phylotypecommand.h

   1 #ifndef PHYLOTYPECOMMAND_H
   2 #define PHYLOTYPECOMMAND_H
   3
   4
   5 /*
   6  *  phylotypecommand.h
   7  *  Mothur
   8  *
   9  *  Created by westcott on 11/20/09.
  10  *  Copyright 2009 Schloss Lab. All rights reserved.
  11  *
  12  */
  13
  14 #include "taxonomyequalizer.h"
  15 #include "command.hpp"
  16
  17 /*************************************************************************/
  18
  19 class PhylotypeCommand : public Command {
  20
  21 public:
  22         PhylotypeCommand(string);
  23         ~PhylotypeCommand();
  24         int execute();
  25         void help();
  26
  27 private:
  28         bool abort, allLines;
  29         string taxonomyFileName, label, outputDir, namefile;
  30         set<string> labels; //holds labels to be used
  31         int cutoff;
  32         map<string, string> namemap;
  33
  34         map<int, int> currentNodes;
  35         map<int, int> parentNodes;
  36         map<int, int>::iterator itCurrent;
  37
  38         int readNamesFile();
  39
  40 };
  41
  42
  43 /*************************************************************************/
  44
  45
  46 #endif
  47
  48
  49