PredictorMfeSeedOnly.h

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#ifndef INTARNA_PREDICTORMFESEEDONLY_H_
#define INTARNA_PREDICTORMFESEEDONLY_H_
 
#include "IntaRNA/PredictorMfe.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
 
namespace IntaRNA {
 
class PredictorMfeSeedOnly: public PredictorMfe {
 
public:
 
 
    PredictorMfeSeedOnly(
            const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , SeedHandler * seedHandler );
 
 
    virtual ~PredictorMfeSeedOnly();
 
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) );
 
 
protected:
 
 
    using PredictorMfe::energy;
 
    using PredictorMfe::output;
 
    using PredictorMfe::reportedInteractions;
 
    SeedHandlerIdxOffset seedHandler;
 
    size_t seedLastPos1;
    size_t seedLastPos2;
 
protected:
 
    virtual
    void
    traceBack( Interaction & interaction );
 
};
 
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFESEEDONLY_H_ */