Class FigTreeApplication

src/figtree/application/FigTreeApplication.java:67–447

Application class for FigTree including main() method for invoking it. Uses JAM Application classes to create a MultiDoc Application. @author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$

 * $LastChangedRevision$
 */
public class FigTreeApplication extends MultiDocApplication {

    public static final String VERSION = "1.4.4";
    public static final String DATES = "2006-2018";

    public static FigTreeApplication application;

    public FigTreeApplication(MenuBarFactory menuBarFactory, String nameString,  String titleString, String aboutString, Icon icon,
                              String websiteURLString,
                              String helpURLString) {
        super(menuBarFactory, nameString, titleString, aboutString, icon, websiteURLString, helpURLString);

//        addPreferencesSection(new GeneralPreferencesSection());
        addPreferencesSection(new AppearancePreferencesSection());
        addPreferencesSection(new FontsPreferencesSection());
//        addPreferencesSection(new AdvancedPreferencesSection());
    }

    public DocumentFrame doOpenFile(File file) {
        DocumentFrame documentFrame = getUpperDocumentFrame();
        if (documentFrame != null && documentFrame.getFile() == null) {
            documentFrame.openFile(file);
            return documentFrame;
        } else {
            return super.doOpenFile(file);
        }
    }

    public void doPaste() {

    }

    static public void createGraphic(String graphicFormat, int width, int height, String treeFileName, String graphicFileName) {

        try {
            BufferedReader bufferedReader = new BufferedReader(new FileReader(treeFileName));
            String line = bufferedReader.readLine();
            while (line != null && line.length() == 0) {
                line = bufferedReader.readLine();
            }

            bufferedReader.close();

            boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));

            Reader reader = new FileReader(treeFileName);

            Map<String, Object> settings = new HashMap<String, Object>();

            ExtendedTreeViewer treeViewer = new ExtendedTreeViewer();
            ControlPalette controlPalette = new BasicControlPalette(FigTreePanel.CONTROL_PALETTE_WIDTH, BasicControlPalette.DisplayMode.ONLY_ONE_OPEN);
            FigTreePanel figTreePanel = new FigTreePanel(null, treeViewer, controlPalette);

            // First of all, fully populate the settings map so that
            // all the settings have defaults
            controlPalette.getSettings(settings);

            List<Tree> trees = new ArrayList<Tree>();