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         ~PhylotypeCommand();
  25         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33         bool abort, allLines;
  34         string taxonomyFileName, label, outputDir, namefile;
  35         set<string> labels; //holds labels to be used
  36         int cutoff;
  37         map<string, string> namemap;
  38         vector<string> outputNames;
  39         map<string, vector<string> > outputTypes;
  40
  41         map<int, int> currentNodes;
  42         map<int, int> parentNodes;
  43         map<int, int>::iterator itCurrent;
  44
  45         int readNamesFile();
  46
  47 };
  48
  49
  50 /*************************************************************************/
  51
  52
  53 #endif
  54
  55
  56