- TreeSelectionChanged((Sequence)ob);\r
- repaint();\r
- return;\r
-\r
- } else if (ob instanceof SequenceNode) {\r
- SequenceNode tmpnode = (SequenceNode)ob;\r
- tree.swapNodes(tmpnode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- } else {\r
- // Find threshold\r
-\r
- if (tree.getMaxHeight() != 0) {\r
- float fthreshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);\r
- this.threshold = x;\r
- tree.getGroups().removeAllElements();\r
- tree.groupNodes(tree.getTopNode(),fthreshold);\r
- setColor(tree.getTopNode(),Color.black);\r
-\r
- for (int i=0; i < tree.getGroups().size(); i++) {\r
-\r
- int tmp = i%(7);\r
- Color col = new Color((int)(Math.random()*255),\r
- (int)(Math.random()*255),\r
- (int)(Math.random()*255));\r
-\r
- setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());\r
-\r
- // l is vector of Objects\r
- Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());\r
-\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