+ SequenceGroup sg = new SequenceGroup(sequences,\r
+ "TreeGroup", cs, true, true, false,\r
+ 0,\r
+ av.alignment.getWidth() - 1);\r
+\r
+ if (av.getGlobalColourScheme() != null\r
+ && av.getGlobalColourScheme().conservationApplied())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(false),\r
+ sg.getStartRes(), sg.getEndRes());\r
+\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+ sg.cs.setConservation(c);\r
+ }\r
+\r
+ av.alignment.addGroup(sg);\r
+ }\r
+\r