), identificationFeaturesGenerator, peptideShakerGUI.getMetrics(), peptideShakerGUI.getIdentification(), coverageShowAllPeptidesJRadioButtonMenuItem.isSelected(), searchParameters, coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem.isSelected());
        // Dirty fix for a bloc-level annotation
        HashMap<Integer, ArrayList<ResidueAnnotation>> blocTooltips = new HashMap<>();
        int aaCpt = 0, blocCpt = 0;
        for (JSparklinesDataSeries jSparklinesDataSeries : sparkLineDataSeriesCoverage) {
            double sparkLineLength = jSparklinesDataSeries.getData().get(0);
            ArrayList<ResidueAnnotation> blocAnnotation = new ArrayList<>();
            for (int j = 0; j < sparkLineLength; j++, aaCpt++) {
                ArrayList<ResidueAnnotation> aaAnnotation = proteinTooltips.get(aaCpt);
                if (aaAnnotation != null) {
                    for (ResidueAnnotation residueAnnotation : aaAnnotation) {
                        if (!blocAnnotation.contains(residueAnnotation)) {
                            blocAnnotation.add(residueAnnotation);
                        }
                    }
                }
            }
            blocTooltips.put(blocCpt, blocAnnotation);
            blocCpt++;
        }
        proteinSequencePanel = new ProteinSequencePanel(Color.WHITE);
        coverageChart = proteinSequencePanel.getSequencePlot(this, new JSparklinesDataset(sparkLineDataSeriesCoverage), blocTooltips, true, true);
        // make sure that the range is the same for all the sequence annotation charts
        coverageChart.getChart().addChangeListener(new ChartChangeListener() {

            @Override
            public void chartChanged(ChartChangeEvent cce) {
                if (ptmChart != null) {
                    Range range = ((CategoryPlot) coverageChart.getChart().getPlot()).getRangeAxis().getRange();
                    ((CategoryPlot) ptmChart.getChart().getPlot()).getRangeAxis().setRange(range);
                    ptmChart.revalidate();
                    ptmChart.repaint();
                }
                if (peptideVariationsChart != null) {
                    Range range = ((CategoryPlot) coverageChart.getChart().getPlot()).getRangeAxis().getRange();
                    ((CategoryPlot) peptideVariationsChart.getChart().getPlot()).getRangeAxis().setRange(range);
                    peptideVariationsChart.revalidate();
                    peptideVariationsChart.repaint();
                }
            }
        });
        sequenceCoverageInnerPanel.removeAll();
        sequenceCoverageInnerPanel.add(coverageChart);
        sequenceCoverageInnerPanel.revalidate();
        sequenceCoverageInnerPanel.repaint();
    } catch (ClassCastException e) {
    // ignore   @TODO: this should not happen, but can happen if the table does not update fast enough for the filtering
    }
}