- // int threshold = 80;\r
-\r
- while (i <= end && i < length) {\r
- Color c = getResidueBoxColour(cs,seq,i);\r
+ Color tempColour = null;\r
+ while (i <= end && i < length)\r
+ {\r
+ if(inCurrentSequenceGroup(i))\r
+ {\r
+ if( currentSequenceGroup.getDisplayBoxes())\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
+ else if(av.getShowBoxes())\r
+ getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+ else\r
+ resBoxColour = Color.white;\r