PredictorMfe2dHeuristicSeed.h

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#ifndef INTARNA_PREDICTORMFE2DHEURISTICSEED_H_
#define INTARNA_PREDICTORMFE2DHEURISTICSEED_H_
 
#include "IntaRNA/PredictorMfe2dHeuristic.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
 
namespace IntaRNA {
 
 
class PredictorMfe2dHeuristicSeed: public PredictorMfe2dHeuristic {
 
 
    typedef PredictorMfe2dHeuristic::E2dMatrix E2dMatrix;
 
public:
 
    PredictorMfe2dHeuristicSeed( const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , SeedHandler* seedHandler );
 
    virtual ~PredictorMfe2dHeuristicSeed();
 
    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;
 
    E2dMatrix hybridE_seed;
 
    SeedHandlerIdxOffset seedHandler;
 
protected:
 
    virtual
    void
    traceBack( Interaction & interaction );
 
 
    virtual
    void
    fillHybridE();
 
 
    virtual
    void
    getNextBest( Interaction & curBest );
 
 
};
 
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFE2DHEURISTICSEED_H_ */