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#ifndef Mothur_createdatabasecommand_h
#define Mothur_createdatabasecommand_h
//
// createdatabasecommand.h
// Mothur
//
// Created by Sarah Westcott on 3/28/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "listvector.hpp"
#include "sequence.hpp"
#include "sharedrabundfloatvectors.hpp"
class CreateDatabaseCommand : public Command {
public:
CreateDatabaseCommand(string);
~CreateDatabaseCommand(){}
vector<string> setParameters();
string getCommandName() { return "create.database"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
string getDescription() { return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string relabundfile, sharedfile, listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, countfile;
vector<string> outputNames;
vector<int> readFasta(vector<Sequence>&);
vector<int> readTax(vector<string>&, vector<string>&);
ListVector* getList();
SharedRAbundVectors* getShared();
SharedRAbundFloatVectors* getRelabund();
int findIndex(vector<string>&, string);
};
#endif
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