Method readData

src/figtree/application/FigTreeFrame.java:727–789

(Reader reader, boolean isNexus)

    }

    protected boolean readData(Reader reader, boolean isNexus) throws IOException {

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

        boolean hasSettings = false;

        try {
            Map<String, Object> settings = new HashMap<String, Object>();
            // First of all, fully populate the settings map so that
            // all the settings have defaults
            controlPalette.getSettings(settings);

            if (isNexus) {
                FigTreeNexusImporter importer = new FigTreeNexusImporter(reader);
                while (importer.hasTree()) {
                    Tree tree = importer.importNextTree();
                    trees.add(tree);
                }
                // Try to find a figtree block and if found, parse the settings
                while (true) {
                    try {
                        importer.findNextBlock();
                        if (importer.getNextBlockName().equalsIgnoreCase("FIGTREE")) {
                            importer.parseFigTreeBlock(settings);
                            hasSettings = true;
                        }
                    } catch (EOFException ex) {
                        break;
                    }
                }
            } else {
                NewickImporter importer = new NewickImporter(reader, true);
                while (importer.hasTree()) {
                    Tree tree = importer.importNextTree();
                    trees.add(tree);
                }
            }

            if (trees.size() == 0) {
                throw new ImportException("This file contained no trees.");
            }

            checkLabelAttribute(trees);

            treeViewer.setTrees(trees);
            controlPalette.setSettings(settings);
        } catch (ImportException ie) {
            JOptionPane.showMessageDialog(this, "Error reading tree file: \n" + ie.getMessage(),
                    "Import Error",
                    JOptionPane.ERROR_MESSAGE);
            return false;
        }

        if (!hasSettings) {
            // If there weren't settings in the file then this wasn't a TreeDraw
            // created document so we don't want to be able to overwrite it without
            // explicit action of the user...
            setDirty();