chimerarealigner.h

   1 #ifndef CHIMERAREALIGNER_H
   2 #define CHIMERAREALIGNER_H
   3
   4 /*
   5  *  chimerarealigner.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 2/12/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "chimera.h"
  14 #include "alignment.hpp"
  15
  16 /***********************************************************/
  17
  18 class ChimeraReAligner  {
  19
  20         public:
  21                 ChimeraReAligner(vector<Sequence*>, int, int);
  22                 ~ChimeraReAligner();
  23
  24                 void reAlign(Sequence*, vector<results>);
  25
  26         private:
  27                 Sequence* querySeq;
  28                 Alignment* alignment;
  29                 vector<Sequence*> templateSeqs;
  30                 int match, misMatch;
  31
  32                 Sequence* getSequence(string);  //find sequence from name
  33 };
  34 /***********************************************************/
  35
  36 #endif
  37