class oneGapDist : public Dist {
public:
+
+ oneGapDist() {}
+
void calcDist(Sequence A, Sequence B){
int difference = 0;
for(int i=start;i<alignLength;i++){
if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '.' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.')){ ; }
+ else if(seqA[i] == '.' && seqB[i] == '.'){
+ break;
+ }
else if(seqB[i] != '-' && (seqA[i] == '-' || seqA[i] == '.')){
if(openGapA == 0){
difference++;
openGapB = 0;
}
}
-
- else if(seqA[i] == '.' && seqB[i] == '.'){
- break;
- }
}
if(minLength == 0) { dist = 1.0000; }