AccessibilityBasePair.h

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#ifndef INTARNA_ACCESSIBILITYBASEPAIR_H_
#define INTARNA_ACCESSIBILITYBASEPAIR_H_
 
#include "IntaRNA/general.h"
#include "IntaRNA/RnaSequence.h"
#include "IntaRNA/Accessibility.h"
#include "IntaRNA/AccessibilityConstraint.h"
#include "IntaRNA/NussinovHandler.h"
 
 
namespace IntaRNA {
 
class AccessibilityBasePair: public Accessibility {
 
public:
  /***
   * Constructor of AccessibilityBasePair
   * @param seq The sequence the accessibility data belongs to
   * @param maxLength the maximal length of accessible regions (>0) to be
   *          considered. 0 defaults to the full sequence's length, otherwise
   *          is is internally set to min(maxLength,seq.length).
   * @param accConstr optional accessibility constraint
   * @param basePairEnergy The energy value of the base pairs
   * @param RT The temperature energy constant
   * @param minLoopLength the minimum loop length
   */
  AccessibilityBasePair(
      const RnaSequence& seq,
      const size_t maxLength,
      const AccessibilityConstraint * const accConstr,
      const E_type basePairEnergy = Ekcal_2_E(-1.0),
      const Z_type RT = 1,
      const size_t minLoopLength = 3);
 
  /***
   * Destructor of AccessibilityBasePair
   */
  virtual ~AccessibilityBasePair();
 
  /***
   * Returns the accessibility energy value between the indices (from, to)
   * in the given sequence.
   * @param from The start index of the region
   * @param to The end index of the region
   *
   * @return The ED Value
   *
   * @throw std::runtime_error in case it does not hold 0 <= from <= to < seq.length
   */
    virtual E_type getED( const size_t from, const size_t to ) const;
 
protected:
 
    const E_type basePairEnergy;
    const Z_type RT;
  const Z_type basePairWeight;
  const size_t minLoopLength;
 
  /***
   * Results of getED lookup table
   */
  NussinovHandler::E2dMatrix logPu;
 
};
 
}  // namespace IntaRNA
 
#endif /* INTARNA_ACCESSIBILITYBASEPAIR_H_ */