- if (s.equals(max))\r
- return new Color(154, 154, 255);\r
- else if (ResidueProperties.getBLOSUM62(max, s) > 0)\r
+ if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
+ {\r
+ String max = (String)hash.get("maxResidue");\r
+\r
+ if (max.indexOf(s)>-1)\r
+ return new Color(154, 154, 255);\r
+ else {\r
+\r
+ int c = 0,\r
+ max_aa=0,\r
+ n=max.length();\r
+ do {\r
+ c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);\r
+ } while (++max_aa<n);\r
+\r
+ if (c>0)\r