eachgapignore.h

   1 #ifndef EACHGAPIGNORE_H
   2 #define EACHGAPIGNORE_H
   3 /*
   4  *  eachgapignore.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 5/7/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12
  13 #include "dist.h"
  14
  15 /**************************************************************************************************/
  16
  17 class eachGapIgnoreTermGapDist : public Dist {
  18
  19 public:
  20
  21         void calcDist(Sequence A, Sequence B){
  22                 int diff = 0;
  23                 int length = 0;
  24                 int start = 0;
  25                 int end = 0;
  26                 bool overlap = false;
  27
  28                 string seqA = A.getAligned();
  29                 string seqB = B.getAligned();
  30                 int alignLength = seqA.length();
  31
  32                 for(int i=0;i<alignLength;i++){
  33                         if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
  34                                 start = i;
  35 //                              cout << "start: " << start << endl;
  36                                 overlap = true;
  37                                 break;
  38                         }
  39                 }
  40                 for(int i=alignLength-1;i>=0;i--){
  41                         if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
  42                                 end = i;
  43 //                              cout << "end: " << end << endl;
  44                                 overlap = true;
  45                                 break;
  46                         }
  47                 }
  48
  49                 for(int i=start;i<=end;i++){
  50                         if(seqA[i] == '.' || seqB[i] == '.'){
  51                                 break;
  52                         }
  53                         else if(seqA[i] != '-' || seqB[i] != '-'){
  54                                 if(seqA[i] != seqB[i]){
  55                                         diff++;
  56                                 }
  57                                 length++;
  58                         }
  59                 }
  60
  61                 //non-overlapping sequences
  62                 if (!overlap) { length = 0; }
  63
  64                 if(length == 0) {       dist = 1.0000;                                                          }
  65                 else                    {       dist = ((double)diff  / (double)length);        }
  66
  67         }
  68
  69 };
  70
  71 /**************************************************************************************************/
  72
  73 #endif
  74
  75