private void setStatusMessage() { Tree tree = treesPanel.getTree(); if (tree != null) { String message = ""; message += "Tree loaded, " + tree.getTaxonCount() + " taxa"; TemporalRooting tr = treesPanel.getTemporalRooting(); if (tr.isContemporaneous()) { message += ", contemporaneous tips"; } else { NumberFormatter nf = new NumberFormatter(3); message += ", dated tips with range " + nf.format(tr.getDateRange()); } statusLabel.setText(message); } }
protected void writeTimeTreeFile(PrintStream ps) throws IOException { FlexibleTree tree = new FlexibleTree(treesPanel.getTreeAsViewed()); Regression r = treesPanel.getTemporalRooting().getRootToTipRegression(treesPanel.getTreeAsViewed()); for (int i = 0; i < tree.getInternalNodeCount(); i++) { NodeRef node = tree.getInternalNode(i); double height = tree.getNodeHeight(node); tree.setNodeHeight(node, height / r.getGradient()); } TreeUtils.setHeightsFromDates(tree); NexusExporter nexusExporter = new NexusExporter(new PrintStream(ps)); nexusExporter.exportTree(tree); }
protected void writeTreeFile(PrintStream ps, boolean newickFormat) throws IOException { Tree tree = treesPanel.getTreeAsViewed(); // if (newickFormat) { // NewickExporter newickExporter = new NewickExporter(ps); // newickExporter.exportTree(tree); // } else { NexusExporter nexusExporter = new NexusExporter(new PrintStream(ps)); nexusExporter.exportTree(tree); // } }
@Override public void doCopy() { StringWriter writer = new StringWriter(); PrintWriter pwriter = new PrintWriter(writer); for (String tip : treesPanel.getSelectedTips()) { pwriter.println(tip); } Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard(); StringSelection selection = new StringSelection(writer.toString()); clipboard.setContents(selection, selection); }
protected void doExportData() { FileDialog dialog = new FileDialog(this, "Export Data File...", FileDialog.SAVE); dialog.setVisible(true); if (dialog.getFile() != null) { File file = new File(dialog.getDirectory(), dialog.getFile()); Writer writer = null; try { writer = new PrintWriter(file); treesPanel.writeDataFile(writer); writer.close(); } catch (IOException ioe) { JOptionPane.showMessageDialog( this, "Error writing data file: " + ioe.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } } }
public void timeScaleChanged() { treesPanel.timeScaleChanged(); setStatusMessage(); }