eachgapdistignorens.h

   1 #ifndef EACHGAPDISTIGNORENS_H
   2 #define EACHGAPDISTIGNORENS_H
   3
   4 /*
   5  *  eachgapdistignorens.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 4/20/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "dist.h"
  15
  16 /**************************************************************************************************/
  17
  18 class eachGapDistIgnoreNs : public Dist {
  19
  20 public:
  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
  29                 int alignLength = seqA.length();
  30
  31                 for(int i=0; i<alignLength; i++){
  32                         if(seqA[i] != '.' || seqB[i] != '.'){
  33                                 start = i;
  34                                 break;
  35                         }
  36                 }
  37
  38                 for(int i=start;i<alignLength;i++){
  39                         if(seqA[i] == '.' && seqB[i] == '.'){
  40                                 break;
  41                         }
  42                         else if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-') || seqA[i] == 'N' || seqB[i] == 'N'){;}
  43                         else{
  44                                 if(seqA[i] != seqB[i]){
  45                                         diff++;
  46                                 }
  47                                 length++;
  48                         }
  49                 }
  50
  51                 if(length == 0) {       dist = 1.0000;                                                          }
  52                 else                    {       dist = ((double)diff  / (double)length);        }
  53         }
  54 };
  55
  56 /**************************************************************************************************/
  57
  58 #endif