binsequencecommand.h

   1 #ifndef BINSEQCOMMAND_H
   2 #define BINSEQCOMMAND_H
   3 /*
   4  *  binsequencecommand.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 4/3/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "listvector.hpp"
  16 #include "readmatrix.hpp"
  17 #include "fastamap.h"
  18
  19
  20 class GlobalData;
  21
  22 class BinSeqCommand : public Command {
  23
  24 public:
  25         BinSeqCommand();
  26         ~BinSeqCommand();
  27         int execute();
  28
  29 private:
  30         GlobalData* globaldata;
  31         ListVector* list;
  32         ReadMatrix* read;
  33         InputData* input;
  34         FastaMap* fasta;
  35         string filename, fastafile, namesfile;
  36         ofstream out;
  37         ifstream in, inNames;
  38
  39         void readNamesFile();
  40 };
  41
  42 #endif