+ SequenceGroup sg = null;\r
+ for (int j = 0; j < l.size(); j++)\r
+ {\r
+ SequenceNode sn = (SequenceNode) l.elementAt(j);\r
+ if(sg==null)\r
+ sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());\r
+\r
+ sg.addSequence( (Sequence) sn.element());\r
+ }\r
+\r
+ if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, sg.getStartRes(),\r
+ sg.getEndRes());\r
+\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
+\r
+ sg.cs = ccs;\r
+\r
+ }\r
+\r
+\r
+\r
+ av.alignment.addGroup(sg);\r