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
  13 #include "dist.h"
  14
  15 /**************************************************************************************************/
  16
  17 class oneGapIgnoreTermGapDist : 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                 int end = 0;
  28
  29                 string seqA = A.getAligned();
  30                 string seqB = B.getAligned();
  31                 int alignLength = seqA.length();
  32
  33                 // this assumes that sequences start and end with '.'s instead of'-'s.
  34                 for(int i=0;i<alignLength;i++){
  35                         if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
  36                                 start = i;
  37                                 cout << "start: " << start << endl;
  38                                 break;
  39                         }
  40                 }
  41                 for(int i=alignLength-1;i>=0;i--){
  42                         if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
  43                                 end = i;
  44                                 cout << "end: " << end << endl;
  45                                 break;
  46                         }
  47                 }
  48
  49                 for(int i=start;i<=end;i++){
  50                         if(seqA[i] == '-' && seqB[i] == '-'){   ;       }
  51                         else if(seqB[i] != '-' && seqA[i] == '-'){
  52                                 if(openGapA == 0){
  53                                         difference++;
  54                                         minLength++;
  55                                         openGapA = 1;
  56                                         openGapB = 0;
  57                                 }
  58                         }
  59                         else if(seqA[i] != '-' && seqB[i] == '-'){
  60                                 if(openGapB == 0){
  61                                         difference++;
  62                                         minLength++;
  63                                         openGapA = 0;
  64                                         openGapB = 1;
  65                                 }
  66                         }
  67                         else if(seqA[i] != '-' && seqB[i] != '-'){
  68                                 if(seqA[i] != seqB[i]){
  69                                         difference++;
  70                                 }
  71                                 minLength++;
  72                                 openGapA = 0;
  73                                 openGapB = 0;
  74                         }
  75                 }
  76
  77                 if(minLength == 0)      {       dist = 1.0000;                                                  }
  78                 else                            {       dist = (double)difference / minLength;  }
  79         }
  80
  81 };
  82
  83 /**************************************************************************************************/
  84
  85 #endif
  86