*
*/
+
#include "dist.h"
/**************************************************************************************************/
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] != '.'){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
start = i;
+ cout << "start: " << start << endl;
break;
}
}
for(int i=alignLength-1;i>=0;i--){
- if(seqA[i] != '.' && seqB[i] != '.'){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
end = i;
+ cout << "end: " << end << endl;
break;
}
}