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bio::organic::Organism Class Reference

#include <Organism.h>

+ Inheritance diagram for bio::organic::Organism:
+ Collaboration diagram for bio::organic::Organism:

Public Member Functions

 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (cellular, Organism) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(cellular
 
 filter::Organic ()) virtual ~Organism()
 
virtual Code Morphogenesis ()
 
OrganismPerspective::Instance ()
 
- Public Member Functions inherited from bio::cellular::Class< Organism >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (genetic, Organism) Class(Organism *object
 
- Public Member Functions inherited from bio::genetic::Class< T >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, T) Class(T *object
 
- Public Member Functions inherited from bio::molecular::Class< T >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, T) Class(T *object
 
- Public Member Functions inherited from bio::chemical::Class< T >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, T) Class(T *object
 
- Public Member Functions inherited from bio::physical::Class< T >
 Class (T *object, Symmetry *symmetry=NULL)
 
virtual ~Class ()
 
virtual WaveAsWave ()
 
virtual const WaveAsWave () const
 
virtual WaveClone () const
 
T * Convert (Wave *wave)
 
virtual operator T* ()
 
virtual operator Wave * ()
 
- Public Member Functions inherited from bio::physical::Wave
 Wave (Symmetry *symmetry=NULL)
 
virtual ~Wave ()
 
virtual chemical::AtomAsAtom ()
 
virtual const chemical::AtomAsAtom () const
 
virtual WaveAsWave ()
 
virtual const WaveAsWave () const
 
virtual Code Attenuate (const Wave *other)
 
virtual WaveClone () const
 
virtual WaveDemodulate ()
 
virtual const WaveDemodulate () const
 
virtual Code Disattenuate (const Wave *other)
 
virtual Properties GetProperties () const
 
virtual WaveModulate (Wave *signal)
 
virtual Waveoperator* ()
 
virtual const Waveoperator* () const
 
virtual Waveoperator* (Wave *signal)
 
virtual void operator+ (const Wave *other)
 
virtual void operator- (const Wave *other)
 
virtual void operator| (Symmetry *symmetry)
 
virtual Code Reify (Symmetry *symmetry)
 
virtual SymmetrySpin () const
 
- Public Member Functions inherited from bio::physical::Identifiable< StandardDimension >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspective
 
void CloneIntoName (Name name)
 
- Public Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
 Observer (const Observer &other)
 
 Observer (Perspective *perspective=NULL)
 
virtual ~Observer ()
 
virtual PerspectiveGetPerspective () const
 
virtual void SetPerspective (Perspective *perspective)
 
- Public Member Functions inherited from bio::physical::Class< Identifiable< StandardDimension > >
 Class (Identifiable< StandardDimension > *object, Symmetry *symmetry=NULL)
 
virtual ~Class ()
 
virtual WaveAsWave ()
 
virtual const WaveAsWave () const
 
virtual WaveClone () const
 
Identifiable< StandardDimension > * Convert (Wave *wave)
 
virtual operator Identifiable< StandardDimension > * ()
 
virtual operator Wave * ()
 
- Public Member Functions inherited from bio::log::Writer
 Writer (Engine *logEngine, Filter logFilter)
 
virtual ~Writer ()
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Writer) Writer()
 
void ExternalLog (Filter logFilter, Level level, const char *format,...) const
 
EngineGetLogEngine ()
 
const EngineGetLogEngine () const
 
bool HasLogEngine () const
 
virtual void SetLogEngine (Engine *logEngine)
 
- Public Member Functions inherited from bio::physical::Filterable
 Filterable (Filter filter)
 
virtual ~Filterable ()
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Filterable) Filterable()
 
Filter GetFilter () const
 
virtual void InitializeImplementation (ByteStreams args)
 
virtual Code Reify (Symmetry *symmetry)
 
virtual void SetFilter (Filter filter)
 
virtual SymmetrySpin () const
 
- Public Member Functions inherited from bio::physical::Class< Filterable >
 Class (Filterable *object, Symmetry *symmetry=NULL)
 
virtual ~Class ()
 
virtual WaveAsWave ()
 
virtual const WaveAsWave () const
 
virtual WaveClone () const
 
FilterableConvert (Wave *wave)
 
virtual operator Filterable * ()
 
virtual operator Wave * ()
 
- Public Member Functions inherited from bio::physical::Class< Writer >
 Class (Writer *object, Symmetry *symmetry=NULL)
 
virtual ~Class ()
 
virtual WaveAsWave ()
 
virtual const WaveAsWave () const
 
virtual WaveClone () const
 
Writer * Convert (Wave *wave)
 
virtual operator Wave * ()
 
virtual operator Writer * ()
 
- Public Member Functions inherited from bio::chemical::Atom
 Atom (const Atom &other)
 
virtual ~Atom ()
 
template<typename T >
As ()
 
template<typename T >
const T As () const
 
template<typename T >
AsBonded ()
 
template<typename T >
const T AsBonded () const
 
template<typename T >
AsBondedQuantum ()
 
template<typename T >
const T AsBondedQuantum () const
 
virtual Code Attenuate (const Wave *other)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Atom) explicit Atom()
 
template<typename T >
bool BreakBond (T toDisassociate, BondType type=bond_type::Unknown())
 
virtual Code Disattenuate (const Wave *other)
 
template<typename T >
bool FormBond (T toBond, BondType type=bond_type::Unknown())
 
BondsGetAllBonds ()
 
const BondsGetAllBonds () const
 
WaveGetBonded (Valence position)
 
const WaveGetBonded (Valence position) const
 
template<typename T >
Valence GetBondPosition () const
 
Valence GetBondPosition (AtomicNumber bondedId) const
 
Valence GetBondPosition (Name typeName) const
 
template<typename T >
BondType GetBondType () const
 
BondType GetBondType (Valence position) const
 
template<typename T >
 operator T ()
 
virtual Code Reify (physical::Symmetry *symmetry)
 
virtual physical::SymmetrySpin () const
 
- Public Member Functions inherited from bio::physical::Class< Atom >
 Class (Atom *object, Symmetry *symmetry=NULL)
 
virtual ~Class ()
 
virtual WaveAsWave ()
 
virtual const WaveAsWave () const
 
virtual WaveClone () const
 
Atom * Convert (Wave *wave)
 
virtual operator Atom * ()
 
virtual operator Wave * ()
 
- Public Member Functions inherited from bio::chemical::Substance
Substance Substance (const typename UnorderedMotif< Property >::Contents *properties, const typename UnorderedMotif< State >::Contents *states)
 
virtual ~Substance ()
 
 BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON (chemical, Substance, &SubstancePerspective::Instance(), filter::Chemical()) BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical
 
virtual void Disable ()
 
virtual void Enable ()
 
virtual bool IsEnabled () 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 >
Add (const T t)
 
template<typename T >
void Clear ()
 
template<typename T >
ContainerGetAll ()
 
template<typename T >
const ContainerGetAll () const
 
template<typename T >
std::vector< T > GetAllAsVector ()
 
template<typename T >
const std::vector< T > GetAllAsVector () const
 
template<typename T >
unsigned long GetCount () const
 
template<typename T >
unsigned int GetNumMatching (const Container *other) const
 
template<typename T >
std::string GetStringFrom (std::string separator=", ")
 
template<typename T >
bool Has (T content) const
 
template<typename T >
bool HasAll (const Container *contents) const
 
template<typename T >
void Import (const std::vector< T > &other)
 
template<typename T >
void Import (const UnorderedMotif< T > *other)
 
Code ImportAll (const physical::Wave *other)
 
template<typename T >
Remove (const T t)
 
- Public Member Functions inherited from bio::ThreadSafe
 ThreadSafe ()
 
 ThreadSafe (const ThreadSafe &toCopy)
 
virtual ~ThreadSafe ()
 
void LockThread () const
 
void UnlockThread () const
 
- Public Member Functions inherited from bio::chemical::LinearStructureInterface
 LinearStructureInterface ()
 
virtual ~LinearStructureInterface ()
 
template<typename T >
Emission ForEach (ExcitationBase *excitation)
 
template<typename T >
GetById (StandardDimension id)
 
template<typename T >
const T GetById (StandardDimension id) const
 
template<typename T >
GetByName (Name name)
 
template<typename T >
const T GetByName (Name name) const
 
template<typename T >
GetOrCreateById (StandardDimension id)
 
template<typename T >
GetOrCreateByName (Name name)
 
template<typename T >
Code Insert (T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)
 
- Public Member Functions inherited from bio::chemical::Class< Substance >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Substance) Class(Substance *object
 
- Public Member Functions inherited from bio::chemical::UnorderedMotif< Property >
 UnorderedMotif (const Contents *contents)
 
 UnorderedMotif (const UnorderedMotif< Property > *toCopy)
 
virtual ~UnorderedMotif ()
 
virtual Property AddImplementation (const Property content)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Property >) UnorderedMotif()
 
virtual void ClearImplementation ()
 
virtual unsigned long GetCountImplementation () const
 
virtual unsigned int GetNumMatchingImplementation (const Container *other) const
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
virtual bool HasAllImplementation (const Container *contents) const
 
virtual bool HasImplementation (const Property content) const
 
virtual void ImportImplementation (const UnorderedMotif< Property > *other)
 
virtual Property RemoveImplementation (const Property content)
 
- Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Property > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Property >) Class(UnorderedMotif< Property > *object
 
- Public Member Functions inherited from bio::chemical::AbstractMotif
 AbstractMotif ()
 
virtual ~AbstractMotif ()
 
virtual void ClearImplementation ()
 
virtual ContainerGetAllImplementation ()
 
virtual const ContainerGetAllImplementation () const
 
virtual unsigned long GetCountImplementation () const
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
virtual void ImportImplementation (const void *other)
 
- Public Member Functions inherited from bio::chemical::UnorderedMotif< State >
 UnorderedMotif (const Contents *contents)
 
 UnorderedMotif (const UnorderedMotif< State > *toCopy)
 
virtual ~UnorderedMotif ()
 
virtual State AddImplementation (const State content)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< State >) UnorderedMotif()
 
virtual void ClearImplementation ()
 
virtual unsigned long GetCountImplementation () const
 
virtual unsigned int GetNumMatchingImplementation (const Container *other) const
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
virtual bool HasAllImplementation (const Container *contents) const
 
virtual bool HasImplementation (const State content) const
 
virtual void ImportImplementation (const UnorderedMotif< State > *other)
 
virtual State RemoveImplementation (const State content)
 
- Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< State > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< State >) Class(UnorderedMotif< State > *object
 
- Public Member Functions inherited from bio::molecular::Molecule
virtual ~Molecule ()
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, Molecule) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(molecular
 
StandardDimension Define (Name varName)
 
template<typename T >
StandardDimension Define (Name varName)
 
template<typename T >
StandardDimension Define (Name varName, const T &assignment)
 
virtual bool DuplicateFrom (Molecule *source, Name surface)
 
 filter::Molecular ()) Molecule(const Molecule &toCopy)
 
MoleculePerspective::Instance ()
 
virtual Moleculeoperator<< (Molecule *source)
 
virtual Moleculeoperator<< (Surface *source)
 
virtual Moleculeoperator>> (Molecule *target)
 
virtual Surfaceoperator>> (Surface *target)
 
virtual Code Reify (physical::Symmetry *symmetry)
 
virtual SurfaceRotateTo (Name surfaceName)
 
virtual const SurfaceRotateTo (Name surfaceName) const
 
template<typename T >
RotateTo (Name surfaceName) const
 
virtual SurfaceRotateTo (StandardDimension surfaceId)
 
virtual const SurfaceRotateTo (StandardDimension surfaceId) const
 
template<typename T >
RotateTo (StandardDimension surfaceId) const
 
virtual physical::SymmetrySpin () const
 
virtual bool TransferFrom (Molecule *source, Name surface)
 
template<typename T >
StandardDimension Use (Name varName, T *varPtr)
 
virtual Surfaceoperator() (StandardDimension surfaceId)
 
virtual const Surfaceoperator() (StandardDimension surfaceId) const
 
template<typename T >
Surfaceoperator() (StandardDimension surfaceId)
 
virtual Surfaceoperator() (Name name)
 
virtual const Surfaceoperator() (Name name) const
 
template<typename T >
Surfaceoperator() (Name surfaceName)
 
- Public Member Functions inherited from bio::molecular::Class< Molecule >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, Molecule) Class(Molecule *object
 
- Public Member Functions inherited from bio::physical::Perspective< StandardDimension >
 Perspective ()
 
virtual ~Perspective ()
 
virtual bool AssociateType (Id id, Wave *type)
 
virtual bool DisassociateType (Id id)
 
Hadits::iterator Find (Id id)
 
Hadits::const_iterator Find (Id id) const
 
virtual Id GetIdFromName (Name name)
 
virtual Id GetIdWithoutCreation (Name name) const
 
virtual Name GetNameFromId (Id id) const
 
virtual WaveGetNewObjectFromId (Id id) const
 
GetNewObjectFromIdAs (Id id)
 
virtual WaveGetNewObjectFromName (Name name)
 
GetNewObjectFromNameAs (Name name)
 
virtual Id GetNumUsedIds () const
 
virtual const WaveGetTypeFromId (Id id) const
 
const T GetTypeFromIdAs (Id id) const
 
virtual const WaveGetTypeFromName (Name name) const
 
const T GetTypeFromNameAs (Name name) const
 
virtual Id GetUniqueIdFor (Name name)
 
- Public Member Functions inherited from bio::chemical::LinearMotif< Surface * >
 LinearMotif (const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)
 
 LinearMotif (const LinearMotif< Surface * > &toCopy)
 
 LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)
 
virtual ~LinearMotif ()
 
virtual Surface * AddImplementation (Surface * content)
 
virtual Code Attenuate (const physical::Wave *other)
 
 BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Surface * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical
 
virtual void ClearImplementation ()
 
virtual Surface * CreateImplementation (StandardDimension id)
 
virtual Code Disattenuate (const physical::Wave *other)
 
virtual Emission ForEachImplementation (ExcitationBase *excitation)
 
virtual Surface * GetByIdImplementation (StandardDimension id)
 
virtual const Surface * GetByIdImplementation (StandardDimension id) const
 
virtual Surface * GetByNameImplementation (Name name)
 
virtual const Surface * GetByNameImplementation (Name name) const
 
virtual Surface * GetOrCreateByIdImplementation (StandardDimension id)
 
virtual Surface * GetOrCreateByNameImplementation (Name name)
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
physical::Perspective< StandardDimension > * GetStructuralPerspective ()
 
const physical::Perspective< StandardDimension > * GetStructuralPerspective () const
 
virtual bool HasImplementation (const Surface * &content) const
 
virtual void ImportImplementation (const LinearMotif< Surface * > *other)
 
virtual Code InsertImplementation (Surface * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)
 
- Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< Surface * > >
 Elementary ()
 
 Elementary (const Properties properties)
 
virtual ~Elementary ()
 
void RegisterProperties (const Properties properties)
 
- Public Member Functions inherited from bio::chemical::Class< LinearMotif< Surface * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Surface * >) Class(LinearMotif< Surface * > *object
 
- Public Member Functions inherited from bio::chemical::UnorderedMotif< Surface * >
 UnorderedMotif (const Contents *contents)
 
 UnorderedMotif (const UnorderedMotif< Surface * > *toCopy)
 
virtual ~UnorderedMotif ()
 
virtual Surface * AddImplementation (const Surface * content)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Surface * >) UnorderedMotif()
 
virtual void ClearImplementation ()
 
virtual unsigned long GetCountImplementation () const
 
virtual unsigned int GetNumMatchingImplementation (const Container *other) const
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
virtual bool HasAllImplementation (const Container *contents) const
 
virtual bool HasImplementation (const Surface * content) const
 
virtual void ImportImplementation (const UnorderedMotif< Surface * > *other)
 
virtual Surface * RemoveImplementation (const Surface * content)
 
- Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Surface * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Surface * >) Class(UnorderedMotif< Surface * > *object
 
- Public Member Functions inherited from bio::physical::Periodic
 Periodic (TimeUS interval=GetDefaultInterval())
 
virtual ~Periodic ()
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Periodic) static TimeUS GetDefaultInterval()
 
virtual void CheckIn ()
 
TimeUS GetInterval () const
 
float GetIntervalInSeconds () const
 
virtual Properties GetProperties () const
 
Timestamp GetTimeLastPeaked () const
 
virtual void InitializeImplementation (ByteStreams args)
 
virtual Code Peak ()
 
virtual Code Reify (Symmetry *symmetry)
 
virtual void SetInterval (TimeUS interval)
 
virtual void SetLastPeakTimestamp (Timestamp lastPeak)
 
virtual SymmetrySpin () const
 
- Public Member Functions inherited from bio::physical::Class< Periodic >
 Class (Periodic *object, Symmetry *symmetry=NULL)
 
virtual ~Class ()
 
virtual WaveAsWave ()
 
virtual const WaveAsWave () const
 
virtual WaveClone () const
 
PeriodicConvert (Wave *wave)
 
virtual operator Periodic * ()
 
virtual operator Wave * ()
 
- Public Member Functions inherited from bio::molecular::Vesicle
virtual ~Vesicle ()
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, Vesicle) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(molecular
 
 filter::Molecular ()) Vesicle(const Vesicle &toCopy)
 
virtual Vesicleoperator<<= (Vesicle *source)
 
virtual Vesicleoperator>>= (Vesicle *target)
 
VesiclePerspective::Instance ()
 
virtual Moleculeoperator[] (StandardDimension moleculeId)
 
virtual const Moleculeoperator[] (StandardDimension moleculeId) const
 
template<typename T >
Moleculeoperator[] (StandardDimension moleculeId)
 
virtual Moleculeoperator[] (Name moleculeName)
 
virtual const Moleculeoperator[] (Name moleculeName) const
 
template<typename T >
Moleculeoperator[] (Name moleculeName)
 
- Public Member Functions inherited from bio::molecular::Class< Vesicle >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, Vesicle) Class(Vesicle *object
 
- Public Member Functions inherited from bio::chemical::LinearMotif< Molecule * >
 LinearMotif (const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)
 
 LinearMotif (const LinearMotif< Molecule * > &toCopy)
 
 LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)
 
virtual ~LinearMotif ()
 
virtual Molecule * AddImplementation (Molecule * content)
 
virtual Code Attenuate (const physical::Wave *other)
 
 BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Molecule * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical
 
virtual void ClearImplementation ()
 
virtual Molecule * CreateImplementation (StandardDimension id)
 
virtual Code Disattenuate (const physical::Wave *other)
 
virtual Emission ForEachImplementation (ExcitationBase *excitation)
 
virtual Molecule * GetByIdImplementation (StandardDimension id)
 
virtual const Molecule * GetByIdImplementation (StandardDimension id) const
 
virtual Molecule * GetByNameImplementation (Name name)
 
virtual const Molecule * GetByNameImplementation (Name name) const
 
virtual Molecule * GetOrCreateByIdImplementation (StandardDimension id)
 
virtual Molecule * GetOrCreateByNameImplementation (Name name)
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
physical::Perspective< StandardDimension > * GetStructuralPerspective ()
 
const physical::Perspective< StandardDimension > * GetStructuralPerspective () const
 
virtual bool HasImplementation (const Molecule * &content) const
 
virtual void ImportImplementation (const LinearMotif< Molecule * > *other)
 
virtual Code InsertImplementation (Molecule * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)
 
- Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< Molecule * > >
 Elementary ()
 
 Elementary (const Properties properties)
 
virtual ~Elementary ()
 
void RegisterProperties (const Properties properties)
 
- Public Member Functions inherited from bio::chemical::Class< LinearMotif< Molecule * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Molecule * >) Class(LinearMotif< Molecule * > *object
 
- Public Member Functions inherited from bio::chemical::UnorderedMotif< Molecule * >
 UnorderedMotif (const Contents *contents)
 
 UnorderedMotif (const UnorderedMotif< Molecule * > *toCopy)
 
virtual ~UnorderedMotif ()
 
virtual Molecule * AddImplementation (const Molecule * content)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Molecule * >) UnorderedMotif()
 
virtual void ClearImplementation ()
 
virtual unsigned long GetCountImplementation () const
 
virtual unsigned int GetNumMatchingImplementation (const Container *other) const
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
virtual bool HasAllImplementation (const Container *contents) const
 
virtual bool HasImplementation (const Molecule * content) const
 
virtual void ImportImplementation (const UnorderedMotif< Molecule * > *other)
 
virtual Molecule * RemoveImplementation (const Molecule * content)
 
- Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Molecule * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Molecule * >) Class(UnorderedMotif< Molecule * > *object
 
- Public Member Functions inherited from bio::chemical::LinearMotif< cellular::OrganSystem * >
 LinearMotif (const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)
 
 LinearMotif (const LinearMotif< cellular::OrganSystem * > &toCopy)
 
 LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)
 
virtual ~LinearMotif ()
 
virtual cellular::OrganSystemAddImplementation (cellular::OrganSystem * content)
 
virtual Code Attenuate (const physical::Wave *other)
 
 BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< cellular::OrganSystem * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical
 
virtual void ClearImplementation ()
 
virtual cellular::OrganSystemCreateImplementation (StandardDimension id)
 
virtual Code Disattenuate (const physical::Wave *other)
 
virtual Emission ForEachImplementation (ExcitationBase *excitation)
 
virtual cellular::OrganSystemGetByIdImplementation (StandardDimension id)
 
virtual const cellular::OrganSystemGetByIdImplementation (StandardDimension id) const
 
virtual cellular::OrganSystemGetByNameImplementation (Name name)
 
virtual const cellular::OrganSystemGetByNameImplementation (Name name) const
 
virtual cellular::OrganSystemGetOrCreateByIdImplementation (StandardDimension id)
 
virtual cellular::OrganSystemGetOrCreateByNameImplementation (Name name)
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
physical::Perspective< StandardDimension > * GetStructuralPerspective ()
 
const physical::Perspective< StandardDimension > * GetStructuralPerspective () const
 
virtual bool HasImplementation (const cellular::OrganSystem * &content) const
 
virtual void ImportImplementation (const LinearMotif< cellular::OrganSystem * > *other)
 
virtual Code InsertImplementation (cellular::OrganSystem * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)
 
- Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< cellular::OrganSystem * > >
 Elementary ()
 
 Elementary (const Properties properties)
 
virtual ~Elementary ()
 
void RegisterProperties (const Properties properties)
 
- Public Member Functions inherited from bio::chemical::Class< LinearMotif< cellular::OrganSystem * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< cellular::OrganSystem * >) Class(LinearMotif< cellular::OrganSystem * > *object
 
- Public Member Functions inherited from bio::chemical::UnorderedMotif< cellular::OrganSystem * >
 UnorderedMotif (const Contents *contents)
 
 UnorderedMotif (const UnorderedMotif< cellular::OrganSystem * > *toCopy)
 
virtual ~UnorderedMotif ()
 
virtual cellular::OrganSystemAddImplementation (const cellular::OrganSystem * content)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< cellular::OrganSystem * >) UnorderedMotif()
 
virtual void ClearImplementation ()
 
virtual unsigned long GetCountImplementation () const
 
virtual unsigned int GetNumMatchingImplementation (const Container *other) const
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
virtual bool HasAllImplementation (const Container *contents) const
 
virtual bool HasImplementation (const cellular::OrganSystem * content) const
 
virtual void ImportImplementation (const UnorderedMotif< cellular::OrganSystem * > *other)
 
virtual cellular::OrganSystemRemoveImplementation (const cellular::OrganSystem * content)
 
- Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< cellular::OrganSystem * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< cellular::OrganSystem * >) Class(UnorderedMotif< cellular::OrganSystem * > *object
 
- Public Member Functions inherited from bio::molecular::EnvironmentDependent< Habitat >
 EnvironmentDependent (Habitat *environment=NULL)
 
virtual ~EnvironmentDependent ()
 
virtual Habitat * GetEnvironment ()
 
virtual const Habitat * GetEnvironment () const
 
virtual void SetEnvironment (Habitat *environment)
 

Public Attributes

 Organism
 
- Public Attributes inherited from bio::cellular::Class< Organism >
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::genetic::Class< T >
physical::Perspective< StandardDimension > * perspective = NULL
 
- Public Attributes inherited from bio::molecular::Class< T >
physical::Perspective< StandardDimension > Filter filter = filter::Default()
 
physical::Perspective< StandardDimension > * perspective = NULL
 
- Public Attributes inherited from bio::chemical::Class< T >
physical::Perspective< StandardDimension > Filter filter = filter::Default()
 
physical::Perspective< StandardDimension > * perspective = NULL
 
- Public Attributes inherited from bio::physical::Identifiable< StandardDimension >
Id m_id
 
- Public Attributes inherited from bio::chemical::Class< Substance >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Property > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< State > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::molecular::Molecule
 Molecule
 
- Public Attributes inherited from bio::molecular::Class< Molecule >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::LinearMotif< Surface * >
physical::Perspective< StandardDimension > * m_perspective
 
- Public Attributes inherited from bio::chemical::Class< LinearMotif< Surface * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Surface * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::molecular::Vesicle
 Vesicle
 
- Public Attributes inherited from bio::molecular::Class< Vesicle >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::LinearMotif< Molecule * >
physical::Perspective< StandardDimension > * m_perspective
 
- Public Attributes inherited from bio::chemical::Class< LinearMotif< Molecule * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Molecule * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::LinearMotif< cellular::OrganSystem * >
physical::Perspective< StandardDimension > * m_perspective
 
- Public Attributes inherited from bio::chemical::Class< LinearMotif< cellular::OrganSystem * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< cellular::OrganSystem * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 

Additional Inherited Members

- Public Types inherited from bio::physical::Identifiable< StandardDimension >
typedef StandardDimension Id
 
typedef std::vector< IdIds
 
- Public Types inherited from bio::physical::Observer< Perspective< StandardDimension > >
typedef Perspective< StandardDimension > Perspective
 
- Public Types inherited from bio::chemical::UnorderedMotif< Property >
typedef physical::Arrangement< Property > Contents
 
- Public Types inherited from bio::chemical::UnorderedMotif< State >
typedef physical::Arrangement< State > Contents
 
- Public Types inherited from bio::physical::Perspective< StandardDimension >
typedef std::vector< Hadit > Hadits
 
typedef StandardDimension Id
 
typedef std::vector< IdIds
 
- Public Types inherited from bio::chemical::LinearMotif< Surface * >
typedef physical::Line Contents
 
- Public Types inherited from bio::chemical::UnorderedMotif< Surface * >
typedef physical::Arrangement< Surface * > Contents
 
- Public Types inherited from bio::chemical::LinearMotif< Molecule * >
typedef physical::Line Contents
 
- Public Types inherited from bio::chemical::UnorderedMotif< Molecule * >
typedef physical::Arrangement< Molecule * > Contents
 
- Public Types inherited from bio::chemical::LinearMotif< cellular::OrganSystem * >
typedef physical::Line Contents
 
- Public Types inherited from bio::chemical::UnorderedMotif< cellular::OrganSystem * >
typedef physical::Arrangement< cellular::OrganSystem * > Contents
 
- Static Public Member Functions inherited from bio::physical::Wave
static Properties GetResonanceBetween (const Wave *wave, const Properties &properties)
 
static Properties GetResonanceBetween (const Wave *wave1, const Wave *wave2)
 
static Properties GetResonanceBetween (ConstWaves waves)
 
- Static Public Member Functions inherited from bio::chemical::AbstractMotif
static Properties GetClassProperties ()
 
- Static Public Member Functions inherited from bio::physical::Perspective< StandardDimension >
static Id InvalidId ()
 
static Name InvalidName ()
 
- Static Public Member Functions inherited from bio::chemical::LinearMotif< Surface * >
static LinearMotif< Surface * > Properties GetClassProperties ()
 
- Static Public Member Functions inherited from bio::physical::Periodic
static Properties GetClassProperties ()
 
- Static Public Member Functions inherited from bio::chemical::LinearMotif< Molecule * >
static LinearMotif< Molecule * > Properties GetClassProperties ()
 
- Static Public Member Functions inherited from bio::chemical::LinearMotif< cellular::OrganSystem * >
static LinearMotif< cellular::OrganSystem * > Properties GetClassProperties ()
 
- Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Surface * > >
static bool hasRegistered
 
- Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Molecule * > >
static bool hasRegistered
 
- Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< cellular::OrganSystem * > >
static bool hasRegistered
 
- Protected Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
virtual void InitializeImplementation (ByteStreams args)
 
- Protected Member Functions inherited from bio::VirtualBase
 VirtualBase ()
 
virtual ~VirtualBase ()
 
void Initialize (ByteStream arg1)
 
void Initialize (ByteStream arg1, ByteStream arg2)
 
void Initialize (ByteStream arg1, ByteStream arg2, ByteStream arg3)
 
void Initialize (ByteStreams args)
 
virtual void InitializeImplementation (ByteStreams args)=0
 
- Protected Member Functions inherited from bio::log::Writer
virtual void InitializeImplementation (ByteStreams args)
 
void Log (Level level, const char *format,...) const
 
- Protected Member Functions inherited from bio::chemical::Atom
virtual bool BreakBondImplementation (Wave *toDisassociate, AtomicNumber id, BondType type)
 
virtual bool FormBondImplementation (Wave *toBond, AtomicNumber id, BondType type)
 
- Protected Attributes inherited from bio::physical::Class< T >
T * m_object
 
- Protected Attributes inherited from bio::physical::Wave
Wavem_signal
 
Symmetrym_symmetry
 
- Protected Attributes inherited from bio::VirtualBase
bool m_hasBeenInitialized
 
- Protected Attributes inherited from bio::physical::Class< Identifiable< StandardDimension > >
Identifiable< StandardDimension > * m_object
 
- Protected Attributes inherited from bio::physical::Filterable
Filter m_filter
 
- Protected Attributes inherited from bio::physical::Class< Filterable >
Filterablem_object
 
- Protected Attributes inherited from bio::physical::Class< Writer >
Writer * m_object
 
- Protected Attributes inherited from bio::chemical::Atom
Bonds m_bonds
 
- Protected Attributes inherited from bio::physical::Class< Atom >
Atom * m_object
 
- Protected Attributes inherited from bio::chemical::AbstractMotif
Containerm_contents
 
- Protected Attributes inherited from bio::physical::Perspective< StandardDimension >
Hadits m_hadits
 
Id m_nextId
 
- Protected Attributes inherited from bio::physical::Periodic
TimeUS m_interval
 
Timestamp m_lastPeakTimestamp
 
- Protected Attributes inherited from bio::physical::Class< Periodic >
Periodicm_object
 
- Protected Attributes inherited from bio::molecular::EnvironmentDependent< Habitat >
Habitat * m_environment
 

Detailed Description

Organisms are the basic units of "life" within Biology. They are organized in a hierarchical, Cell-centric manner. They grow and develop through Morphogenesis(). They can respond to stimuli, depending on the interface. They can reproduce, if you Clone() them. They can adapt to new environments, if you add in dynamic Plasmid & TranscriptionFactor rules. They "metabolize" time & data into their own organization. This is the primary difference between computational and biological (proper) life and makes these Organisms more "electric" or "ethereal" than "real". They do not age except perhaps through outside influences, like bitrot.

Does newing an Organism create life? Does deleting end it? How different are microbes from these designs? How different are we? Have fun!

Definition at line 47 of file Organism.h.

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::organic::Organism::BIO_DISAMBIGUATE_ALL_CLASS_METHODS ( cellular  ,
Organism   
)

Ensure virtual methods point to Class implementations. Standard ctors.

◆ filter::Organic()

bio::organic::Organism::filter::Organic ( )

◆ Morphogenesis()

Code bio::organic::Organism::Morphogenesis ( )
virtual

new your OrganSystems here, then call the parent method (Organism::Morphogenesis()), which will handle the Organ, Tissue, & Cell Differentiation, producing a fully functional Organism.

Definition at line 31 of file Organism.cpp.

32{
33 Code ret = code::Success();
34 Container* organSystems = GetAll< cellular::OrganSystem* >();
35 BIO_SANITIZE(organSystems, ,
37 cellular::OrganSystem* systemBuffer;
38 for (
39 SmartIterator sys = organSystems->Begin();
40 !sys.IsAtEnd();
41 ++sys
42 )
43 {
44 systemBuffer = sys;
45 if (systemBuffer->Organogenesis() != code::Success() && ret == code::Success())
46 {
47 ret = code::UnknownError();
48 }
49 }
50 return ret;
51}
#define BIO_SANITIZE(test, success, failure)
Code CouldNotFindValue1()
Code UnknownError()
Code Success()

References bio::Container::Begin(), BIO_SANITIZE, bio::code::CouldNotFindValue1(), bio::SmartIterator::IsAtEnd(), bio::cellular::OrganSystem::Organogenesis(), bio::code::Success(), and bio::code::UnknownError().

Referenced by bio::organic::Habitat::AdaptInhabitants().

◆ OrganismPerspective::Instance()

& bio::organic::Organism::OrganismPerspective::Instance ( )

Member Data Documentation

◆ Organism

bio::organic::Organism::Organism

Definition at line 63 of file Organism.h.


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