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         ~GetSAbundCommand();
  26         vector<string> getRequiredParameters();
  27         vector<string> getValidParameters();
  28         vector<string> getRequiredFiles();
  29         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  30         int execute();
  31         void help();
  32
  33 private:
  34         GlobalData* globaldata;
  35         string filename, format;
  36         ofstream out;
  37         ReadOTUFile* read;
  38         OrderVector* order;
  39         InputData* input;
  40         SAbundVector* sabund;
  41         vector<string> outputNames;
  42         map<string, vector<string> > outputTypes;
  43
  44         bool abort, allLines;
  45         set<string> labels; //holds labels to be used
  46         string label;
  47
  48 };
  49
  50 #endif