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 class GlobalData;
  18
  19 class ReadTreeCommand : public Command {
  20 public:
  21         ReadTreeCommand(string);
  22         ReadTreeCommand() { abort = true; calledHelp = true; }
  23         ~ReadTreeCommand();
  24         vector<string> getRequiredParameters();
  25         vector<string> getValidParameters();
  26         vector<string> getRequiredFiles();
  27         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28         int execute();
  29         void help();
  30
  31 private:
  32         GlobalData* globaldata;
  33         ReadTree* read;
  34         TreeMap* treeMap;
  35         string filename, treefile, groupfile, namefile;
  36         bool abort;
  37         map<string, string> nameMap;
  38         vector<string> outputNames;
  39         map<string, vector<string> > outputTypes;
  40
  41         int readNamesFile();
  42         int numUniquesInName;
  43
  44 };
  45
  46
  47 #endif