PredictorMfeEns2d.h

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#ifndef INTARNA_PREDICTORMFEENS2D_H_
#define INTARNA_PREDICTORMFEENS2D_H_
 
#include "IntaRNA/PredictorMfeEns.h"
#include "IntaRNA/BasePairProbabilities.h"
#include "IntaRNA/Interaction.h"
 
#include "IntaRNA/Matrix.h"
 
namespace IntaRNA {
 
class PredictorMfeEns2d: public PredictorMfeEns {
 
protected:
 
    typedef Matrix<Z_type> Z2dMatrix;
 
public:
 
    PredictorMfeEns2d( const InteractionEnergy & energy
                    , OutputHandler & output
                    , PredictionTracker * predTracker
                    , BasePairProbabilities * pairProbabilities = nullptr );
 
    virtual ~PredictorMfeEns2d() override;
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos)
            ) override;
 
protected:
 
    BasePairProbabilities * pairProbabilities;
 
    using PredictorMfeEns::energy;
 
    using PredictorMfeEns::output;
 
    Z2dMatrix hybridZ;
 
protected:
 
    void predictRegion(const IndexRange & r1,const IndexRange & r2);
 
    void accumulatePairMasses(size_t j1,size_t j2,Z2dMatrix & outside,
            Z2dMatrix & masses,Z_type & denominator) const;
 
    virtual
    void
    fillHybridZ( const size_t j1, const size_t j2
                , const size_t i1init, const size_t i2init
                , const bool callUpdateZ
                );
 
};
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFEENS2D_H_ */