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
  21         oneGapDist() {}
  22
  23         void calcDist(Sequence A, Sequence B){
  24
  25                 int difference = 0;
  26                 int minLength = 0;
  27                 int openGapA = 0;
  28                 int openGapB = 0;
  29                 int start = 0;
  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                                 break;
  39                         }
  40                 }
  41
  42                 for(int i=start;i<alignLength;i++){
  43                         if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '.' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.')){     ;       }
  44                         else if(seqA[i] == '.' && seqB[i] == '.'){
  45                                 break;
  46                         }
  47                         else if(seqB[i] != '-' && (seqA[i] == '-' || seqA[i] == '.')){
  48                                 if(openGapA == 0){
  49                                         difference++;
  50                                         minLength++;
  51                                         openGapA = 1;
  52                                         openGapB = 0;
  53                                 }
  54                         }
  55                         else if(seqA[i] != '-' && (seqB[i] == '-' || seqB[i] == '.')){
  56                                 if(openGapB == 0){
  57                                         difference++;
  58                                         minLength++;
  59                                         openGapA = 0;
  60                                         openGapB = 1;
  61                                 }
  62                         }
  63                         else if(seqA[i] != '-' && seqB[i] != '-'){
  64                                 if(seqA[i] != seqB[i]){
  65                                         difference++;
  66                                         minLength++;
  67                                         openGapA = 0;
  68                                         openGapB = 0;
  69                                 }
  70                                 else{
  71                                         minLength++;
  72                                         openGapA = 0;
  73                                         openGapB = 0;
  74                                 }
  75                         }
  76                 }
  77
  78                 if(minLength == 0)      {       dist = 1.0000;                                                  }
  79                 else                            {       dist = (double)difference / minLength;  }
  80         }
  81
  82 };
  83
  84 /**************************************************************************************************/
  85
  86 #endif