*/\r
public void recalcConservation()\r
{\r
- if (cs != null)\r
- {\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
- }\r
+ if(cs == null)\r
+ return;\r
+\r
+ cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
}\r
\r
- if (cs instanceof ConservationColourScheme)\r
+\r
+ if (cs.conservationApplied())\r
{\r
Conservation c = new Conservation(groupName,\r
ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
c.calculate();\r
c.verdict(false, 25);\r
\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
- ccs.conserve = c;\r
\r
- if (ccs.cs instanceof ClustalxColourScheme)\r
+ cs.setConservation(c);\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme) ccs.cs).resetClustalX(sequences,\r
+ ((ClustalxColourScheme) cs).resetClustalX(sequences,\r
getWidth());\r
}\r
}\r