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                 for(int i=0; i<A.getLength(); i++){
  25                         if(A.getAligned()[i] != '.' || B.getAligned()[i] != '.'){
  26                                 start = i;
  27                                 break;
  28                         }
  29                 }
  30
  31                 for(int i=start;i<A.getLength();i++){
  32                         if((A.getAligned()[i] == '-' || B.getAligned()[i] == '-') && (A.getAligned()[i] == '.' || B.getAligned()[i] == '.')){}
  33                         else if(A.getAligned()[i] == '.' && B.getAligned()[i] == '.'){
  34                                 break;
  35                         }
  36                         else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
  37                                 if(A.getAligned()[i] != B.getAligned()[i]){
  38                                         diff++;
  39                                 }
  40                                 length++;
  41                         }
  42                         else if(A.getAligned()[i] != '-' || B.getAligned()[i] != '-'){
  43                                 diff++;
  44                                 length++;
  45                         }
  46                 }
  47
  48                 if(length == 0) {       dist = 1.0000;                                                          }
  49                 else                    {       dist = ((double)diff  / (double)length);        }
  50
  51         }
  52 };
  53
  54 /**************************************************************************************************/
  55
  56 #endif