#include <Neuron.h>

Inheritance diagram for bio::neural::Neuron:

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Collaboration diagram for bio::neural::Neuron:

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Public Member Functions
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (neural, Neuron, filter::Neural()) virtual ~Neuron()

virtual Code	CacheProteins ()

virtual Code	CreateDefaultProteins ()

virtual bool	ExciteTrigger () const

virtual void	PreCrest ()

virtual void	Learn ()

bool	DetermineAndCallImpulseTriggers ()

void	StartAtRisingEdge ()

void	ActiveNow ()

void	ActiveUntil (Timestamp time)

Timestamp	GetTimeLastActive () const

bool	IsActive () const

void	UpdateImpulseCallers ()

void	CreateImpulse (const FiringCondition &trigger, const Name &impulseName, bool shouldBeActive=true)

FiringCondition	GetReasonForFiring () const

bool	IsPersisting (const Timestamp now) const

bool	IsPersisting () const

void	PersistFor (const Milliseconds ms)

void	PersistUntil (const Timestamp time)

Pointer< Synapse >	ConnectTo (Pointer< Neuron > target, Pointer< const Synapse > synapseType)

void	RequestProcessingOf (Pointer< Dendrite > dendrite)

virtual void	PreSend ()

virtual Code	Transmit (Pointer< ::bio::Affinity > selection=NULL)

virtual void	PostSend ()

virtual Code	DepotentiateSentData (Pointer< ::bio::Affinity > selection=NULL)

Index	DetachOutgoingSynapsesTopologyNoDelete ()

Index	DetachIncomingSynapsesTopologyNoDelete ()

Index	DetachAllSynapsesTopologyNoDelete ()

Index	PruneAllSynapses ()

virtual bool	CheckIn ()

virtual Code	Crest ()

virtual Code	Apoptose ()

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

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

	Class (Pointer< Neuron > 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	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::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	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::Covalent< chemical::LinearMotif< Impulse > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

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

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

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

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

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

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

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

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

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

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

Protected Member Functions
virtual void	CommonConstructor ()

virtual bool	DetermineImpulseTriggers (bool trigger)

virtual void	PotentiateDendrite (Pointer< Dendrite > dendrite)

virtual void	DepotentiateDendrite (Pointer< Dendrite > dendrite)

virtual void	ProcessDendrites (Pointer< ::bio::Affinity > selection=NULL)

virtual Code	ProcessDendrite (Pointer< Dendrite > dendrite)

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< molecular::Protein >	mcRisingEdge

Pointer< molecular::Protein >	mcContinuing

Pointer< molecular::Protein >	mcFallingEdge

Pointer< molecular::Protein >	mcPreCrest

Pointer< molecular::Protein >	mcPreSend

Pointer< molecular::Protein >	mcPostSend

Pointer< molecular::Protein >	mcLearn

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::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::Covalent< chemical::LinearMotif< Impulse > >
Pointer< chemical::LinearMotif< Impulse > >	mT

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

Protected Attributes inherited from bio::Covalent< chemical::LinearMotif< Axon > >
Pointer< chemical::LinearMotif< Axon > >	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)

Detailed Description

When to use a Neuron:

You want explicit control over who can use what data when (structure).
You want to process many signals in many different threads (asynchronicity).
If Diffusing many signals through the Solution system is cumbersome and Neurons are more efficient.

To use a Neuron, you must define the following:

The Neuron child class; this is a Cell which holds whatever values and does whatever work you want.
Define an ExciteTrigger which will determine what data is sent through which Neurites when (see below for more on that).
Define the Neuron's Neurites, which connect it to other Neurons; this is the structure of your Organism's nervous system.

In real-life biology, neurons are implemented with solutions, membranes / vesicles, and proteins. These neurons (in theory) diffuse an arbitrary number of solutes (aka potentials) at once, and equalize carefully crafted imbalances in electrochemical gradients. Thus, neurons allow for fast, optimized delivery of information through structured channels which enforce requirements of how and when data may be accessed.
This is the spirit which we attempt to emulate here.

Member Function Documentation

◆ ActiveNow()

void bio::neural::Neuron::ActiveNow ( )

Set the time active to the current timestamp.

◆ ActiveUntil()

void bio::neural::Neuron::ActiveUntil ( Timestamp time )

Manually set the time active.

Parameters

time

◆ Apoptose()

Code bio::neural::Neuron::Apoptose ( )

virtual

Optional cellular method.

Returns: StemCell::Apoptose() by default.

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

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

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

Disambiguate Class methods.

◆ CacheProteins()

Code bio::neural::Neuron::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 >.

◆ CheckIn()

bool bio::neural::Neuron::CheckIn ( )

virtual

physical::Periodic method; called every clock tick.
Performs all upkeep operations.

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

◆ CommonConstructor()

void bio::neural::Neuron::CommonConstructor ( )

protectedvirtual

◆ ConnectTo()

Pointer< Synapse > bio::neural::Neuron::ConnectTo	(	Pointer< Neuron >	target,
		Pointer< const Synapse >	synapseType
	)

Utilizes the Synapse::ConfigureFor method to create a new Synapse between this and the target
The target is whatever you want *this to send data to.
The synapseType specifies how you want to send that data.
The synapseType can be as simple as a Synapse with some TranscriptionFactors added or as complex as a custom derived class.
If a Synapse to the same target and of the same Id already exists, the existing Synapse will be RETURNED but not re-added.

Parameters

target	the Neuron to send data to.
synapseType	the Synapse to use to send data.

Returns: : the configured Synapse that has been added to *this.

◆ CreateDefaultProteins()

Code bio::neural::Neuron::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 >.

◆ CreateImpulse()

void bio::neural::Neuron::CreateImpulse	(	const FiringCondition &	trigger,
		const Name &	impulseName,
		bool	shouldBeActive = `true`
	)

Creates an Impulse and adds it to *this.
This will create a new top-level-protein, if one does not exist.

Parameters

trigger	the FiringCondition that will cause this Impulse to be sent.
impulseName	the Name of the Protein that will be used to process the Impulse.
shouldBeActive	whether or not this Impulse should cause *this to be active.

◆ Crest()

Code bio::neural::Neuron::Crest ( )

virtual

Optional cellular method.

Returns: StemCell::Crest() by default.

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

◆ DepotentiateDendrite()

void bio::neural::Neuron::DepotentiateDendrite ( Pointer< Dendrite > dendrite )

protectedvirtual

Remove the data sent by the given Dendrite from *this.

Parameters

dendrite

◆ DepotentiateSentData()

Code bio::neural::Neuron::DepotentiateSentData ( Pointer< ::bio::Affinity > selection = NULL )

virtual

Sends an DepotentiateSignal() to all downstream neurons.
This signifies the data from *this are no longer relevant and should be ignored/removed.

Parameters

selection (optional) the Affinity to use for selecting which Axons to expire data from.

◆ DetachAllSynapsesTopologyNoDelete()

Index bio::neural::Neuron::DetachAllSynapsesTopologyNoDelete ( )

Release all incoming and outgoing synapse topology without deleting synapse objects. Callers must quiesce scheduling before calling this method.

Returns: number of distinct synapses visited.

◆ DetachIncomingSynapsesTopologyNoDelete()

Index bio::neural::Neuron::DetachIncomingSynapsesTopologyNoDelete ( )

Release all incoming synapse topology without deleting the synapse objects. Callers must quiesce scheduling before calling this method.

Returns: number of synapses whose topology was released or already detached.

◆ DetachOutgoingSynapsesTopologyNoDelete()

Index bio::neural::Neuron::DetachOutgoingSynapsesTopologyNoDelete ( )

Release all outgoing synapse topology without deleting the synapse objects. Callers must quiesce scheduling before calling this method.

Returns: number of synapses whose topology was released or already detached.

◆ DetermineAndCallImpulseTriggers()

bool bio::neural::Neuron::DetermineAndCallImpulseTriggers ( )

This uses ExciteTrigger to set the FiringCondition of *this and calls whatever _____Impulse() method is appropriate. See firing_condition::Trigger, below for more on how those calls are made.

Returns: whether or not *this should be active.

◆ DetermineImpulseTriggers()

bool bio::neural::Neuron::DetermineImpulseTriggers ( bool trigger )

protectedvirtual

If you define your own firing conditions, make sure to overload this!
You'll want to make this handle the logic for how to set mFiringReason.
See the current definition for an example.

Parameters

trigger

Returns: whether or not there is a impulse to send

◆ ExciteTrigger()

virtual bool bio::neural::Neuron::ExciteTrigger ( ) const

inlinevirtual

It is up to each individual Neuron to determine what is appropriate here.

Returns: whether or not *this should be active

◆ GetReasonForFiring()

FiringCondition bio::neural::Neuron::GetReasonForFiring ( ) const

This is ONLY set by DetermineAndCallImpulseTriggers.
If you would like to control this manually, please adjust your ExciteTrigger so that DetermineAndCallImpulseTriggers gives the results you desire.

Returns: : the FiringCondition that caused *this to be active.

◆ GetTimeLastActive()

Timestamp bio::neural::Neuron::GetTimeLastActive ( ) const

See ActiveNow, above.

Returns: : last time *this was active

◆ IsActive()

bool bio::neural::Neuron::IsActive ( ) const

NOTE: activity may also by checked like this->Has< State >(::bio::state::Active()).

Returns: : whether or not *this is active.

◆ IsPersisting() [1/2]

bool bio::neural::Neuron::IsPersisting ( ) const

inline

Returns: whether or not *this is "active" due to persistence.

◆ IsPersisting() [2/2]

bool bio::neural::Neuron::IsPersisting ( const Timestamp now ) const

Parameters

now	the current timestamp.

Returns: whether or not *this is "active" due to persistence.

◆ Learn()

void bio::neural::Neuron::Learn ( )

virtual

Learn tells the Neuron when to apply any learning operations.
This is a no-op unless the Learning plasmid is used.
While this method is virtual, it is NOT advised you override it, unless you know exactly what you are doing and have your own learning system to integrate with.
-—WHEN TO USE-—
Consider what you want your system to learn about.
If you want to learn/predict when a Neuron will be active, call this when the Neuron becomes active. NOTE that you might not want this done on RisingEdgeImpulse or some other location that could be just as easily triggered by any incoming excitatory Synapse as innate activity. For example, sensors call Learn when they receive data from a driver That way, any neurons connected to them will start predicting real world inputs (as opposed to other neural activity).
For learning to other inputs, Learn will be called on addition of a "DriveLearning" Synapse. For more info, see the mod_learning-neural docs.

◆ PersistFor()

void bio::neural::Neuron::PersistFor ( const Milliseconds ms )

Always applied.

Parameters

ms	the number of milliseconds that *this should persist for.

◆ PersistUntil()

void bio::neural::Neuron::PersistUntil ( const Timestamp time )

Sets PersistFor with (time-now).

Parameters

time

◆ PostSend()

void bio::neural::Neuron::PostSend ( )

virtual

This is called directly after sending a datum.
Activates "PostSend" protein by default.

◆ PotentiateDendrite()

void bio::neural::Neuron::PotentiateDendrite ( Pointer< Dendrite > dendrite )

protectedvirtual

Add the data sent by the given Dendrite to *this.

Parameters

dendrite

◆ PreCrest()

void bio::neural::Neuron::PreCrest ( )

virtual

Activated at the just before Crest(), before internal stuffs and before Crest().

◆ PreSend()

void bio::neural::Neuron::PreSend ( )

virtual

This is called directly before sending a datum.
Activates "PreSend" protein by default.

◆ ProcessDendrite()

Code bio::neural::Neuron::ProcessDendrite ( Pointer< Dendrite > dendrite )

protectedvirtual

How a single Dendrite is processed.

Parameters

dendrite

◆ ProcessDendrites()

void bio::neural::Neuron::ProcessDendrites ( Pointer< ::bio::Affinity > selection = NULL )

protectedvirtual

Handles new and expired data.

Parameters

selection (optional) the Affinity to use for selecting which Dendrites to bring data in from.

◆ PruneAllSynapses()

Index bio::neural::Neuron::PruneAllSynapses ( )

TERMINAL (for the synapses, not for *this): detach AND delete every synapse touching this Neuron — every incoming (Dendrite-motif, postsynaptic == this) and every outgoing (Axon-motif) Synapse. A self-edge appears in the distinct set exactly ONCE and is therefore deleted exactly once (no double-free). Each distinct synapse is FULL-detached (no-delete), free-stood from any Neuropil owner motif, and then deleted — the same free-stand release block the quiesced-detach API uses.

The distinct-by-pointer snapshot is taken up-front, so deleting synapses does not invalidate the iteration. After this returns this holds no live synapse topology. The caller MUST quiesce scheduling first (same precondition as the Detach API). NON-VIRTUAL / ABI-neutral.

Returns: number of distinct synapses deleted.

◆ RequestProcessingOf()

void bio::neural::Neuron::RequestProcessingOf ( Pointer< Dendrite > dendrite )

RequestProcessingOf checks if the data coming from the given Dendrite should be added (or removed) and will perform the necessary proteins.
The only reason to use this method, as opposed to letting Crest check the given Dendrite, is to have it be processed before another Dendrite i.e. this method gives you more control over the order in which Dendrites are processed. With that said, Crest will still process Dendrite in the order they are added, it will just skip any Dendrites which have already been processed, either by a previous Crest or by this method.

Parameters

dendrite

◆ StartAtRisingEdge()

void bio::neural::Neuron::StartAtRisingEdge ( )

Causes DetermineAndCallImpulseTriggers() to start at RisingEdgeImpulse(), if it would otherwise call ContinuingImpulse().

◆ Transmit()

Code bio::neural::Neuron::Transmit ( Pointer< ::bio::Affinity > selection = NULL )

virtual

Calls Synapse::ProcessOutgoing for each Axon.

Parameters

selection (optional) the Affinity to use for selecting which Axons to send data through.

◆ UpdateImpulseCallers()

void bio::neural::Neuron::UpdateImpulseCallers ( )

This updates all Impulses to use *this as their caller.
This must be called whenever *this is copied, cloned, etc.

Member Data Documentation

◆ mcContinuing

Pointer< molecular::Protein > bio::neural::Neuron::mcContinuing

protected

◆ mcFallingEdge

Pointer< molecular::Protein > bio::neural::Neuron::mcFallingEdge

protected

◆ mcLearn

Pointer< molecular::Protein > bio::neural::Neuron::mcLearn

protected

◆ mcPostSend

Pointer< molecular::Protein > bio::neural::Neuron::mcPostSend

protected

◆ mcPreCrest

Pointer< molecular::Protein > bio::neural::Neuron::mcPreCrest

protected

◆ mcPreSend

Pointer< molecular::Protein > bio::neural::Neuron::mcPreSend

protected

◆ mcRisingEdge

Pointer< molecular::Protein > bio::neural::Neuron::mcRisingEdge

protected

Proteins (see cellular::Cell.h for more information)

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

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ ActiveNow()

◆ ActiveUntil()

◆ Apoptose()

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

◆ CacheProteins()

◆ CheckIn()

◆ CommonConstructor()

◆ ConnectTo()

◆ CreateDefaultProteins()

◆ CreateImpulse()

◆ Crest()

◆ DepotentiateDendrite()

◆ DepotentiateSentData()

◆ DetachAllSynapsesTopologyNoDelete()

◆ DetachIncomingSynapsesTopologyNoDelete()

◆ DetachOutgoingSynapsesTopologyNoDelete()

◆ DetermineAndCallImpulseTriggers()

◆ DetermineImpulseTriggers()

◆ ExciteTrigger()

◆ GetReasonForFiring()

◆ GetTimeLastActive()

◆ IsActive()

◆ IsPersisting() [1/2]

◆ IsPersisting() [2/2]

◆ Learn()

◆ PersistFor()

◆ PersistUntil()

◆ PostSend()

◆ PotentiateDendrite()

◆ PreCrest()

◆ PreSend()

◆ ProcessDendrite()

◆ ProcessDendrites()

◆ PruneAllSynapses()

◆ RequestProcessingOf()

◆ StartAtRisingEdge()

◆ Transmit()

◆ UpdateImpulseCallers()

Member Data Documentation

◆ mcContinuing

◆ mcFallingEdge

◆ mcLearn

◆ mcPostSend

◆ mcPreCrest

◆ mcPreSend

◆ mcRisingEdge