Examples with AxesSetupDialog net.sf.mzmine.util.dialogs.AxesSetupDialog used on opensource projects

Example 6 with AxesSetupDialog

use of net.sf.mzmine.util.dialogs.AxesSetupDialog in project mzmine2 by mzmine.

the class ScatterPlotChart method actionPerformed.

public void actionPerformed(ActionEvent event) {
    super.actionPerformed(event);
    String command = event.getActionCommand();
    if (command.equals("SETUP_AXES")) {
        AxesSetupDialog dialog = new AxesSetupDialog(window, plot);
        dialog.setVisible(true);
        return;
    }
    if (command.equals("TIC")) {
        double valueX = plot.getDomainCrosshairValue();
        double valueY = plot.getRangeCrosshairValue();
        PeakListRow selectedRow = mainDataSet.getRow(valueX, valueY);
        if (selectedRow == null) {
            MZmineCore.getDesktop().displayErrorMessage(window, "No peak is selected");
            return;
        }
        Feature[] peaks = selectedRow.getPeaks();
        Range<Double> rtRange = peakList.getRowsRTRange();
        Range<Double> mzRange = PeakUtils.findMZRange(peaks);
        // Label best peak with preferred identity.
        final Feature bestPeak = selectedRow.getBestPeak();
        final PeakIdentity peakIdentity = selectedRow.getPreferredPeakIdentity();
        final Map<Feature, String> labelMap = new HashMap<Feature, String>(1);
        if (bestPeak != null && peakIdentity != null) {
            labelMap.put(bestPeak, peakIdentity.getName());
        }
        ScanSelection scanSelection = new ScanSelection(rtRange, 1);
        TICVisualizerModule.showNewTICVisualizerWindow(peakList.getRawDataFiles(), peaks, labelMap, scanSelection, TICPlotType.BASEPEAK, mzRange);
    }
    if ("SAVE_EMF".equals(command)) {
        JFileChooser chooser = new JFileChooser();
        FileNameExtensionFilter filter = new FileNameExtensionFilter("EMF Image", "EMF");
        chooser.setFileFilter(filter);
        int returnVal = chooser.showSaveDialog(null);
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            String file = chooser.getSelectedFile().getPath();
            if (!file.toLowerCase().endsWith(".emf"))
                file += ".emf";
            int width = (int) this.getSize().getWidth();
            int height = (int) this.getSize().getHeight();
            // Save image
            SaveImage SI = new SaveImage(getChart(), file, width, height, FileType.EMF);
            new Thread(SI).start();
        }
    }
    if ("SAVE_EPS".equals(command)) {
        JFileChooser chooser = new JFileChooser();
        FileNameExtensionFilter filter = new FileNameExtensionFilter("EPS Image", "EPS");
        chooser.setFileFilter(filter);
        int returnVal = chooser.showSaveDialog(null);
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            String file = chooser.getSelectedFile().getPath();
            if (!file.toLowerCase().endsWith(".eps"))
                file += ".eps";
            int width = (int) this.getSize().getWidth();
            int height = (int) this.getSize().getHeight();
            // Save image
            SaveImage SI = new SaveImage(getChart(), file, width, height, FileType.EPS);
            new Thread(SI).start();
        }
    }
}

Example 7 with AxesSetupDialog

use of net.sf.mzmine.util.dialogs.AxesSetupDialog in project mzmine2 by mzmine.

the class MsMsVisualizerWindow method actionPerformed.

/**
 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
 */
public void actionPerformed(ActionEvent event) {
    String command = event.getActionCommand();
    if (command.equals("SHOW_SPECTRUM")) {
        CursorPosition pos = getCursorPosition();
        if (pos != null) {
            SpectraVisualizerModule.showNewSpectrumWindow(pos.getDataFile(), pos.getScanNumber());
        }
    }
    if (command.equals("SETUP_AXES")) {
        AxesSetupDialog dialog = new AxesSetupDialog(this, IDAPlot.getXYPlot());
        dialog.setVisible(true);
    }
    if (command.equals("SHOW_DATA_POINTS")) {
        IDAPlot.switchDataPointsVisible();
    }
    if (command.equals("SWITCH_TOOLTIPS")) {
        if (tooltipMode) {
            IDAPlot.showPeaksTooltips(false);
            toolBar.setTooltipButton(false);
            tooltipMode = false;
        } else {
            IDAPlot.showPeaksTooltips(true);
            toolBar.setTooltipButton(true);
            tooltipMode = true;
        }
    }
    if (command.equals("FIND_SPECTRA")) {
        // Parameters
        final DoubleParameter inputMZ = new DoubleParameter("Ion m/z", "m/z value of ion to search for.");
        final MZToleranceParameter inputMZTolerance = new MZToleranceParameter();
        final DoubleParameter inputIntensity = new DoubleParameter("Min. ion intensity", "Only ions with intensities above this value will be searched for.");
        final BooleanParameter inputNL = new BooleanParameter("Neutral Loss", "If selected, the ion to be searched for will be a neutral loss ion.\nIn this case, only ions above the min. intensity will be examined.", false);
        final ComboParameter<Colors> inputColors = new ComboParameter<Colors>("Color", "The color which the data points will be marked with.", Colors.values());
        Parameter<?>[] parameters = new Parameter<?>[5];
        parameters[0] = inputMZ;
        parameters[1] = inputMZTolerance;
        parameters[2] = inputIntensity;
        parameters[3] = inputNL;
        parameters[4] = inputColors;
        final ParameterSet parametersSearch = new SimpleParameterSet(parameters);
        ExitCode exitCode = parametersSearch.showSetupDialog(this, true);
        if (exitCode != ExitCode.OK)
            return;
        double searchMZ = parametersSearch.getParameter(inputMZ).getValue();
        MZTolerance searchMZTolerance = parametersSearch.getParameter(inputMZTolerance).getValue();
        double minIntensity = parametersSearch.getParameter(inputIntensity).getValue();
        boolean neutralLoss = parametersSearch.getParameter(inputNL).getValue();
        Color highligtColor = Color.red;
        ;
        if (parametersSearch.getParameter(inputColors).getValue().equals(Colors.green)) {
            highligtColor = Color.green;
        }
        if (parametersSearch.getParameter(inputColors).getValue().equals(Colors.blue)) {
            highligtColor = Color.blue;
        }
        // Find and highlight spectra with specific ion
        dataset.highlightSpectra(searchMZ, searchMZTolerance, minIntensity, neutralLoss, highligtColor);
        // Add legend entry
        LegendItemCollection chartLegend = IDAPlot.getXYPlot().getLegendItems();
        chartLegend.add(new LegendItem("Ion: " + searchMZ, "", "MS/MS spectra which contain the " + searchMZ + " ion\nTolerance: " + searchMZTolerance.toString() + "\nMin intensity: " + minIntensity, "", new Ellipse2D.Double(0, 0, 7, 7), highligtColor));
        IDAPlot.getXYPlot().setFixedLegendItems(chartLegend);
    }
}

Example 8 with AxesSetupDialog

use of net.sf.mzmine.util.dialogs.AxesSetupDialog in project mzmine2 by mzmine.

the class TICPlot method actionPerformed.

@Override
public void actionPerformed(final ActionEvent event) {
    super.actionPerformed(event);
    final String command = event.getActionCommand();
    if ("SHOW_DATA_POINTS".equals(command)) {
        switchDataPointsVisible();
    }
    if ("SHOW_ANNOTATIONS".equals(command)) {
        switchItemLabelsVisible();
    }
    if ("SETUP_AXES".equals(command)) {
        JFrame parent = null;
        if (visualizer instanceof JFrame)
            parent = (JFrame) visualizer;
        new AxesSetupDialog(parent, getXYPlot()).setVisible(true);
    }
    if ("ZOOM_IN".equals(command)) {
        getXYPlot().getDomainAxis().resizeRange(1.0 / ZOOM_FACTOR);
        getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
    }
    // Set tick size to auto when zooming
    String[] zoomList = new String[] { "ZOOM_IN_BOTH", "ZOOM_IN_DOMAIN", "ZOOM_IN_RANGE", "ZOOM_OUT_BOTH", "ZOOM_DOMAIN_BOTH", "ZOOM_RANGE_BOTH", "ZOOM_RESET_BOTH", "ZOOM_RESET_DOMAIN", "ZOOM_RESET_RANGE" };
    if (Arrays.asList(zoomList).contains(command)) {
        getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
        getXYPlot().getRangeAxis().setAutoTickUnitSelection(true);
    }
    if ("ZOOM_OUT".equals(command)) {
        getXYPlot().getDomainAxis().resizeRange(ZOOM_FACTOR);
        getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
    // if (getXYPlot().getDomainAxis().getRange().contains(0.0000001)) {
    // getXYPlot().getDomainAxis().setAutoRange(true);
    // getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
    // }
    }
    if ("ZOOM_AUTO".equals(command)) {
        getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
        getXYPlot().getRangeAxis().setAutoTickUnitSelection(true);
        restoreAutoDomainBounds();
        restoreAutoRangeBounds();
    }
    if ("SET_SAME_RANGE".equals(command)) {
        // Get current axes range.
        final NumberAxis xAxis = (NumberAxis) getXYPlot().getDomainAxis();
        final NumberAxis yAxis = (NumberAxis) getXYPlot().getRangeAxis();
        final double xMin = xAxis.getRange().getLowerBound();
        final double xMax = xAxis.getRange().getUpperBound();
        final double xTick = xAxis.getTickUnit().getSize();
        final double yMin = yAxis.getRange().getLowerBound();
        final double yMax = yAxis.getRange().getUpperBound();
        final double yTick = yAxis.getTickUnit().getSize();
        // Set the range of these frames
        for (final Window frame : JFrame.getWindows()) {
            if (frame instanceof TICVisualizerWindow) {
                final TICVisualizerWindow ticFrame = (TICVisualizerWindow) frame;
                ticFrame.setAxesRange(xMin, xMax, xTick, yMin, yMax, yTick);
            }
        }
    }
    if ("SHOW_SPECTRUM".equals(command)) {
        visualizer.actionPerformed(event);
    }
    if ("SHOW_LEGEND".equals(command)) {
        // Toggle legend visibility.
        final LegendTitle legend = getChart().getLegend();
        legend.setVisible(!legend.isVisible());
    }
    if ("GRAY_BACKGROUND".equals(command)) {
        // Toggle background color
        final Paint color = getChart().getPlot().getBackgroundPaint();
        Color bgColor, liColor;
        if (color.equals(Color.lightGray)) {
            bgColor = Color.white;
            liColor = Color.lightGray;
        } else {
            bgColor = Color.lightGray;
            liColor = Color.white;
        }
        getChart().getPlot().setBackgroundPaint(bgColor);
        getChart().getXYPlot().setDomainGridlinePaint(liColor);
        getChart().getXYPlot().setRangeGridlinePaint(liColor);
    }
    if ("SAVE_EMF".equals(command)) {
        JFileChooser chooser = new JFileChooser();
        FileNameExtensionFilter filter = new FileNameExtensionFilter("EMF Image", "EMF");
        chooser.setFileFilter(filter);
        int returnVal = chooser.showSaveDialog(null);
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            String file = chooser.getSelectedFile().getPath();
            if (!file.toLowerCase().endsWith(".emf"))
                file += ".emf";
            int width = (int) this.getSize().getWidth();
            int height = (int) this.getSize().getHeight();
            // Save image
            SaveImage SI = new SaveImage(getChart(), file, width, height, FileType.EMF);
            new Thread(SI).start();
        }
    }
    if ("SAVE_EPS".equals(command)) {
        JFileChooser chooser = new JFileChooser();
        FileNameExtensionFilter filter = new FileNameExtensionFilter("EPS Image", "EPS");
        chooser.setFileFilter(filter);
        int returnVal = chooser.showSaveDialog(null);
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            String file = chooser.getSelectedFile().getPath();
            if (!file.toLowerCase().endsWith(".eps"))
                file += ".eps";
            int width = (int) this.getSize().getWidth();
            int height = (int) this.getSize().getHeight();
            // Save image
            SaveImage SI = new SaveImage(getChart(), file, width, height, FileType.EPS);
            new Thread(SI).start();
        }
    }
}