catchallcommand.h

   1 #ifndef CATCHALLCOMMAND_H
   2 #define CATCHALLCOMMAND_H
   3
   4 /*
   5  *  catchallcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 5/11/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "readotu.h"
  16 #include "sabundvector.hpp"
  17
  18 /*
  19  citation goes here
  20  */
  21
  22 /****************************************************************************/
  23
  24 class CatchAllCommand : public Command {
  25
  26 public:
  27
  28         CatchAllCommand(string);
  29         ~CatchAllCommand() {};
  30         int execute();
  31         void help();
  32
  33 private:
  34
  35         GlobalData* globaldata;
  36         ReadOTUFile* read;
  37         InputData* input;
  38
  39         string outputDir, sabundfile, rabundfile, listfile, format;
  40         bool abort, allLines;
  41         set<string> labels;
  42
  43         string process(SAbundVector*);
  44 };
  45
  46 /****************************************************************************/
  47
  48 #endif
  49
  50