readtreecommand.h

   1 #ifndef READTREECOMMAND_H
   2 #define READTREECOMMAND_H
   3
   4 /*
   5  *  readtreecommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 1/23/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "readtree.h"
  15 #include "treemap.h"
  16
  17
  18 class ReadTreeCommand : public Command {
  19 public:
  20         ReadTreeCommand(string);
  21         ReadTreeCommand() { abort = true; calledHelp = true; }
  22         ~ReadTreeCommand() {}
  23
  24         vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
  25         string getCommandName()                 { return "read.tree";   }
  26         string getCommandCategory()             { return "Hidden";      }
  27         string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like unifrac.unweighted."; }
  28         string getCitation() { return "http://www.mothur.org/wiki/Read.tree"; }
  29         string getDescription()         { return "read.tree"; }
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35         ReadTree* read;
  36         TreeMap* treeMap;
  37         string filename, treefile, groupfile, namefile;
  38         bool abort;
  39         map<string, string> nameMap;
  40         vector<string> outputNames;
  41
  42         int readNamesFile();
  43         int numUniquesInName;
  44
  45 };
  46
  47
  48 #endif