1 #ifndef Mothur_createdatabasecommand_h
2 #define Mothur_createdatabasecommand_h
5 // createdatabasecommand.h
8 // Created by Sarah Westcott on 3/28/12.
9 // Copyright (c) 2012 Schloss Lab. All rights reserved.
12 #include "command.hpp"
13 #include "listvector.hpp"
14 #include "sequence.hpp"
16 class CreateDatabaseCommand : public Command {
18 CreateDatabaseCommand(string);
19 CreateDatabaseCommand();
20 ~CreateDatabaseCommand(){}
22 vector<string> setParameters();
23 string getCommandName() { return "create.database"; }
24 string getCommandCategory() { return "OTU-Based Approaches"; }
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"; }
33 void help() { m->mothurOut(getHelpString()); }
38 string sharedfile, listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir, countfile;
40 vector<string> outputNames;
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);