int diff = 0;
int length = 0;
int start = 0;
+ int end = 0;
+ bool overlap = false;
string seqA = A.getAligned();
string seqB = B.getAligned();
int alignLength = seqA.length();
- for(int i=0; i<alignLength; i++){
- if(seqA[i] != '.' && seqB[i] != '.'){
+ 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=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<alignLength;i++){
+ for(int i=start;i<=end;i++){
if(seqA[i] == '.' || seqB[i] == '.'){
break;
}
}
}
+ //non-overlapping sequences
+ if (!overlap) { length = 0; }
+
if(length == 0) { dist = 1.0000; }
else { dist = ((double)diff / (double)length); }