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 "sharedrabundvector.h"
  18 #include "inputdata.h"
  19
  20 //**********************************************************************************************************************
  21 class GetSharedOTUCommand : public Command {
  22
  23         public:
  24
  25                 GetSharedOTUCommand(string);
  26                 GetSharedOTUCommand();
  27                 ~GetSharedOTUCommand() {}
  28
  29                 vector<string> setParameters();
  30                 string getCommandName()                 { return "get.sharedseqs";                      }
  31                 string getCommandCategory()             { return "OTU-Based Approaches";        }
  32                 string getRequiredCommand()             { return "none";                                        }
  33
  34         string getHelpString();
  35     string getOutputPattern(string);
  36                 string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
  37                 string getDescription()         { return "identifies sequences that are either unique or shared by specific groups"; }
  38
  39                 int execute();
  40                 void help() { m->mothurOut(getHelpString()); }
  41
  42
  43
  44         private:
  45                 ListVector* list;
  46                 GroupMap* groupMap;
  47
  48                 set<string> labels;
  49                 string fastafile, label, groups, listfile, groupfile, sharedfile, output, userGroups, outputDir, format;
  50                 bool abort, allLines, unique;
  51                 vector<string> Groups;
  52                 map<string, string> groupFinder;
  53                 map<string, string>::iterator it;
  54                 vector<Sequence> seqs;
  55                 vector<string> outputNames;
  56
  57                 int process(ListVector*);
  58         int process(vector<SharedRAbundVector*>&);
  59         int runShared();
  60
  61 };
  62 //**********************************************************************************************************************
  63
  64 #endif
  65