- tree = new NJTree(seq, type, pwtype, start, end);\r
-\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
- treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- setViewStateFromTreeCanvas(treeCanvas);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- scrollPane.setViewportView(treeCanvas);\r
-\r
- }\r
- private void setViewStateFromTreeCanvas(TreeCanvas tree) {\r
- // update view menu state from treeCanvas render state\r
- distanceMenu.setSelected(tree.showDistances);\r
- bootstrapMenu.setSelected(tree.showBootstrap);\r
- placeholdersMenu.setSelected(tree.markPlaceholders);\r
- }\r
-\r
- private void setTreeCanvasFromViewState(TreeCanvas tree) {\r
- // update view menu state from treeCanvas render state\r
- tree.showDistances = distanceMenu.isSelected();\r
- tree.showBootstrap = bootstrapMenu.isSelected();\r
- tree.markPlaceholders = placeholdersMenu.isSelected();\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
+ {\r
+ super();\r
+ initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+ }\r
+\r
+ public AlignmentI getAlignment()\r
+ {\r
+ return treeCanvas.av.getAlignment();\r