+\r
+ // Y O Y CLUSTALX\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
+ if(ccs.cs instanceof ClustalxColourScheme)\r
+ {\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
+ ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;\r
+ cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());\r
+ ccs = new ConservationColourScheme(c, cxs);\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
+\r