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
  15 class CreateDatabaseCommand : public Command {
  16 public:
  17         CreateDatabaseCommand(string);
  18         CreateDatabaseCommand();
  19         ~CreateDatabaseCommand(){}
  20
  21         vector<string> setParameters();
  22         string getCommandName()                 { return "create.database";             }
  23         string getCommandCategory()             { return "OTU-Based Approaches"; }
  24         string getHelpString();
  25         string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
  26         string getDescription()         { return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
  27
  28
  29         int execute() {};
  30         void help() { m->mothurOut(getHelpString()); }
  31
  32 private:
  33
  34         bool abort;
  35         string listfile, groupfile, repfastafile, repnamesfile, constaxonomyfile, label, outputDir;
  36
  37         vector<string> outputNames;
  38
  39         int readFasta();
  40         int readNames();
  41     int readTax();
  42         int processList(ListVector*&);
  43
  44 };
  45
  46
  47
  48
  49 #endif