#include <BALL/CONCEPT/composite.h>

Inheritance diagram for BALL::Composite:

Classes
class	AncestorIteratorTraits

class	ChildCompositeIteratorTraits

class	CompositeIteratorTraits

Public Types
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

Type Definitions and Enums
enum	StampType { MODIFICATION = 1, SELECTION = 2, BOTH = 3 }

typedef UnaryPredicate< Composite >	KernelPredicateType

Public Member Functions
template<typename T >
bool	applyLevel (ConstUnaryProcessor< T > &processor, long level) const

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)

template<typename T >
BALL_INLINE bool	apply (UnaryProcessor< T > &processor)

template<typename T >
BALL_INLINE bool	apply (ConstUnaryProcessor< T > &processor) const

template<typename T >
BALL_INLINE T *	getAncestor (const T &)

template<typename T >
BALL_INLINE const T *	getAncestor (const T &) const

template<typename T >
BALL_INLINE T *	getPrevious (const T &)

template<typename T >
BALL_INLINE const T *	getPrevious (const T &dummy) const

template<typename T >
BALL_INLINE T *	getNext (const T &)

template<typename T >
BALL_INLINE const T *	getNext (const T &dummy) const

template<typename T >
BALL_INLINE bool	hasAncestor (const T &dummy) const

Construction and Destruction
	Composite ()

	Composite (const Composite &composite, bool deep=true)

virtual	~Composite ()

virtual void	clear ()

virtual void	destroy ()

void	destroy (bool virtual_destroy)

void *	clone (Composite &root) const

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

virtual void	persistentRead (PersistenceManager &pm)

Predicates
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

Type predicates
These predicates should be used for type checking instead of dynamic_casts as a virtual function call is orders of magnitudes faster.
virtual bool	isAtom () const

virtual bool	isMolecule () const

virtual bool	isProtein () const

virtual bool	isFragment () const

virtual bool	isResidue () const

virtual bool	isChain () const

Debugging and Diagnostics
virtual bool	isValid () const

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

Application and Hosting
void	host (Visitor< Composite > &visitor)

template<typename T >
bool	applyAncestor (UnaryProcessor< T > &processor)

template<typename T >
bool	applyAncestor (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyChild (UnaryProcessor< T > &processor)

template<typename T >
bool	applyChild (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPreorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPostorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendant (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendant (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPreorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPostorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	apply (UnaryProcessor< T > &processor)

template<typename T >
bool	apply (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyLevel (UnaryProcessor< T > &processor, long level)

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. More...

	Object (const Object &object)
	Copy constructor. More...

virtual	~Object ()
	Destructor. More...

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

Static Public Attributes
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR

static KernelPredicateType	DEFAULT_UNARY_PREDICATE

Friends
class	AncestorIteratorTraits

class	ChildCompositeIteratorTraits

class	CompositeIteratorTraits

Modifying and Accessing the Tree
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 ()

static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)

Additional Inherited Members
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 ()

Protected Member Functions inherited from BALL::AutoDeletable
	AutoDeletable ()

	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)

Protected Attributes inherited from BALL::Selectable
bool	selected_

Detailed Description

Composite Class. This class implements a variant of the composite design pattern. A Composite may contain an arbitrary number of other composites, thus forming a tree. All BALL kernel classes are derived from Composite. This provides a unique interface for all kernel classes.

: The composite class provides a selection mechanism that allows hierarchical selection and deselection of arbitrary subtrees. The time of the last selection/deselection operation is stored as well as the time of the last modification operation in time stamps that can be accessed via getModificationTime and getSelectionTime . Selecting or deselecting a Composite automatically selects or deselects all its children (recursively!). Selecting or deselecting all children of a node deselects their parent as well. Selection information is propagated upwards in the tree.

: Composites are persistent objects.

Definition at line 71 of file composite.h.

Member Typedef Documentation

typedef ConstForwardIterator<Composite, Composite, Composite*, AncestorIteratorTraits> BALL::Composite::AncestorConstIterator

Definition at line 1064 of file composite.h.

typedef ForwardIterator<Composite, Composite, Composite*, AncestorIteratorTraits> BALL::Composite::AncestorIterator

Definition at line 1051 of file composite.h.

typedef ConstBidirectionalIterator<Composite, Composite, Composite *, ChildCompositeIteratorTraits> BALL::Composite::ChildCompositeConstIterator

Definition at line 1188 of file composite.h.

typedef std::reverse_iterator<ChildCompositeConstIterator> BALL::Composite::ChildCompositeConstReverseIterator

Definition at line 1218 of file composite.h.

typedef BidirectionalIterator<Composite, Composite, Composite *, ChildCompositeIteratorTraits> BALL::Composite::ChildCompositeIterator

Definition at line 1171 of file composite.h.

typedef std::reverse_iterator<ChildCompositeIterator> BALL::Composite::ChildCompositeReverseIterator

Definition at line 1204 of file composite.h.

typedef ConstBidirectionalIterator<Composite, Composite, Composite*, CompositeIteratorTraits> BALL::Composite::CompositeConstIterator

Definition at line 1475 of file composite.h.

typedef std::reverse_iterator<CompositeConstIterator> BALL::Composite::CompositeConstReverseIterator

Definition at line 1501 of file composite.h.

typedef BidirectionalIterator<Composite, Composite, Composite*, CompositeIteratorTraits> BALL::Composite::CompositeIterator

Definition at line 1468 of file composite.h.

typedef std::reverse_iterator<CompositeIterator> BALL::Composite::CompositeReverseIterator

Definition at line 1488 of file composite.h.

typedef UnaryPredicate<Composite> BALL::Composite::KernelPredicateType

Composite predicate type. This type declares a predicate operating on composites. As it is used as a predicate for all kernel classes, it is named KernelPredicateType.

Definition at line 88 of file composite.h.

Member Enumeration Documentation

enum BALL::Composite::StampType

Time stamp type.

Enumerator
MODIFICATION
SELECTION
BOTH

Definition at line 93 of file composite.h.

Constructor & Destructor Documentation

BALL::Composite::Composite ( )

Default constructor. This constructor creates an empty composite object.

BALL::Composite::Composite	(	const Composite &	composite,
		bool	deep = `true`
	)

Copy constructor. Creates a copy of a composite. Deep copies include the whole composite tree, shallow copies contain anly a single composite.

Parameters

composite	the composite to be cloned (the root of the tree in the case of a deep copy)
deep	make a deep copy (true) or shallow copy (false)

virtual BALL::Composite::~Composite ( )

virtual

Destructor. The destructor calls destroy to remove the composite from potential tree structures. It also recursively destructs all children of the composite.

Member Function Documentation

void BALL::Composite::appendChild ( Composite & composite )

Insert a composite as the last child of this composite. Updates the modification time stamp. Note that this method alters the composite tree from which composite is taken, if there is such a tree.

See also: stamp

Parameters

composite the composite to be inserted

template<typename T >

bool BALL::Composite::apply ( UnaryProcessor< T > & processor )

Apply a processor to the node and its subtree. applyPreorder is used.

See also: applyPreorder

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

template<typename T >

bool BALL::Composite::apply ( ConstUnaryProcessor< T > & processor ) const

Apply a const processor to the node and its subtree. applyPreorder is used.

See also: applyPreorder

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

template<typename T >

BALL_INLINE bool BALL::Composite::apply ( UnaryProcessor< T > & processor )

Definition at line 2049 of file composite.h.

template<typename T >

BALL_INLINE bool BALL::Composite::apply ( ConstUnaryProcessor< T > & processor ) const

Definition at line 2056 of file composite.h.

template<typename T >

bool BALL::Composite::applyAncestor ( UnaryProcessor< T > & processor )

Apply a processor to all ancestors of this node.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1600 of file composite.h.

template<typename T >

bool BALL::Composite::applyAncestor ( ConstUnaryProcessor< T > & processor ) const

Apply a const processor to all ancestors of this node.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1626 of file composite.h.

template<typename T >

bool BALL::Composite::applyChild ( UnaryProcessor< T > & processor )

Apply a processor to all children of this node.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1652 of file composite.h.

template<typename T >

bool BALL::Composite::applyChild ( ConstUnaryProcessor< T > & processor ) const

Apply a const processor to all children of this node.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1658 of file composite.h.

template<typename T >

bool BALL::Composite::applyDescendant ( UnaryProcessor< T > & processor )

Apply a processor to all descendents of this node. The node itself is not processed. applyDescendantPreorder is used.

See also: applyDescendantPreorder

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 2024 of file composite.h.

template<typename T >

bool BALL::Composite::applyDescendant ( ConstUnaryProcessor< T > & processor ) const

Apply a const processor to all descendents of this node. The node itself is not processed. applyDescendantPreorder is used.

See also: applyDescendantPreorder

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 2030 of file composite.h.

template<typename T >

bool BALL::Composite::applyDescendantPostorder ( UnaryProcessor< T > & processor )

Apply a processor to all descendents of this node. The node itself is not processed. The root of a subtree is accessed after the nodes in its left and right subtree.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1776 of file composite.h.

template<typename T >

bool BALL::Composite::applyDescendantPostorder ( ConstUnaryProcessor< T > & processor ) const

Apply a const processor to all descendents of this node. The node itself is not processed. The root of a subtree is accessed after the nodes in its left and right subtree.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1782 of file composite.h.

template<typename T >

bool BALL::Composite::applyDescendantPreorder ( UnaryProcessor< T > & processor )

Apply a processor to all descendents of this node. The node itself is not processed. The root of a subtree is accessed before the nodes in its left and right subtree.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1708 of file composite.h.

template<typename T >

bool BALL::Composite::applyDescendantPreorder ( ConstUnaryProcessor< T > & processor ) const

Apply a const processor to all descendents of this node. The node itself is not processed. The root of a subtree is accessed before the nodes in its left and right subtree.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1714 of file composite.h.

template<typename T >

bool BALL::Composite::applyLevel	(	UnaryProcessor< T > &	processor,
		long	level
	)

Apply a processor to the node and its siblings.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1877 of file composite.h.

template<typename T >

bool BALL::Composite::applyLevel	(	ConstUnaryProcessor< T > &	processor,
		long	level
	)		const

Apply a const processor to the node and its siblings.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1883 of file composite.h.

template<typename T >

bool BALL::Composite::applyPostorder ( UnaryProcessor< T > & processor )

Apply a processor to the node and its subtree. The root of a subtree is accessed after the nodes in its left and right subtree.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1846 of file composite.h.

template<typename T >

bool BALL::Composite::applyPostorder ( ConstUnaryProcessor< T > & processor ) const

Apply a const processor to the node and its subtree. The root of a subtree is accessed after the nodes in its left and right subtree.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 1861 of file composite.h.

template<typename T >

bool BALL::Composite::applyPreorder ( UnaryProcessor< T > & processor )

Apply a processor to the node and its subtree. The root of a subtree is accessed before the nodes in its left and right subtree.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 2036 of file composite.h.

template<typename T >

bool BALL::Composite::applyPreorder ( ConstUnaryProcessor< T > & processor ) const

Apply a const processor to the node and its subtree. The root of a subtree is accessed before the nodes in its left and right subtree.

Returns: true if the processor could be applied.

Exceptions

Exception::GeneralException

Definition at line 2042 of file composite.h.

AncestorIterator BALL::Composite::beginAncestor ( )

inline

Definition at line 1053 of file composite.h.

AncestorConstIterator BALL::Composite::beginAncestor ( ) const

inline

Definition at line 1066 of file composite.h.

ChildCompositeIterator BALL::Composite::beginChildComposite ( )

inline

Definition at line 1173 of file composite.h.

ChildCompositeConstIterator BALL::Composite::beginChildComposite ( ) const

inline

Definition at line 1190 of file composite.h.

CompositeIterator BALL::Composite::beginComposite ( )

inline

Definition at line 1470 of file composite.h.

CompositeConstIterator BALL::Composite::beginComposite ( ) const

inline

Definition at line 1477 of file composite.h.

virtual void BALL::Composite::clear ( )

virtual

Clear the composite properties. This method removes the composite's children and destructs them if they are auto-deletable.

: It does not remove the composite from any parental structure.

: This method updates the modification time stamp of this.

See also: stamp; AutoDeletable; destroy

Reimplemented from BALL::Selectable.

Reimplemented in BALL::Atom, BALL::Bond, BALL::PDBAtom, BALL::Residue, BALL::Nucleotide, BALL::SecondaryStructure, BALL::AtomContainer, BALL::NucleicAcid, and BALL::Protein.

void* BALL::Composite::clone ( Composite & root ) const

Clone with a predicate. This method copies the attributes of this composite to root (shallow copy) and then adds recursively each of its children.

Parameters

root	the cloning target root is `destroy`ed prior to any copying

Returns: a pointer to the root composite (&root)

bool BALL::Composite::containsSelection ( ) const

Return true if any descendant is selected. This method does not check all nodes recursively. Instead, on each modification of the tree, internal flags are updated and the information is propagated upwards in the tree.

: Complexity: O(1)

Returns: bool true if any node in the subtree is selected

Size BALL::Composite::count ( const KernelPredicateType & predicate ) const

Count the number of nodes fulfilling a predicate in this subtree.

Parameters

predicate the predicate

Returns: Size the number of nodes in the subtree satisfying the predicate

Size BALL::Composite::countDescendants ( ) const

Count the number of descendants.

Returns: Size the number of descendants of this node

void BALL::Composite::deleteChildrenList_ ( std::list< Composite * > & composites )

virtual void BALL::Composite::deselect ( )

virtual

Deselect a composite. This method deselects the composite and all the composites therein.

: If the state of this composite is modified, its selection time stamp is updated and that of its ancestors (up to and including the root composite) as well. The time stamps of descendants that changed their selection state are update, too.

Reimplemented from BALL::Selectable.

virtual void BALL::Composite::destroy ( )

virtual

Destroy the composite. This method removes the composite from potential parental structures and then calls clear to destruct all children.

: This method updates the modification time stamp of this.

See also: stamp; ~Composite; clear

Reimplemented in BALL::Atom, BALL::Bond, BALL::PDBAtom, BALL::Residue, BALL::Nucleotide, BALL::AtomContainer, BALL::SecondaryStructure, BALL::NucleicAcid, and BALL::Protein.

void BALL::Composite::destroy ( bool virtual_destroy )

Non-virtual destroy method. This method behaves exactly like destroy except for a small difference: when called with true, it calls the virtual clear function. If called with false it calls the original clear function of Composite. This is useful when implementing the behaviour of derived classes.

: This method updates the modification time stamp of this.

See also: stamp

Parameters

virtual_destroy call the virtual clear method (true) or Composite::clear() (false)

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

virtual

Dump the constent of this instance to an ostream.

Parameters

s	the stream to which we will dump
depth	the indentation depth of the output

Reimplemented in BALL::Atom, BALL::Bond, BALL::Residue, BALL::AtomContainer, BALL::Chain, BALL::SecondaryStructure, BALL::Protein, BALL::PDBAtom, BALL::Nucleotide, BALL::Molecule, BALL::NucleicAcid, and BALL::Fragment.

AncestorIterator BALL::Composite::endAncestor ( )

inline

Definition at line 1058 of file composite.h.

AncestorConstIterator BALL::Composite::endAncestor ( ) const

inline

Definition at line 1071 of file composite.h.

ChildCompositeIterator BALL::Composite::endChildComposite ( )

inline

Definition at line 1179 of file composite.h.

ChildCompositeConstIterator BALL::Composite::endChildComposite ( ) const

inline

Definition at line 1196 of file composite.h.

CompositeIterator BALL::Composite::endComposite ( )

inline

Definition at line 1472 of file composite.h.

CompositeConstIterator BALL::Composite::endComposite ( ) const

inline

Definition at line 1482 of file composite.h.

void BALL::Composite::get	(	Composite &	composite,
		bool	deep = `true`
	)		const

Assignment of a tree to another. Create a deep (deep = true) or shallow copy of a composite and assign it to composite. composite is destroyed first.

Parameters

composite	the composite to assign the copy to
deep	true for a deep copy

template<typename T >

T* BALL::Composite::getAncestor ( const T & )

Find the first ancestor of type T. This method walks up the tree from parent to parent and checks whether the composite object is a kind of T. This method is useful to identify special container classes.

Returns: a pointer to the first composite found that is a kind of T or 0 if no matching composite was found up to the root of the tree

template<typename T >

const T* BALL::Composite::getAncestor ( const T & ) const

Find the first ancestor of type T (const method). This method operates also on constant trees.

Returns: a pointer to the first composite found that is a kind of T or 0 if no matching composite was found to the root of the tree

template<typename T >

BALL_INLINE T* BALL::Composite::getAncestor ( const T & )

Definition at line 2063 of file composite.h.

template<typename T >

BALL_INLINE const T* BALL::Composite::getAncestor ( const T & ) const

Definition at line 2083 of file composite.h.

Composite* BALL::Composite::getChild ( Index index )

Return the index th child of this composite. If no such child exists, 0 is returned. The index of the first child is 0.

Parameters

index the index of the child to return

Returns: a pointer to the child or 0 if there is no such child.

const Composite* BALL::Composite::getChild ( Index index ) const

Return a const pointer to the index th child of this composite. If no such child exists, 0 is returned. The index of the first child is 0.

Parameters

index the index of the child to return

Returns: a const pointer to the child or 0 if there is no such child.

Size BALL::Composite::getDegree ( ) const

Return the degree of the node. This method returns the number of children of a composite object.

Returns: Size the number of children

Size BALL::Composite::getDepth ( ) const

Get the depth of this item in its tree. The depth of a root item is 0.

Returns: Size the depth

Composite* BALL::Composite::getFirstChild ( )

Return a pointer to the first child.

Returns: a pointer to the first child or 0 if there is no child.

const Composite* BALL::Composite::getFirstChild ( ) const

Return a const pointer to the first child.

Returns: a const pointer to the first child or 0 if there is no child.

Size BALL::Composite::getHeight ( ) const

Get the height of this item in its tree. The hight of a leaf is 0.

Returns: Size the height

Composite* BALL::Composite::getLastChild ( )

Return a pointer to the last child.

Returns: a pointer to the last child or 0 if there is no child.

const Composite* BALL::Composite::getLastChild ( ) const

Return a const pointer to the last child.

Returns: a const pointer to the last child or 0 if there is no child.

Composite* BALL::Composite::getLowestCommonAncestor ( const Composite & composite )

Get the lowest common ancestor of this item with an other. If no common ancestor exists 0 is returned.

Returns: Composite& the lowest common ancestor

const Composite* BALL::Composite::getLowestCommonAncestor ( const Composite & composite ) const

Get a const reference to the lowest common ancestor of this item with an other. If no common ancestor exists, 0 is returned.

Returns: Composite& the lowest common ancestor

const PreciseTime& BALL::Composite::getModificationTime ( ) const

Return the time of last modification

Returns: the last modification time

template<typename T >

T* BALL::Composite::getNext ( const T & )

Find the next composite of type T. This method walks backward in the tree from composite to composite and checks whether the composite object is a kind of T.

Returns: a pointer to the first composite found that is a kind of T or 0 if no matching composite was found up to the root of the tree

template<typename T >

const T* BALL::Composite::getNext ( const T & dummy ) const

Find the next composite of type T (const method). This method walks backward in the tree from composite to composite and checks whether the composite object is a kind of T.

Returns: a pointer to the first composite found that is a kind of T or 0 if no matching composite was found up to the root of the tree

template<typename T >

BALL_INLINE T* BALL::Composite::getNext ( const T & )

Definition at line 2144 of file composite.h.

template<typename T >

BALL_INLINE const T* BALL::Composite::getNext ( const T & dummy ) const

Definition at line 2174 of file composite.h.

Composite* BALL::Composite::getParent ( )

Return the composite's parent.

Returns: a pointer to the parent composite or 0 if no parent exists

const Composite* BALL::Composite::getParent ( ) const

Return the composite's parent (const method).

Returns: a pointer to the parent composite or 0 if no parent exists

Size BALL::Composite::getPathLength ( const Composite & composite ) const

Get the length of the path between two composite objects. If no path exists INVALID_SIZE is returned.

Parameters

composite the second object

Returns: Size the size of the path

template<typename T >

T* BALL::Composite::getPrevious ( const T & )

Find the nearest previous composite of type T. This method walks backward in the tree from composite to composite and checks whether the composite object is a kind of T.

Returns: a pointer to the first composite found that is a kind of T or 0 if no matching composite was found up to the root of the tree

template<typename T >

const T* BALL::Composite::getPrevious ( const T & dummy ) const

Find the nearest previous composite of type T (const method). This method walks backward in the tree from composite to composite and checks whether the composite object is a kind of T.

Returns: a pointer to the first composite found that is a kind of T or 0 if no matching composite was found up to the root of the tree

template<typename T >

BALL_INLINE T* BALL::Composite::getPrevious ( const T & )

Definition at line 2101 of file composite.h.

template<typename T >

BALL_INLINE const T* BALL::Composite::getPrevious ( const T & dummy ) const

Definition at line 2133 of file composite.h.

Composite& BALL::Composite::getRoot ( )

Get the root of this item.

Returns: Composite& the root

const Composite& BALL::Composite::getRoot ( ) const

Get a const reference to the root of this item.

Returns: Composite& the root

const PreciseTime& BALL::Composite::getSelectionTime ( ) const

Return the time of last change of selection.

Returns: the last time of change of selection

Composite* BALL::Composite::getSibling ( Index index )

Return a pointer to the sibling index positions from this composite. A pointer to the sibling index positions to the right (for positive values of index) or -index positions to the left (for negative values of index) is returned. For Index = 0 the this-pointer is returned.

Parameters

index the index of the sibling

Returns: a pointer to the child or 0 if there is no such sibling.

const Composite* BALL::Composite::getSibling ( Index index ) const

Return a const pointer to the sibling index positions from this composite. A pointer to the sibling index positions to the right (for positive values of index) or -index positions to the left (for negative values of index) is returned. For Index = 0 the this-pointer is returned.

Parameters

index the index of the sibling

Returns: a const pointer to the child or 0 if there is no such sibling.

template<typename T >

bool BALL::Composite::hasAncestor ( const T & dummy ) const

Return true if the node has a ancestor of the same type as dummy.

template<typename T >

BALL_INLINE bool BALL::Composite::hasAncestor ( const T & dummy ) const

Definition at line 2185 of file composite.h.

bool BALL::Composite::hasChild ( ) const

Return true if the node has a child.

bool BALL::Composite::hasNextSibling ( ) const

Return true if the node has a previous sibling. (Its parent has a child after this.)

bool BALL::Composite::hasParent ( ) const

Return true if the node has a parent.

bool BALL::Composite::hasPreviousSibling ( ) const

Return true if the node has a previous sibling. (Its parent has a child before this.)

bool BALL::Composite::hasSibling ( ) const

Return true if the node has a sibling. (Its parent has other childs.)

void BALL::Composite::host ( Visitor< Composite > & visitor )

Visitor host method. Composites may be visited. For an example look into Composite_test.C

Parameters

visitor the visitor

Exceptions

Exception::GeneralException

void BALL::Composite::insertAfter ( Composite & composite )

Insert a node after this node. This method inserts composite after this node, if this node has a parent and is not a descendant of composite. Self-insertion is recognized and ignored (nothing is done).

: This method updates the modification time stamp.

See also: stamp

Parameters

composite the node to be inserted in the tree after of this

void BALL::Composite::insertBefore ( Composite & composite )

Insert a node before this node. This method inserts composite before this node, if this node has a parent and is not a descendant of composite. Self-insertion is recognized and ignored (nothing is done).

: This method updates the modification time stamp.

See also: stamp

Parameters

composite the node to be inserted in the tree before this

static bool BALL::Composite::insertParent	(	Composite &	parent,
		Composite &	first,
		Composite &	last,
		bool	destroy_parent = `true`
	)

static

Insert a new parent node. This method is used to combine a range of nodes into a single parent. First, the parent composite is destroyed. Then, all nodes from first through last are inserted into parent and parent is inserted in the former position of first. The method returns false, if { first} or last have differing parents, if parent is identical with either first or last, or if first is already a descendant of parent.

: This method updates the modification time stamp.

See also: stamp

Parameters

parent	the new parent of the nodes from `first` through `last`
first	the first of the nodes to be inserted into `parent`
last	the last of the nodes to be inserted into `parent`
destroy_parent	keeps the current contents of `parent` if set to `true`

bool BALL::Composite::isAncestorOf ( const Composite & composite ) const

Return true if the node has composite as descendent.

virtual bool BALL::Composite::isAtom ( ) const

inlinevirtual

Test if the Composite is an Atom

Reimplemented in BALL::Atom.

Definition at line 757 of file composite.h.

virtual bool BALL::Composite::isChain ( ) const

inlinevirtual

Test if the Composite is a Chain

Reimplemented in BALL::Chain.

Definition at line 782 of file composite.h.

bool BALL::Composite::isChildOf ( const Composite & composite ) const

Return true if the node has the parent composite.

bool BALL::Composite::isDescendantOf ( const Composite & composite ) const

Return true if the node is a descendent of composite.

bool BALL::Composite::isEmpty ( ) const

Return true if the node does not contain children.

Returns: bool true if number_of_children_ == 0

bool BALL::Composite::isFirstChild ( ) const

Return true if the node is the first child of its parent.

bool BALL::Composite::isFirstChildOf ( const Composite & composite ) const

Return true if the node is the first child of composite.

virtual bool BALL::Composite::isFragment ( ) const

inlinevirtual

Test if the Composite is a Fragment

Reimplemented in BALL::Fragment.

Definition at line 772 of file composite.h.

bool BALL::Composite::isHomomorph ( const Composite & composite ) const

Return true if composite is homomorph to this node. (The subtrees of the two instances have to be of the same form.)

bool BALL::Composite::isInterior ( ) const

Return true if the node is not the root or a leaf.

bool BALL::Composite::isLastChild ( ) const

Return true if the node is the last child of its parent.

bool BALL::Composite::isLastChildOf ( const Composite & composite ) const

Return true if the node is the last child of composite.

virtual bool BALL::Composite::isMolecule ( ) const

inlinevirtual

Test if the Composite is a Molecule

Reimplemented in BALL::Molecule.

Definition at line 762 of file composite.h.

bool BALL::Composite::isNextSiblingOf ( const Composite & composite ) const

Return true if the node is a next sibling of composite.

bool BALL::Composite::isParentOf ( const Composite & composite ) const

Return true if the node is the parent of composite.

bool BALL::Composite::isPreviousSiblingOf ( const Composite & composite ) const

Return true if the node is a previous sibling of composite.

virtual bool BALL::Composite::isProtein ( ) const

inlinevirtual

Test if the Composite is a Protein

Reimplemented in BALL::Protein.

Definition at line 767 of file composite.h.

bool BALL::Composite::isRelatedWith ( const Composite & composite ) const

Return true if the node has composite as ancestor or composite is ancestor of this node.

virtual bool BALL::Composite::isResidue ( ) const

inlinevirtual

Test if the Composite is a Residue

Reimplemented in BALL::Residue.

Definition at line 777 of file composite.h.

bool BALL::Composite::isRoot ( ) const

Return true if the node has no parent.

Returns: bool true if parent_ == 0

bool BALL::Composite::isRootOf ( const Composite & composite ) const

Return true if the node is root of composite.

bool BALL::Composite::isSiblingOf ( const Composite & composite ) const

Return true if the node is a sibling of composite.

virtual bool BALL::Composite::isValid ( ) const

virtual

Test if the subtree with this node as root is valid. (The structure of the subtree has to be valid.)

Reimplemented from BALL::Object.

Reimplemented in BALL::Atom, BALL::Bond, BALL::Residue, BALL::AtomContainer, BALL::SecondaryStructure, BALL::Protein, BALL::Nucleotide, and BALL::NucleicAcid.

bool BALL::Composite::operator!= ( const Composite & composite ) const

Inequality operator.

See also: operator == B

Composite& BALL::Composite::operator= ( const Composite & composite )

Assignment operator.

Parameters

composite the Composite tree to assign from

Returns: a const reference to this

bool BALL::Composite::operator== ( const Composite & composite ) const

Equality operator. Compares the handles of two Composite objects, therefore two Composite objects can never be equal.

See also: Object::operator ==

Parameters

composite the composite against which equality will be tested

virtual void BALL::Composite::persistentRead ( PersistenceManager & pm )

virtual

Read a persistent object.

Parameters

pm	the persistence manager

Exceptions

Exception::GeneralException

Reimplemented from BALL::PersistentObject.

Reimplemented in BALL::Atom, BALL::Bond, BALL::PDBAtom, BALL::Residue, BALL::SecondaryStructure, BALL::Nucleotide, BALL::AtomContainer, BALL::NucleicAcid, BALL::Molecule, BALL::Protein, BALL::Chain, BALL::System, and BALL::Fragment.

virtual void BALL::Composite::persistentWrite	(	PersistenceManager &	pm,
		const char *	name = `0`
	)		const

virtual

Write a persistent copy of the object.

Parameters

pm	the persistence manager
name	the object name

Exceptions

Exception::GeneralException

Reimplemented from BALL::PersistentObject.

Reimplemented in BALL::Atom, BALL::Bond, BALL::PDBAtom, BALL::Residue, BALL::SecondaryStructure, BALL::Nucleotide, BALL::AtomContainer, BALL::NucleicAcid, BALL::Molecule, BALL::Protein, BALL::Chain, BALL::System, and BALL::Fragment.

void BALL::Composite::prependChild ( Composite & composite )

Insert a composite as the first child of this composite. Updates the modification time stamp.

See also: stamp

Parameters

composite the composite to be inserted

ChildCompositeReverseIterator BALL::Composite::rbeginChildComposite ( )

inline

Definition at line 1206 of file composite.h.

ChildCompositeConstReverseIterator BALL::Composite::rbeginChildComposite ( ) const

inline

Definition at line 1220 of file composite.h.

CompositeReverseIterator BALL::Composite::rbeginComposite ( )

inline

Definition at line 1490 of file composite.h.

CompositeConstReverseIterator BALL::Composite::rbeginComposite ( ) const

inline

Definition at line 1503 of file composite.h.

bool BALL::Composite::removeChild ( Composite & child )

Remove a child from its parent. child is only removed, if it is a true child of this.

: This method updates the modification time stamp of this.

See also: stamp

Parameters

child the child to remove

Returns: false if child could not be removed

Size BALL::Composite::removeSelected ( )

Remove selected subcomposites. This method iterates over all children of the current composite and removes all selected composites by deleteing them. If the respective Composite are not AutoDeletable, they are just remove d from the hierarchy, but not deleted.

This method is useful in combination with the Selector class in order to remove unwanted partitions of kernel data structures.

Returns: the number of composites deleted.

Size BALL::Composite::removeUnselected ( )

Remove unselected subcomposites. This method iterates over all children of the current composite and removes all unselected composites by deleteing them. If the respective Composite are not AutoDeletable, they are just remove d from the hierarchy, but not deleted.

This method is useful in combination with the Selector class in order to remove unwanted partitions of kernel data structures.

Returns: the number of composites deleted.

ChildCompositeReverseIterator BALL::Composite::rendChildComposite ( )

inline

Definition at line 1211 of file composite.h.

ChildCompositeConstReverseIterator BALL::Composite::rendChildComposite ( ) const

inline

Definition at line 1225 of file composite.h.

CompositeReverseIterator BALL::Composite::rendComposite ( )

inline

Definition at line 1495 of file composite.h.

CompositeConstReverseIterator BALL::Composite::rendComposite ( ) const

inline

Definition at line 1508 of file composite.h.

void BALL::Composite::replace ( Composite & composite )

This instance and its subtree is removed form its tree and replaced by composite and its subtree.

: This method updates the modification time stamp of this and composite.

See also: stamp

Parameters

composite the composite which will be inserted

virtual void BALL::Composite::select ( )

virtual

Select a composite. This method selects the composite and all the composites therein.

: If the state of this composite is modified, its selection time stamp is updated and that of its ancestors (up to and including the root composite) as well. The time stamps of descendants that changed their selection state are update, too.

Reimplemented from BALL::Selectable.

void BALL::Composite::set	(	const Composite &	composite,
		bool	deep = `true`
	)

Assignment.

Parameters

composite	the Composite tree to assign from
deep	a `bool` deciding whether the assignment will be deep or shallow.

void BALL::Composite::splice ( Composite & composite )

Insert the children of composite into this composite. The children of composite are inserted at the position of composite if composite is a child of this. Otherwise the children are inserted using spliceBefore .

: This method updates the modification time stamp.

See also: stamp

Parameters

composite the composite to be spliced

void BALL::Composite::spliceAfter ( Composite & composite )

Append all children of composite to the children of this composite. The method does nothing, if composite is identical to this or is a descendent of this.

: This method updates the modification time stamp.

See also: stamp

Parameters

composite the composite to be spliced

void BALL::Composite::spliceBefore ( Composite & composite )

Prepend all children of composite to the children of this composite. The method does nothing, if composite is identical to this or is a descendent of this.

: This method updates the modification time stamp.

See also: stamp

Parameters

the	composite to be spliced

void BALL::Composite::stamp ( StampType stamp = BOTH )

Modify a time stamp. Update one or both of the two time stamps with the current time. The time stamp is then propagated up to the root of the composite tree. Each composite contains two stamps. the modification stamp is updated each time the tree structure changes, while the selection stamp is updated each time the selection status changes.

Parameters

stamp the time stamp type

void BALL::Composite::swap ( Composite & composite )

Swap the contents of two composites.

: This method updates the modification time stamp of this and composite.

See also: stamp

Parameters

composite the composite with which the contents will be swapped

Friends And Related Function Documentation

friend class AncestorIteratorTraits

friend

Definition at line 1048 of file composite.h.

friend class ChildCompositeIteratorTraits

friend

Definition at line 1168 of file composite.h.

friend class CompositeIteratorTraits

friend

Definition at line 1465 of file composite.h.

Member Data Documentation

UnaryProcessor<Composite> BALL::Composite::DEFAULT_PROCESSOR

static

Definition at line 109 of file composite.h.

KernelPredicateType BALL::Composite::DEFAULT_UNARY_PREDICATE

static

Definition at line 110 of file composite.h.

Classes

Public Types

Public Member Functions

Static Public Attributes

Friends

Modifying and Accessing the Tree

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation