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
  18 //**********************************************************************************************************************
  19 class GetSharedOTUCommand : public Command {
  20
  21         public:
  22
  23                 GetSharedOTUCommand(string);
  24                 GetSharedOTUCommand();
  25                 ~GetSharedOTUCommand() {}
  26
  27                 vector<string> setParameters();
  28                 string getCommandName()                 { return "get.sharedseqs";                      }
  29                 string getCommandCategory()             { return "OTU-Based Approaches";        }
  30                 string getRequiredCommand()             { return "none";                                        }
  31                 string getHelpString();
  32                 string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
  33                 string getDescription()         { return "identifies sequences that are either unique or shared by specific groups"; }
  34
  35                 int execute();
  36                 void help() { m->mothurOut(getHelpString()); }
  37
  38
  39
  40         private:
  41                 ListVector* list;
  42                 GroupMap* groupMap;
  43
  44                 set<string> labels;
  45                 string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir, format;
  46                 bool abort, allLines, unique;
  47                 vector<string> Groups;
  48                 map<string, string> groupFinder;
  49                 map<string, string>::iterator it;
  50                 vector<Sequence> seqs;
  51                 vector<string> outputNames;
  52
  53                 int process(ListVector*);
  54
  55 };
  56 //**********************************************************************************************************************
  57
  58 #endif
  59