otuhierarchycommand.h

   1 #ifndef OTUHIERARCHYCOMMAND_H
   2 #define OTUHIERARCHYCOMMAND_H
   3 /*
   4  *  otuhierarchycommand.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 1/19/10.
   8  *  Copyright 2010 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "listvector.hpp"
  14
  15 //**********************************************************************************************************************
  16
  17 class OtuHierarchyCommand : public Command {
  18
  19 public:
  20         OtuHierarchyCommand(string);
  21         OtuHierarchyCommand();
  22         ~OtuHierarchyCommand(){}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "otu.hierarchy";                       }
  26         string getCommandCategory()             { return "OTU-Based Approaches";        }
  27         string getOutputFileNameTag(string, string);
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
  30         string getDescription()         { return "relates OTUs at different distances"; }
  31
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36
  37 private:
  38         bool abort;
  39         set<string> labels; //holds labels to be used
  40         string label, listFile, outputDir, output;
  41         vector<string> outputNames;
  42
  43         vector<ListVector> getListVectors();
  44
  45 };
  46
  47 //**********************************************************************************************************************
  48
  49 #endif
  50
  51