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