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                 for(int i=0;i<A.getLength();i++){
  28                         if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
  29                         }
  30                         else{
  31                                 start = i;
  32                                 break;
  33                         }
  34                 }
  35                 for(int i=A.getLength()-1;i>=0;i--){
  36                         if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
  37                         }
  38                         else{
  39                                 end = i;
  40                                 break;
  41                         }
  42                 }
  43
  44                 for(int i=start;i<=end;i++){
  45                         if(A.getAligned()[i] == '-' && B.getAligned()[i] == '-'){}
  46                         else if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
  47                                 break;
  48                         }
  49                         else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
  50                                 if(A.getAligned()[i] != B.getAligned()[i]){
  51                                         diff++;
  52                                 }
  53                                 length++;
  54                         }
  55                         else if(A.getAligned()[i] != '-' || B.getAligned()[i] != '-'){
  56                                 diff++;
  57                                 length++;
  58                         }
  59                 }
  60
  61                 if(length == 0) {       dist = 1.0000;                                                          }
  62                 else                    {       dist = ((double)diff  / (double)length);        }
  63
  64         }
  65
  66 };
  67
  68 /**************************************************************************************************/
  69
  70 #endif
  71
  72