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 "inputdata.h"
  14 #include "groupmap.h"
  15 #include "sharedcommand.h"
  16
  17 class ReadOtuCommand : public Command {
  18 public:
  19         ReadOtuCommand(string);
  20         ReadOtuCommand();
  21         ~ReadOtuCommand() {}
  22
  23         vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
  24         string getCommandName()                 { return "read.otu";    }
  25         string getCommandCategory()             { return "Hidden";      }
  26         string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }
  27
  28         int execute();
  29         void help() { m->mothurOut(getHelpString()); }
  30
  31 private:
  32         InputData* input;
  33         Command* shared;
  34         GroupMap* groupMap;
  35         string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
  36         vector<string> Groups, outputNames;
  37         map<string, vector<string> > outputTypes;
  38
  39         bool abort, allLines;
  40         set<string> labels; //holds labels to be used
  41
  42 };
  43
  44 #endif