BALL::NucleicAcid Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/nucleicAcid.h>

Inheritance diagram for BALL::NucleicAcid:

List of all members.

Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES }
Public Member Functions
bool	operator== (const NucleicAcid &nucleic_acid) const
bool	operator!= (const NucleicAcid &nucleic_acid) const
Constructors and Destructors
	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 ()
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
Assignment Methods
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)
Accessors
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
Debugging and Diagnostics
virtual bool	isValid () const
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
Private Attributes
String	id_

---

Detailed Description

Nucleic acid class.

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Member Enumeration Documentation

enum BALL::NucleicAcid::Property

Properties

Enumerator:

NUMBER_OF_PROPERTIES

Reimplemented from BALL::Molecule.

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Constructor & Destructor Documentation

BALL::NucleicAcid::NucleicAcid

(

)

Default constructor.

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

Copy constructor.

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

Detailed constructor.

virtual BALL::NucleicAcid::~NucleicAcid

(

)

[virtual]

Destructor.

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Member Function Documentation

virtual void BALL::NucleicAcid::clear

(

)

[virtual]

Clear the contents of the nucleic acid.

Reimplemented from BALL::AtomContainer.

Size BALL::NucleicAcid::countNucleotides

(

)

const

Return the number of Nucleotides contained in this instance NucleicAcid.

Returns:

Size - number of Nucleotides

virtual void BALL::NucleicAcid::destroy

(

)

[virtual]

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

Reimplemented from BALL::AtomContainer.

virtual void BALL::NucleicAcid::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
	depth	- the dumping depth

Reimplemented from BALL::Molecule.

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

Assign a NucleicAcid object from another.

const Nucleotide* BALL::NucleicAcid::get3Prime

(

)

const

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* BALL::NucleicAcid::get3Prime

(

)

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* BALL::NucleicAcid::get5Prime

(

)

const

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* BALL::NucleicAcid::get5Prime

(

)

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& BALL::NucleicAcid::getID

(

)

const

Retrieve the ID of the NucleicAcid.

Returns:

String the ID

const Nucleotide* BALL::NucleicAcid::getNucleotide

(

Position

position

)

const

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* BALL::NucleicAcid::getNucleotide

(

Position

position

)

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 BALL::NucleicAcid::isValid

(

)

const [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 BALL::AtomContainer.

bool BALL::NucleicAcid::operator!=

(

const NucleicAcid &

nucleic_acid

)

const

Inequality operator

See also:

operator ==

NucleicAcid& BALL::NucleicAcid::operator=

(

const NucleicAcid &

nucleic_acid

)

Assignment operator.

bool BALL::NucleicAcid::operator==

(

const NucleicAcid &

nucleic_acid

)

const

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

See also:

Object::operator ==.

void BALL::NucleicAcid::persistentRead

(

PersistenceManager &

pm

)

throw (Exception::GeneralException) [virtual]

Reads a NucleicAcid object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Molecule.

void BALL::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 BALL::Molecule.

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

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 BALL::NucleicAcid::setID

(

const String &

id

)

Set the ID of the NucleicAcid.

Parameters:

id

the new ID

void BALL::NucleicAcid::swap

(

NucleicAcid &

nucleic_acid

)

Swap the contents of two NucleicAcid objects.

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Member Data Documentation

String BALL::NucleicAcid::id_ [private]