ignoregaps.h

   1 #ifndef IGNOREGAPS_H
   2 #define IGNOREGAPS_H
   3 /*
   4  *  ignoregaps.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 //      this class calculates distances by ignoring all gap characters.  so if seq a has an "A" and seq
  17 //      b has a '-', there is no penalty
  18
  19 class ignoreGaps : public Dist {
  20
  21 public:
  22
  23         void calcDist(Sequence A, Sequence B){
  24                 int diff = 0;
  25                 int length = 0;
  26                 int start = 0;
  27                 int end = 0;
  28
  29                 for(int i=0;i<A.getLength();i++){
  30                         if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
  31                         }
  32                         else{
  33                                 start = i;
  34                                 break;
  35                         }
  36                 }
  37                 for(int i=A.getLength()-1;i>=0;i--){
  38                         if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
  39                         }
  40                         else{
  41                                 end = i;
  42                                 break;
  43                         }
  44                 }
  45
  46                 for(int i=start; i<=end; i++){
  47                         if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.'){
  48                                 break;
  49                         }
  50                         else if((A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-')){
  51                                 if(A.getUnaligned()[i] != B.getUnaligned()[i]){
  52                                         diff++;
  53                                 }
  54                                 length++;
  55                         }
  56                 }
  57
  58                 if(length == 0)         {       dist = 1.0000;                                                          }
  59                 else                            {       dist = ((double)diff  / (double)length);        }
  60
  61         }
  62
  63 };
  64
  65 /**************************************************************************************************/
  66 #endif
  67