PredictorMfe2dSeed.h

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/*
 * PredictorMfe2dSeed.h
 *
 *  Created on: 13.10.2016
 *      Author: Mmann
 */
 
#ifndef INTARNA_PREDICTORMFE2DSEED_H_
#define INTARNA_PREDICTORMFE2DSEED_H_
 
#include "IntaRNA/PredictorMfe2d.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
 
namespace IntaRNA {
 
class PredictorMfe2dSeed: public PredictorMfe2d {
 
protected:
 
    typedef PredictorMfe2d::E2dMatrix E2dMatrix;
 
public:
 
 
    PredictorMfe2dSeed(
            const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , SeedHandler * seedHandler );
 
 
    virtual ~PredictorMfe2dSeed();
 
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) );
 
 
protected:
 
 
    using PredictorMfe2d::energy;
 
    using PredictorMfe2d::output;
 
    using PredictorMfe2d::hybridE_pq;
 
    SeedHandlerIdxOffset seedHandler;
 
    E2dMatrix hybridE_pq_seed;
 
protected:
 
    virtual
    void
    fillHybridE( const size_t j1, const size_t j2
                , const size_t i1init, const size_t i2init
                , const bool callUpdateOptima
                );
 
    virtual
    void
    traceBack( Interaction & interaction );
 
};
 
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFE2DSEED_H_ */