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 #include "dist.h"
  13
  14 /**************************************************************************************************/
  15
  16 class eachGapDist : public Dist {
  17
  18 public:
  19         void calcDist(Sequence A, Sequence B){
  20                 int diff = 0;
  21                 int length = 0;
  22                 int start = 0;
  23
  24                 string seqA = A.getAligned();
  25                 string seqB = B.getAligned();
  26
  27                 int alignLength = seqA.length();
  28
  29                 for(int i=0; i<alignLength; i++){
  30                         if(seqA[i] != '.' || seqB[i] != '.'){
  31                                 start = i;
  32                                 break;
  33                         }
  34                 }
  35
  36                 for(int i=start;i<alignLength;i++){
  37                         if(seqA[i] == '.' && seqB[i] == '.'){
  38                                 break;
  39                         }
  40                         else if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-')){;}
  41                         else{
  42                                 if(seqA[i] != seqB[i]){
  43                                         diff++;
  44                                 }
  45                                 length++;
  46                         }
  47                 }
  48
  49                 if(length == 0) {       dist = 1.0000;                                                          }
  50                 else                    {       dist = ((double)diff  / (double)length);        }
  51
  52
  53         }
  54 };
  55
  56 /**************************************************************************************************/
  57
  58 #endif