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         oneGapDist(const oneGapDist& ddb) {}
  23
  24         void calcDist(Sequence A, Sequence B){
  25
  26                 int difference = 0;
  27                 int minLength = 0;
  28                 int openGapA = 0;
  29                 int openGapB = 0;
  30                 int start = 0;
  31
  32                 string seqA = A.getAligned();
  33                 string seqB = B.getAligned();
  34                 int alignLength = seqA.length();
  35
  36                 for(int i=0;i<alignLength;i++){
  37                         if((seqA[i] != '.' || seqB[i] != '.')){
  38                                 start = i;
  39                                 break;
  40                         }
  41                 }
  42
  43                 for(int i=start;i<alignLength;i++){
  44                         if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '.' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.')){     ;       }
  45                         else if(seqA[i] == '.' && seqB[i] == '.'){
  46                                 break;
  47                         }
  48                         else if(seqB[i] != '-' && (seqA[i] == '-' || seqA[i] == '.')){
  49                                 if(openGapA == 0){
  50                                         difference++;
  51                                         minLength++;
  52                                         openGapA = 1;
  53                                         openGapB = 0;
  54                                 }
  55                         }
  56                         else if(seqA[i] != '-' && (seqB[i] == '-' || seqB[i] == '.')){
  57                                 if(openGapB == 0){
  58                                         difference++;
  59                                         minLength++;
  60                                         openGapA = 0;
  61                                         openGapB = 1;
  62                                 }
  63                         }
  64                         else if(seqA[i] != '-' && seqB[i] != '-'){
  65                                 if(seqA[i] != seqB[i]){
  66                                         difference++;
  67                                         minLength++;
  68                                         openGapA = 0;
  69                                         openGapB = 0;
  70                                 }
  71                                 else{
  72                                         minLength++;
  73                                         openGapA = 0;
  74                                         openGapB = 0;
  75                                 }
  76                         }
  77                 }
  78
  79                 if(minLength == 0)      {       dist = 1.0000;                                                  }
  80                 else                            {       dist = (double)difference / minLength;  }
  81         }
  82
  83 };
  84
  85 /**************************************************************************************************/
  86
  87 #endif