nucleotideMapping.h

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#ifndef BALL_STRUCTURE_NUCLEOTIDEMAPPING_H
#define BALL_STRUCTURE_NUCLEOTIDEMAPPING_H

#include <string>

#include <BALL/DATATYPE/hashMap.h>

namespace BALL
{
  class Chain;
  class Residue;

  class BALL_EXPORT NucleotideMapping
  {
    public:
      typedef std::pair<const std::string, const std::string> Alignment;

      NucleotideMapping();


      static NucleotideMapping assignNaively(Chain& a, Chain& b, unsigned int offset_a = 0, unsigned int offset_b = 0);

      static NucleotideMapping assignFromDistances(Chain& a, Chain& b);

      static NucleotideMapping assignFromAlignment(Chain& a, Chain& b, const Alignment& alignment);



      Chain* getFirstStrand() const;

      Chain* getSecondStrand() const;

      Residue* firstToSecond(Residue* a) const;

      Residue* secondToFirst(Residue* b) const;

    private:
      typedef HashMap<Residue*, Residue*> NucleotideMap;
      NucleotideMapping(Chain& a, Chain& b, const NucleotideMap& a_to_b, const NucleotideMap& b_to_a);

      Chain* a_;
      Chain* b_;

      NucleotideMap a_to_b_;
      NucleotideMap b_to_a_;
  };
}

#endif //BALL_STRUCTURE_NUCLEOTIDEMAPPING_H