+ if(cs!=null)\r
+ {\r
+ if (cs.conservationApplied())\r
+ {\r
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ 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)cs).\r
+ 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
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
+ av.setGlobalColourScheme(cs);\r
+ }\r
+ }\r