getcoremicrobiomcommand.h

   1 #ifndef Mothur_getcoremicrobiomcommand_h
   2 #define Mothur_getcoremicrobiomcommand_h
   3
   4
   5 //
   6 //  getcoremicrobiomcommand.h
   7 //  Mothur
   8 //
   9 //  Created by John Westcott on 5/8/12.
  10 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
  11 //
  12
  13
  14 #include "command.hpp"
  15 #include "inputdata.h"
  16
  17 /**************************************************************************************************/
  18
  19 class GetCoreMicroBiomCommand : public Command {
  20 public:
  21     GetCoreMicroBiomCommand(string);
  22     GetCoreMicroBiomCommand();
  23     ~GetCoreMicroBiomCommand(){}
  24
  25     vector<string> setParameters();
  26     string getCommandName()                     { return "get.coremicrobiom";                   }
  27     string getCommandCategory()         { return "OTU-Based Approaches";                }
  28     //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
  29     string getHelpString();
  30     string getCitation() { return "http://www.mothur.org/wiki/get.coremicrobio"; }
  31     string getDescription()             { return "description"; }
  32
  33     int execute();
  34     void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37     string relabundfile, sharedfile, inputFileName, format;
  38     bool allLines;
  39     vector<string> Groups;
  40     set<string> labels;
  41     bool abort;
  42     string outputDir;
  43     vector<string> outputNames;
  44
  45     int createTable(vector<SharedRAbundFloatVector*>&);
  46
  47 };
  48
  49 /**************************************************************************************************/
  50
  51
  52
  53
  54 #endif