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 ReadOtuCommand : public Command {
  19 public:
  20         ReadOtuCommand(string);
  21         ReadOtuCommand();
  22         ~ReadOtuCommand() {}
  23
  24         vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
  25         string getCommandName()                 { return "read.otu";    }
  26         string getCommandCategory()             { return "Hidden";      }
  27         string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }
  28
  29         int execute();
  30         void help() { m->mothurOut(getHelpString()); }
  31
  32 private:
  33         InputData* input;
  34         Command* shared;
  35         GroupMap* groupMap;
  36         string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
  37         vector<string> Groups, outputNames;
  38         map<string, vector<string> > outputTypes;
  39
  40         bool abort, allLines;
  41         set<string> labels; //holds labels to be used
  42
  43 };
  44
  45 #endif