readlistcommand.h

   1 /*
   2  *  readlistcommand.h
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/20/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #ifndef READLISTFILECOMMAND_H
  11 #define READLISTFILECOMMAND_H
  12 /*
  13  *  readlistcommand.h
  14  *  Mothur
  15  *
  16  *  Created by Sarah Westcott on 1/20/09.
  17  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  18  *
  19  */
  20
  21 #include <Carbon/Carbon.h>
  22 #include <iostream>
  23 #include <fstream>
  24 #include "command.hpp"
  25 #include "readmatrix.hpp"
  26 #include "inputdata.h"
  27 #include "groupmap.h"
  28 #include "sharedcommand.h"
  29 #include "parselistcommand.h"
  30
  31
  32 /* The read.list command parameter options are listfile and groupfile.
  33 The read.list command should be in the following format:
  34 read.shared(listfile=yourListFile, groupfile=yourGroupFile).
  35 The listfile parameter and groupfile paramaters are required. */
  36
  37
  38 class GlobalData;
  39
  40 class ReadListFileCommand : public Command {
  41 public:
  42         ReadListFileCommand();
  43         ~ReadListFileCommand();
  44         int execute();
  45
  46 private:
  47         GlobalData* globaldata;
  48         Command* shared;
  49         Command* parselist;
  50         GroupMap* groupMap;
  51         ReadMatrix* read;
  52         InputData* input;
  53         string filename;
  54 };
  55
  56 #endif