PredictorMfeEns2dSeedExtension.h

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#ifndef INTARNA_PREDICTORMFEENS2DSEEDEXTENSION_H_
#define INTARNA_PREDICTORMFEENS2DSEEDEXTENSION_H_
 
#include "IntaRNA/PredictorMfeEns.h"
#include "IntaRNA/BasePairProbabilities.h"
#include "IntaRNA/Matrix.h"
#include "IntaRNA/SeedHandlerIdxOffset.h"
#include "IntaRNA/StackSeedDomain.h"
#include <functional>
#include <memory>
 
namespace IntaRNA {
 
class PredictorMfeEns2dSeedExtension: public PredictorMfeEns {
 
protected:
    void addSeedPartition(Interaction::BasePair seed, Interaction::BasePair left,
            Interaction::BasePair right, Z_type hybridZ);
 
    typedef Matrix<Z_type> Z2dMatrix;
 
public:
 
 
    PredictorMfeEns2dSeedExtension(
            const InteractionEnergy & energy
            , OutputHandler & output
            , PredictionTracker * predTracker
            , SeedHandler * seedHandler
            , BasePairProbabilities * pairProbabilities = nullptr );
 
 
    virtual ~PredictorMfeEns2dSeedExtension() override;
 
 
    virtual
    void
    predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos)
            , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override;
 
 
protected:
 
    virtual Z_type exactBoundaryWeight(size_t i1,size_t j1,size_t i2,size_t j2) const;
    void predictStackSeeds(const IndexRange & r1,const IndexRange & r2);
    virtual void prepareStackSeedExtensions(size_t n,size_t m,const StackSeedDomain & seeds);
    virtual std::function<Interaction::BasePair(Interaction::BasePair,Interaction::BasePair)>
    stackSeedRightSelector() const;
 
    struct ExtensionProbabilityTrace;
    std::unique_ptr<ExtensionProbabilityTrace> extensionProbabilityTrace;
    void initExtensionProbabilities(size_t n,size_t m);
    void beginExtensionProbabilitySeed(size_t i1,size_t i2);
    void addExtensionProbabilityRoot(size_t i1,size_t j1,size_t i2,size_t j2,
            Z_type partZ,bool left,bool right);
    void finishExtensionProbabilitySeed();
    void commitExtensionProbabilities();
    std::vector<Interaction::BasePair> extensionSeedPrefix(size_t i1,size_t i2,size_t before) const;
 
    BasePairProbabilities * pairProbabilities;
 
    using PredictorMfeEns::energy;
 
    using PredictorMfeEns::output;
 
    Z2dMatrix hybridZ_left;
 
    SeedHandlerIdxOffset seedHandler;
 
    Z2dMatrix hybridZ_right;
 
protected:
 
    virtual
    void
    fillHybridZ_left( const size_t j1, const size_t j2 );
 
    virtual
    void
    fillHybridZ_right( const size_t i1, const size_t i2 );
 
    virtual
    void
    traceBack( Interaction & interaction ) override;
 
    virtual
    E_type
    getNonOverlappingEnergy( const size_t si1, const size_t si2, const size_t sj1, const size_t sj2 );
 
    // debug function
    void
    printMatrix( const Z2dMatrix & matrix );
 
};
 
} // namespace
 
#endif /* INTARNA_PREDICTORMFEENS2DSEEDEXTENSION_H_ */