Examples with MolStructureViewer net.sf.mzmine.modules.visualization.molstructure.MolStructureViewer used on opensource projects

Example 1 with MolStructureViewer

use of net.sf.mzmine.modules.visualization.molstructure.MolStructureViewer in project mzmine2 by mzmine.

the class ResultWindow method actionPerformed.

public void actionPerformed(ActionEvent e) {
    String command = e.getActionCommand();
    if (command.equals("ADD")) {
        int index = IDList.getSelectedRow();
        if (index < 0) {
            MZmineCore.getDesktop().displayMessage(this, "Select one result to add as compound identity");
            return;
        }
        index = IDList.convertRowIndexToModel(index);
        peakListRow.addPeakIdentity(listElementModel.getCompoundAt(index), false);
        // Notify the GUI about the change in the project
        MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(peakListRow, false);
        // Repaint the window to reflect the change in the feature list
        MZmineCore.getDesktop().getMainWindow().repaint();
        dispose();
    }
    if (command.equals("VIEWER")) {
        int index = IDList.getSelectedRow();
        if (index < 0) {
            MZmineCore.getDesktop().displayMessage(this, "Select one result to display molecule structure");
            return;
        }
        index = IDList.convertRowIndexToModel(index);
        DBCompound compound = listElementModel.getCompoundAt(index);
        URL url2D = compound.get2DStructureURL();
        URL url3D = compound.get3DStructureURL();
        String name = compound.getName() + " (" + compound.getPropertyValue(PeakIdentity.PROPERTY_ID) + ")";
        MolStructureViewer viewer = new MolStructureViewer(name, url2D, url3D);
        viewer.setVisible(true);
    }
    if (command.equals("ISOTOPE_VIEWER")) {
        int index = IDList.getSelectedRow();
        if (index < 0) {
            MZmineCore.getDesktop().displayMessage(this, "Select one result to display the isotope pattern");
            return;
        }
        index = IDList.convertRowIndexToModel(index);
        final IsotopePattern predictedPattern = listElementModel.getCompoundAt(index).getIsotopePattern();
        if (predictedPattern == null)
            return;
        Feature peak = peakListRow.getBestPeak();
        RawDataFile dataFile = peak.getDataFile();
        int scanNumber = peak.getRepresentativeScanNumber();
        SpectraVisualizerModule.showNewSpectrumWindow(dataFile, scanNumber, null, peak.getIsotopePattern(), predictedPattern);
    }
    if (command.equals("BROWSER")) {
        int index = IDList.getSelectedRow();
        if (index < 0) {
            MZmineCore.getDesktop().displayMessage(this, "Select one compound to display in a web browser");
            return;
        }
        index = IDList.convertRowIndexToModel(index);
        logger.finest("Launching default browser to display compound details");
        java.awt.Desktop desktop = java.awt.Desktop.getDesktop();
        DBCompound compound = listElementModel.getCompoundAt(index);
        String urlString = compound.getPropertyValue(PeakIdentity.PROPERTY_URL);
        if ((urlString == null) || (urlString.length() == 0))
            return;
        try {
            URL compoundURL = new URL(urlString);
            desktop.browse(compoundURL.toURI());
        } catch (Exception ex) {
            logger.severe("Error trying to launch default browser: " + ex.getMessage());
        }
    }
}