- if (av.getSelectionGroup() != null)\r
- {\r
- av.getSelectionGroup().recalcConservation();\r
- }\r
-\r
- if (cs.conservationApplied())\r
- {\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, av.alignment.getSequences(),\r
- 0, av.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
- cxs.resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- cs.setConservation(c);\r
- av.setGlobalColourScheme(cs);\r
- }\r
- else\r
- {\r
- cs.setConservation(c);\r
- av.setGlobalColourScheme(cs);\r
- }\r
- }\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ((ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- av.setGlobalColourScheme(cs);\r
- }\r