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