{\r
StringTokenizer st = new StringTokenizer(paramValue, ";");\r
StringTokenizer st2;\r
- String token=null, colour, residues, residue;\r
+ String token=null, colour, residues;\r
try{\r
while (st.hasMoreElements())\r
{\r
while (st2.hasMoreTokens())\r
{\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
+ //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+\r
if(token.equalsIgnoreCase("lowerCase"))\r
{\r
if (lowerCaseColours == null)\r
continue;\r
}\r
\r
- int colIndex =\r
- ( (Integer) ResidueProperties.aaHash.\r
- get(token)).intValue();\r
-\r
if(token.equals(token.toLowerCase()))\r
{\r
if(lowerCaseColours==null)\r
\r
public Color findColour(String s, int j)\r
{\r
- int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();\r
+ int index = ResidueProperties.aaIndex[s.charAt(0)];\r
\r
if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
{\r
+ //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')\r
currentColour = lowerCaseColours[index];\r
else\r