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 {
20 eachGapIgnoreTermGapDist() {}
21 eachGapIgnoreTermGapDist(const eachGapIgnoreTermGapDist& ddb) {}
23 void calcDist(Sequence A, Sequence B){
30 string seqA = A.getAligned();
31 string seqB = B.getAligned();
32 int alignLength = seqA.length();
34 for(int i=0;i<alignLength;i++){
35 if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
37 // cout << "start: " << start << endl;
42 for(int i=alignLength-1;i>=0;i--){
43 if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
45 // cout << "end: " << end << endl;
51 for(int i=start;i<=end;i++){
52 if(seqA[i] == '.' || seqB[i] == '.'){
55 else if(seqA[i] != '-' || seqB[i] != '-'){
56 if(seqA[i] != seqB[i]){
63 //non-overlapping sequences
64 if (!overlap) { length = 0; }
66 if(length == 0) { dist = 1.0000; }
67 else { dist = ((double)diff / (double)length); }
73 /**************************************************************************************************/