- c = new Conservation("All", al.cons,\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- al.getWidth());\r
- c.calculate();\r
- c.verdict(false, 100);\r
- sg.setConservation(c);\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- ccs.conserve = c;*/\r
+ // Y O Y CLUSTALX\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+\r
+ if(av.getSelectionGroup()!=null)\r
+ av.getSelectionGroup().recalcConservation();\r
+\r
+\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ av.alignment.getSequences(), 0,\r
+ av.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+\r
+ if (ccs.cs instanceof ClustalxColourScheme)\r
+ {\r
+\r
+ ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;\r
+ cxs.resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
+ ccs = new ConservationColourScheme(c, cxs);\r
+ av.setGlobalColourScheme(ccs);\r
+ }\r
+ else\r
+ {\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
+ av.setGlobalColourScheme(ccs);\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