PredictorMfeEns2dHeuristicSeedExtension.h

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#ifndef INTARNA_PREDICTORMFEENS2DHEURISTICSEEDEXTENSION_H_
#define INTARNA_PREDICTORMFEENS2DHEURISTICSEEDEXTENSION_H_
 
#include "IntaRNA/PredictorMfeEns2dSeedExtension.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
#include <unordered_map>
 
namespace IntaRNA {
 
class PredictorMfeEns2dHeuristicSeedExtension: public PredictorMfeEns2dSeedExtension {
 
public:
 
 
    PredictorMfeEns2dHeuristicSeedExtension(
            const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , SeedHandler * seedHandler
            , BasePairProbabilities * pairProbabilities = nullptr );
 
 
    virtual ~PredictorMfeEns2dHeuristicSeedExtension() override;
 
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override;
 
 
protected:
 
    void prepareStackSeedExtensions(size_t n,size_t m,const StackSeedDomain & seeds) override;
    std::function<Interaction::BasePair(Interaction::BasePair,Interaction::BasePair)>
    stackSeedRightSelector() const override;
 
    bool selectingStackSeedRight = false;
    std::unordered_map<Interaction::BasePair,Interaction::BasePair,Interaction::BasePair::Hash> stackSeedRight;
 
 
    using PredictorMfeEns2dSeedExtension::energy;
 
    using PredictorMfeEns2dSeedExtension::output;
 
    using PredictorMfeEns2dSeedExtension::seedHandler;
 
    using PredictorMfeEns2dSeedExtension::hybridZ_left;
 
    using PredictorMfeEns2dSeedExtension::hybridZ_right;
 
    Z_type E_right_opt = E_INF;
 
    size_t j1opt, j2opt;
 
protected:
 
    virtual
    void
    updateOptRightZ( const size_t i1, const size_t j1
            , const size_t i2, const size_t j2
            , const E_type hybridE );
 
    virtual
    void
    fillHybridZ_right( const size_t i1, const size_t i2
                , const size_t si1, const size_t si2
                );
 
    virtual
    void
    fillHybridZ_left( const size_t j1, const size_t j2 ) override;
 
};
 
 
inline
void
PredictorMfeEns2dHeuristicSeedExtension::
updateOptRightZ( const size_t i1, const size_t j1
        , const size_t i2, const size_t j2
        , const E_type hybridE )
{
    // store boundaries and energy of the optimal right extension
    E_type fullE = energy.getE( i1, j1, i2, j2, hybridE );
    if (fullE < E_right_opt
            && (!output.getOutputConstraint().noGUend || !energy.isGU(j1,j2)))
    {
        E_right_opt = fullE;
        j1opt = j1;
        j2opt = j2;
    }
}
 
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFEENS2DHEURISTICSEEDEXTENSION_H_ */