- for(int i=0;i<A.getLength();i++){
- if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
- }
- else{
+ string seqA = A.getAligned();
+ string seqB = B.getAligned();
+ int alignLength = seqA.length();
+
+ // this assumes that sequences start and end with '.'s instead of'-'s.
+ for(int i=0;i<alignLength;i++){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){