\r
int start, end;\r
\r
- if ( (sg != null) && (sg.getSize(false) >= 1))\r
+ if ( (sg != null) && (sg.getSize() >= 1))\r
{\r
originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
start = sg.getStartRes();\r
\r
if(omitHidden==null)\r
{\r
- seqi = originalSequences[i].getSequence(start, end);\r
- seqj = originalSequences[j].getSequence(start, end);\r
+ seqi = originalSequences[i].getSequenceAsString(start, end);\r
+ seqj = originalSequences[j].getSequenceAsString(start, end);\r
}\r
else\r
{\r