7 * Created by Sarah Westcott on 5/7/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 /**************************************************************************************************/
16 class eachGapDist : public Dist {
19 void calcDist(Sequence A, Sequence B){
24 for(int i=0; i<A.getLength(); i++){
25 if(A.getUnaligned()[i] != '.' || B.getUnaligned()[i] != '.'){
31 for(int i=start;i<A.getLength();i++){
32 if((A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-') && (A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.')){}
33 else if(A.getUnaligned()[i] == '.' && B.getUnaligned()[i] == '.'){
36 else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-'){
37 if(A.getUnaligned()[i] != B.getUnaligned()[i]){
42 else if(A.getUnaligned()[i] != '-' || B.getUnaligned()[i] != '-'){
48 if(length == 0) { dist = 1.0000; }
49 else { dist = ((double)diff / (double)length); }
54 /**************************************************************************************************/