+ if (av.getGlobalColourScheme() instanceof UserColourScheme)\r
+ {\r
+ cs = new UserColourScheme(\r
+ ( (UserColourScheme) av.getGlobalColourScheme()).getColours());\r
+\r
+ }\r
+ else\r
+ cs = ColourSchemeProperty.getColour(sequences,\r
+ av.alignment.getWidth(),\r
+ ColourSchemeProperty.getColourName(\r
+ av.getGlobalColourScheme()));\r
+\r
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),\r
+ av.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",\r
+ cs, true, true,\r
+ false, 0, av.alignment.getWidth()-1);\r
+\r
+\r
+ if ( av.getGlobalColourScheme()!=null\r
+ && av.getGlobalColourScheme().conservationApplied())\r
+ {\r