getsabundcommand.h

   1 #ifndef GETSABUNDCOMMAND_H
   2 #define GETSABUNDCOMMAND_H
   3
   4 /*
   5  *  getsabundcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 6/2/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "inputdata.h"
  16 #include "readotu.h"
  17 #include "sabundvector.hpp"
  18
  19 class GlobalData;
  20
  21 class GetSAbundCommand : public Command {
  22 public:
  23         GetSAbundCommand(string);
  24         ~GetSAbundCommand();
  25         int execute();
  26         void help();
  27
  28 private:
  29         GlobalData* globaldata;
  30         string filename, format;
  31         ofstream out;
  32         ReadOTUFile* read;
  33         OrderVector* order;
  34         OrderVector* lastOrder;
  35         InputData* input;
  36         SAbundVector* sabund;
  37         OptionParser* parser;
  38         map<string, string> parameters;
  39         map<string, string>::iterator it;
  40         bool abort, allLines;
  41         set<int> lines; //hold lines to be used
  42         set<string> labels; //holds labels to be used
  43         string line, label;
  44
  45 };
  46
  47 #endif