PredictorMfeEns2dSeedExtension.h

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#ifndef INTARNA_PREDICTORMFEENS2DSEEDEXTENSION_H_
#define INTARNA_PREDICTORMFEENS2DSEEDEXTENSION_H_
 
#include "IntaRNA/PredictorMfeEns.h"
#include "IntaRNA/Matrix.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
 
namespace IntaRNA {
 
class PredictorMfeEns2dSeedExtension: public PredictorMfeEns {
 
protected:
 
    typedef Matrix<Z_type> Z2dMatrix;
 
public:
 
 
    PredictorMfeEns2dSeedExtension(
            const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , SeedHandler * seedHandler );
 
 
    virtual ~PredictorMfeEns2dSeedExtension();
 
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) );
 
 
protected:
 
 
    using PredictorMfeEns::energy;
 
    using PredictorMfeEns::output;
 
    Z2dMatrix hybridZ_left;
 
    SeedHandlerIdxOffset seedHandler;
 
    Z2dMatrix hybridZ_right;
 
protected:
 
    virtual
    void
    fillHybridZ_left( const size_t j1, const size_t j2 );
 
    virtual
    void
    fillHybridZ_right( const size_t i1, const size_t i2 );
 
    virtual
    void
    traceBack( Interaction & interaction );
 
    virtual
    E_type
    getNonOverlappingEnergy( const size_t si1, const size_t si2, const size_t sj1, const size_t sj2 );
 
    // debug function
    void
    printMatrix( const Z2dMatrix & matrix );
 
};
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFEENS2DSEEDEXTENSION_H_ */