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
  28         string getHelpString();
  29     string getOutputPattern(string);
  30         string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
  31         string getDescription()         { return "relates OTUs at different distances"; }
  32
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37
  38 private:
  39         bool abort;
  40         set<string> labels; //holds labels to be used
  41         string label, listFile, outputDir, output;
  42         vector<string> outputNames;
  43
  44         vector<ListVector> getListVectors();
  45
  46 };
  47
  48 //**********************************************************************************************************************
  49
  50 #endif
  51
  52