PredictorMfe2d.h

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#ifndef INTARNA_PREDICTORMFE2D_H_
#define INTARNA_PREDICTORMFE2D_H_
 
#include "IntaRNA/PredictorMfe.h"
#include "IntaRNA/Interaction.h"
 
#include "IntaRNA/Matrix.h"
 
namespace IntaRNA {
 
class PredictorMfe2d: public PredictorMfe {
 
protected:
 
    typedef Matrix<E_type> E2dMatrix;
 
public:
 
    PredictorMfe2d( const InteractionEnergy & energy
                    , OutputHandler & output
                    , PredictionTracker * predTracker );
 
    virtual ~PredictorMfe2d();
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos)
            );
 
protected:
 
    using PredictorMfe::energy;
 
    using PredictorMfe::output;
 
    E2dMatrix hybridE_pq;
 
protected:
 
    virtual
    void
    fillHybridE( const size_t j1, const size_t j2
                , const size_t i1init, const size_t i2init
                , const bool callUpdateOptima
                );
 
    virtual
    void
    traceBack( Interaction & interaction );
 
};
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFE2D_H_ */