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
  32         string getHelpString();
  33     string getOutputPattern(string);
  34                 string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
  35                 string getDescription()         { return "identifies sequences that are either unique or shared by specific groups"; }
  36
  37                 int execute();
  38                 void help() { m->mothurOut(getHelpString()); }
  39
  40
  41
  42         private:
  43                 ListVector* list;
  44                 GroupMap* groupMap;
  45
  46                 set<string> labels;
  47                 string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir, format;
  48                 bool abort, allLines, unique;
  49                 vector<string> Groups;
  50                 map<string, string> groupFinder;
  51                 map<string, string>::iterator it;
  52                 vector<Sequence> seqs;
  53                 vector<string> outputNames;
  54
  55                 int process(ListVector*);
  56
  57 };
  58 //**********************************************************************************************************************
  59
  60 #endif
  61