+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void textbox_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+\r
+ StringBuffer buffer = new StringBuffer();\r
+\r
+ if (type.equals("AV"))\r
+ {\r
+ buffer.append("Average distance tree using ");\r
+ }\r
+ else\r
+ {\r
+ buffer.append("Neighbour joining tree using ");\r
+ }\r
+\r
+ if (pwtype.equals("BL"))\r
+ {\r
+ buffer.append("BLOSUM62");\r
+ }\r
+ else\r
+ {\r
+ buffer.append("PID");\r
+ }\r
+\r
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
+\r
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void saveAsNewick_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save tree as newick file");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(null);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ try\r
+ {\r
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
+ String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
+ java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
+ choice));\r
+ out.println(output);\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void printMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ //Putting in a thread avoids Swing painting problems\r
+ treeCanvas.startPrinting();\r
+ }\r
+\r