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
  26                 string seqA = A.getAligned();
  27                 string seqB = B.getAligned();
  28                 int alignLength = seqA.length();
  29
  30                 for(int i=0; i<alignLength; i++){
  31                         if(seqA[i] != '.' && seqB[i] != '.'){
  32                                 start = i;
  33                                 break;
  34                         }
  35                 }
  36
  37                 for(int i=start;i<alignLength;i++){
  38                         if(seqA[i] == '.' || seqB[i] == '.'){
  39                                 break;
  40                         }
  41                         else if(seqA[i] != '-' || seqB[i] != '-'){
  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
  59
  60