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                 int end = 0;
  26
  27                 string seqA = A.getAligned();
  28                 string seqB = B.getAligned();
  29                 int alignLength = seqA.length();
  30
  31                 for(int i=0;i<alignLength;i++){
  32                         if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
  33                                 start = i;
  34                                 cout << "start: " << start << endl;
  35                                 break;
  36                         }
  37                 }
  38                 for(int i=alignLength-1;i>=0;i--){
  39                         if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
  40                                 end = i;
  41                                 cout << "end: " << end << endl;
  42                                 break;
  43                         }
  44                 }
  45
  46                 for(int i=start;i<=end;i++){
  47                         if(seqA[i] == '.' || seqB[i] == '.'){
  48                                 break;
  49                         }
  50                         else if(seqA[i] != '-' || seqB[i] != '-'){
  51                                 if(seqA[i] != seqB[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
  67 #endif
  68
  69