rnastructure_plugin.h

/******************************************************************************
 *   Copyright (C) 2014  Juan Antonio Garcia Martin , Peter Clote, Ivan Dotu  *
 *                                                                            *
 *  This program 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.                                       *
 *                                                                            *
 *  This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.     *
 ******************************************************************************/

#include <string>

using namespace std;
#ifndef RNASTRUCTURE_PLUGIN
#define _RNASTRUCTURE_PLUGIN

#include "rna_plugin.h"
#include "RNAstructure/RNA_class/RNA.h"
#include "RNAstructure/RNA_class/HybridRNA.h"

class RNAstructurePlugin : public RNAPlugin {
	public:
		RNAstructurePlugin(){};
		RNAstructurePlugin(int size);
		RNAstructurePlugin(int size,int dangles);
		~RNAstructurePlugin();
	
		void initMe(std::string name, int d);
		void setSequence(std::string seq);
		void setStructure(std::string str);
		void setTestStructure(std::string str);
		double fold();
		string getStructure();
		double energyOfStruct(); 
		double energyOfEnsemble(); 
		double probOfStruct();
		int* getBasePairs();
		int* getBasePairs1Index();
		void fillBasePairs1Index(int *bprs);
		double* basePairProbsArray();  
		double** basePairProbsMatrix();
		double* basePairProbsArrayCofold();
		double** basePairProbsMatrixCofold();
		void setWindowSize(int ws);
		void setTemperature(double t);
		void setCutPoint(int p);
		double cofold();
		void freeMe();
		void setDangles(int d);
		void setEnergyModel(std::string energy_model);
	private:
		string _name;
		string _seq;
		string _str;
		string _tstr;
		structure* _structure;
		vector<int> _vtstr;
		int _winSize;
		int _maxLoop;
		double _temp;
		int _cutpoint;
		int _d;

};

#endif