\r
for (j = 1; j <= len; j++)\r
{\r
- sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(\r
- sq.substring(j - 1, j)))).intValue(); // yuk\r
+ sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(String.valueOf(\r
+ sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash\r
}\r
\r
seqNums.setElementAt(sqnum, i);\r
\r
if (sequence.length() > i)\r
{\r
- res = sequence.substring(i, i + 1);\r
+ res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));\r
\r
if (residueHash.containsKey(res))\r
{\r
continue;\r
}\r
\r
- c = ((Sequence) sequences.elementAt(i)).getCharAt(j);\r
+ c = ((Sequence) sequences.elementAt(i)).getCharAt(j); // gaps do not have upper/lower case\r
\r
if (jalview.util.Comparison.isGap((c)))\r
{\r