NucleicAcid Class Reference
[Molecular Datastructures]

Nucleic acid class. More...

#include <nucleicAcid.h>

Inheritance diagram for NucleicAcid:

List of all members.

Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES }
	Properties.
Public Member Functions
bool	operator== (const NucleicAcid &nucleic_acid) const throw ()
	Equality operator.
bool	operator!= (const NucleicAcid &nucleic_acid) const throw ()
	Inequality operator.
Constructors and Destructors
	NucleicAcid () throw ()
	Default constructor.
	NucleicAcid (const NucleicAcid &nucleic_acid, bool deep=true) throw ()
	Copy constructor.
	NucleicAcid (const String &name, const String &id=BALL_NUCLEICACID_DEFAULT_ID) throw ()
	Detailed constructor.
virtual	~NucleicAcid () throw ()
	Destructor.
virtual void	clear () throw ()
	Clear the contents of the nucleic acid.
virtual void	destroy () throw ()
	Clear the contents of the nucleic acid and remove it from parent kernel objects.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Writes a NucleicAcid object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Reads a NucleicAcid object from a persistent stream.
Assignment Methods
void	set (const NucleicAcid &nucleic_acid, bool deep=true) throw ()
	Assignment with cloning facility.
NucleicAcid &	operator= (const NucleicAcid &nucleic_acid) throw ()
	Assignment operator.
void	get (NucleicAcid &nucleic_acid, bool deep=true) const throw ()
	Assign a NucleicAcid object from another.
void	swap (NucleicAcid &nucleic_acid) throw ()
	Swap the contents of two NucleicAcid objects.
Accessors
Nucleotide *	getNucleotide (Position position) throw ()
	Get a pointer to a child Nucleotide at a given position.
const Nucleotide *	getNucleotide (Position position) const throw ()
	Get a pointer to a child Nucleotide at a given position.
Nucleotide *	get3Prime () throw ()
	Retrieve a pointer to the Nucleotide at the 3'-end of this instance.
const Nucleotide *	get3Prime () const throw ()
	Retrieve a const pointer to the nucleotide at the 3'-end of this instance.
Nucleotide *	get5Prime () throw ()
	Retrieve a pointer to the Nucleotide at the 5'-end of this instance.
const Nucleotide *	get5Prime () const throw ()
	Retrieve a const pointer to the Nucleotide at the 5'-end of this instance.
void	setID (const String &id) throw ()
	Set the ID of the NucleicAcid.
const String &	getID () const throw ()
	Retrieve the ID of the NucleicAcid.
Size	countNucleotides () const throw ()
	Return the number of Nucleotides contained in this instance NucleicAcid.
Debugging and Diagnostics
virtual bool	isValid () const throw ()
	Internal state and consistency self-validation.
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const throw ()
	Internal state dump.

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Detailed Description

Nucleic acid class.

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Constructor & Destructor Documentation

NucleicAcid::NucleicAcid (   )  throw ()

Default constructor.

NucleicAcid::NucleicAcid (  const NucleicAcid &  nucleic_acid, bool  deep = true )  throw ()

Copy constructor.

NucleicAcid::NucleicAcid (  const String &  name, const String &  id = BALL_NUCLEICACID_DEFAULT_ID )  throw ()

Detailed constructor.

virtual NucleicAcid::~NucleicAcid (   )  throw () [virtual]

Destructor.

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Member Function Documentation

virtual void NucleicAcid::clear (   )  throw () [virtual]

Clear the contents of the nucleic acid. Reimplemented from AtomContainer.

Size NucleicAcid::countNucleotides (   )  const throw ()

Return the number of Nucleotides contained in this instance NucleicAcid. Returns: Size - number of Nucleotides

virtual void NucleicAcid::destroy (   )  throw () [virtual]

Clear the contents of the nucleic acid and remove it from parent kernel objects. Reimplemented from AtomContainer.

virtual void NucleicAcid::dump (  std::ostream &  s = std::cout, Size  depth = 0 )  const throw () [virtual]

Internal state dump. Dump the current internal state of this instance to the output ostream s with dumping depth depth . Parameters: s  - output stream where to output the internal state of this instance depth  - the dumping depth Reimplemented from Molecule.

void NucleicAcid::get (  NucleicAcid &  nucleic_acid, bool  deep = true )  const throw ()

Assign a NucleicAcid object from another.

const Nucleotide* NucleicAcid::get3Prime (   )  const throw ()

Retrieve a const pointer to the nucleotide at the 3'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide. Returns: Nucleotide* - constant pointer to the first child Nucleotide

Nucleotide* NucleicAcid::get3Prime (   )  throw ()

Retrieve a pointer to the Nucleotide at the 3'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide. Returns: Nucleotide* - mutable pointer to the first child Nucleotide

const Nucleotide* NucleicAcid::get5Prime (   )  const throw ()

Retrieve a const pointer to the Nucleotide at the 5'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide. Returns: Nucleotide* - constant pointer to the last child Nucleotide

Nucleotide* NucleicAcid::get5Prime (   )  throw ()

Retrieve a pointer to the Nucleotide at the 5'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide. Returns: Nucleotide* - mutable pointer to the last child Nucleotide

const String& NucleicAcid::getID (   )  const throw ()

Retrieve the ID of the NucleicAcid. Returns: String the ID

const Nucleotide* NucleicAcid::getNucleotide (  Position  position  )  const throw ()

Get a pointer to a child Nucleotide at a given position. The pointer is 0 if this instance does not have a Nucleotide at the given position. Parameters: position  the position of the child Nucleotide Returns: Nucleotide* - constant pointer to the child Nucleotide at positon

Nucleotide* NucleicAcid::getNucleotide (  Position  position  )  throw ()

Get a pointer to a child Nucleotide at a given position. The pointer is 0 if this instance does not have a Nucleotide at the given position. Parameters: position  the position of the child Nucleotide Returns: Nucleotide* - mutable pointer to the child Nucleotide at positon

virtual bool NucleicAcid::isValid (   )  const throw () [virtual]

Internal state and consistency self-validation. Returns: bool - true if the internal state of this instance atom is correct (self-validated) and consistent, false otherwise Reimplemented from AtomContainer.

bool NucleicAcid::operator!= (  const NucleicAcid &  nucleic_acid  )  const throw ()

Inequality operator. See also: operator ==

NucleicAcid& NucleicAcid::operator= (  const NucleicAcid &  nucleic_acid  )  throw ()

Assignment operator.

bool NucleicAcid::operator== (  const NucleicAcid &  nucleic_acid  )  const throw ()

Equality operator. Two nucleic acids are equal if they have the same handle. See also: Object::operator ==.

void NucleicAcid::persistentRead (  PersistenceManager &  pm  )  throw (Exception::GeneralException) [virtual]

Reads a NucleicAcid object from a persistent stream. Parameters: pm  the persistence manager Reimplemented from Molecule.

void NucleicAcid::persistentWrite (  PersistenceManager &  pm, const char *  name = 0 )  const throw (Exception::GeneralException) [virtual]

Writes a NucleicAcid object to a persistent stream. Parameters: pm  the persistence manager Reimplemented from Molecule.

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

Assignment with cloning facility. The assignment is either deep or shallow (default). Parameters: nucleic_acid  the NucleicAcid to be copied (cloned) deep  make a deep (=true) or shallow (=false) copy

void NucleicAcid::setID (  const String &  id  )  throw ()

Set the ID of the NucleicAcid. Parameters: id  the new ID

void NucleicAcid::swap (  NucleicAcid &  nucleic_acid  )  throw ()

Swap the contents of two NucleicAcid objects.