createdatabasecommand.h

   1 #ifndef Mothur_createdatabasecommand_h
   2 #define Mothur_createdatabasecommand_h
   3
   4 //
   5 //  createdatabasecommand.h
   6 //  Mothur
   7 //
   8 //  Created by Sarah Westcott on 3/28/12.
   9 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
  10 //
  11
  12 #include "command.hpp"
  13 #include "listvector.hpp"
  14 #include "sequence.hpp"
  15
  16 class CreateDatabaseCommand : public Command {
  17 public:
  18         CreateDatabaseCommand(string);
  19         CreateDatabaseCommand();
  20         ~CreateDatabaseCommand(){}
  21
  22         vector<string> setParameters();
  23         string getCommandName()                 { return "create.database";             }
  24         string getCommandCategory()             { return "OTU-Based Approaches"; }
  25         string getHelpString();
  26         string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
  27         string getDescription()         { return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
  28
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33 private:
  34
  35         bool abort;
  36         string listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
  37
  38         vector<string> outputNames;
  39
  40         vector<int> readFasta(vector<Sequence>&);
  41     vector<int> readTax(vector<string>&);
  42     int readNames(map<string, string>&);
  43         ListVector* getList();
  44
  45 };
  46
  47
  48
  49
  50 #endif