- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
-\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- scrollPane.setViewportView(treeCanvas);\r
- treeCanvas.setMarkPlaceholders(has_placeholders);\r
- setViewStateFromTreeCanvas(treeCanvas);\r
-\r
- // JBPNote TODO: preference for always marking placeholders in new associated tree\r
- }\r
-\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
- private void setViewStateFromTreeCanvas(TreeCanvas tree)\r
- {\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
- {\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
-\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
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
+\r
+ if (lf.isPlaceholder())\r
+ {\r
+ has_placeholders = true;\r
+ }\r
+\r
+ if (longestName.length() < ((Sequence) lf.element()).getName()\r
+ .length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ((Sequence) lf.element()).getName();\r
+ }\r
+ }\r
+\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+\r
+ treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+ treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
+ treeCanvas.setShowDistances(newtree.HasDistances());\r
+ scrollPane.setViewportView(treeCanvas);\r
+ treeCanvas.setMarkPlaceholders(has_placeholders);\r
+ setViewStateFromTreeCanvas(treeCanvas);\r
+\r
+ // JBPNote TODO: preference for always marking placeholders in new associated tree\r