int end;\r
TreeCanvas treeCanvas;\r
NJTree tree;\r
+ AlignViewport av;\r
\r
/**\r
* Creates a new TreePanel object.\r
initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
}\r
\r
+ public AlignmentI getAlignment()\r
+ {\r
+ return treeCanvas.av.getAlignment();\r
+ }\r
+\r
\r
void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
String pwtype, int s, int e, NewickFile newTree)\r
}\r
});\r
\r
+ this.av = av;\r
+\r
\r
TreeLoader tl = new TreeLoader(newTree);\r
tl.start();\r
\r
treeCanvas.repaint();\r
\r
+ av.setCurrentTree(tree);\r
+\r
}\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(false, true));\r
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
}\r
\r
/**\r
try\r
{\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- String output = fout.print(false, true); // distances only\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