BALL::NucleicAcid Class Reference

#include <BALL/KERNEL/nucleicAcid.h>

Inheritance diagram for BALL::NucleicAcid:

Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES }
Public Types inherited from BALL::Molecule
enum	Property { IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES, NUMBER_OF_PROPERTIES }
Public Types inherited from BALL::AtomContainer
enum	Property { NUMBER_OF_PROPERTIES = 0 }
	The number of predefined properties for AtomContainer. More...
Public Types inherited from BALL::Composite
typedef ForwardIterator < Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorIterator
typedef ConstForwardIterator < Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorConstIterator
typedef BidirectionalIterator < Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeIterator
typedef ConstBidirectionalIterator < Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeConstIterator
typedef std::reverse_iterator < ChildCompositeIterator >	ChildCompositeReverseIterator
typedef std::reverse_iterator < ChildCompositeConstIterator >	ChildCompositeConstReverseIterator
typedef BidirectionalIterator < Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeIterator
typedef ConstBidirectionalIterator < Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeConstIterator
typedef std::reverse_iterator < CompositeIterator >	CompositeReverseIterator
typedef std::reverse_iterator < CompositeConstIterator >	CompositeConstReverseIterator
enum	StampType { MODIFICATION = 1, SELECTION = 2, BOTH = 3 }
typedef UnaryPredicate< Composite >	KernelPredicateType

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
void	persistentRead (PersistenceManager &pm)
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
Public Member Functions inherited from BALL::Molecule
bool	operator== (const Molecule &molecule) const
bool	operator!= (const Molecule &molecule) const
	Molecule ()
	Molecule (const Molecule &molecule, bool deep=true)
	Molecule (const String &name)
virtual	~Molecule ()
void	set (const Molecule &molecule, bool deep=true)
Molecule &	operator= (const Molecule &molecule)
void	get (Molecule &molecule, bool deep=true) const
void	swap (Molecule &molecule)
System *	getSystem ()
const System *	getSystem () 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	prepend (AtomContainer &atom_container)
void	append (AtomContainer &atom_container)
void	insert (AtomContainer &atom_container)
void	insertBefore (AtomContainer &atom_container, Composite &before)
void	insertAfter (AtomContainer &atom_container, Composite &after)
void	spliceBefore (AtomContainer &atom_container)
void	spliceAfter (AtomContainer &atom_container)
void	splice (AtomContainer &atom_container)
bool	remove (AtomContainer &atom_container)
Public Member Functions inherited from BALL::AtomContainer
	AtomContainer ()
	AtomContainer (const AtomContainer &atom_container, bool deep=true)
	AtomContainer (const String &name)
virtual	~AtomContainer ()
void	set (const AtomContainer &atom_container, bool deep=true)
AtomContainer &	operator= (const AtomContainer &atom_container)
void	get (AtomContainer &atom_container, bool deep=true) const
void	swap (AtomContainer &atom_container)
bool	operator== (const AtomContainer &atom_container) const
bool	operator!= (const AtomContainer &atom_container) const
bool	isSuperAtomContainerOf (const AtomContainer &atom_container) const
void	setName (const String &name)
const String &	getName () const
AtomContainer *	getAtomContainer (Position position)
const AtomContainer *	getAtomContainer (Position position) const
Atom *	getAtom (Position position)
const Atom *	getAtom (Position position) const
Atom *	getAtom (const String &name)
const Atom *	getAtom (const String &name) const
Size	countAtomContainers () const
Size	countAtoms () const
Size	countBonds () const
Size	countInterBonds () const
Size	countIntraBonds () const
Size	removeHavingProperty (BALL::Property p)
Size	removeNotHavingProperty (BALL::Property p)
Size	removeHavingProperty (const string &name)
Size	removeNotHavingProperty (const string &name)
void	destroyBonds ()
bool	applyIntraBond (UnaryProcessor< Bond > &processor)
	Apply to all bonds connecting two atoms inside this AtomContainer.
bool	applyInterBond (UnaryProcessor< Bond > &processor)
	Apply to all bonds connected to atoms outside this AtomContainer.
Public Member Functions inherited from BALL::Composite
AncestorIterator	beginAncestor ()
AncestorIterator	endAncestor ()
AncestorConstIterator	beginAncestor () const
AncestorConstIterator	endAncestor () const
ChildCompositeIterator	beginChildComposite ()
ChildCompositeIterator	endChildComposite ()
ChildCompositeConstIterator	beginChildComposite () const
ChildCompositeConstIterator	endChildComposite () const
ChildCompositeReverseIterator	rbeginChildComposite ()
ChildCompositeReverseIterator	rendChildComposite ()
ChildCompositeConstReverseIterator	rbeginChildComposite () const
ChildCompositeConstReverseIterator	rendChildComposite () const
CompositeIterator	beginComposite ()
CompositeIterator	endComposite ()
CompositeConstIterator	beginComposite () const
CompositeConstIterator	endComposite () const
CompositeReverseIterator	rbeginComposite ()
CompositeReverseIterator	rendComposite ()
CompositeConstReverseIterator	rbeginComposite () const
CompositeConstReverseIterator	rendComposite () const
void	deleteChildrenList_ (std::list< Composite * > &composites)
	Composite ()
	Composite (const Composite &composite, bool deep=true)
virtual	~Composite ()
void	destroy (bool virtual_destroy)
void *	clone (Composite &root) const
bool	operator== (const Composite &composite) const
bool	operator!= (const Composite &composite) const
bool	isEmpty () const
bool	isRoot () const
bool	isRootOf (const Composite &composite) const
bool	isInterior () const
bool	hasChild () const
bool	isChildOf (const Composite &composite) const
bool	isFirstChild () const
bool	isFirstChildOf (const Composite &composite) const
bool	isLastChild () const
bool	isLastChildOf (const Composite &composite) const
bool	hasParent () const
bool	isParentOf (const Composite &composite) const
bool	hasSibling () const
bool	isSiblingOf (const Composite &composite) const
bool	hasPreviousSibling () const
bool	isPreviousSiblingOf (const Composite &composite) const
bool	hasNextSibling () const
bool	isNextSiblingOf (const Composite &composite) const
bool	isDescendantOf (const Composite &composite) const
template<typename T >
bool	hasAncestor (const T &dummy) const
bool	isAncestorOf (const Composite &composite) const
bool	isRelatedWith (const Composite &composite) const
bool	isHomomorph (const Composite &composite) const
bool	containsSelection () const
void	host (Visitor< Composite > &visitor)
template<typename T >
bool	applyAncestor (UnaryProcessor< T > &processor)
template<typename T >
bool	applyChild (UnaryProcessor< T > &processor)
template<typename T >
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)
template<typename T >
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)
template<typename T >
bool	applyDescendant (UnaryProcessor< T > &processor)
template<typename T >
bool	applyPreorder (UnaryProcessor< T > &processor)
template<typename T >
bool	applyPostorder (UnaryProcessor< T > &processor)
template<typename T >
bool	apply (UnaryProcessor< T > &processor)
template<typename T >
bool	applyLevel (UnaryProcessor< T > &processor, long level)
void	set (const Composite &composite, bool deep=true)
Composite &	operator= (const Composite &composite)
void	get (Composite &composite, bool deep=true) const
Size	getDegree () const
Size	count (const KernelPredicateType &predicate) const
Size	countDescendants () const
Size	getPathLength (const Composite &composite) const
Size	getDepth () const
Size	getHeight () const
Composite &	getRoot ()
const Composite &	getRoot () const
Composite *	getLowestCommonAncestor (const Composite &composite)
const Composite *	getLowestCommonAncestor (const Composite &composite) const
template<typename T >
T *	getAncestor (const T &)
template<typename T >
const T *	getAncestor (const T &) const
template<typename T >
T *	getPrevious (const T &)
template<typename T >
const T *	getPrevious (const T &dummy) const
template<typename T >
T *	getNext (const T &)
template<typename T >
const T *	getNext (const T &dummy) const
Composite *	getParent ()
const Composite *	getParent () const
Composite *	getChild (Index index)
const Composite *	getChild (Index index) const
Composite *	getSibling (Index index)
const Composite *	getSibling (Index index) const
Composite *	getFirstChild ()
const Composite *	getFirstChild () const
Composite *	getLastChild ()
const Composite *	getLastChild () const
const PreciseTime &	getModificationTime () const
const PreciseTime &	getSelectionTime () const
void	stamp (StampType stamp=BOTH)
void	prependChild (Composite &composite)
void	appendChild (Composite &composite)
void	insertBefore (Composite &composite)
void	insertAfter (Composite &composite)
void	spliceBefore (Composite &composite)
void	spliceAfter (Composite &composite)
void	splice (Composite &composite)
bool	removeChild (Composite &child)
Size	removeSelected ()
Size	removeUnselected ()
void	replace (Composite &composite)
void	swap (Composite &composite)
virtual void	select ()
virtual void	deselect ()
Public Member Functions inherited from BALL::PersistentObject
	PersistentObject ()
virtual	~PersistentObject ()
PersistenceManager &	operator>> (PersistenceManager &pm) const
virtual void	finalize ()
Public Member Functions inherited from BALL::Object
	Object ()
	Default constructor.
	Object (const Object &object)
	Copy constructor.
virtual	~Object ()
	Destructor.
const Object &	operator= (const Object &)
bool	operator== (const Object &object) const
bool	operator!= (const Object &object) const
bool	operator< (const Object &object) const
bool	operator<= (const Object &object) const
bool	operator>= (const Object &object) const
bool	operator> (const Object &object) const
int	compare (const Object &object) const
virtual void	dump (::std::ostream &s=std::cout, Size depth=0) const
Handle	getHandle () const
Public Member Functions inherited from BALL::AutoDeletable
virtual	~AutoDeletable ()
void *	operator new (size_t size)
void	operator delete (void *ptr)
void *	operator new (size_t size, void *ptr)
void	operator delete (void *ptr, void *)
bool	isAutoDeletable () const
void	setAutoDeletable (bool enable)
Public Member Functions inherited from BALL::Selectable
	Selectable ()
	Selectable (const Selectable &selectable, bool deep=true)
virtual	~Selectable ()
void	set (const Selectable &selectable, bool deep=true)
const Selectable &	operator= (const Selectable &selectable)
void	get (Selectable &selectable, bool deep=true) const
void	swap (Selectable &selectable)
virtual void	setSelected (bool selected)
bool	isSelected () const
bool	operator== (const Selectable &selectable) const
bool	operator!= (const Selectable &selectable) const
void	write (PersistenceManager &pm) const
bool	read (PersistenceManager &pm)
virtual void	dump (::std::ostream &s=std::cout, Size depth=0) const
Public Member Functions inherited from BALL::PropertyManager
BALL_INLINE	PropertyManager ()
	Default constructor.
BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor.
virtual	~PropertyManager ()
	Destructor.
void	set (const PropertyManager &property_manager)
const PropertyManager &	operator= (const PropertyManager &property_manager)
void	get (PropertyManager &property_manager) const
void	swap (PropertyManager &property_manager)
BitVector &	getBitVector ()
const BitVector &	getBitVector () const
	operator BitVector & ()
void	setProperty (Property property)
void	clearProperty (Property property)
void	toggleProperty (Property property)
Size	countProperties () const
const NamedProperty &	getNamedProperty (Position index) const
NamedProperty &	getNamedProperty (Position index)
void	setProperty (const NamedProperty &property)
void	setProperty (const string &name)
void	setProperty (const string &name, bool value)
void	setProperty (const string &name, int value)
void	setProperty (const string &name, unsigned int value)
void	setProperty (const string &name, float value)
void	setProperty (const string &name, double value)
void	setProperty (const string &name, const string &value)
void	setProperty (const string &name, const PersistentObject &value)
const NamedProperty &	getProperty (const string &name) const
NamedPropertyIterator	beginNamedProperty ()
NamedPropertyIterator	endNamedProperty ()
void	clearProperty (const string &name)
Size	countNamedProperties () const
bool	hasProperty (Property property) const
	Query for an unnamed property.
bool	hasProperty (const string &name) const
	Query for a named property.
bool	operator== (const PropertyManager &pm) const
bool	operator!= (const PropertyManager &pm) const
	Inequality operator.
void	write (PersistenceManager &pm) const
	Persistent stream writing.
bool	read (PersistenceManager &pm)
	Persistent stream reading.

Private Attributes
String	id_

Additional Inherited Members
Static Public Member Functions inherited from BALL::Composite
static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)
Static Public Member Functions inherited from BALL::Object
static Handle	getNextHandle ()
static Handle	getNewHandle ()
Static Public Member Functions inherited from BALL::AutoDeletable
static void	clearLastPtr ()
Static Public Attributes inherited from BALL::Composite
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR
static KernelPredicateType	DEFAULT_UNARY_PREDICATE
Protected Member Functions inherited from BALL::Molecule
Molecule *	getMolecule ()
const Molecule *	getMolecule () const
AtomContainer *	getSuperAtomContainer ()
const AtomContainer *	getSuperAtomContainer () const
void	prepend (Molecule &molecule)
void	append (Molecule &molecule)
void	insert (Molecule &molecule)
void	insertBefore (Molecule &molecule, Composite &composite)
void	insertAfter (Molecule &molecule, Composite &composite)
bool	remove (Molecule &molecule)
bool	isSubAtomContainerOf (const AtomContainer &atom_container) const
Protected Attributes inherited from BALL::Selectable
bool	selected_

Detailed Description

Nucleic acid class.

Definition at line 27 of file nucleicAcid.h.

Member Enumeration Documentation

enum BALL::NucleicAcid::Property

Enumerator:

NUMBER_OF_PROPERTIES

Definition at line 40 of file nucleicAcid.h.

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.

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.

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::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::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 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

const String& BALL::NucleicAcid::getID

(

)

const

Retrieve the ID of the NucleicAcid.

Returns

String the ID

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

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

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 )

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

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.

Member Data Documentation

String BALL::NucleicAcid::id_

private

Definition at line 231 of file nucleicAcid.h.