deuniquetreecommand.h

   1 #ifndef DEUNIQUETREECOMMAND_H
   2 #define DEUNIQUETREECOMMAND_H
   3
   4 /*
   5  *  deuniquetreecommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 5/27/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "treemap.h"
  16 #include "sharedutilities.h"
  17 #include "readtree.h"
  18
  19 class DeuniqueTreeCommand : public Command {
  20
  21 public:
  22         DeuniqueTreeCommand(string);
  23         DeuniqueTreeCommand();
  24         ~DeuniqueTreeCommand() {}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "deunique.tree";               }
  28         string getCommandCategory()             { return "Hypothesis Testing";          }
  29         string getHelpString();
  30         string getCitation() { return "http://www.mothur.org/wiki/Deunique.tree"; }
  31         string getDescription()         { return "add the redundant sequence names back into a tree of unique sequences"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36
  37 private:
  38         TreeMap* tmap;
  39         int numUniquesInName;
  40
  41         bool abort;
  42         string outputDir, treefile, namefile;
  43         vector<string> outputNames;
  44         map<string, string> nameMap;
  45         int readNamesFile();
  46 };
  47
  48 #endif