- Color col = new Color((int)(Math.random()*255),\r
- (int)(Math.random()*255),\r
- (int)(Math.random()*255));\r
- setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());\r
+ return;\r
+ }\r
+ else if (ob instanceof SequenceNode)\r
+ {\r
+ SequenceNode tmpnode = (SequenceNode) ob;\r
+ tree.swapNodes(tmpnode);\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+ }\r
+ else\r
+ {\r
+ // Find threshold\r
+ if (tree.getMaxHeight() != 0)\r
+ {\r
+ threshold = (float) (x - offx) / (float) (getWidth() -\r
+ labelLength - (2 * offx));\r
+\r
+ tree.getGroups().removeAllElements();\r
+ tree.groupNodes(tree.getTopNode(), threshold);\r
+ setColor(tree.getTopNode(), Color.black);\r
+\r
+ av.setSelectionGroup(null);\r
+ av.alignment.deleteAllGroups();\r
+\r
+ for (int i = 0; i < tree.getGroups().size(); i++)\r
+ {\r
+ Color col = new Color( (int) (Math.random() * 255),\r
+ (int) (Math.random() * 255),\r
+ (int) (Math.random() * 255));\r
+ setColor( (SequenceNode) tree.getGroups().elementAt(i),\r
+ col.brighter());\r
+\r
+ Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()\r
+ .elementAt(i),\r
+ new Vector());\r
+\r
+ Vector sequences = new Vector();\r
+ for (int j = 0; j < l.size(); j++)\r
+ {\r
+ sequences.add( (Sequence)((SequenceNode) l.elementAt(j)).element());\r
+ }\r