*
*/
+
#include "dist.h"
/**************************************************************************************************/
int start = 0;
int end = 0;
- for(int i=0;i<A.getLength();i++){
- if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
- }
- else{
+ 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] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
start = i;
+ cout << "start: " << start << endl;
break;
}
}
- for(int i=A.getLength()-1;i>=0;i--){
- if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
- }
- else{
+ for(int i=alignLength-1;i>=0;i--){
+ if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
end = i;
+ cout << "end: " << end << endl;
break;
}
}
-
for(int i=start;i<=end;i++){
- if(A.getAligned()[i] == '-' && B.getAligned()[i] == '-'){}
- else if(A.getAligned()[i] == '-' && B.getAligned()[i] != '-'){
+ if(seqA[i] == '-' && seqB[i] == '-'){ ; }
+ else if(seqB[i] != '-' && seqA[i] == '-'){
if(openGapA == 0){
difference++;
minLength++;
openGapB = 0;
}
}
- else if(A.getAligned()[i] != '-' && B.getAligned()[i] == '-'){
+ else if(seqA[i] != '-' && seqB[i] == '-'){
if(openGapB == 0){
difference++;
minLength++;
openGapB = 1;
}
}
- else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
- if(A.getAligned()[i] != B.getAligned()[i]){
+ else if(seqA[i] != '-' && seqB[i] != '-'){
+ if(seqA[i] != seqB[i]){
difference++;
- minLength++;
- openGapA = 0;
- openGapB = 0;
- }
- else{
- minLength++;
- openGapA = 0;
- openGapB = 0;
}
+ minLength++;
+ openGapA = 0;
+ openGapB = 0;
}
}
+
if(minLength == 0) { dist = 1.0000; }
else { dist = (double)difference / minLength; }
}