PredictorMfe2dHeuristicSeedExtension.h

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#ifndef INTARNA_PREDICTORMFE2DHEURISTICSEEDEXTENSION_H_
#define INTARNA_PREDICTORMFE2DHEURISTICSEEDEXTENSION_H_
 
#include "IntaRNA/PredictorMfe2dSeedExtension.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
 
namespace IntaRNA {
 
class PredictorMfe2dHeuristicSeedExtension: public PredictorMfe2dSeedExtension {
 
protected:
 
    typedef PredictorMfe2dSeedExtension::E2dMatrix E2dMatrix;
 
public:
 
 
    PredictorMfe2dHeuristicSeedExtension(
            const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , SeedHandler * seedHandler );
 
 
    virtual ~PredictorMfe2dHeuristicSeedExtension();
 
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) );
 
 
protected:
 
 
    using PredictorMfe2dSeedExtension::energy;
 
    using PredictorMfe2dSeedExtension::output;
 
    using PredictorMfe2dSeedExtension::hybridE_left;
 
    using PredictorMfe2dSeedExtension::seedHandler;
 
    using PredictorMfe2dSeedExtension::hybridE_right;
 
    E_type E_right_opt;
 
    size_t j1opt, j2opt;
 
protected:
 
    virtual
    void
    updateOptimalRightExt( const size_t i1, const size_t j1
            , const size_t i2, const size_t j2
            , const E_type energy
            , const bool isHybridE );
 
    void
    fillHybridE_right( const size_t i1, const size_t i2
                , const size_t si1, const size_t si2 );
 
    void
    fillHybridE_left( const size_t j1, const size_t j2 );
 
    void
    printMatrix( const E2dMatrix & matrix );
 
};
 
 
inline
void
PredictorMfe2dHeuristicSeedExtension::
updateOptimalRightExt( const size_t i1, const size_t j1
        , const size_t i2, const size_t j2
        , const E_type energy
        , const bool isHybridE )
{
    E_type fullE = isHybridE ? this->energy.getE(i1,j1,i2,j2,energy) : energy;
    // if energy lower
    // if valid right boundary
    if (fullE < E_right_opt
            && (!output.getOutputConstraint().noGUend || !this->energy.isGU(j1,j2)))
    {
        // store boundaries and energy of the optimal right extension
        E_right_opt = fullE;
        j1opt = j1;
        j2opt = j2;
    }
}
 
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFE2DHEURISTICSEEDEXTENSION_H_ */