int length = 0;
int start = 0;
int end = 0;
+ bool overlap = false;
- 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();
+
+ for(int i=0;i<alignLength;i++){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
start = i;
+// cout << "start: " << start << endl;
+ overlap = true;
break;
}
}
- for(int i=A.getLength()-1;i>=0;i--){
- if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
- }
- else{
+ for(int i=alignLength-1;i>=0;i--){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
end = i;
+// cout << "end: " << end << endl;
+ overlap = true;
break;
}
}
for(int i=start;i<=end;i++){
- if(A.getUnaligned()[i] == '-' && B.getUnaligned()[i] == '-'){}
- else if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.'){
+ if(seqA[i] == '.' || seqB[i] == '.'){
break;
}
- else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-'){
- if(A.getUnaligned()[i] != B.getUnaligned()[i]){
+ else if(seqA[i] != '-' || seqB[i] != '-'){
+ if(seqA[i] != seqB[i]){
diff++;
}
length++;
}
- else if(A.getUnaligned()[i] != '-' || B.getUnaligned()[i] != '-'){
- diff++;
- length++;
- }
}
+ //non-overlapping sequences
+ if (!overlap) { length = 0; }
+
if(length == 0) { dist = 1.0000; }
else { dist = ((double)diff / (double)length); }