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