int length = 0;
int start = 0;
- for(int i=0; i<A.getLength(); i++){
- if(A.getUnaligned()[i] != '.' || B.getUnaligned()[i] != '.'){
+ string seqA = A.getAligned();
+ string seqB = B.getAligned();
+ int alignLength = seqA.length();
+
+ for(int i=0; i<alignLength; i++){
+ if(seqA[i] != '.' || seqB[i] != '.'){
start = i;
break;
}
}
-
- for(int i=start;i<A.getLength();i++){
- if((A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-') && (A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.')){}
- else if(A.getUnaligned()[i] == '.' && B.getUnaligned()[i] == '.'){
+
+ for(int i=start;i<alignLength;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] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-')){;}
+ else{
+ if(seqA[i] != seqB[i]){
diff++;
}
length++;
}
- else if(A.getUnaligned()[i] != '-' || B.getUnaligned()[i] != '-'){
- diff++;
- length++;
- }
}
if(length == 0) { dist = 1.0000; }
/**************************************************************************************************/
-#endif
\ No newline at end of file
+#endif