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                 for(int i=0;i<A.getLength();i++){
  29                         if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
  30                         }
  31                         else{
  32                                 start = i;
  33                                 break;
  34                         }
  35                 }
  36                 for(int i=A.getLength()-1;i>=0;i--){
  37                         if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
  38                         }
  39                         else{
  40                                 end = i;
  41                                 break;
  42                         }
  43                 }
  44
  45
  46                 for(int i=start;i<=end;i++){
  47                         if(A.getAligned()[i] == '-' && B.getAligned()[i] == '-'){}
  48                         else if(A.getAligned()[i] == '-' && B.getAligned()[i] != '-'){
  49                                 if(openGapA == 0){
  50                                         difference++;
  51                                         minLength++;
  52                                         openGapA = 1;
  53                                         openGapB = 0;
  54                                 }
  55                         }
  56                         else if(A.getAligned()[i] != '-' && B.getAligned()[i] == '-'){
  57                                 if(openGapB == 0){
  58                                         difference++;
  59                                         minLength++;
  60                                         openGapA = 0;
  61                                         openGapB = 1;
  62                                 }
  63                         }
  64                         else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
  65                                 if(A.getAligned()[i] != B.getAligned()[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                 if(minLength == 0)      {       dist = 1.0000;                                                  }
  79                 else                            {       dist = (double)difference / minLength;  }
  80         }
  81
  82 };
  83
  84 /**************************************************************************************************/
  85
  86 #endif
  87