onegapdist.h

   1 #ifndef ONEGAPDIST_H
   2 #define ONEGAPDIST_H
   3 /*
   4  *  onegapdist.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
  17 class oneGapDist : public Dist {
  18
  19 public:
  20         void calcDist(Sequence A, Sequence B){
  21
  22                 int difference = 0;
  23                 int minLength = 0;
  24                 int openGapA = 0;
  25                 int openGapB = 0;
  26                 int start = 0;
  27
  28                 string seqA = A.getAligned();
  29                 string seqB = B.getAligned();
  30                 int alignLength = seqA.length();
  31
  32                 for(int i=0;i<alignLength;i++){
  33                         if((seqA[i] != '.' || seqB[i] != '.')){
  34                                 start = i;
  35                                 break;
  36                         }
  37                 }
  38
  39                 for(int i=start;i<alignLength;i++){
  40                         if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '.' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.')){     ;       }
  41                         else if(seqA[i] == '.' && seqB[i] == '.'){
  42                                 break;
  43                         }
  44                         else if(seqB[i] != '-' && (seqA[i] == '-' || seqA[i] == '.')){
  45                                 if(openGapA == 0){
  46                                         difference++;
  47                                         minLength++;
  48                                         openGapA = 1;
  49                                         openGapB = 0;
  50                                 }
  51                         }
  52                         else if(seqA[i] != '-' && (seqB[i] == '-' || seqB[i] == '.')){
  53                                 if(openGapB == 0){
  54                                         difference++;
  55                                         minLength++;
  56                                         openGapA = 0;
  57                                         openGapB = 1;
  58                                 }
  59                         }
  60                         else if(seqA[i] != '-' && seqB[i] != '-'){
  61                                 if(seqA[i] != seqB[i]){
  62                                         difference++;
  63                                         minLength++;
  64                                         openGapA = 0;
  65                                         openGapB = 0;
  66                                 }
  67                                 else{
  68                                         minLength++;
  69                                         openGapA = 0;
  70                                         openGapB = 0;
  71                                 }
  72                         }
  73                 }
  74
  75                 if(minLength == 0)      {       dist = 1.0000;                                                  }
  76                 else                            {       dist = (double)difference / minLength;  }
  77         }
  78
  79 };
  80
  81 /**************************************************************************************************/
  82
  83 #endif