Examples with TICPlot net.sf.mzmine.modules.visualization.tic.TICPlot used on opensource projects

Example 1 with TICPlot

use of net.sf.mzmine.modules.visualization.tic.TICPlot in project mzmine2 by mzmine.

the class PeakResolverSetupDialog method addDialogComponents.

/**
 * This function add all the additional components for this dialog over the original
 * ParameterSetupDialog.
 */
@Override
protected void addDialogComponents() {
    super.addDialogComponents();
    final PeakList[] peakLists = MZmineCore.getProjectManager().getCurrentProject().getPeakLists();
    // Elements of panel.
    preview = new JCheckBox("Show preview");
    preview.addActionListener(this);
    preview.setHorizontalAlignment(SwingConstants.CENTER);
    preview.setEnabled(peakLists.length > 0);
    // Preview panel.
    final JPanel previewPanel = new JPanel(new BorderLayout());
    previewPanel.add(new JSeparator(), BorderLayout.NORTH);
    previewPanel.add(preview, BorderLayout.CENTER);
    previewPanel.add(Box.createVerticalStrut(10), BorderLayout.SOUTH);
    // Feature list combo-box.
    comboPeakList = new JComboBox<PeakList>();
    comboPeakList.setFont(COMBO_FONT);
    for (final PeakList peakList : peakLists) {
        if (peakList.getNumberOfRawDataFiles() == 1) {
            comboPeakList.addItem(peakList);
        }
    }
    comboPeakList.addActionListener(this);
    // Peaks combo box.
    comboPeak = new JComboBox<PeakListRow>();
    comboPeak.setFont(COMBO_FONT);
    comboPeak.setRenderer(new PeakPreviewComboRenderer());
    comboPeak.setPreferredSize(new Dimension(PREFERRED_PEAK_COMBO_WIDTH, comboPeak.getPreferredSize().height));
    pnlLabelsFields = GUIUtils.makeTablePanel(2, 2, new JComponent[] { new JLabel("Feature list"), comboPeakList, new JLabel("Chromatogram"), comboPeak });
    // Put all together.
    pnlVisible = new JPanel(new BorderLayout());
    pnlVisible.add(previewPanel, BorderLayout.NORTH);
    // TIC plot.
    ticPlot = new TICPlot(this);
    ticPlot.setMinimumSize(MINIMUM_TIC_DIMENSIONS);
    // Tool bar.
    final TICToolBar toolBar = new TICToolBar(ticPlot);
    toolBar.getComponentAtIndex(0).setVisible(false);
    // Panel for XYPlot.
    pnlPlotXY = new JPanel(new BorderLayout());
    pnlPlotXY.setBackground(Color.white);
    pnlPlotXY.add(ticPlot, BorderLayout.CENTER);
    pnlPlotXY.add(toolBar, BorderLayout.EAST);
    GUIUtils.addMarginAndBorder(pnlPlotXY, 10);
    mainPanel.add(pnlVisible, 0, getNumberOfParameters() + 3, 2, 1, 0, 0, GridBagConstraints.HORIZONTAL);
    // Layout and position.
    updateBounds();
}

Example 2 with TICPlot

use of net.sf.mzmine.modules.visualization.tic.TICPlot in project mzmine2 by mzmine.

the class MultiSpectraVisualizerWindow method addSpectra.

private JPanel addSpectra(int scan) {
    JPanel panel = new JPanel(new BorderLayout());
    // Split pane for eic plot (top) and spectrum (bottom)
    JSplitPane bottomPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
    // Create EIC plot
    // labels for TIC visualizer
    Map<Feature, String> labelsMap = new HashMap<Feature, String>(0);
    Feature peak = row.getPeak(activeRaw);
    // scan selection
    ScanSelection scanSelection = new ScanSelection(activeRaw.getDataRTRange(1), 1);
    // mz range
    Range<Double> mzRange = null;
    mzRange = peak.getRawDataPointsMZRange();
    // optimize output by extending the range
    double upper = mzRange.upperEndpoint();
    double lower = mzRange.lowerEndpoint();
    double fiveppm = (upper * 5E-6);
    mzRange = Range.closed(lower - fiveppm, upper + fiveppm);
    // labels
    labelsMap.put(peak, peak.toString());
    // get EIC window
    TICVisualizerWindow window = new // raw
    TICVisualizerWindow(// raw
    new RawDataFile[] { activeRaw }, // plot type
    TICPlotType.BASEPEAK, // scan selection
    scanSelection, // mz range
    mzRange, // selected features
    new Feature[] { peak }, // labels
    labelsMap);
    // get EIC Plot
    TICPlot ticPlot = window.getTICPlot();
    ticPlot.setPreferredSize(new Dimension(600, 200));
    ticPlot.getChart().getLegend().setVisible(false);
    // add a retention time Marker to the EIC
    ValueMarker marker = new ValueMarker(activeRaw.getScan(scan).getRetentionTime());
    marker.setPaint(Color.RED);
    marker.setStroke(new BasicStroke(3.0f));
    XYPlot plot = (XYPlot) ticPlot.getChart().getPlot();
    plot.addDomainMarker(marker);
    bottomPane.add(ticPlot);
    bottomPane.setResizeWeight(0.5);
    bottomPane.setEnabled(true);
    bottomPane.setDividerSize(5);
    bottomPane.setDividerLocation(200);
    JSplitPane spectrumPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
    // get MS/MS spectra window
    SpectraVisualizerWindow spectraWindow = new SpectraVisualizerWindow(activeRaw);
    spectraWindow.loadRawData(activeRaw.getScan(scan));
    // get MS/MS spectra plot
    SpectraPlot spectrumPlot = spectraWindow.getSpectrumPlot();
    spectrumPlot.getChart().getLegend().setVisible(false);
    spectrumPlot.setPreferredSize(new Dimension(600, 400));
    spectrumPane.add(spectrumPlot);
    spectrumPane.add(spectraWindow.getToolBar());
    spectrumPane.setResizeWeight(1);
    spectrumPane.setEnabled(false);
    spectrumPane.setDividerSize(0);
    bottomPane.add(spectrumPane);
    panel.add(bottomPane);
    panel.setBorder(BorderFactory.createLineBorder(Color.black));
    return panel;
}

Example 3 with TICPlot

use of net.sf.mzmine.modules.visualization.tic.TICPlot in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method updateChart.

private void updateChart() {
    updateParameterSetFromComponents();
    if (selectedDataFile == null)
        return;
    try {
        // old charts axes ranges
        org.jfree.data.Range domainZoom = chart == null ? null : chart.getChart().getXYPlot().getDomainAxis().getRange();
        org.jfree.data.Range rangeZoom = chart == null ? null : chart.getChart().getXYPlot().getRangeAxis().getRange();
        Range<Double> rangeMZ = parameterSet.getParameter(KovatsIndexExtractionParameters.mzRange).getValue();
        Range<Double> rangeRT = parameterSet.getParameter(KovatsIndexExtractionParameters.rtRange).getValue();
        if (rangeMZ == null) {
            // set range to specific alkane fragment
            rangeMZ = Range.closed(56.6, 57.5);
            ((MZRangeComponent) getComponentForParameter(KovatsIndexExtractionParameters.mzRange)).setValue(rangeMZ);
        }
        if (rangeRT == null) {
            rangeRT = selectedDataFile[0].getDataRTRange();
            ((RTRangeComponent) getComponentForParameter(KovatsIndexExtractionParameters.rtRange)).setValue(rangeRT);
        }
        // create dataset
        TICSumDataSet data = new TICSumDataSet(selectedDataFile, rangeRT, rangeMZ, null, TICPlotType.BASEPEAK);
        chart = new TICPlot(this);
        chart.addTICDataset(data);
        if (domainZoom != null)
            chart.getChart().getXYPlot().getDomainAxis().setRange(domainZoom);
        if (rangeZoom != null)
            chart.getChart().getXYPlot().getRangeAxis().setRange(rangeZoom);
        // add control for markers
        chart.getGestureAdapter().addGestureHandler(new ChartGestureDragDiffHandler(Entity.PLOT, Button.BUTTON1, new Key[] { Key.NONE }, e -> handleMarkerDrag(e)));
        chart.getGestureAdapter().addGestureHandler(new ChartGestureHandler(new ChartGesture(Entity.PLOT, Event.RELEASED), e -> {
            if (chart != null)
                chart.setMouseZoomable(true);
            if (currentlyDraggedMarker != null) {
                // set value of current marker
                logger.info("Marker dragging ended at " + currentlyDraggedMarker.getValue());
                int index = markers.indexOf(currentlyDraggedMarker);
                double value = e.getCoordinates().getX();
                setValue(index, value);
                // 
                currentlyDraggedMarker = null;
            }
        }));
        kovatsValuesChanged();
        pnChart.removeAll();
        pnChart.add(chart, BorderLayout.CENTER);
        revalidate();
        repaint();
    } catch (Exception e) {
        logger.log(Level.WARNING, "Peak picking parameters incorrect");
    }
}

Example 4 with TICPlot

use of net.sf.mzmine.modules.visualization.tic.TICPlot in project mzmine2 by mzmine.

the class XICManualPickerDialog method addDialogComponents.

@Override
protected void addDialogComponents() {
    super.addDialogComponents();
    Color l = new Color(50, 255, 50, 150), u = new Color(255, 50, 50, 150);
    Stroke stroke = new BasicStroke(1.0f);
    // make new panel, put tic into the middle of a border layout.
    remove(this.mainPanel);
    rtRangeComp = new DoubleRangeComponent(MZmineCore.getConfiguration().getRTFormat());
    mzRangeComp = new DoubleRangeComponent(MZmineCore.getConfiguration().getMZFormat());
    applyMassRange = new JButton("Set");
    applyMassRange.addActionListener(a -> setMassRange());
    addListenertoRTComp(rtRangeComp);
    JLabel rtLabel = new JLabel("Retention time range");
    JLabel mzLabel = new JLabel("m/z range");
    mainPanel.add(rtLabel, 0, getNumberOfParameters() + 1);
    mainPanel.add(rtRangeComp, 1, getNumberOfParameters() + 1);
    mainPanel.add(mzLabel, 0, getNumberOfParameters() + 2);
    mainPanel.add(mzRangeComp, 1, getNumberOfParameters() + 2);
    mainPanel.add(applyMassRange, 2, getNumberOfParameters() + 2);
    BorderLayout borderLayout = new BorderLayout();
    Panel pnlNewMain = new Panel(borderLayout);
    // put another border layout for south of the new main panel, so we can place controls and
    // integration specific stuff there
    Panel pnlControlsAndParameters = new Panel(new BorderLayout());
    pnlControlsAndParameters.add(this.mainPanel, BorderLayout.CENTER);
    pnlNewMain.add(pnlControlsAndParameters, BorderLayout.SOUTH);
    // now make another panel to put the integration specific stuff, like the buttons and the
    // current area
    Panel pnlIntegration = new Panel(new FlowLayout());
    setLower = GUIUtils.addButton(pnlIntegration, null, icoLower, this, "SETLOWER", "Set the lower integration boundary.");
    setUpper = GUIUtils.addButton(pnlIntegration, null, icoUpper, this, "SETUPPER", "Set the upper integration boundary.");
    GUIUtils.addSeparator(pnlIntegration);
    pnlIntegration.add(new Label("Area: "));
    txtArea = new JTextField(10);
    txtArea.setEditable(false);
    pnlIntegration.add(txtArea);
    pnlControlsAndParameters.add(pnlIntegration, BorderLayout.NORTH);
    ticPlot = new TICPlot(this);
    ticPlot.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.RAISED));
    ticPlot.setMinimumSize(new Dimension(400, 200));
    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
    ticPlot.setPreferredSize(new Dimension((int) (screenSize.getWidth() / 1.3d), (int) (screenSize.getHeight() / 1.8d)));
    pnlNewMain.add(ticPlot, BorderLayout.CENTER);
    // add a mouse listener to place the boundaries
    getTicPlot().addChartMouseListener(new ChartMouseListener() {

        // https://stackoverflow.com/questions/1512112/jfreechart-get-mouse-coordinates
        // draw a marker at the current position
        @Override
        public void chartMouseMoved(ChartMouseEvent event) {
            Point2D p = ticPlot.translateScreenToJava2D(event.getTrigger().getPoint());
            Rectangle2D plotArea = ticPlot.getScreenDataArea();
            XYPlot plot = ticPlot.getXYPlot();
            double rtValue = plot.getDomainAxis().java2DToValue(p.getX(), plotArea, plot.getDomainAxisEdge());
            Color clr = (nextBorder == NextBorder.LOWER) ? l : u;
            addMarkers();
            plot.addDomainMarker(new ValueMarker(rtValue, clr, stroke));
        }

        @Override
        public void chartMouseClicked(ChartMouseEvent event) {
            Point2D p = ticPlot.translateScreenToJava2D(event.getTrigger().getPoint());
            Rectangle2D plotArea = ticPlot.getScreenDataArea();
            XYPlot plot = ticPlot.getXYPlot();
            double rtValue = plot.getDomainAxis().java2DToValue(p.getX(), plotArea, plot.getDomainAxisEdge());
            inputSource = InputSource.GRAPH;
            setRTBoundary(rtValue);
            inputSource = InputSource.OTHER;
        }
    });
    add(pnlNewMain);
    pack();
}

Example 5 with TICPlot

use of net.sf.mzmine.modules.visualization.tic.TICPlot in project mzmine2 by mzmine.

the class ShapeModelerSetupDialog method addComponents.

/**
 * This function add all the additional components for this dialog over the original
 * ParameterSetupDialog.
 */
private void addComponents() {
    PeakList[] peakLists = MZmineCore.getProjectManager().getCurrentProject().getPeakLists();
    // Elements of pnlpreview
    JPanel pnlpreview = new JPanel(new BorderLayout());
    preview = new JCheckBox(" Show preview of peak building ");
    preview.addActionListener(this);
    preview.setHorizontalAlignment(SwingConstants.CENTER);
    preview.setEnabled(peakLists.length > 0);
    pnlpreview.add(new JSeparator(), BorderLayout.NORTH);
    pnlpreview.add(preview, BorderLayout.CENTER);
    pnlpreview.add(Box.createVerticalStrut(10), BorderLayout.SOUTH);
    JComponent[] tableComponents = new JComponent[4];
    tableComponents[0] = new JLabel("Feature list");
    comboPeakList = new JComboBox<PeakList>();
    for (PeakList peakList : peakLists) {
        comboPeakList.addItem(peakList);
    }
    comboPeakList.setFont(comboFont);
    comboPeakList.addActionListener(this);
    tableComponents[1] = comboPeakList;
    comboPeak = new JComboBox<PeakListRow>();
    comboPeak.setFont(comboFont);
    comboPeak.setRenderer(new PeakPreviewComboRenderer());
    tableComponents[2] = new JLabel("Peak");
    tableComponents[3] = comboPeak;
    pnlLabelsFields = GUIUtils.makeTablePanel(2, 2, tableComponents);
    // Put all together
    pnlVisible = new JPanel(new BorderLayout());
    pnlVisible.add(pnlpreview, BorderLayout.NORTH);
    // Panel for XYPlot
    pnlPlotXY = new JPanel(new BorderLayout());
    GUIUtils.addMarginAndBorder(pnlPlotXY, 10);
    pnlPlotXY.setBackground(Color.white);
    ticPlot = new TICPlot((ActionListener) this);
    pnlPlotXY.add(ticPlot, BorderLayout.CENTER);
    toolBar = new TICToolBar(ticPlot);
    toolBar.getComponentAtIndex(0).setVisible(false);
    pnlPlotXY.add(toolBar, BorderLayout.EAST);
    mainPanel.add(pnlVisible, 0, getNumberOfParameters() + 3, 3, 1, 0, 0);
    updateMinimumSize();
    pack();
    setLocationRelativeTo(MZmineCore.getDesktop().getMainWindow());
}