Examples with MZToleranceParameter net.sf.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter used on opensource projects

Example 1 with MZToleranceParameter

use of net.sf.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter 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);
    }
}