getsharedotucommand.h

   1 #ifndef GETSHAREDOTUCOMMAND_H
   2 #define GETSHAREDOTUCOMMAND_H
   3
   4 /*
   5  *  getsharedotucommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/22/09.
   9  *  Copyright 2009 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "listvector.hpp"
  15 #include "sequence.hpp"
  16 #include "groupmap.h"
  17 #include "globaldata.hpp"
  18
  19 //**********************************************************************************************************************
  20 class GetSharedOTUCommand : public Command {
  21
  22         public:
  23
  24                 GetSharedOTUCommand(string);
  25                 ~GetSharedOTUCommand();
  26                 int execute();
  27                 void help();
  28
  29         private:
  30
  31                 GlobalData* globaldata;
  32                 ListVector* list;
  33                 GroupMap* groupMap;
  34
  35                 set<string> labels;
  36                 string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir;
  37                 bool abort, allLines, unique;
  38                 vector<string> Groups;
  39                 map<string, string> groupFinder;
  40                 map<string, string>::iterator it;
  41                 vector<Sequence> seqs;
  42                 vector<string> outputNames;
  43
  44                 int process(ListVector*);
  45
  46 };
  47 //**********************************************************************************************************************
  48
  49 #endif
  50