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 getOutputFileNameTag(string, string);
  26         string getHelpString();
  27         string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
  28         string getDescription()         { return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
  29
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35
  36         bool abort;
  37         string sharedfile, listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
  38
  39         vector<string> outputNames;
  40
  41         vector<int> readFasta(vector<Sequence>&);
  42     vector<int> readTax(vector<string>&, vector<string>&);
  43         ListVector* getList();
  44     vector<SharedRAbundVector*> getShared();
  45     int findIndex(vector<string>&, string);
  46
  47 };
  48
  49
  50
  51
  52 #endif