PredictorMfe2dHelixBlockHeuristic.h

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#ifndef INTARNA_PREDICTORMFE2DHELIXBLOCKHEURISTIC_H_
#define INTARNA_PREDICTORMFE2DHELIXBLOCKHEURISTIC_H_
 
#include "IntaRNA/PredictorMfe2dHeuristic.h"
#include "IntaRNA/Interaction.h"
#include "IntaRNA/HelixHandlerIdxOffset.h"
 
 
namespace IntaRNA {
 
class PredictorMfe2dHelixBlockHeuristic: public PredictorMfe2dHeuristic {
 
protected:
 
    typedef PredictorMfe2dHeuristic::E2dMatrix E2dMatrix;
 
public:
 
    PredictorMfe2dHelixBlockHeuristic( const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , const HelixConstraint & helixConstraint);
 
    virtual ~PredictorMfe2dHelixBlockHeuristic();
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) );
 
protected:
 
    using PredictorMfe2dHeuristic::energy;
 
    using PredictorMfe2dHeuristic::output;
 
    using PredictorMfe2dHeuristic::reportedInteractions;
 
    using PredictorMfe2dHeuristic::hybridE;
 
    //HelixHandler helixHandler;
    HelixHandlerIdxOffset helixHandler;
 
protected:
 
    virtual
    void
    fillHybridE();
 
    virtual
    void
    traceBack( Interaction & interaction );
 
    virtual
    void
    getNextBest( Interaction & curBest );
 
    virtual
    void
    updateMfe4leftEnd(const size_t i1, const size_t j1
                    , const size_t i2, const size_t j2
                    , const Interaction & curInteraction );
 
};
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFE2DHELIXBLOCKHEURISTIC_H_ */