- seqi = (SequenceI) sel.elementAt(i);\r
- seqj = (SequenceI) sel.elementAt(j);\r
-\r
- if (sg != null)\r
- pid = Comparison.PID( seqi,\r
- seqj,\r
- sg.getStartRes(), sg.getEndRes());\r
+ if(omitHidden==null)\r
+ {\r
+ seqi = originalSequences[i].getSequence(start, end);\r
+ seqj = originalSequences[j].getSequence(start, end);\r
+ }\r