- SequenceI[] seq;\r
- String type;\r
- String pwtype;\r
- AlignViewport av;\r
- int start;\r
- int end;\r
- TreeCanvas treeCanvas;\r
- NJTree tree;\r
-\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
- public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
- {\r
- super();\r
-\r
- this.type = type;\r
- this.pwtype = pwtype;\r
-\r
- start = s;\r
- end = e;\r
-\r
- String longestName = "";\r
- seq = new Sequence [seqVector.size()];\r
- for (int i=0;i < seqVector.size();i++)\r
+ SequenceI[] seq;\r
+ String type;\r
+ String pwtype;\r
+ int start;\r
+ int end;\r
+ TreeCanvas treeCanvas;\r
+ NJTree tree;\r
+ AlignViewport av;\r
+\r
+ /**\r
+ * Creates a new TreePanel object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param seqVector DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ * @param pwtype DOCUMENT ME!\r
+ * @param s DOCUMENT ME!\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public TreePanel(AlignViewport av, Vector seqVector, String type,\r
+ String pwtype, int s, int e)\r
+ {\r
+ super();\r
+ initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+\r
+ // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
+ showDistances(true);\r
+ }\r
+\r
+ /**\r
+ * Creates a new TreePanel object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param seqVector DOCUMENT ME!\r
+ * @param newtree DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ * @param pwtype DOCUMENT ME!\r
+ */\r
+ public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
+ String type, String pwtype)\r