nucleicAcid.h

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

#ifndef BALL_KERNEL_NUCLEICACID_H
#define BALL_KERNEL_NUCLEICACID_H

#ifndef BALL_KERNEL_MOLECULE_H
# include <BALL/KERNEL/molecule.h>
#endif

#ifndef BALL_KERNEL_NUCLEOTIDE_H
# include <BALL/KERNEL/nucleotide.h>
#endif

#define BALL_NUCLEICACID_DEFAULT_ID   ""

namespace BALL 
{
  class BALL_EXPORT NucleicAcid
    : public Molecule
  {
    public:

    BALL_CREATE_DEEP(NucleicAcid)

    
      
    
    enum Property
    {
      NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES
    };



    NucleicAcid();
  
    NucleicAcid(const NucleicAcid& nucleic_acid, bool deep = true);
  
    NucleicAcid(const String& name,
        const String& id = BALL_NUCLEICACID_DEFAULT_ID);

    virtual ~NucleicAcid();
  
    virtual void clear();
  
    virtual void destroy();


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

    void persistentRead(PersistenceManager& pm);



    void set(const NucleicAcid& nucleic_acid, bool deep = true);

    NucleicAcid& operator = (const NucleicAcid& nucleic_acid);

    void get(NucleicAcid& nucleic_acid, bool deep = true) const;
  
    void swap(NucleicAcid& nucleic_acid);
  

    bool operator == (const NucleicAcid& nucleic_acid) const;

    bool operator != (const NucleicAcid& nucleic_acid) const;


    Nucleotide* getNucleotide(Position position);
  
    const Nucleotide* getNucleotide(Position position) const;

    Nucleotide* get3Prime();

    const Nucleotide* get3Prime() const;

    Nucleotide* get5Prime();

    const Nucleotide* get5Prime() const;

    void setID(const String& id);

    const String& getID() const;

    Size countNucleotides() const;


    using Molecule::prepend;
    using Molecule::append;
    using Molecule::insert;
    using Molecule::insertBefore;
    using Molecule::insertAfter;
    using Molecule::remove;
    using Molecule::splice;
    using Molecule::spliceBefore;
    using Molecule::spliceAfter;


    virtual bool isValid() const;

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


    // --- EXTERNAL ITERATORS

    BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Nucleotide)
    

    private:

    // --- ATTRIBUTES

    String id_;
  };
} // namespace BALL

#endif // BALL_KERNEL_NUCLEICACID_H

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