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         vector<string> getRequiredParameters();
  23         vector<string> getValidParameters();
  24         vector<string> getRequiredFiles();
  25         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  26         int execute();
  27         void help();
  28
  29 private:
  30
  31         vector<string> outputNames;
  32         map<string, vector<string> > outputTypes;
  33         bool abort;
  34
  35         string clearTypes;
  36         vector<string> types;
  37
  38         string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
  39         string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
  40
  41
  42 };
  43
  44 #endif
  45
  46