clusterdoturcommand.h

   1 #ifndef CLUSTERDOTURCOMMAND_H
   2 #define CLUSTERDOTURCOMMAND_H
   3
   4 /*
   5  *  clusterdoturcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 10/27/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "nameassignment.hpp"
  15 #include "globaldata.hpp"
  16 #include "rabundvector.hpp"
  17 #include "sabundvector.hpp"
  18 #include "listvector.hpp"
  19
  20
  21 class ClusterDoturCommand : public Command {
  22
  23 public:
  24         ClusterDoturCommand(string);
  25         ClusterDoturCommand();
  26         ~ClusterDoturCommand();
  27         vector<string> getRequiredParameters();
  28         vector<string> getValidParameters();
  29         vector<string> getRequiredFiles();
  30         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  31         int execute();
  32         void help();
  33
  34 private:
  35         bool abort, hard;
  36         string method, fileroot, tag, outputDir, phylipfile, namefile;
  37         double cutoff;
  38         int precision, length;
  39         ofstream sabundFile, rabundFile, listFile;
  40         NameAssignment* nameMap;
  41         ListVector* list;
  42         RAbundVector* rabund;
  43         RAbundVector oldRAbund;
  44         ListVector oldList;
  45
  46         void printData(string label);
  47         vector<string> outputNames;
  48         map<string, vector<string> > outputTypes;
  49 };
  50
  51 #endif
  52