aligncommand.h

   1 #ifndef ALIGNCOMMAND_H
   2 #define ALIGNCOMMAND_H
   3
   4 /*
   5  *  aligncommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 5/15/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "globaldata.hpp"
  15
  16 class AlignCommand : public Command {
  17
  18         public:
  19                 AlignCommand();
  20                 ~AlignCommand();
  21                 int execute();
  22
  23         private:
  24                 GlobalData* globaldata;
  25                 string candidateFileName, templateFileName, distanceFileName;
  26                 int kmerSize;
  27                 float match, misMatch, gapOpen, gapExtend;
  28                 ofstream out;
  29                 ifstream in;
  30
  31 };
  32
  33
  34
  35 #endif