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bio::cellular::Organ Class Reference

#include <Organ.h>

+ Inheritance diagram for bio::cellular::Organ:
+ Collaboration diagram for bio::cellular::Organ:

Public Member Functions

 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (cellular, Organ) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(cellular
 
virtual Code BuildMobilome ()
 
 filter::Cellular ()) virtual ~Organ()
 
virtual Code GrowTissues ()
 
OrganPerspective::Instance ()
 
virtual Code SpecializeTissues ()
 
- Public Member Functions inherited from bio::cellular::Class< Organ >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (genetic, Organ) Class(Organ *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< genetic::Plasmid * >
 LinearMotif (const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)
 
 LinearMotif (const LinearMotif< genetic::Plasmid * > &toCopy)
 
 LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)
 
virtual ~LinearMotif ()
 
virtual genetic::PlasmidAddImplementation (genetic::Plasmid * content)
 
virtual Code Attenuate (const physical::Wave *other)
 
 BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< genetic::Plasmid * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical
 
virtual void ClearImplementation ()
 
virtual genetic::PlasmidCreateImplementation (StandardDimension id)
 
virtual Code Disattenuate (const physical::Wave *other)
 
virtual Emission ForEachImplementation (ExcitationBase *excitation)
 
virtual genetic::PlasmidGetByIdImplementation (StandardDimension id)
 
virtual const genetic::PlasmidGetByIdImplementation (StandardDimension id) const
 
virtual genetic::PlasmidGetByNameImplementation (Name name)
 
virtual const genetic::PlasmidGetByNameImplementation (Name name) const
 
virtual genetic::PlasmidGetOrCreateByIdImplementation (StandardDimension id)
 
virtual genetic::PlasmidGetOrCreateByNameImplementation (Name name)
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
physical::Perspective< StandardDimension > * GetStructuralPerspective ()
 
const physical::Perspective< StandardDimension > * GetStructuralPerspective () const
 
virtual bool HasImplementation (const genetic::Plasmid * &content) const
 
virtual void ImportImplementation (const LinearMotif< genetic::Plasmid * > *other)
 
virtual Code InsertImplementation (genetic::Plasmid * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)
 
- Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< genetic::Plasmid * > >
 Elementary ()
 
 Elementary (const Properties properties)
 
virtual ~Elementary ()
 
void RegisterProperties (const Properties properties)
 
- Public Member Functions inherited from bio::chemical::Class< LinearMotif< genetic::Plasmid * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< genetic::Plasmid * >) Class(LinearMotif< genetic::Plasmid * > *object
 
- Public Member Functions inherited from bio::chemical::UnorderedMotif< genetic::Plasmid * >
 UnorderedMotif (const Contents *contents)
 
 UnorderedMotif (const UnorderedMotif< genetic::Plasmid * > *toCopy)
 
virtual ~UnorderedMotif ()
 
virtual genetic::PlasmidAddImplementation (const genetic::Plasmid * content)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< genetic::Plasmid * >) 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 genetic::Plasmid * content) const
 
virtual void ImportImplementation (const UnorderedMotif< genetic::Plasmid * > *other)
 
virtual genetic::PlasmidRemoveImplementation (const genetic::Plasmid * content)
 
- Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< genetic::Plasmid * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< genetic::Plasmid * >) Class(UnorderedMotif< genetic::Plasmid * > *object
 
- Public Member Functions inherited from bio::chemical::LinearMotif< Tissue * >
 LinearMotif (const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)
 
 LinearMotif (const LinearMotif< Tissue * > &toCopy)
 
 LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)
 
virtual ~LinearMotif ()
 
virtual Tissue * AddImplementation (Tissue * content)
 
virtual Code Attenuate (const physical::Wave *other)
 
 BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Tissue * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical
 
virtual void ClearImplementation ()
 
virtual Tissue * CreateImplementation (StandardDimension id)
 
virtual Code Disattenuate (const physical::Wave *other)
 
virtual Emission ForEachImplementation (ExcitationBase *excitation)
 
virtual Tissue * GetByIdImplementation (StandardDimension id)
 
virtual const Tissue * GetByIdImplementation (StandardDimension id) const
 
virtual Tissue * GetByNameImplementation (Name name)
 
virtual const Tissue * GetByNameImplementation (Name name) const
 
virtual Tissue * GetOrCreateByIdImplementation (StandardDimension id)
 
virtual Tissue * GetOrCreateByNameImplementation (Name name)
 
virtual std::string GetStringFromImplementation (std::string separator=", ")
 
physical::Perspective< StandardDimension > * GetStructuralPerspective ()
 
const physical::Perspective< StandardDimension > * GetStructuralPerspective () const
 
virtual bool HasImplementation (const Tissue * &content) const
 
virtual void ImportImplementation (const LinearMotif< Tissue * > *other)
 
virtual Code InsertImplementation (Tissue * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)
 
- Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< Tissue * > >
 Elementary ()
 
 Elementary (const Properties properties)
 
virtual ~Elementary ()
 
void RegisterProperties (const Properties properties)
 
- Public Member Functions inherited from bio::chemical::Class< LinearMotif< Tissue * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Tissue * >) Class(LinearMotif< Tissue * > *object
 
- Public Member Functions inherited from bio::chemical::UnorderedMotif< Tissue * >
 UnorderedMotif (const Contents *contents)
 
 UnorderedMotif (const UnorderedMotif< Tissue * > *toCopy)
 
virtual ~UnorderedMotif ()
 
virtual Tissue * AddImplementation (const Tissue * content)
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Tissue * >) 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 Tissue * content) const
 
virtual void ImportImplementation (const UnorderedMotif< Tissue * > *other)
 
virtual Tissue * RemoveImplementation (const Tissue * content)
 
- Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Tissue * > >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Tissue * >) Class(UnorderedMotif< Tissue * > *object
 
- Public Member Functions inherited from bio::molecular::EnvironmentDependent< OrganSystem >
 EnvironmentDependent (OrganSystem *environment=NULL)
 
virtual ~EnvironmentDependent ()
 
virtual OrganSystem * GetEnvironment ()
 
virtual const OrganSystem * GetEnvironment () const
 
virtual void SetEnvironment (OrganSystem *environment)
 

Public Attributes

 Organ
 
- Public Attributes inherited from bio::cellular::Class< Organ >
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< genetic::Plasmid * >
physical::Perspective< StandardDimension > * m_perspective
 
- Public Attributes inherited from bio::chemical::Class< LinearMotif< genetic::Plasmid * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< genetic::Plasmid * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::LinearMotif< Tissue * >
physical::Perspective< StandardDimension > * m_perspective
 
- Public Attributes inherited from bio::chemical::Class< LinearMotif< Tissue * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Tissue * > >
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< genetic::Plasmid * >
typedef physical::Line Contents
 
- Public Types inherited from bio::chemical::UnorderedMotif< genetic::Plasmid * >
typedef physical::Arrangement< genetic::Plasmid * > Contents
 
- Public Types inherited from bio::chemical::LinearMotif< Tissue * >
typedef physical::Line Contents
 
- Public Types inherited from bio::chemical::UnorderedMotif< Tissue * >
typedef physical::Arrangement< Tissue * > 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< genetic::Plasmid * >
static LinearMotif< genetic::Plasmid * > Properties GetClassProperties ()
 
- Static Public Member Functions inherited from bio::chemical::LinearMotif< Tissue * >
static LinearMotif< Tissue * > 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< genetic::Plasmid * > >
static bool hasRegistered
 
- Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Tissue * > >
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< OrganSystem >
OrganSystem * m_environment
 

Detailed Description

An Organ is a collection of Tissues that can operate on its own. Similar to how Plasmids are packages of Genes, Organs are packages of Tissues. In this way, Organs are like pseudo-binaries that can be integrated into other binaries.

Organs contain all of the DNA (Plasmids) they need to create all of their Cells. This means you should new the Plasmids necessary for your Organ within the BuildMobilome method.

Once your Organ is prepared, you can initialize it with SpecializeTissues() and run it with Peak. However, these will be done for you through the parent OrganSystem.

Definition at line 50 of file Organ.h.

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::cellular::Organ::BIO_DISAMBIGUATE_ALL_CLASS_METHODS ( cellular  ,
Organ   
)

Ensure virtual methods point to Class implementations. Standard ctors.

◆ BuildMobilome()

virtual Code bio::cellular::Organ::BuildMobilome ( )
inlinevirtual

new all necessary Plasmids. Does NOT distribute them. See SpecializeTissues for that. NOTE: we pronounce "mobilome" as "mobile-lee-ome" because it's more fun.

Definition at line 78 of file Organ.h.

79 {
80 // CREATE YOUR PLASMIDS HERE!
81
82 return code::NotImplemented();
83 }
Code NotImplemented()

References bio::code::NotImplemented().

Referenced by bio::cellular::OrganSystem::Organogenesis().

◆ filter::Cellular()

bio::cellular::Organ::filter::Cellular ( )

◆ GrowTissues()

virtual Code bio::cellular::Organ::GrowTissues ( )
inlinevirtual

new all Tissues. Does NOT Differentiate them. See SpecializeTissues for that.

Definition at line 89 of file Organ.h.

90 {
91 // CREATE YOUR TISSUES HERE!
92
93 return code::NotImplemented();
94 }

References bio::code::NotImplemented().

Referenced by bio::cellular::OrganSystem::Organogenesis().

◆ OrganPerspective::Instance()

& bio::cellular::Organ::OrganPerspective::Instance ( )

◆ SpecializeTissues()

Code bio::cellular::Organ::SpecializeTissues ( )
virtual

Differentiate all Cells in all Tissues.

Definition at line 33 of file Organ.cpp.

34{
35 Code ret = code::Success();
36 Container* tissues = GetAll< Tissue* >();
37 BIO_SANITIZE(tissues, ,
39 Tissue* tissueBuffer;
40 for (
41 SmartIterator tis = tissues->Begin();
42 !tis.IsAtEnd();
43 ++tis
44 )
45 {
46 tissueBuffer = tis;
47 if (tissueBuffer->DifferentiateCells() != code::Success() && ret == code::Success())
48 {
49 ret = code::UnknownError();
50 }
51 }
52 return ret;
53}
#define BIO_SANITIZE(test, success, failure)
Code CouldNotFindValue1()
Code UnknownError()
Code Success()

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

Referenced by bio::cellular::OrganSystem::Organogenesis().

Member Data Documentation

◆ Organ

bio::cellular::Organ::Organ

Definition at line 67 of file Organ.h.


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