*/\r
public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
{\r
- String si = ii.getSequence();\r
- String sj = jj.getSequence();\r
+ String si = ii.getSequenceAsString();\r
+ String sj = jj.getSequenceAsString();\r
\r
int ilen = si.length() - 1;\r
int jlen = sj.length() - 1;\r