#include <Synapse.h>

Inheritance diagram for bio::neural::Synapse:

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Collaboration diagram for bio::neural::Synapse:

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

virtual	~Synapse ()

virtual Code	CacheProteins ()

virtual Code	CreateDefaultProteins ()

virtual void	Update (Timestamp whenToPotentiate)

Pointer< Synapse >	ConfigureFor (Pointer< const Neuron > presynapticNeuron, Pointer< Neuron > postsynapticNeuron) const

void	ClearPresynapticEndpoint ()

void	ClearPostsynapticEndpoint ()

void	ClearAllEndpointsNoDelete ()

SynapseDetachReport	DetachTopologyNoDelete (bool touchPresynaptic, bool touchPostsynaptic)

SynapseDetachReport	DetachTopologyNoDelete ()

bool	IsTopologyDetached () const

void	DisconnectAndDelete ()

virtual void	AdditionalConfiguration (Pointer< const Neuron > presynapticNeuron, Pointer< Neuron > postsynapticNeuron)

virtual bool	ShouldBePotentiated () const

virtual bool	ShouldBeDepotentiated () const

virtual void	ExtendTimeoutUntil (Timestamp timeToDepotentiate)

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

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

	Class (Pointer< Synapse > 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::Dendrite
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (neural, Dendrite, filter::Neural()) void CommonConstructor()

virtual	~Dendrite ()

virtual Timestamp	PrepareForPotentiation (Timestamp whenToPotentiate)

virtual void	PrepareForDepotentiation ()

virtual Code	ProcessPotentiation ()

virtual Code	ProcessDepotentiation ()

virtual Code	PostPotentiation ()

virtual Code	PostDepotentiation ()

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::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

Public Member Functions inherited from bio::neural::Axon
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (neural, Axon, filter::Neural()) void CommonConstructor()

virtual	~Axon ()

virtual Code	ProcessOutgoing ()

virtual void	Callback (Pointer< const molecular::Molecule > arg)

virtual Timestamp	GetTimeLastUpdated () const

virtual Milliseconds	GetTimeout () const

virtual void	SetTimeout (Milliseconds lastFor)

virtual void	DepotentiateSignal ()

Pointer< const Neuron >	GetPresynapticNeuron () const

Name	GetPresynapticName () const

Id	GetPresynapticId () const

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

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

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

virtual	~Class ()

Protected Attributes
Pointer< molecular::Protein >	mcAdditionalConfiguration

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::Dendrite
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::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

Protected Attributes inherited from bio::neural::Axon
Pointer< const Neuron >	mPresynapticNeuron

Pointer< molecular::Protein >	mcProcessOutgoing

Pointer< molecular::Protein >	mCallback

Pointer< molecular::Protein >	mcDepotentiateSignal

Timestamp	mLastUpdated

Milliseconds	mTimeout

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

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 Member Functions inherited from bio::neural::Dendrite
virtual void	NoLongerReady ()

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)

Detailed Description

Synapses take data from one Neuron, the "presynapticNeuron", and make it available to another Neuron, the "postsynapticNeuron".
Synapses are Cells. This is unusual. However, if we think of the proteins within the synaptic cleft as a specialized & distinct unit, this starts to make sense. The only major difference then is the lack of a membrane around the synaptic cleft.
So, in our Biology framework, Synapses have their own Genes, Proteins, local Dissolved Substances, and can be specialized just like any other Cell.

In order to remove data that was previously added while simultaneously allowing more data to be pushed through *this, a history of the data in *this must be kept.
This history need only be a single value (i.e. not a complete history).
The reason for this is that if a new datum is pushed through this that would overwrite data that has not been added, the previous, unadded data are no longer useful and can be freely overwritten.
Similarly, if the old datum always represents what is currently added to to the postsynapticNeuron, there is no need to maintain a history of more than this single datum.
For example a Synapse that passes a float might have: float mUnprocessed float mProcessed This type of 2 value system will be a common motif among bio::Synapses. The unprocessed, or "new", value is a value from the presynapticNeuron that has not yet been added to the postsynapticNeuron. Once this value is added, it becomes processed, or "old".
In general, Synapses look like: [SOURCE]-—[*this]-—>[TARGET]
When sending data, [SOURCE]-->ProcessOutgoing()-->Update() [SOURCE]-->DepotentiateSignal() (totally optional)
When receiving data, ProcessPotentiation()-->[TARGET] (postsynapticNeuron calls ProcessPotentiation, which affects ProcessDepotentiation()-->[TARGET] the postsynapticNeuron in some way)

NOTE: Creating synapses outside of Neuron::ConnectTo(...) is not supported.

To use *this between any pair of neurons, use ConfigureFor() (below).

Constructor & Destructor Documentation

◆ ~Synapse()

bio::neural::Synapse::~Synapse ( )

virtual

Member Function Documentation

◆ AdditionalConfiguration()

void bio::neural::Synapse::AdditionalConfiguration	(	Pointer< const Neuron >	presynapticNeuron,
		Pointer< Neuron >	postsynapticNeuron
	)

virtual

PROTEIN BASED.
Called when *this is configured for use between the two given neurons.
This will be called on a newly created Clone() of *this.

Parameters

presynapticNeuron	the Neuron that will be sending data through *this.
postsynapticNeuron	the Neuron that will be receiving data through *this.

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

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

Disambiguate all class methods.
Initialise the cached Protein* fields to NULL. Belt-and-suspenders companion to lib/bio f97fc89 (which moved CacheProteins to fire before ConfigureFor's rebuild guard); ensures any future direct deref of mcAdditionalConfiguration on a freshly-constructed Synapse hits a NULL (clean diagnostic) rather than heap garbage.

◆ CacheProteins()

Code bio::neural::Synapse::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 >.

◆ ClearAllEndpointsNoDelete()

void bio::neural::Synapse::ClearAllEndpointsNoDelete ( )

Clear BOTH endpoint pointers (pre + post) without touching any motif and without deleting. Used by the whole-Neuropil teardown sweep to make every contained synapse inert before the base Clear deletes it.

◆ ClearPostsynapticEndpoint()

void bio::neural::Synapse::ClearPostsynapticEndpoint ( )

Clear the postsynaptic (Dendrite) endpoint pointer and Id ONLY. No motif touch, no delete. NON-VIRTUAL / ABI-neutral.

◆ ClearPresynapticEndpoint()

void bio::neural::Synapse::ClearPresynapticEndpoint ( )

Clear the presynaptic (Axon) endpoint pointer ONLY. No motif touch, no delete. Synapse IS-A Axon, so it may write its own protected base field; this and ClearPostsynapticEndpoint are the only writers of the endpoint fields outside ConfigureFor. NON-VIRTUAL / ABI-neutral.

◆ ConfigureFor()

Pointer< Synapse > bio::neural::Synapse::ConfigureFor	(	Pointer< const Neuron >	presynapticNeuron,
		Pointer< Neuron >	postsynapticNeuron
	)		const

ConfigureFor is used by Neuron::ConnectTo to clone *this such that it may be added between the given presynapticNeuron and postsynapticNeuron
This will call postsynapticNeuron->AddDendrite()

Parameters

presynapticNeuron	the Neuron that will send data to the new Neurite
postsynapticNeuron	the Neuron that will receive data from the new Neurite

Returns: a Clone of *this but with the given postsynapticNeuron

◆ CreateDefaultProteins()

Code bio::neural::Synapse::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 >.

◆ DetachTopologyNoDelete() [1/2]

SynapseDetachReport bio::neural::Synapse::DetachTopologyNoDelete ( )

Release this synapse from its presynaptic Axon motif and postsynaptic Dendrite motif without deleting this object and without running user Proteins. Callers must quiesce scheduling before calling this method.

The normal ConnectTo topology is source-owned and target-referenced. This method removes the target reference first, then releases the source-owned wrapper with ownership suppressed, and finally clears raw endpoint pointers. The returned report records which wrappers existed and whether either wrapper had been owning. Equivalent to DetachTopologyNoDelete(true, true).

◆ DetachTopologyNoDelete() [2/2]

SynapseDetachReport bio::neural::Synapse::DetachTopologyNoDelete	(	bool	touchPresynaptic,
		bool	touchPostsynaptic
	)

Side-selectable no-delete topology detach. Releases this synapse from the selected endpoint motif(s) by pointer identity (no-delete release) and then clears the corresponding raw endpoint pointer(s). Idempotent when both endpoints are already NULL. NEVER touches the Neuropil owner motif — the base ~Cell (Mechanism 1) handles owner release, env-guarded.

Parameters

touchPresynaptic	release/clear the source-side Axon endpoint.
touchPostsynaptic	release/clear the target-side Dendrite endpoint.

Returns: report of which wrappers existed and whether either was owning.

◆ DisconnectAndDelete()

void bio::neural::Synapse::DisconnectAndDelete ( )

TERMINAL: fully detach this synapse from its topology and then delete it.

If this synapse is not already topology-detached, it is FULL-detached (DetachTopologyNoDelete(true, true)) so neither the source Axon motif nor the target Dendrite motif is left holding a dangling pointer. If this synapse is tissued (has a Neuropil owner via its environment), it is then free-stood from that owner motif — released from the owner Cell motif and its environment nulled, exactly as the Neuron quiesced-detach API does — so nothing else frees it. Finally delete this runs.

After this call returns this has been destroyed: the caller MUST NOT touch *this again. The caller MUST quiesce scheduling before calling this method (same precondition as the Detach API) — a synapse that may still be RequestProcessingOf'd must not be deleted out from under the scheduler. NON-VIRTUAL / ABI-neutral.

◆ ExtendTimeoutUntil()

void bio::neural::Synapse::ExtendTimeoutUntil ( Timestamp timeToDepotentiate )

virtual

Sets the expiration time such that *this will expire at the given time.
Has no effect if the given time is later than the current time.

Parameters

timeToDepotentiate the time that *this should expire at.

Reimplemented from bio::neural::Axon.

◆ IsTopologyDetached()

bool bio::neural::Synapse::IsTopologyDetached ( ) const

Returns: true when both endpoint pointers have been cleared.

◆ ShouldBeDepotentiated()

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

virtual

Returns: true if *this has expired.

Reimplemented from bio::neural::Dendrite.

◆ ShouldBePotentiated()

bool bio::neural::Synapse::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 from bio::neural::Dendrite.

◆ Update()

void bio::neural::Synapse::Update ( Timestamp whenToPotentiate )

virtual

This should be called with ProcessOutgoing
When this is called, ShouldBeProcessed will return true on or after addDatumAt and before addDatumAt + timeout See ShouldBeProcessed for more info.
IMPORTANT: when overriding this, make sure to call this method too!

Parameters

whenToPotentiate the time at which *this should be added to the postsynapticNeuron

Reimplemented from bio::neural::Axon.

Member Data Documentation

◆ mcAdditionalConfiguration

Pointer< molecular::Protein > bio::neural::Synapse::mcAdditionalConfiguration

protected

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~Synapse()

Member Function Documentation

◆ AdditionalConfiguration()

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

◆ CacheProteins()

◆ ClearAllEndpointsNoDelete()

◆ ClearPostsynapticEndpoint()

◆ ClearPresynapticEndpoint()

◆ ConfigureFor()

◆ CreateDefaultProteins()

◆ DetachTopologyNoDelete() [1/2]

◆ DetachTopologyNoDelete() [2/2]

◆ DisconnectAndDelete()

◆ ExtendTimeoutUntil()

◆ IsTopologyDetached()

◆ ShouldBeDepotentiated()

◆ ShouldBePotentiated()

◆ Update()

Member Data Documentation

◆ mcAdditionalConfiguration