setcurrentcommand.h

   1 #ifndef SETCURRENTCOMMAND_H
   2 #define SETCURRENTCOMMAND_H
   3
   4 /*
   5  *  setcurrentcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 3/16/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15
  16 class SetCurrentCommand : public Command {
  17
  18 public:
  19         SetCurrentCommand(string);
  20         SetCurrentCommand();
  21         ~SetCurrentCommand() {}
  22
  23         vector<string> setParameters();
  24         string getCommandName()                 { return "set.current"; }
  25         string getCommandCategory()             { return "General";             }
  26         string getOutputFileNameTag(string, string) { return ""; }
  27         string getHelpString();
  28         string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
  29         string getDescription()         { return "set current files for mothur"; }
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35
  36         vector<string> outputNames;
  37         bool abort;
  38
  39         string clearTypes;
  40         vector<string> types;
  41
  42         string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile;
  43         string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
  44
  45
  46 };
  47
  48 #endif
  49
  50