otuhierarchycommand.h

   1 #ifndef OTUHIERARCHYCOMMAND_H
   2 #define OTUHIERARCHYCOMMAND_H
   3 /*
   4  *  otuhierarchycommand.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 1/19/10.
   8  *  Copyright 2010 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "listvector.hpp"
  14
  15 //**********************************************************************************************************************
  16
  17 class OtuHierarchyCommand : public Command {
  18
  19 public:
  20         OtuHierarchyCommand(string);
  21         OtuHierarchyCommand();
  22         ~OtuHierarchyCommand();
  23         vector<string> getRequiredParameters();
  24         vector<string> getValidParameters();
  25         vector<string> getRequiredFiles();
  26         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  27         int execute();
  28         void help();
  29
  30 private:
  31         bool abort;
  32         set<string> labels; //holds labels to be used
  33         string label, listFile, outputDir, output;
  34         vector<string> outputNames;
  35         map<string, vector<string> > outputTypes;
  36
  37         vector<ListVector> getListVectors();
  38
  39 };
  40
  41 //**********************************************************************************************************************
  42
  43 #endif
  44
  45