#include <DependentMotif.h>

Inheritance diagram for bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >:

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Collaboration diagram for bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >:

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Public Member Functions
virtual Code	Attenuate (Pointer< const physical::Wave > other)

virtual Code	Disattenuate (Pointer< const physical::Wave > other)

	DependentMotif (EnvironmentPointer environment=NULL)

	DependentMotif (const typename LinearMotif< CONTENT_TYPE >::Contents *contents, EnvironmentPointer environment=NULL)

	DependentMotif (const DependentMotif< CONTENT_TYPE, ENVIRONMENT > &toCopy)

virtual	~DependentMotif ()

virtual void	SetEnvironment (EnvironmentPointer environment)

virtual ContentPointer	AddImplementation (ContentPointer content)

virtual Code	InsertImplementation (ContentPointer toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false)

Public Member Functions inherited from bio::chemical::Class< DependentMotif< CONTENT_TYPE, ENVIRONMENT > >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< DependentMotif< CONTENT_TYPE, ENVIRONMENT > > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< DependentMotif< CONTENT_TYPE, ENVIRONMENT > > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< DependentMotif< CONTENT_TYPE, ENVIRONMENT > > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual	~Class ()

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

Public Member Functions inherited from bio::physical::Class< T >
	Class (Pointer< T > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< T > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< T >	GetWaveObject ()

virtual Pointer< const T >	GetWaveObject () const

virtual	operator T& ()

virtual	operator const T & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::physical::Wave
	Wave (Pointer< Symmetry > symmetry=NULL)

	Wave (const Wave &other)

Wave &	operator= (const Wave &other)

virtual	~Wave ()

Pointer< const Symmetry >	GetSymmetry () const

virtual bool	Superpose (Pointer< const Wave > displacement, Pointer< Interference > pattern)

virtual Pointer< Wave >	Superpose (const ConstWaves &displacement, Pointer< Interference > pattern)

virtual Pointer< Wave >	Modulate (Pointer< Wave > signal)

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual void	operator\| (Pointer< Symmetry > symmetry)

virtual Pointer< Wave >	operator* (Pointer< Wave > signal)

virtual Pointer< Wave >	operator* ()

virtual Pointer< const Wave >	operator* () const

virtual void	operator+ (Pointer< const Wave > other)

virtual void	operator- (Pointer< const Wave > other)

uint16_t	GetTypeId () const

void	SetTypeId (uint16_t typeId)

Public Member Functions inherited from bio::physical::Identifiable< Id >
	Identifiable (Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Name &name, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (Identifier id, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Identifiable &other)

virtual	~Identifiable ()

virtual	operator Id () const

virtual bool	operator== (const Identifier id) const

virtual bool	operator== (const Name &name) const

virtual bool	operator== (const Identifiable< Id > &other) const

virtual Name	GetName () const

virtual Identifier	GetId () const

virtual bool	SetName (const Name &name)

virtual bool	SetId (Identifier id)

virtual bool	IsName (const Name &name) const

virtual bool	IsNameInsensitive (const Name &name) const

virtual bool	IsId (Identifier id) const

virtual void	SetPerspective (Pointer< Perspective< Id > > perspective)

Public Member Functions inherited from bio::physical::Observer< PERSPECTIVE >
	Observer (Pointer< Perspective > perspective=NULL)

	Observer (const Observer &other)

virtual	~Observer ()

virtual void	SetPerspective (Pointer< Perspective > perspective)

virtual Pointer< Perspective >	GetPerspective () const

Public Member Functions inherited from bio::log::Writer
	Writer ()

	Writer (Filter logFilter)

virtual	~Writer ()

virtual Pointer< const Writer >	AsLogWriter () const

bool	IsEnabled (LogLevel level) const

virtual void	Log (LogLevel level, const char *format, va_list args) const

Public Member Functions inherited from bio::physical::Class< Writer >
	Class (Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Writer > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Writer >	GetWaveObject ()

virtual Pointer< const Writer >	GetWaveObject () const

virtual	operator Writer & ()

virtual	operator const Writer & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::physical::Filterable
	Filterable ()

	Filterable (Filter filter)

virtual	~Filterable ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual void	SetFilter (Filter filter)

Filter	GetFilter () const

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

Public Member Functions inherited from bio::physical::Class< Filterable >
	Class (Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Filterable > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Filterable >	GetWaveObject ()

virtual Pointer< const Filterable >	GetWaveObject () const

virtual	operator Filterable & ()

virtual	operator const Filterable & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::chemical::Atom
	Atom ()

	Atom (const Atom &other)

virtual	~Atom ()

void	CloneBondsFrom (const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy)

virtual Pointer< const physical::Symmetry >	Spin () const

virtual Code	Reify (Pointer< const physical::Symmetry > symmetry)

Pointer< physical::Wave >	GetBonded (Valence position)

Pointer< const physical::Wave >	GetBonded (Valence position) const

Pointer< const physical::Wave >	ResolveBondedForReadById (AtomicNumber bondId) const

Pointer< physical::Wave >	ResolveBondedForWriteById (AtomicNumber bondId)

template<typename T >
Cow< T >	AsBonded () const

template<typename T >
Pointer< T >	AsBondedQuantum () const

template<typename T >
atom_detail::AsResultType< T, type::IsWaveImplementation< typenametype::RemovePointer< T >::Type >::sValue >::Type	As () const

template<typename T >
	operator T () const

template<typename T >
Valence	FormBond (T toBond, BondType type=bond_type::Unknown())

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (const Name &typeName) const

Valence	GetBondPositionLocked (AtomicNumber bondedId) const

template<typename T >
Valence	GetBondPosition () const

BondType	GetBondType (Valence position) const

template<typename T >
BondType	GetBondType () const

Pointer< Bonds >	GetAllBonds ()

Pointer< const Bonds >	GetAllBonds () const

void	ForEachBond (BondVisitor visitor, void *context=NULL) const

void	ForEachBondMutable (BondMutator mutator, void *context=NULL)

virtual Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type)

Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

Valence	FormBondImplementationLocked (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

virtual bool	BreakBondImplementation (AtomicNumber id, BondType type)

bool	BreakBondImplementationLocked (AtomicNumber id, BondType type)

Public Member Functions inherited from bio::physical::Class< Atom >
	Class (Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Atom > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Atom >	GetWaveObject ()

virtual Pointer< const Atom >	GetWaveObject () const

virtual	operator Atom & ()

virtual	operator const Atom & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

ThreadSafe &	operator= (const ThreadSafe &toCopy)

	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

void	LockMutexShared () const

void	UnlockMutexShared () const

Public Member Functions inherited from bio::chemical::LinearMotif< CONTENT_TYPE >
	LinearMotif ()

	LinearMotif (const Contents *contents)

	LinearMotif (const LinearMotif< CONTENT_TYPE > &toCopy)

virtual	~LinearMotif ()

virtual AtomicNumber	GetContentTypeId () const

virtual bool	AddWaveByContentType (Pointer< physical::Wave > wave)

virtual bool	AddSharedWaveByContentType (Pointer< physical::Wave > wave)

virtual ContentPointer	AddImplementation (ContentPointer content)

virtual ContentPointer	AddSharedImplementation (ContentPointer content)

void	ReleaseContentOwnership ()

ReleaseResult	ReleaseImplementation (const ContentPointer content)

virtual Code	RemoveImplementation (const ContentPointer content)

virtual Code	InsertImplementation (ContentPointer toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false)

virtual ContentPointer	GetByIdImplementation (const Id &id)

virtual const ContentPointer	GetByIdImplementation (const Id &id) const

virtual ContentPointer	GetByNameImplementation (const Name &name)

virtual const ContentPointer	GetByNameImplementation (const Name &name) const

virtual ContentPointer	CreateImplementation ()

virtual ContentPointer	CreateWithIdImplementation (const Id &id)

virtual ContentPointer	CreateWithNameImplementation (const Name &name)

virtual ContentPointer	GetOrCreateByIdImplementation (const Id &id)

virtual ContentPointer	GetOrCreateByNameImplementation (const Name &name)

virtual Code	RemoveByIdImplementation (const Id &id)

virtual Code	RemoveByNameImplementation (const Name &name)

virtual bool	HasImplementation (const ContentPointer &content) const

virtual void	ImportImplementation (Pointer< const LinearMotif< CONTENT_TYPE > > other)

virtual void	ImportImplementation (const void *other)

virtual Contents	GetAllLikeImplementation (Pointer< const Affinity > affinity) const

virtual Emission	ForEachImplementation (Pointer< const ExcitationBase > excitation)

virtual ::std::string	GetStringFromImplementation (std::string separator=", ")

virtual void	ClearImplementation ()

virtual Pointer< Container >	GetAllImplementation ()

virtual Pointer< const Container >	GetAllImplementation () const

Public Member Functions inherited from bio::chemical::Class< LinearMotif< CONTENT_TYPE > >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< LinearMotif< CONTENT_TYPE > > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< LinearMotif< CONTENT_TYPE > > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< LinearMotif< CONTENT_TYPE > > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual	~Class ()

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

Public Member Functions inherited from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >
	UnorderedMotif ()

	UnorderedMotif (Pointer< const Contents > contents)

	UnorderedMotif (Pointer< const UnorderedMotif< Pointer< CONTENT_TYPE > > > toCopy)

	UnorderedMotif (const UnorderedMotif< Pointer< CONTENT_TYPE > > &toCopy)

UnorderedMotif< Pointer< CONTENT_TYPE > > &	operator= (const UnorderedMotif< Pointer< CONTENT_TYPE > > &toCopy)

virtual	~UnorderedMotif ()

virtual Index	GetCountImplementation () const

virtual Code	RemoveImplementation (const Pointer< CONTENT_TYPE > content)

virtual bool	HasImplementation (const Pointer< CONTENT_TYPE > content) const

virtual void	ImportImplementation (Pointer< const UnorderedMotif< Pointer< CONTENT_TYPE > > > other)

virtual unsigned int	GetNumMatchingImplementation (Pointer< const Container > other) const

virtual bool	HasAllImplementation (Pointer< const Container > contents) const

virtual String	GetStringFromImplementation (String separator=", ")

virtual void	LogImplementation (const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId())

Public Member Functions inherited from bio::chemical::Class< T >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< T > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< T > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< T > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual	~Class ()

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

Public Member Functions inherited from bio::chemical::AbstractMotif
	AbstractMotif ()

	AbstractMotif (const AbstractMotif &other)

AbstractMotif &	operator= (const AbstractMotif &other)

virtual	~AbstractMotif ()

virtual ::std::string	GetStringFromImplementation (std::string separator=", ")

Public Member Functions inherited from bio::chemical::EnvironmentDependent< ENVIRONMENT >
	EnvironmentDependent (EnvironmentPointer environment=NULL)

virtual	~EnvironmentDependent ()

virtual EnvironmentPointer	GetEnvironment ()

virtual const EnvironmentPointer	GetEnvironment () const

virtual void	SetEnvironment (EnvironmentPointer environment)

Additional Inherited Members
Public Types inherited from bio::physical::Identifiable< Id >
typedef Id	Identifier

typedef Arrangement< Identifier >	Ids

Public Types inherited from bio::physical::Observer< PERSPECTIVE >
typedef PERSPECTIVE	Perspective

Public Types inherited from bio::chemical::Atom
typedef BondCloneAction(*	BondClonePolicy) (const Bond &bond)

typedef void(*	BondVisitor) (const Bond &bond, void *context)

typedef BondCloneAction(*	BondMutator) (Bond &bond, void *context)

Public Types inherited from bio::chemical::LinearMotif< CONTENT_TYPE >
typedef physical::Line	Contents

Public Types inherited from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >
typedef Arrangement< Pointer< CONTENT_TYPE > >	Contents

Public Types inherited from bio::chemical::EnvironmentDependent< ENVIRONMENT >
typedef type::RemovePointer< ENVIRONMENT >::Type	EnvironmentType

typedef Pointer< EnvironmentType >	EnvironmentPointer

Static Public Member Functions inherited from bio::physical::Class< T >
static Pointer< T >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::physical::Wave
static Properties	GetResonanceBetween (ConstWaves waves)

static Properties	GetResonanceBetween (Pointer< const Wave > wave1, Pointer< const Wave > wave2)

static Properties	GetResonanceBetween (Pointer< const Wave > wave, const Properties &properties)

Static Public Member Functions inherited from bio::log::Writer
static void	Log (Pointer< const Writer > writer, LogLevel level, const char *format,...)

static bool	ShouldLog (Pointer< const Writer > writer, LogLevel level)

Static Public Member Functions inherited from bio::physical::Class< Writer >
static Pointer< Writer >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::physical::Class< Filterable >
static Pointer< Filterable >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::chemical::Atom
static BondCloneAction	DefaultBondClonePolicy (const Bond &bond)

template<typename T >
static AtomicNumber	GetBondId ()

Static Public Member Functions inherited from bio::physical::Class< Atom >
static Pointer< Atom >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::chemical::LinearMotif< CONTENT_TYPE >
static Properties	GetClassProperties ()

Static Public Member Functions inherited from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >
static Contents *	NewContents (Index expectedSize)

static Contents *	NewContents (const Contents &contents)

static Contents *	NewContents (Pointer< const Container > contents)

Static Public Member Functions inherited from bio::chemical::AbstractMotif
static Properties	GetClassProperties ()

Public Attributes inherited from bio::chemical::LinearMotif< CONTENT_TYPE >
AtomicNumber	mContentId

Protected Types inherited from bio::physical::Identifiable< Id >
typedef Id	Identifier

typedef Arrangement< Identifier >	Ids

Protected Types inherited from bio::physical::Observer< PERSPECTIVE >
typedef PERSPECTIVE	Perspective

Protected Types inherited from bio::chemical::Atom
typedef BondCloneAction(*	BondClonePolicy) (const Bond &bond)

typedef void(*	BondVisitor) (const Bond &bond, void *context)

typedef BondCloneAction(*	BondMutator) (Bond &bond, void *context)

Protected Types inherited from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >
enum	ContentsAllocation

Protected Member Functions inherited from bio::chemical::Elementary< T >
void	RegisterType ()

	Elementary (const Properties properties)

	Elementary ()

virtual	~Elementary ()

Protected Member Functions inherited from bio::physical::Identifiable< Id >
virtual void	InitializeImplementation (ByteStreams &args)

friend::std::ostream &	operator<< (std::ostream &out, const Identifiable< Id > &t)

	Identifiable (Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Name &name, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (Identifier id, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Identifiable &other)

virtual	~Identifiable ()

virtual	operator Id () const

virtual bool	operator== (const Identifier id) const

virtual bool	operator== (const Name &name) const

virtual bool	operator== (const Identifiable< Id > &other) const

virtual Name	GetName () const

virtual Identifier	GetId () const

virtual bool	SetName (const Name &name)

virtual bool	SetId (Identifier id)

virtual bool	IsName (const Name &name) const

virtual bool	IsNameInsensitive (const Name &name) const

virtual bool	IsId (Identifier id) const

virtual void	SetPerspective (Pointer< Perspective< Id > > perspective)

Protected Member Functions inherited from bio::physical::Observer< PERSPECTIVE >
	Observer (Pointer< Perspective > perspective=NULL)

	Observer (const Observer &other)

virtual	~Observer ()

virtual void	SetPerspective (Pointer< Perspective > perspective)

virtual Pointer< Perspective >	GetPerspective () const

Protected Member Functions inherited from bio::VirtualBase
	VirtualBase ()

virtual	~VirtualBase ()

void	Initialize (ByteStreams &args)

void	Initialize (ByteStream arg1)

void	Initialize (ByteStream arg1, ByteStream arg2)

void	Initialize (ByteStream arg1, ByteStream arg2, ByteStream arg3)

Protected Member Functions inherited from bio::log::Writer
	Writer ()

	Writer (Filter logFilter)

virtual	~Writer ()

virtual Pointer< const Writer >	AsLogWriter () const

bool	IsEnabled (LogLevel level) const

virtual void	Log (LogLevel level, const char *format, va_list args) const

Protected Member Functions inherited from bio::physical::Class< Writer >
	Class (Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Writer > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Writer >	GetWaveObject ()

virtual Pointer< const Writer >	GetWaveObject () const

virtual	operator Writer & ()

virtual	operator const Writer & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::physical::Filterable
	Filterable ()

	Filterable (Filter filter)

virtual	~Filterable ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual void	SetFilter (Filter filter)

Filter	GetFilter () const

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

Protected Member Functions inherited from bio::physical::Class< Filterable >
	Class (Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Filterable > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Filterable >	GetWaveObject ()

virtual Pointer< const Filterable >	GetWaveObject () const

virtual	operator Filterable & ()

virtual	operator const Filterable & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::chemical::Atom
void	IndexBond (AtomicNumber bondedId, Valence position)

void	UnindexBond (AtomicNumber bondedId)

	Atom ()

	Atom (const Atom &other)

virtual	~Atom ()

void	CloneBondsFrom (const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy)

virtual Pointer< const physical::Symmetry >	Spin () const

virtual Code	Reify (Pointer< const physical::Symmetry > symmetry)

Pointer< physical::Wave >	GetBonded (Valence position)

Pointer< const physical::Wave >	GetBonded (Valence position) const

Pointer< const physical::Wave >	ResolveBondedForReadById (AtomicNumber bondId) const

Pointer< physical::Wave >	ResolveBondedForWriteById (AtomicNumber bondId)

template<typename T >
Cow< T >	AsBonded () const

template<typename T >
Pointer< T >	AsBondedQuantum () const

template<typename T >
atom_detail::AsResultType< T, type::IsWaveImplementation< typenametype::RemovePointer< T >::Type >::sValue >::Type	As () const

template<typename T >
	operator T () const

template<typename T >
Valence	FormBond (T toBond, BondType type=bond_type::Unknown())

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (const Name &typeName) const

Valence	GetBondPositionLocked (AtomicNumber bondedId) const

template<typename T >
Valence	GetBondPosition () const

BondType	GetBondType (Valence position) const

template<typename T >
BondType	GetBondType () const

Pointer< Bonds >	GetAllBonds ()

Pointer< const Bonds >	GetAllBonds () const

void	ForEachBond (BondVisitor visitor, void *context=NULL) const

void	ForEachBondMutable (BondMutator mutator, void *context=NULL)

virtual Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type)

Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

Valence	FormBondImplementationLocked (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

virtual bool	BreakBondImplementation (AtomicNumber id, BondType type)

bool	BreakBondImplementationLocked (AtomicNumber id, BondType type)

Protected Member Functions inherited from bio::physical::Class< Atom >
	Class (Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Atom > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Atom >	GetWaveObject ()

virtual Pointer< const Atom >	GetWaveObject () const

virtual	operator Atom & ()

virtual	operator const Atom & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

ThreadSafe &	operator= (const ThreadSafe &toCopy)

	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

void	LockMutexShared () const

void	UnlockMutexShared () const

Protected Member Functions inherited from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >
	UnorderedMotif (ContentsAllocation allocation)

Static Protected Member Functions inherited from bio::log::Writer
static void	Log (Pointer< const Writer > writer, LogLevel level, const char *format,...)

static bool	ShouldLog (Pointer< const Writer > writer, LogLevel level)

Static Protected Member Functions inherited from bio::physical::Class< Writer >
static Pointer< Writer >	Convert (Pointer< Wave > wave)

Static Protected Member Functions inherited from bio::physical::Class< Filterable >
static Pointer< Filterable >	Convert (Pointer< Wave > wave)

Static Protected Member Functions inherited from bio::chemical::Atom
static BondCloneAction	DefaultBondClonePolicy (const Bond &bond)

template<typename T >
static AtomicNumber	GetBondId ()

Static Protected Member Functions inherited from bio::physical::Class< Atom >
static Pointer< Atom >	Convert (Pointer< Wave > wave)

Protected Attributes inherited from bio::physical::Class< T >
Pointer< T >	mObject

Protected Attributes inherited from bio::physical::Wave
LazyPointer< Symmetry >	mSymmetry

bool	mHasSignal

uint16_t	mTypeId

Protected Attributes inherited from bio::VirtualBase
bool	mHasBeenInitialized

Protected Attributes inherited from bio::physical::Class< Writer >
Pointer< Writer >	mObject

Protected Attributes inherited from bio::physical::Filterable
Filter	mFilter

Protected Attributes inherited from bio::physical::Class< Filterable >
Pointer< Filterable >	mObject

Protected Attributes inherited from bio::chemical::Atom
Bonds	mBonds

::std::map< AtomicNumber, Valence >	mBondIndex

Arrangement< Pointer< const physical::Wave > >	mBackflowPreventer

Protected Attributes inherited from bio::physical::Class< Atom >
Pointer< Atom >	mObject

Protected Attributes inherited from bio::chemical::AbstractMotif
CowPtr< Container >	mContents

Protected Attributes inherited from bio::chemical::EnvironmentDependent< ENVIRONMENT >
EnvironmentPointer	mEnvironment

Detailed Description

template<typename CONTENT_TYPE, typename ENVIRONMENT>
class bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >

DependentMotifs extend LinearMotifs by adding support for EnvironmentDependent objects.
Template arguments name the domain object types. DependentMotif< Cell, Tissue > stores Pointer< Cell > contents and a Pointer< Tissue > environment. This intentionally breaks WYSIWYG template spelling in the same way as LinearMotif<T>: callers spell the biological types, while Pointer<> remains an implementation and API value detail.
When an object is added to a DependentMotif, the object's Environment is Set as that stored in *this.

Constructor & Destructor Documentation

◆ DependentMotif() [1/3]

template<typename CONTENT_TYPE , typename ENVIRONMENT >

bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::DependentMotif ( EnvironmentPointer environment = NULL )

inlineexplicit

Parameters

environment

◆ DependentMotif() [2/3]

template<typename CONTENT_TYPE , typename ENVIRONMENT >

bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::DependentMotif	(	const typename LinearMotif< CONTENT_TYPE >::Contents *	contents,
		EnvironmentPointer	environment = `NULL`
	)

inlineexplicit

Parameters

contents
environment

◆ DependentMotif() [3/3]

template<typename CONTENT_TYPE , typename ENVIRONMENT >

bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::DependentMotif ( const DependentMotif< CONTENT_TYPE, ENVIRONMENT > & toCopy )

inline

Copying a DependentMotif will Clone all contents in toCopy into *this.
Keep in mind that dtor will delete the contents of *this.

Parameters

toCopy

◆ ~DependentMotif()

template<typename CONTENT_TYPE , typename ENVIRONMENT >

virtual bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::~DependentMotif ( )

inlinevirtual

Member Function Documentation

◆ AddImplementation()

template<typename CONTENT_TYPE , typename ENVIRONMENT >

virtual ContentPointer bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::AddImplementation ( ContentPointer content )

inlinevirtual

Adds content to *this.
Added objects are "owned" (not physical::Linear::IsShared()) and will be deleted with *this.

Parameters

content

Returns: t or NULL.

Reimplemented from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >.

◆ Attenuate()

template<typename CONTENT_TYPE , typename ENVIRONMENT >

virtual Code bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::Attenuate ( Pointer< const physical::Wave > other )

inlinevirtual

Ensure virtual methods point to Class implementations.
We want to define our own Attenuate & Disattenuate, so we have to ignore the optional class methods for the chemical class.

Reimplemented from bio::chemical::Class< DependentMotif< CONTENT_TYPE, ENVIRONMENT > >.

◆ Disattenuate()

template<typename CONTENT_TYPE , typename ENVIRONMENT >

virtual Code bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::Disattenuate ( Pointer< const physical::Wave > other )

inlinevirtual

Disambiguate Wave method. See that class for details.

Parameters

other

Returns: result of Wave::Disattenuation.

Reimplemented from bio::chemical::Class< DependentMotif< CONTENT_TYPE, ENVIRONMENT > >.

◆ InsertImplementation()

template<typename CONTENT_TYPE , typename ENVIRONMENT >

virtual Code bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::InsertImplementation	(	ContentPointer	toAdd,
		const Position	position = `BOTTOM`,
		const Id	optionalPositionArg = `0`,
		const bool	transferSubContents = `false`
	)

inlinevirtual

Adds a Content in *this at the indicated position.
Multiple contents of the same id will cause the previously existing Content to be removed.

NOTE: THIS DESTROYS INDEX INTEGRITY.
Indices will be rearranged to accommodate the insertion, making any cached Index invalid.

Parameters

toAdd	what to add. IMPORTANT: This must not already be in a DependentMotif (i.e. create a clone() before adding it to another destination).
position	determines where in *this the Content is added.
optionalPositionArg	If a position is specified, the optionalPositionArg is the id of the Content referenced (e.g. BEFORE, MyContentId()).
transferSubContents	allows all of the Contents within a conflicting Content to be copied into the new Content, before the conflicting Content is deleted (similar to renaming an upper directory while preserving it's contents).

Returns: Status of addition (e.g. success or failure).

◆ SetEnvironment()

template<typename CONTENT_TYPE , typename ENVIRONMENT >

virtual void bio::chemical::DependentMotif< CONTENT_TYPE, ENVIRONMENT >::SetEnvironment ( EnvironmentPointer environment )

inlinevirtual

Sets the Environment of *this and all mContents.
Don't let the environment go out of scope or be deleted before *this!

Parameters

environment

The documentation for this class was generated from the following file:

DependentMotif.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DependentMotif() [1/3]

◆ DependentMotif() [2/3]

◆ DependentMotif() [3/3]

◆ ~DependentMotif()

Member Function Documentation

◆ AddImplementation()

◆ Attenuate()

◆ Disattenuate()

◆ InsertImplementation()

◆ SetEnvironment()