1 #ifndef EACHGAPIGNORE_H
2 #define EACHGAPIGNORE_H
7 * Created by Sarah Westcott on 5/7/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
15 /**************************************************************************************************/
17 class eachGapIgnoreTermGapDist : public Dist {
21 void calcDist(Sequence A, Sequence B){
27 for(int i=0;i<A.getLength();i++){
28 if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
35 for(int i=A.getLength()-1;i>=0;i--){
36 if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
44 for(int i=start;i<=end;i++){
45 if(A.getUnaligned()[i] == '-' && B.getUnaligned()[i] == '-'){}
46 else if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.'){
49 else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-'){
50 if(A.getUnaligned()[i] != B.getUnaligned()[i]){
55 else if(A.getUnaligned()[i] != '-' || B.getUnaligned()[i] != '-'){
61 if(length == 0) { dist = 1.0000; }
62 else { dist = ((double)diff / (double)length); }
68 /**************************************************************************************************/