SeedHandler.h

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#ifndef INTARNA_SEEDHANDLER_H_
#define INTARNA_SEEDHANDLER_H_
 
#include "IntaRNA/InteractionEnergy.h"
#include "IntaRNA/SeedConstraint.h"
 
#include <boost/multi_array.hpp>
 
 
namespace IntaRNA {
 
class SeedHandler
{
 
public:
 
    virtual bool guaranteesStackOnlySeeds() const;
 
 
    SeedHandler(
            const InteractionEnergy & energy
            , const SeedConstraint & seedConstraint
            );
 
    virtual ~SeedHandler();
 
    virtual
    const SeedConstraint&
    getConstraint() const;
 
    virtual
    const InteractionEnergy&
    getInteractionEnergy() const;
 
 
    virtual
    size_t
    fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) = 0;
 
    virtual
    void
    traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const = 0;
 
 
    virtual
    E_type
    getSeedE( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    bool
    isSeedBound( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    size_t
    getSeedLength1( const size_t i1, const size_t i2 ) const = 0;
 
    virtual
    size_t
    getSeedLength2( const size_t i1, const size_t i2 ) const = 0;
 
 
    virtual
    bool
    updateToNextSeed( size_t & i1, size_t & i2
            , const size_t i1min = 0, const size_t i1max = RnaSequence::lastPos
            , const size_t i2min = 0, const size_t i2max = RnaSequence::lastPos
            ) const;
 
    virtual
    void
    addSeeds( Interaction & i ) const;
 
    virtual
    bool
    areLoopOverlapping( const size_t i1, const size_t i2
                    , const size_t k1, const size_t k2 ) const;
 
    virtual
    bool
    isFeasibleSeedBasePair( const size_t i1
                        , const size_t i2
                        , const bool atEndOfSeed = false ) const;
 
protected:
 
    const InteractionEnergy& energy;
 
    const SeedConstraint & seedConstraint;
 
 
 
};
 
 
 
 
inline
SeedHandler::SeedHandler(
        const InteractionEnergy & energy
        , const SeedConstraint & seedConstraint
        )
    :
        energy(energy)
        , seedConstraint(seedConstraint)
{
}
 
 
inline
SeedHandler::~SeedHandler()
{
}
 
 
inline
const SeedConstraint&
SeedHandler::
getConstraint() const
{
    return seedConstraint;
}
 
 
inline
const InteractionEnergy&
SeedHandler::
getInteractionEnergy() const
{
    return energy;
}
 
 
inline bool
SeedHandler::guaranteesStackOnlySeeds() const
{
    return false;
}
 
} // namespace
 
#endif /* SEEDHANDLER_H_ */