PredictorMfe2dHelixBlockHeuristicSeed.h

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#ifndef INTARNA_PREDICTORMFE2DHELIXBLOCKHEURISTICSEED_H
#define INTARNA_PREDICTORMFE2DHELIXBLOCKHEURISTICSEED_H
 
#include "IntaRNA/PredictorMfe2dHelixBlockHeuristic.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
 
namespace IntaRNA {
 
 
class PredictorMfe2dHelixBlockHeuristicSeed: public PredictorMfe2dHelixBlockHeuristic {
 
 
    typedef PredictorMfe2dHeuristic::E2dMatrix E2dMatrix;
 
public:
 
    PredictorMfe2dHelixBlockHeuristicSeed( const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , const HelixConstraint & helixConstraint
            , SeedHandler * seedHandlerInstance
    );
 
    virtual ~PredictorMfe2dHelixBlockHeuristicSeed();
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos));
 
protected:
 
    using PredictorMfe2dHelixBlockHeuristic::energy;
 
    using PredictorMfe2dHelixBlockHeuristic::output;
 
    using PredictorMfe2dHelixBlockHeuristic::reportedInteractions;
 
    using PredictorMfe2dHelixBlockHeuristic::hybridE;
 
    using PredictorMfe2dHelixBlockHeuristic::helixHandler;
 
    E2dMatrix hybridE_seed;
 
    //
    SeedHandlerIdxOffset seedHandler;
 
protected:
 
    virtual
    void
    traceBack( Interaction & interaction );
 
 
    virtual
    void
    getNextBest( Interaction & curBest );
 
    virtual
    void
    updateOptima( const size_t i1, const size_t j1
            , const size_t i2, const size_t j2
            , const E_type energy
            , const bool isHybridE );
 
 
};
 
 
inline
void
PredictorMfe2dHelixBlockHeuristicSeed::
updateOptima( const size_t i1, const size_t j1
        , const size_t i2, const size_t j2
        , const E_type energy
        , const bool isHybridE )
{
    // temporarily disable tracker
    PredictionTracker * curPredTracker = this->predTracker;
    this->predTracker = NULL;
    // update optimum information, such that we might skip this sequence pair
    PredictorMfe2dHeuristic::updateOptima(i1,j1,i2,j2,energy,isHybridE,false);
    // reenable tracker
    this->predTracker = curPredTracker;
}
 
 
} // namespace
#endif //INTARNA_PREDICTORMFE2DHELIXBLOCKHEURISTICSEED_H