- AlignSeq as = new AlignSeq((SequenceI) selsubset.elementAt(i),\r
- (SequenceI) selsubset.elementAt(j), "pep");\r
+ AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],\r
+ seqs[j], seqStrings[j], "pep");\r
+\r
+ if(as.s1str.length()==0 || as.s2str.length()==0)\r
+ {\r
+ continue;\r
+ }\r
+\r