\r
if (sg.cs != null)\r
{\r
- ((ResidueColourScheme) sg.cs).setThreshold(25, av.getIgnoreGapsConsensus());\r
+ sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());\r
}\r
\r
- if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
+ if (av.getGlobalColourScheme().conservationApplied())\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3, sg.sequences,\r
sg.getStartRes(), sg.getEndRes());\r
\r
c.calculate();\r
c.verdict(false, av.ConsPercGaps);\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
-\r
- sg.cs = ccs;\r
+ sg.cs.setConservation(c);\r
}\r
\r
av.alignment.addGroup(sg);\r