+ if(viewport.getColourAppliesToAllGroups())\r
+ {\r
+ Vector groups = viewport.alignment.getGroups();\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ sg.cs = cs;\r
+\r
+ if(abovePIDThreshold.isSelected())\r
+ abovePIDThreshold_actionPerformed(null);\r
+ else if( viewport.getConservationSelected() )\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, sg.getStartRes(),\r
+ sg.getEndRes());\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+\r
+ sg.cs = ccs;\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+\r
+ if ( viewport.getAbovePIDThreshold())\r
+ {\r
+ int threshold = 0;\r
+ threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
+ Desktop.hideConservationSlider();\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+ else if (cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) cs).setThreshold(threshold);\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+\r
+ }\r
+ else\r
+ if (cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) cs).setThreshold(0);\r
+ else if (cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) cs).setThreshold(0);\r
+\r
+\r