readotucommand.h

   1 #ifndef READOTUCOMMAND_H
   2 #define READOTUCOMMAND_H
   3 /*
   4  *  readotu.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 1/20/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "readotu.h"
  14 #include "inputdata.h"
  15 #include "groupmap.h"
  16 #include "sharedcommand.h"
  17
  18 class GlobalData;
  19
  20 class ReadOtuCommand : public Command {
  21 public:
  22         ReadOtuCommand(string);
  23         ReadOtuCommand();
  24         ~ReadOtuCommand();
  25         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33         GlobalData* globaldata;
  34         InputData* input;
  35         Command* shared;
  36         GroupMap* groupMap;
  37         string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
  38         vector<string> Groups, outputNames;
  39         map<string, vector<string> > outputTypes;
  40
  41         bool abort, allLines;
  42         set<string> labels; //holds labels to be used
  43
  44 };
  45
  46 #endif