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vienna_plugin.h
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/******************************************************************************
* 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 _VIENNA_PLUGIN
#define _VIENNA_PLUGIN
#include "rna_plugin.h"
class ViennaPlugin: public RNAPlugin{
public:
ViennaPlugin(){};
ViennaPlugin(int size);
ViennaPlugin(int size,int dangles);
~ViennaPlugin();
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(string energy_model);
private:
string _name;
string _seq;
string _str;
string _tstr;
char *_cseq;
char *_cstr;
char *_ctstr;
int _winSize;
double _temp;
int _cutpoint;
int _d;
};
#endif