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                 ~GetSharedOTUCommand();
  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
  36                 GlobalData* globaldata;
  37                 ListVector* list;
  38                 GroupMap* groupMap;
  39
  40                 set<string> labels;
  41                 string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir;
  42                 bool abort, allLines, unique;
  43                 vector<string> Groups;
  44                 map<string, string> groupFinder;
  45                 map<string, string>::iterator it;
  46                 vector<Sequence> seqs;
  47                 vector<string> outputNames;
  48                 map<string, vector<string> > outputTypes;
  49
  50                 int process(ListVector*);
  51
  52 };
  53 //**********************************************************************************************************************
  54
  55 #endif
  56