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         eachGapIgnoreTermGapDist() {}
  21         eachGapIgnoreTermGapDist(const eachGapIgnoreTermGapDist& ddb) {}
  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                 bool overlap = false;
  29
  30                 string seqA = A.getAligned();
  31                 string seqB = B.getAligned();
  32                 int alignLength = seqA.length();
  33
  34                 for(int i=0;i<alignLength;i++){
  35                         if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
  36                                 start = i;
  37 //                              cout << "start: " << start << endl;
  38                                 overlap = true;
  39                                 break;
  40                         }
  41                 }
  42                 for(int i=alignLength-1;i>=0;i--){
  43                         if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
  44                                 end = i;
  45 //                              cout << "end: " << end << endl;
  46                                 overlap = true;
  47                                 break;
  48                         }
  49                 }
  50
  51                 for(int i=start;i<=end;i++){
  52                         if(seqA[i] == '.' || seqB[i] == '.'){
  53                                 break;
  54                         }
  55                         else if(seqA[i] != '-' || seqB[i] != '-'){
  56                                 if(seqA[i] != seqB[i]){
  57                                         diff++;
  58                                 }
  59                                 length++;
  60                         }
  61                 }
  62
  63                 //non-overlapping sequences
  64                 if (!overlap) { length = 0; }
  65
  66                 if(length == 0) {       dist = 1.0000;                                                          }
  67                 else                    {       dist = ((double)diff  / (double)length);        }
  68
  69         }
  70
  71 };
  72
  73 /**************************************************************************************************/
  74
  75 #endif
  76
  77