eachgapdist.h

   1 #ifndef EACHGAPDIST_H
   2 #define EACHGAPDIST_H
   3 /*
   4  *  eachgapdist.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 eachGapDist : public Dist {
  18
  19 public:
  20
  21         eachGapDist() {}
  22
  23         void calcDist(Sequence A, Sequence B){
  24                 int diff = 0;
  25                 int length = 0;
  26                 int start = 0;
  27
  28                 string seqA = A.getAligned();
  29                 string seqB = B.getAligned();
  30
  31                 int alignLength = seqA.length();
  32
  33                 for(int i=0; i<alignLength; i++){
  34                         if(seqA[i] != '.' || seqB[i] != '.'){
  35                                 start = i;
  36                                 break;
  37                         }
  38                 }
  39
  40                 for(int i=start;i<alignLength;i++){
  41                         if(seqA[i] == '.' && seqB[i] == '.'){
  42                                 break;
  43                         }
  44                         else if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-')){;}
  45                         else{
  46                                 if(seqA[i] != seqB[i]){
  47                                         diff++;
  48                                 }
  49                                 length++;
  50                         }
  51                 }
  52
  53                 if(length == 0) {       dist = 1.0000;                                                          }
  54                 else                    {       dist = ((double)diff  / (double)length);        }
  55         }
  56 };
  57
  58 /**************************************************************************************************/
  59
  60 #endif