BALL::Nucleotide Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/nucleotide.h>

Inheritance diagram for BALL::Nucleotide:

Public Types
Enums

enum	Property { PROPERTY__5_PRIME = Residue::NUMBER_OF_PROPERTIES + 1, PROPERTY__3_PRIME, PROPERTY__NUCLEOTIDE, NUMBER_OF_PROPERTIES }
	The number of predefined properties for AtomContainer. More...
Public Member Functions
bool	operator== (const Nucleotide &nucleotide) const
bool	operator!= (const Nucleotide &nucleotide) const
Constructors and Destructors

	Nucleotide ()
	Default constructor.
	Nucleotide (const Nucleotide &nucleotide, bool deep=true)
	Copy constructor.
	Nucleotide (const String &name, const String &id=BALL_NUCLEOTIDE_DEFAULT_ID, char insertion_code=BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE)
	Detailled constructor.
virtual	~Nucleotide ()
	Destructor.
virtual void	clear ()
	Clears the nucleotides contents.
virtual void	destroy ()
	Clears the nucleotides contents and removes it from all composite structures.
Persistence

void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
Assignment

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)
Accessors

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)
Predicates

bool	isTerminal () const
bool	is3Prime () const
bool	is5Prime () const
Debugging and Diagnostics

virtual bool	isValid () const
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
Private Member Functions
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
Private Attributes
String	id_
char	insertion_code_

Detailed Description

Nucleotide class. This class is used to represent nucleotides within an NucleicAcid object.

Definition at line 37 of file nucleotide.h.

Member Enumeration Documentation

enum BALL::Nucleotide::Property

The number of predefined properties for AtomContainer.

Enumerator:

PROPERTY__5_PRIME
PROPERTY__3_PRIME
PROPERTY__NUCLEOTIDE
NUMBER_OF_PROPERTIES

Reimplemented from BALL::Fragment.

Definition at line 49 of file nucleotide.h.

Constructor & Destructor Documentation

BALL::Nucleotide::Nucleotide ( )

Default constructor.

BALL::Nucleotide::Nucleotide	(	const Nucleotide &	nucleotide,
		bool	deep = `true`
	)

Copy constructor.

BALL::Nucleotide::Nucleotide	(	const String &	name,
		const String &	id = `BALL_NUCLEOTIDE_DEFAULT_ID`,
		char	insertion_code = `BALL_NUCLEOTIDE_DEFAULT_INSERTION_CODE`
	)

Detailled constructor.

virtual BALL::Nucleotide::~Nucleotide ( ) [virtual]

Destructor.

Member Function Documentation

void BALL::Nucleotide::append ( AtomContainer & atom_container ) [private]

Append an AtomContainer at the last position.

Parameters:

atom_container

the AtomContainer to prepend

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::append ( Atom & atom )

Append an atom after the last position.

Parameters:

atom

the atom to append

Reimplemented from BALL::AtomContainer.

virtual void BALL::Nucleotide::clear ( ) [virtual]

Clears the nucleotides contents.

Reimplemented from BALL::AtomContainer.

Size BALL::Nucleotide::countAtomContainers ( ) const [private]

Count the child AtomContainers.

Returns:: Size the number of AtomContainers

Reimplemented from BALL::AtomContainer.

virtual void BALL::Nucleotide::destroy ( ) [virtual]

Clears the nucleotides contents and removes it from all composite structures.

Reimplemented from BALL::AtomContainer.

virtual void BALL::Nucleotide::dump	(	std::ostream &	s = `std::cout`,
		Size	depth = `0`
	)			const `[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 nucleotide
	depth	the dumping depth

Reimplemented from BALL::Fragment.

void BALL::Nucleotide::get	(	Nucleotide &	nucleotide,
		bool	deep = `true`
	)			const

Copy this instance to nucleotide . The assignment is either deep or shallow (default).

Parameters:

nucleotide

the nucleotide to be assigned to

See also:: nucleotide::set

const AtomContainer* BALL::Nucleotide::getAtomContainer ( Position position ) const [private]

Get a constant pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters:

position

of the child AtomContainer

Returns:: AtomContainer* - constant pointer to the child

Reimplemented from BALL::AtomContainer.

AtomContainer* BALL::Nucleotide::getAtomContainer ( Position position ) [private]

Get a pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters:

position

of the child AtomContainer

Returns:: AtomContainer* - mutable pointer to the child

Reimplemented from BALL::AtomContainer.

const String& BALL::Nucleotide::getID ( ) const

Retrieve the ID of the nucleotide.

Returns:: String the ID (constant)

char BALL::Nucleotide::getInsertionCode ( ) const

Retrieve the insertion code of the nucleotide.

Returns:: String the insertion code (constant)

const NucleicAcid* BALL::Nucleotide::getNucleicAcid ( ) const

Get a pointer to the parent NucleicAcid. The pointer is 0 if this instance nucleotide does not have a parent NucleicAcid.

Returns:: NucleicAcid* - constant pointer to the parent NucleicAcid

NucleicAcid* BALL::Nucleotide::getNucleicAcid ( )

Get a pointer to the parent NucleicAcid. The pointer is 0 if this instance nucleotide does not have a parent NucleicAcid.

Returns:: NucleicAcid* - mutable pointer to the parent NucleicAcid

void BALL::Nucleotide::insert ( AtomContainer & atom_container ) [private]

Insert an AtomContainer at the last position.

Parameters:

atom_container

the AtomContainer to insert

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::insert ( Atom & atom )

Insert an atom after the last position.

Parameters:

atom

the atom to insert

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::insertAfter	(	AtomContainer &	atom_container,
		Composite &	after
	)			`[private]`

Insert an AtomContainer after a given Composite object.

Parameters:

	atom_container	the AtomContainer to insert
	after	the Composite object to insert after

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::insertAfter	(	Atom &	atom,
		Composite &	after
	)

Insert an atom after a given Composite object.

Parameters:

	atom	the atom to insert
	after	the Composite object to insert after

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::insertBefore	(	AtomContainer &	atom_container,
		Composite &	before
	)			`[private]`

Insert an AtomContainer before a given Composite object.

Parameters:

	atom_container	the AtomContainer to insert
	before	the Composite object to insert before

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::insertBefore	(	Atom &	atom,
		Composite &	before
	)

Insert an atom before a given Composite object.

Parameters:

	atom	the atom to insert
	before	the Composite object to insert before

Reimplemented from BALL::AtomContainer.

bool BALL::Nucleotide::is3Prime ( ) const

Test if this instance nucleotide is 3-prime. Returns true, if this instance is the first nucleotide in its parent NucleicAcid.

Returns:: bool

bool BALL::Nucleotide::is5Prime ( ) const

Test if this instance nucleotide is 5-prime. Returns true, if this instance is the last nucleotide in its parent NucleicAcid.

Returns:: bool

bool BALL::Nucleotide::isSuperAtomContainerOf ( const AtomContainer & atom_container ) const [private]

Test if an AtomContainer is the parent.

Parameters:

atom_container

the AtomContainer to test

Reimplemented from BALL::AtomContainer.

bool BALL::Nucleotide::isTerminal ( ) const

Test if this instance nucleotide is terminal. Returns true, if this instance is the first or last nucleotide in its parent NucleicAcid.

Returns:: bool

virtual bool BALL::Nucleotide::isValid ( ) const [virtual]

Internal state and consistency self-validation.

Returns:: bool - true if the internal state of this instance nucleotide is correct (self-validated) and consistent, false otherwise

Reimplemented from BALL::AtomContainer.

bool BALL::Nucleotide::operator!= ( const Nucleotide & nucleotide ) const

Inequality operator

See also:: operator ==

Nucleotide& BALL::Nucleotide::operator= ( const Nucleotide & nucleotide )

Assignment operator. The assignment is either deep or shallow (default).

Parameters:

nucleotide

the nucleotide to be copied (cloned)

Returns:: nucleotide& - this instance nucleotide

See also:: nucleotide::set

bool BALL::Nucleotide::operator== ( const Nucleotide & nucleotide ) const

Equality operator. Two nucleotides are equal if they have the same handle.

See also:: Object::operator ==.

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

Reads a Nucleotide object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Fragment.

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

Writes a Nucleotide object to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Fragment.

void BALL::Nucleotide::prepend ( AtomContainer & atom_container ) [private]

Prepend an AtomContainer at position 0.

Parameters:

atom_container

the AtomContainer to prepend

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::prepend ( Atom & atom )

Prepend an atom at position 0.

Parameters:

atom

the atom to prepend

Reimplemented from BALL::AtomContainer.

bool BALL::Nucleotide::remove ( AtomContainer & atom_container ) [private]

Remove an AtomContainer

Parameters:

atom_container

the AtomContainer to remove

Returns:: false if {atom_container} could not be removed

Reimplemented from BALL::AtomContainer.

bool BALL::Nucleotide::remove ( Atom & atom )

Remove an atom.

Parameters:

atom

the atom to remove

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::set	(	const Nucleotide &	nucleotide,
		bool	deep = `true`
	)

Assignment with cloning facility. The assignment is either deep or shallow (default).

Parameters:

	nucleotide	the nucleotide to be copied (cloned)
	deep	make a deep (=`true`) or shallow (=`false`) copy

void BALL::Nucleotide::setID ( const String & id )

Set the ID of the nucleotide.

Parameters:

id

the new ID

void BALL::Nucleotide::setInsertionCode ( char insertion_code )

Set the insertion code of the nucleotide.

Parameters:

insertion_code

the new insertion code

void BALL::Nucleotide::splice ( AtomContainer & atom_container ) [private]

Move the children of {atom_container} into this instance. The children of atom_container are inserted at its position if it is is a child of this. Otherwise the children are inserted using spliceBefore .

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::splice ( Nucleotide & nucleotide )

Move the children of nucleotide into this instance. The children are inserted using spliceBefore .

void BALL::Nucleotide::spliceAfter ( AtomContainer & atom_container ) [private]

Cut all children of atom_container and append them after the children of this instance.

Parameters:

atom_container

the AtomContainer to access

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::spliceAfter ( Nucleotide & nucleotide )

Cut all children of nucleotide and append them after the children of this instance.

Parameters:

nucleotide

the nucleotide to access

void BALL::Nucleotide::spliceBefore ( AtomContainer & atom_container ) [private]

Cut all children of atom_container and prepend them before the children of this instance.

Parameters:

atom_container

the AtomContainer to access

Reimplemented from BALL::AtomContainer.

void BALL::Nucleotide::spliceBefore ( Nucleotide & nucleotide )

Cut all children of nucleotide and prepend them before the children of this instance.

Parameters:

nucleotide

the nucleotide to access

void BALL::Nucleotide::swap ( Nucleotide & nucleotide )

Swapping of instaces of nucleotide.

Parameters:

nucleotide

the instance of nucleotide to swap with

Member Data Documentation

String BALL::Nucleotide::id_ [private]

Definition at line 309 of file nucleotide.h.

char BALL::Nucleotide::insertion_code_ [private]

Definition at line 311 of file nucleotide.h.

BALL::Nucleotide Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

BALL::Nucleotide Class Reference
[Molecular Datastructures]