- int colIndex =\r
- ( (Integer) ResidueProperties.aaHash.\r
- get(st2.nextToken())).intValue();\r
-\r
- colors[colIndex] = getColourFromString(colour);\r
+ token = st2.nextToken();\r
+\r
+ if (ResidueProperties.aaIndex[token.charAt(0)]==-1)\r
+ continue;\r
+\r
+ int colIndex = ResidueProperties.aaIndex[token.charAt(0)];\r
+\r
+ if(token.equalsIgnoreCase("lowerCase"))\r
+ {\r
+ if (lowerCaseColours == null)\r
+ lowerCaseColours = new Color[23];\r
+ for (int i = 0; i < 23; i++)\r
+ if (lowerCaseColours[i] == null)\r
+ lowerCaseColours[i] = getColourFromString(colour);\r
+\r
+ continue;\r
+ }\r
+\r
+ if(token.equals(token.toLowerCase()))\r
+ {\r
+ if(lowerCaseColours==null)\r
+ {\r
+ lowerCaseColours = new Color[23];\r
+ }\r
+ lowerCaseColours[colIndex] = getColourFromString(colour);\r
+ }\r
+ else\r
+ colors[colIndex] = getColourFromString(colour);\r