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         ignoreGaps() {}
  24
  25         void calcDist(Sequence A, Sequence B){
  26                 int diff = 0;
  27                 int length = 0;
  28                 int start = 0;
  29                 bool overlap = false;
  30
  31                 string seqA = A.getAligned();
  32                 string seqB = B.getAligned();
  33                 int alignLength = seqA.length();
  34
  35                 for(int i=0;i<alignLength;i++){
  36                         if(seqA[i] != '.' && seqB[i] != '.'){
  37                                 start = i;
  38                                 overlap = true;
  39                                 break;
  40                         }
  41                 }
  42
  43                 for(int i=start; i<alignLength; i++){
  44                         if(seqA[i] == '.' || seqB[i] == '.'){
  45                                 break;
  46                         }
  47                         else if((seqA[i] != '-' && seqB[i] != '-')){
  48                                 if(seqA[i] != seqB[i]){
  49                                         diff++;
  50                                 }
  51                                 length++;
  52                         }
  53                 }
  54
  55                 //non-overlapping sequences
  56                 if (!overlap) { length = 0; }
  57
  58                 if(length == 0)         {       dist = 1.0000;                                                          }
  59                 else                            {       dist = ((double)diff  / (double)length);        }
  60
  61         }
  62
  63 };
  64
  65 /**************************************************************************************************/
  66 #endif
  67