+ allGroups = av.alignment.findAllGroups(seq);\r
+\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
+ }\r