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 "rabundvector.hpp"
  16 #include "sabundvector.hpp"
  17 #include "listvector.hpp"
  18
  19
  20 class ClusterDoturCommand : public Command {
  21
  22 public:
  23         ClusterDoturCommand(string);
  24         ClusterDoturCommand();
  25         ~ClusterDoturCommand(){}
  26
  27         vector<string> setParameters();
  28         string getCommandName()                 { return "cluster.classic";             }
  29         string getCommandCategory()             { return "Clustering";                  }
  30         string getHelpString();
  31         string getCitation() { return "http://www.mothur.org/wiki/Cluster.classic"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         bool abort, hard, sim;
  38         string method, fileroot, tag, outputDir, phylipfile, namefile;
  39         double cutoff;
  40         int precision, length;
  41         ofstream sabundFile, rabundFile, listFile;
  42         NameAssignment* nameMap;
  43         ListVector* list;
  44         RAbundVector* rabund;
  45         RAbundVector oldRAbund;
  46         ListVector oldList;
  47
  48         void printData(string label);
  49         vector<string> outputNames;
  50 };
  51
  52 #endif
  53