onegapignore.h

   1 #ifndef ONEIGNOREGAPS_H
   2 #define ONEIGNOREGAPS_H
   3 /*
   4  *  onegapignore.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 class oneGapIgnoreTermGapDist : public Dist {
  17
  18 public:
  19         void calcDist(Sequence A, Sequence B){
  20
  21                 int difference = 0;
  22                 int openGapA = 0;
  23                 int openGapB = 0;
  24                 int minLength = 0;
  25                 int start = 0;
  26                 int end = 0;
  27
  28                 string seqA = A.getAligned();
  29                 string seqB = B.getAligned();
  30                 int alignLength = seqA.length();
  31
  32                 // this assumes that sequences start and end with '.'s instead of'-'s.
  33                 for(int i=0;i<alignLength;i++){
  34                         if(seqA[i] != '.' && seqB[i] != '.'){
  35                                 start = i;
  36                                 break;
  37                         }
  38                 }
  39                 for(int i=alignLength-1;i>=0;i--){
  40                         if(seqA[i] != '.' && seqB[i] != '.'){
  41                                 end = i;
  42                                 break;
  43                         }
  44                 }
  45
  46                 for(int i=start;i<=end;i++){
  47                         if(seqA[i] == '-' && seqB[i] == '-'){   ;       }
  48                         else if(seqB[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] == '-'){
  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                                 }
  68                                 minLength++;
  69                                 openGapA = 0;
  70                                 openGapB = 0;
  71                         }
  72                 }
  73
  74                 if(minLength == 0)      {       dist = 1.0000;                                                  }
  75                 else                            {       dist = (double)difference / minLength;  }
  76         }
  77
  78 };
  79
  80 /**************************************************************************************************/
  81
  82 #endif
  83