nucleotide.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_KERNEL_NUCLEOTIDE_H
#define BALL_KERNEL_NUCLEOTIDE_H

#ifndef BALL_KERNEL_FRAGMENT_H
# include <BALL/KERNEL/fragment.h>
#endif

#ifndef BALL_KERNEL_RESIDUE_H
# include <BALL/KERNEL/residue.h>
#endif

#ifndef BALL_KERNEL_NUCLEOTIDEITERATOR_H
# include <BALL/KERNEL/nucleotideIterator.h>
#endif

 
#define BALL_NUCLEOTIDE_DEFAULT_ID               ""
#define BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE   ' '

namespace BALL 
{
  class NucleicAcid;

  class BALL_EXPORT Nucleotide
    : public Fragment
  {
    public:

    BALL_CREATE_DEEP(Nucleotide)
  
    

    enum Property
    {
      PROPERTY__5_PRIME = Residue::NUMBER_OF_PROPERTIES + 1,
      PROPERTY__3_PRIME,
      PROPERTY__NUCLEOTIDE,

      NUMBER_OF_PROPERTIES
    };


  
    Nucleotide();
  
    Nucleotide(const Nucleotide& nucleotide, bool deep = true);
  
    Nucleotide
      (const String& name,
       const String& id = BALL_NUCLEOTIDE_DEFAULT_ID,
       char insertion_code = BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE);

    virtual ~Nucleotide();

    virtual void clear();
  
    virtual void destroy();
  


    void persistentWrite(PersistenceManager& pm, const char* name = 0) const;

    void persistentRead(PersistenceManager& pm);



    void set(const Nucleotide& nucleotide, bool deep = true);

    Nucleotide& operator = (const Nucleotide& nucleotide);

    void get(Nucleotide& nucleotide, bool deep = true) const;

    void swap(Nucleotide& nucleotide);
  

    bool operator == (const Nucleotide& nucleotide) const;

    bool operator != (const Nucleotide& nucleotide) const;


    NucleicAcid* getNucleicAcid();
    
    const NucleicAcid* getNucleicAcid() const;

    void setID(const String& id);

    const String& getID() const;

    void setInsertionCode(char insertion_code);

    char getInsertionCode() const;

    void prepend(Atom& atom);

    void append(Atom& atom);

    void insert(Atom& atom);

    void insertBefore(Atom& atom, Composite& before);

    void insertAfter(Atom& atom, Composite& after);

    bool remove(Atom& atom);

    void spliceBefore(Nucleotide& nucleotide);

    void spliceAfter(Nucleotide& nucleotide);

    void splice(Nucleotide& nucleotide);



    bool isTerminal() const;
  
    bool is3Prime() const;

    bool is5Prime() const;



    virtual bool isValid() const;

    virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;

 
    private:

    AtomContainer* getAtomContainer(Position position);
  
    const AtomContainer* getAtomContainer(Position position) const;
  
    Size countAtomContainers() const;

    void prepend(AtomContainer& atom_container);

    void append(AtomContainer& atom_container);

    void insert(AtomContainer& atom_container);

    void insertBefore(AtomContainer& atom_container, Composite& composite);

    void insertAfter(AtomContainer& atom_container, Composite& composite);

    void spliceBefore(AtomContainer& atom_container);

    void spliceAfter(AtomContainer& base_ragment);

    void splice(AtomContainer& AtomContainer);

    bool remove(AtomContainer& AtomContainer);

    bool isSuperAtomContainerOf(const AtomContainer& atom_container) const;

    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(AtomContainer)

    // --- ATTRIBUTES

    String  id_;

    char    insertion_code_;
  };


  template <class NucleotideContainerType>
  const Nucleotide* get5Prime(const NucleotideContainerType& nucleotide_container)
  {
    NucleotideConstIterator res_it;
    for ( res_it = nucleotide_container.beginNucleotide(); !res_it.isEnd(); ++res_it)
    {
      return &(*res_it);
    }

    return 0;
  }

  template <class NucleotideContainerType>
  const Nucleotide* get3Prime(const NucleotideContainerType& nucleotide_container)
  {
    for (NucleotideConstIterator res_it = nucleotide_container.rbeginNucleotide(); !res_it.isREnd(); ++res_it)
    {
      return &(*res_it);
    }

    return 0;
  }
 
} // namespace BALL

#endif // BALL_KERNEL_NUCLEOTIDE_H