database.h

/**************************************************************************
 * Copyright (c) 2005-2011 T. M. Murali                                   *
 * Copyright (c) 2008-2011 Naveed Massjouni                               *
 * Copyright (c) 2004 Greg Grothaus                                       *
 *                                                                        *
 * This file is part of Biorithm.                                         *
 *                                                                        *
 * Biorithm is free software: you can redistribute it and/or modify       *
 * it under the terms of the GNU General Public License as published by   *
 * the Free Software Foundation, either version 3 of the License, or      *
 * (at your option) any later version.                                    *
 *                                                                        *
 * Biorithm is distributed in the hope that it will be useful,            *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of         *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          *
 * GNU General Public License for more details.                           *
 *                                                                        *
 * You should have received a copy of the GNU General Public License      *
 * along with Biorithm.  If not, see <http://www.gnu.org/licenses/>.      *
 *                                                                        *
 **************************************************************************/

#include<string>
#include<iostream>
#include<fstream>
#include<vector>
#include<map>
#include<sstream>
#include<set>
#include<mysql++.hh>
#include "setTemplates.C"
#include "motifDataset.h"
using namespace std;

#ifndef DATABASE_MOTIFDATASETGREG
#define DATABASE_MOTIFDATASETGREG

class database : public motifDataset
{
        private:
                vector<string> columnToName,rowToName;
                map<string,int> nameToColumn,nameToRow;
                vector<vector<double> > data;
                vector<vector<bool> > mExists;
                vector<vector<int> > mClassToExperiments;
                vector<vector<int> > mExperimentsToClass;
                vector<string> classLabels;
                Connection *con;
                vector<int> expSet,geneSet;
                int mRunID;

                template<class T> string toa(T in);
                template<class T> T ato(string in);
                void getData(int);
                double atod(string in);
                Result select(string);
                void makeConnection();

        public:
                database(int);
                database(string);
                void writeData(string outfile);
                
                virtual vector<string> probes();
                virtual vector<string> samples();
                virtual double operator()(int,int);
                virtual double operator()(string,string);
                virtual bool exists(int,int);
                virtual bool exists(string,string);
                virtual vector<vector<int> > classToExperiments();
                virtual vector<vector<int> > experimentsToClass();
                virtual vector<string> classes();
};

#endif