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