#include <Dendrite.h>

Inheritance diagram for bio::neural::Dendrite:

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Collaboration diagram for bio::neural::Dendrite:

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Public Member Functions
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (neural, Dendrite, filter::Neural()) void CommonConstructor()

virtual	~Dendrite ()

virtual Code	CacheProteins ()

virtual Code	CreateDefaultProteins ()

virtual Timestamp	PrepareForPotentiation (Timestamp whenToPotentiate)

virtual void	PrepareForDepotentiation ()

virtual Code	ProcessPotentiation ()

virtual Code	ProcessDepotentiation ()

virtual Code	PostPotentiation ()

virtual Code	PostDepotentiation ()

virtual bool	ShouldBePotentiated () const

virtual bool	ShouldBeDepotentiated () const

virtual void	ReReady ()

virtual Timestamp	GetTimeToAdd () const

Pointer< Neuron >	GetPostsynapticNeuron ()

Pointer< const Neuron >	GetPostsynapticNeuron () const

Name	GetPostsynapticName () const

Id	GetPostsynapticId () const

virtual void	Potentiated ()

virtual void	Depotentiated ()

Public Member Functions inherited from bio::neural::Class< Dendrite >
	Class (Pointer< Dendrite > object, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

	Class (Pointer< Dendrite > object, const Name &name, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

	Class (Pointer< Dendrite > object, const Id &id, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

virtual	~Class ()

Public Member Functions inherited from bio::cellular::Class< T >
	Class (Pointer< T > object, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval())

	Class (Pointer< T > object, const Name &name, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval())

	Class (Pointer< T > object, const Id &id, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval())

virtual Code	Apoptose ()

virtual Code	Crest ()

virtual bool	CheckIn ()

virtual Code	SetInterval (Milliseconds period)

Public Member Functions inherited from bio::genetic::Class< T >
	Class (Pointer< T > object, Filter filter=filter::Default())

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

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

Public Member Functions inherited from bio::molecular::Class< T >
	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())

template<typename ENVIRONMENT >
void	SetEnvironment (Pointer< ENVIRONMENT > environment)

template<typename ENVIRONMENT >
Pointer< ENVIRONMENT >	GetEnvironment ()

template<typename ENVIRONMENT >
const Pointer< ENVIRONMENT >	GetEnvironment () const

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 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

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)

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::Substance
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (chemical, Substance, filter::Chemical()) Substance(const UnorderedMotif< Property > &properties

virtual	~Substance ()

virtual void	Enable ()

virtual void	Disable ()

virtual bool	IsEnabled () const

Public Member Functions inherited from bio::chemical::Class< Substance >
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< Substance > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

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

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

	Class (const Class &other)

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

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

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

Public Member Functions inherited from bio::Covalent< UnorderedMotif< Property > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< UnorderedMotif< Property > >	Object ()

Pointer< const UnorderedMotif< Property > >	Object () const

Public Member Functions inherited from bio::Covalent< UnorderedMotif< State > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< UnorderedMotif< State > >	Object ()

Pointer< const UnorderedMotif< State > >	Object () const

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

virtual	~Structure ()

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

virtual	~UnorderedStructureInterface ()

template<typename T >
T	Add (const T t)

template<typename T >
Pointer< T >	Add (Pointer< T > t)

template<typename T >
Code	Remove (const T t)

template<typename T >
Code	Remove (Pointer< T > t)

template<typename T >
void	Import (Pointer< const UnorderedMotif< T > > other)

template<typename T >
void	Import (Pointer< const LinearMotif< T > > other)

template<typename T >
void	Import (const ::bio::Arrangement< T > &other)

Code	ImportAll (Pointer< const physical::Wave > other)

template<typename T >
Index	GetCount () const

template<typename T >
Pointer< Container >	GetAll ()

template<typename T >
Pointer< const Container >	GetAll () const

template<typename T >
bool	Has (T content) const

template<typename T >
bool	Has (Pointer< T > content) const

template<typename T >
unsigned int	GetNumMatching (Pointer< const Container > other) const

template<typename T >
bool	HasAll (Pointer< const Container > contents) const

template<typename T >
void	Clear ()

template<typename T >
std::string	GetStringFrom (std::string separator=", ")

template<typename T >
void	Log (const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId())

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

virtual	~LinearStructureInterface ()

template<typename T >
Code	Insert (typename LinearStructureRequest< T >::PointerType toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false)

template<typename T >
LinearStructureRequest< T >::PointerType	GetById (const Id &id)

template<typename T >
const LinearStructureRequest< T >::PointerType	GetById (const Id &id) const

template<typename T >
LinearStructureRequest< T >::PointerType	GetByName (const Name &name)

template<typename T >
const LinearStructureRequest< T >::PointerType	GetByName (const Name &name) const

template<typename T >
LinearStructureRequest< T >::PointerType	GetOrCreateById (Id id)

template<typename T >
LinearStructureRequest< T >::PointerType	GetOrCreateByName (const Name &name)

template<typename T >
Code	RemoveById (const Id &id)

template<typename T >
Code	RemoveByName (const Name &name)

template<typename T >
LinearMotif< typenameLinearStructureRequest< T >::Pointee >::Contents	GetAllLike (Pointer< const Affinity > affinity) const

template<typename T >
Emission	ForEach (Pointer< ExcitationBase > excitation)

Public Member Functions inherited from bio::molecular::Molecule
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (molecular, Molecule, filter::Molecular()) Molecule(const Molecule &toCopy)

virtual	~Molecule ()

template<typename T >
Id	Use (const Name &varName, Pointer< T > varPtr)

template<typename T >
Id	Use (const Id &id, Pointer< T > varPtr)

Id	Define (const Name &varName)

Id	Define (const Id &id)

template<typename T >
Id	Define (const Name &varName)

template<typename T >
Id	Define (const Id &id)

template<typename T >
Id	Define (const Name &varName, const T &assignment)

template<typename T >
Id	Define (const Id &id, const T &assignment)

virtual Pointer< Surface >	RotateTo (const Id &surfaceId)

virtual Pointer< const Surface >	RotateTo (const Id &surfaceId) const

virtual Pointer< Surface >	RotateTo (const Name &surfaceName)

virtual Pointer< const Surface >	RotateTo (const Name &surfaceName) const

virtual Pointer< Surface >	RotateToOrDefine (const Id &surfaceId)

Pointer< Surface >	RotateToOrDefine (const Name &surfaceName)

template<typename T >
Pointer< Surface >	RotateToOrDefine (const Id &surfaceId, T &assignment)

template<typename T >
Pointer< Surface >	RotateToOrDefine (const Name &surfaceName, T &assignment)

virtual bool	DuplicateFrom (Pointer< Molecule > source, const Name &surface)

virtual bool	TransferFrom (Pointer< Molecule > source, const Name &surface)

virtual Pointer< Surface >	operator() (const Id &surfaceId)

virtual Pointer< const Surface >	operator() (const Id &surfaceId) const

template<typename T >
Pointer< Surface >	operator() (const Id &surfaceId)

virtual Pointer< Surface >	operator() (const Name &name)

virtual Pointer< const Surface >	operator() (const Name &name) const

template<typename T >
Pointer< Surface >	operator() (const Name &surfaceName)

virtual Pointer< Molecule >	operator<< (Pointer< Surface > source)

virtual Pointer< Surface >	operator>> (Pointer< Surface > target)

virtual Pointer< Molecule >	operator<< (Pointer< Molecule > source)

virtual Pointer< Molecule >	operator>> (Pointer< Molecule > target)

Public Member Functions inherited from bio::molecular::Class< Molecule >
	Class (Pointer< Molecule > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

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

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

void	SetEnvironment (Pointer< ENVIRONMENT > environment)

Pointer< ENVIRONMENT >	GetEnvironment ()

const Pointer< ENVIRONMENT >	GetEnvironment () const

Public Member Functions inherited from bio::Metallic< chemical::DependentMotif< Surface, Molecule > >
	Metallic ()

	Metallic (const Metallic &other)

virtual	~Metallic ()

Metallic &	operator= (const Metallic &other)

Pointer< chemical::DependentMotif< Surface, Molecule > >	Object ()

Pointer< const chemical::DependentMotif< Surface, Molecule > >	Object () const

Public Member Functions inherited from bio::genetic::Expressor
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (genetic, Expressor, filter::Genetic()) virtual ~Expressor()

void	CommonConstructor ()

Code	Activate (const Id &proteinId)

Code	Activate (const Name &proteinName)

template<typename T >
Code	Activate ()

template<typename T >
Pointer< molecular::Protein >	GetExpressedProteinByName (const Name &proteinName)

virtual Code	Translate (Pointer< const RNA > mRNA)

virtual Code	AddToTranscriptome (Pointer< const RNA > toExpress)

Public Member Functions inherited from bio::genetic::Class< Expressor >
	Class (Pointer< Expressor > object, Filter filter=filter::Default())

	Class (Pointer< Expressor > object, const Name &name, Filter filter=filter::Default())

	Class (Pointer< Expressor > object, const Id &id, Filter filter=filter::Default())

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

	UnorderedMotif (Pointer< const Contents > contents)

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

	UnorderedMotif (const UnorderedMotif< TranscriptionFactor > &toCopy)

UnorderedMotif< TranscriptionFactor > &	operator= (const UnorderedMotif< TranscriptionFactor > &toCopy)

virtual	~UnorderedMotif ()

virtual Pointer< Container >	GetAllImplementation ()

virtual Pointer< const Container >	GetAllImplementation () const

virtual void	ClearImplementation ()

virtual Index	GetCountImplementation () const

virtual TranscriptionFactor	AddImplementation (const TranscriptionFactor content)

virtual Code	RemoveImplementation (const TranscriptionFactor content)

virtual bool	HasImplementation (const TranscriptionFactor content) const

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

virtual void	ImportImplementation (const void *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::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::Covalent< chemical::LinearMotif< Plasmid > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< chemical::LinearMotif< Plasmid > >	Object ()

Pointer< const chemical::LinearMotif< Plasmid > >	Object () const

Public Member Functions inherited from bio::Covalent< chemical::LinearMotif< molecular::Protein > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< chemical::LinearMotif< molecular::Protein > >	Object ()

Pointer< const chemical::LinearMotif< molecular::Protein > >	Object () const

Public Member Functions inherited from bio::molecular::Vesicle
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS (molecular, Vesicle, filter::Molecular()) Vesicle(const Vesicle &toCopy)

virtual	~Vesicle ()

Public Member Functions inherited from bio::molecular::Class< Vesicle >
	Class (Pointer< Vesicle > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

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

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

void	SetEnvironment (Pointer< ENVIRONMENT > environment)

Pointer< ENVIRONMENT >	GetEnvironment ()

const Pointer< ENVIRONMENT >	GetEnvironment () const

Public Member Functions inherited from bio::physical::Periodic
	Periodic (Milliseconds interval=GetDefaultInterval())

virtual	~Periodic ()

virtual void	InitializeImplementation (ByteStreams &args)

Milliseconds	GetInterval () const

Timestamp	GetTimeLastCrested () const

float	GetIntervalInSeconds () const

virtual void	SetLastCrestTimestamp (Timestamp lastCrest)

virtual Properties	GetProperties () const

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

	Class (Pointer< Periodic > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Periodic >	GetWaveObject ()

virtual Pointer< const Periodic >	GetWaveObject () const

virtual	operator Periodic & ()

virtual	operator const Periodic & () const

virtual Pointer< Wave >	Clone () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::neural::Neurite
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS (neural, Neurite, filter::Neural()) virtual ~Neurite()

virtual bool	IsZero () const

virtual void	MakeZero ()

Public Member Functions inherited from bio::neural::Class< Neurite >
	Class (Pointer< Neurite > object, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

	Class (Pointer< Neurite > object, const Name &name, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

	Class (Pointer< Neurite > object, const Id &id, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

virtual	~Class ()

Public Member Functions inherited from bio::neural::StemCell
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS (neural, StemCell, filter::Neural()) virtual ~StemCell()

virtual Code	Reset (const ::bio::Potential &potential)

virtual Code	ResetAllPossiblePotentials ()

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

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

Public Member Functions inherited from bio::neural::Class< StemCell >
	Class (Pointer< StemCell > object, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

	Class (Pointer< StemCell > object, const Name &name, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

	Class (Pointer< StemCell > object, const Id &id, Filter filter=filter::Default(), Milliseconds interval=physical::Periodic::GetDefaultInterval())

virtual	~Class ()

Public Member Functions inherited from bio::cellular::Cell
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS (cellular, Cell, filter::Cellular()) virtual ~Cell()

virtual Code	ExpressGenes ()

virtual bool	IsWithinTissue (const Id &tissueId) const

virtual bool	IsWithinTissue (const Name &name) const

Code	ApoptoseAndEvict ()

Public Member Functions inherited from bio::cellular::Class< Cell >
	Class (Pointer< Cell > object, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval())

	Class (Pointer< Cell > object, const Name &name, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval())

	Class (Pointer< Cell > object, const Id &id, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval())

virtual	~Class ()

virtual Code	Apoptose ()

virtual Code	Crest ()

virtual bool	CheckIn ()

virtual Code	SetInterval (Milliseconds period)

Public Member Functions inherited from bio::Metallic< chemical::DependentMotif< Organelle, Cell > >
	Metallic ()

	Metallic (const Metallic &other)

virtual	~Metallic ()

Metallic &	operator= (const Metallic &other)

Pointer< chemical::DependentMotif< Organelle, Cell > >	Object ()

Pointer< const chemical::DependentMotif< Organelle, Cell > >	Object () const

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

virtual	~EnvironmentDependent ()

virtual EnvironmentPointer	GetEnvironment ()

virtual const EnvironmentPointer	GetEnvironment () const

virtual void	SetEnvironment (EnvironmentPointer environment)

Public Member Functions inherited from bio::Covalent< chemical::UnorderedMotif< Feature > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< chemical::UnorderedMotif< Feature > >	Object ()

Pointer< const chemical::UnorderedMotif< Feature > >	Object () const

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

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< chemical::LinearMotif< Potential > >	Object ()

Pointer< const chemical::LinearMotif< Potential > >	Object () const

Protected Member Functions
virtual void	NoLongerReady ()

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

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)

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::LinearStructureInterface
template<typename T >
Pointer< LinearMotif< T > >	ResolveLinearMotif ()

template<typename T >
Pointer< const LinearMotif< T > >	ResolveLinearMotif () const

Protected Member Functions inherited from bio::genetic::Expressor
void	ClearTranscriptome ()

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

Protected Member Functions inherited from bio::chemical::Solution
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS (chemical, Solution, filter::Chemical()) virtual Id Dissolve(Pointer< Substance > toDissolve

virtual Pointer< Substance >	Separate (const Id &id)

virtual Id	Influx (const Solute &toInflux)

virtual Solute	Efflux (const Id &soluteId)

virtual const Solute	Efflux (const Id &soluteId) const

virtual Solute	Efflux (const Name &substanceName)

virtual const Solute	Efflux (const Name &substanceName) const

virtual Pointer< physical::Line >	GetAllSolutes ()

virtual Pointer< const physical::Line >	GetAllSolutes () const

Protected Member Functions inherited from bio::chemical::Class< Solution >
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< Solution > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

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

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

	Class (const Class &other)

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

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

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

Protected Member Functions inherited from bio::chemical::DependentMotif< Solute, Solution >
virtual Code	Attenuate (Pointer< const physical::Wave > other)

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

	DependentMotif (EnvironmentPointer environment=NULL)

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

	DependentMotif (const DependentMotif< Solute, Solution > &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)

Protected 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

Protected 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 bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

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

	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 Pointer< CONTENT_TYPE >	AddImplementation (const Pointer< CONTENT_TYPE > content)

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())

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

virtual	~EnvironmentDependent ()

virtual EnvironmentPointer	GetEnvironment ()

virtual const EnvironmentPointer	GetEnvironment () const

virtual void	SetEnvironment (EnvironmentPointer environment)

Protected Attributes
Pointer< Neuron >	mPostsynapticNeuron

Pointer< molecular::Protein >	mcPrepareForPotentiation

Pointer< molecular::Protein >	mcProcessPotentiation

Pointer< molecular::Protein >	mcPostPotentiation

Pointer< molecular::Protein >	mcPrepareForDepotentiation

Pointer< molecular::Protein >	mcProcessDepotentiation

Pointer< molecular::Protein >	mcPostDepotentiation

Pointer< molecular::Protein >	mcReReady

Timestamp	mPotentiateAt

Timestamp	mLastPotentiated

Id	mPostsynapticNeuronId

Protected Attributes inherited from bio::cellular::Class< T >
Pointer< molecular::Protein >	mcApoptosis

Pointer< molecular::Protein >	mcCrest

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::Covalent< UnorderedMotif< Property > >
Pointer< UnorderedMotif< Property > >	mT

Protected Attributes inherited from bio::Covalent< UnorderedMotif< State > >
Pointer< UnorderedMotif< State > >	mT

Protected Attributes inherited from bio::Metallic< chemical::DependentMotif< Surface, Molecule > >
Pointer< chemical::DependentMotif< Surface, Molecule > >	mT

Protected Attributes inherited from bio::genetic::Expressor
Transcriptome	mTranscriptome

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

Protected Attributes inherited from bio::Covalent< chemical::LinearMotif< Plasmid > >
Pointer< chemical::LinearMotif< Plasmid > >	mT

Protected Attributes inherited from bio::Covalent< chemical::LinearMotif< molecular::Protein > >
Pointer< chemical::LinearMotif< molecular::Protein > >	mT

Protected Attributes inherited from bio::chemical::Solution
const DiffusionTime &	diffusionTime = diffusion::time::Destruction()

const DiffusionTime const DiffusionEffort &	diffusionEffort

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

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

Protected Attributes inherited from bio::physical::Periodic
Milliseconds	mInterval

Timestamp	mLastCrestTimestamp

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

Protected Attributes inherited from bio::neural::Neurite
Pointer< molecular::Protein >	mcIsZero

Pointer< molecular::Protein >	mcMakeZero

Protected Attributes inherited from bio::cellular::Class< Cell >
Pointer< molecular::Protein >	mcApoptosis

Pointer< molecular::Protein >	mcCrest

Protected Attributes inherited from bio::Metallic< chemical::DependentMotif< Organelle, Cell > >
Pointer< chemical::DependentMotif< Organelle, Cell > >	mT

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

Protected Attributes inherited from bio::Covalent< chemical::UnorderedMotif< Feature > >
Pointer< chemical::UnorderedMotif< Feature > >	mT

Protected Attributes inherited from bio::Covalent< chemical::LinearMotif< Potential > >
Pointer< chemical::LinearMotif< Potential > >	mT

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::UnorderedMotif< TranscriptionFactor >
typedef Arrangement< TranscriptionFactor >	Contents

Public Types inherited from bio::chemical::EnvironmentDependent< cellular::Tissue >
typedef type::RemovePointer< cellular::Tissue >::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::UnorderedStructureInterface
static void	ImportAllCollectVisitor (const chemical::Bond &bond, void *ctx)

Static Public Member Functions inherited from bio::Metallic< chemical::DependentMotif< Surface, Molecule > >
static void	DonateCollectVisitor (const chemical::Bond &bond, void *ctx)

static void	DonateBonds (Pointer< chemical::Atom > donor, Pointer< chemical::Atom > receiver)

static void	BreakDonatedCollectVisitor (const chemical::Bond &bond, void *ctx)

static void	BreakDonatedBonds (Pointer< chemical::Atom > receiver)

static BondType	GetBondType ()

Static Public Member Functions inherited from bio::chemical::UnorderedMotif< TranscriptionFactor >
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 ()

Static Public Member Functions inherited from bio::physical::Periodic
static Milliseconds	GetDefaultInterval ()

static Properties	GetClassProperties ()

static Symmetry *	MakePeriodicSymmetry ()

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

Static Public Member Functions inherited from bio::Metallic< chemical::DependentMotif< Organelle, Cell > >
static void	DonateCollectVisitor (const chemical::Bond &bond, void *ctx)

static void	DonateBonds (Pointer< chemical::Atom > donor, Pointer< chemical::Atom > receiver)

static void	BreakDonatedCollectVisitor (const chemical::Bond &bond, void *ctx)

static void	BreakDonatedBonds (Pointer< chemical::Atom > receiver)

static BondType	GetBondType ()

Public Attributes inherited from bio::chemical::Substance
const UnorderedMotif< State > &	states

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< TranscriptionFactor >
enum	ContentsAllocation

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

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

typedef Arrangement< Pointer< CONTENT_TYPE > >	Contents

Protected Types inherited from bio::chemical::EnvironmentDependent< T >
typedef type::RemovePointer< T >::Type	EnvironmentType

typedef Pointer< EnvironmentType >	EnvironmentPointer

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)

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

Static Protected 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)

Constructor & Destructor Documentation

◆ ~Dendrite()

bio::neural::Dendrite::~Dendrite ( )

virtual

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

bio::neural::Dendrite::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR	(	neural	,
		Dendrite	,
		filter::Neural()
	)

Disambiguate all class methods.
Initialise the cached Protein* fields to NULL. Without this they inherit whatever heap garbage is at their offset; the consumer methods (PrepareForPotentiation, ProcessPotentiation, etc.) all dereference these unconditionally — so any code path that fires a consumer before CacheProteins has run on a freshly-constructed Dendrite explodes on garbage. Same family of bug as Synapse's mcAdditionalConfiguration (lib/bio f97fc89); same fix applied structurally rather than at the consumer-side guard since these consumers don't have one.

◆ CacheProteins()

Code bio::neural::Dendrite::CacheProteins ( )

virtual

Use this method to populate any member variable Protein*s.
You'll want to do this to speed up your code by bypassing the dynamic execution provided by genetic::Expressor.

Reimplemented from bio::cellular::Class< T >.

Reimplemented in bio::neural::Synapse.

◆ CreateDefaultProteins()

Code bio::neural::Dendrite::CreateDefaultProteins ( )

virtual

If you use CacheProteins, you'll likely want to create your default Proteins here.
This will prevent dereferencing null or garbage pointers when using your cached Proteins.

Reimplemented from bio::cellular::Class< T >.

Reimplemented in bio::neural::Synapse.

◆ Depotentiated()

void bio::neural::Dendrite::Depotentiated ( )

virtual

Hook for when *this is Depotentiated.

◆ GetPostsynapticId()

Id bio::neural::Dendrite::GetPostsynapticId ( ) const

Returns: the Id of what *this sends data to, the target.

◆ GetPostsynapticName()

Name bio::neural::Dendrite::GetPostsynapticName ( ) const

Returns: the Name of what *this sends data to, the target.

◆ GetPostsynapticNeuron() [1/2]

Pointer< Neuron > bio::neural::Dendrite::GetPostsynapticNeuron ( )

Returns: what *this sends data to, the target.

◆ GetPostsynapticNeuron() [2/2]

Pointer< const Neuron > bio::neural::Dendrite::GetPostsynapticNeuron ( ) const

Returns: what *this sends data to, the target.

◆ GetTimeToAdd()

Timestamp bio::neural::Dendrite::GetTimeToAdd ( ) const

virtual

Returns: the timestamp at which *this should be added to the target

◆ NoLongerReady()

void bio::neural::Dendrite::NoLongerReady ( )

protectedvirtual

What to do when *this is no longer ready to be potentiated.

◆ PostDepotentiation()

Code bio::neural::Dendrite::PostDepotentiation ( )

virtual

PROTEIN BASED.
If you would like to do something after *this has been fully removed from the target, put that code in the appropriate Post____() method.

Returns: the result of PostDepotentiation()

◆ PostPotentiation()

Code bio::neural::Dendrite::PostPotentiation ( )

virtual

PROTEIN BASED.
If you would like to do something after *this has been fully added to the target, put that code in the appropriate Post____() method.

Returns: the result of PostPotentiation()

◆ Potentiated()

void bio::neural::Dendrite::Potentiated ( )

virtual

Hook for when *this is Potentiated.

◆ PrepareForDepotentiation()

void bio::neural::Dendrite::PrepareForDepotentiation ( )

virtual

PROTEIN BASED.
Called directly after *this is added, PrepareForDepotentiation does whatever is necessary for ProcessDepotentiation to work.
For example, if *this uses a New and Old value, this method would set Old to New and zero out New.

◆ PrepareForPotentiation()

Timestamp bio::neural::Dendrite::PrepareForPotentiation ( Timestamp whenToPotentiate )

virtual

PROTEIN BASED.
Called after ProcessOutgoing calls Update(time)
For example, if the source says this should be added at the current time, and *this has some sort of delay (perhaps from learning), this method will return the current time plus the indicated delay.

Parameters

whenToPotentiate the time at which the source wants *this to be added.

Returns: the timestamp that Update will use to set the time at which *this should be added.

◆ ProcessDepotentiation()

Code bio::neural::Dendrite::ProcessDepotentiation ( )

virtual

PROTEIN BASED.
Modifies the receiver according to the purpose of *this (e.g. incrementing/decrementing the receiver's value)
Removal is always the opposite of Addition such that: p = Removal(Addition(p)) && p = Addition(Removal(p))
EXTREME care must be taken when the above is not possible.

Returns: the result of removing *this from the target.

◆ ProcessPotentiation()

Code bio::neural::Dendrite::ProcessPotentiation ( )

virtual

PROTEIN BASED.
Modifies the receiver according to the purpose of *this (e.g. incrementing/decrementing the receiver's value)
Removal is always the opposite of Addition such that: p = Removal(Addition(p)) && p = Addition(Removal(p))
EXTREME care must be taken when the above is not possible.

Returns: the result of adding *this to the target.

◆ ReReady()

void bio::neural::Dendrite::ReReady ( )

virtual

PROTEIN BASED.
For rare circumstances, where *this might need to be re-added
TODO: is there a better solution?

◆ ShouldBeDepotentiated()

bool bio::neural::Dendrite::ShouldBeDepotentiated ( ) const

virtual

Returns: true if *this has expired.

Reimplemented in bio::neural::Synapse.

◆ ShouldBePotentiated()

bool bio::neural::Dendrite::ShouldBePotentiated ( ) const

virtual

This method does not need to be overwritten. See the IsZero, above.

Returns: true if *this should be added at the current time, and the value of the data are >0 || AreZerosAllowed is true. false otherwise

Reimplemented in bio::neural::Synapse.

Member Data Documentation

◆ mcPostDepotentiation

Pointer< molecular::Protein > bio::neural::Dendrite::mcPostDepotentiation

protected

◆ mcPostPotentiation

Pointer< molecular::Protein > bio::neural::Dendrite::mcPostPotentiation

protected

◆ mcPrepareForDepotentiation

Pointer< molecular::Protein > bio::neural::Dendrite::mcPrepareForDepotentiation

protected

◆ mcPrepareForPotentiation

Pointer< molecular::Protein > bio::neural::Dendrite::mcPrepareForPotentiation

protected

◆ mcProcessDepotentiation

Pointer< molecular::Protein > bio::neural::Dendrite::mcProcessDepotentiation

protected

◆ mcProcessPotentiation

Pointer< molecular::Protein > bio::neural::Dendrite::mcProcessPotentiation

protected

◆ mcReReady

Pointer< molecular::Protein > bio::neural::Dendrite::mcReReady

protected

◆ mLastPotentiated

Timestamp bio::neural::Dendrite::mLastPotentiated

protected

◆ mPostsynapticNeuron

Pointer< Neuron > bio::neural::Dendrite::mPostsynapticNeuron

protected

◆ mPostsynapticNeuronId

Id bio::neural::Dendrite::mPostsynapticNeuronId

protected

Used when the target object is unknown or has not been created yet.

◆ mPotentiateAt

Timestamp bio::neural::Dendrite::mPotentiateAt

protected

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

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ~Dendrite()

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

◆ CacheProteins()

◆ CreateDefaultProteins()

◆ Depotentiated()

◆ GetPostsynapticId()

◆ GetPostsynapticName()

◆ GetPostsynapticNeuron() [1/2]

◆ GetPostsynapticNeuron() [2/2]

◆ GetTimeToAdd()

◆ NoLongerReady()

◆ PostDepotentiation()

◆ PostPotentiation()

◆ Potentiated()

◆ PrepareForDepotentiation()

◆ PrepareForPotentiation()

◆ ProcessDepotentiation()

◆ ProcessPotentiation()

◆ ReReady()

◆ ShouldBeDepotentiated()

◆ ShouldBePotentiated()

Member Data Documentation

◆ mcPostDepotentiation

◆ mcPostPotentiation

◆ mcPrepareForDepotentiation

◆ mcPrepareForPotentiation

◆ mcProcessDepotentiation

◆ mcProcessPotentiation

◆ mcReReady

◆ mLastPotentiated

◆ mPostsynapticNeuron

◆ mPostsynapticNeuronId

◆ mPotentiateAt