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 Wave * | AsWave () |
| virtual const Wave * | AsWave () const |
| virtual Wave * | Clone () 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::Atom * | AsAtom () |
| virtual const chemical::Atom * | AsAtom () const |
| virtual Wave * | AsWave () |
| virtual const Wave * | AsWave () const |
| virtual Code | Attenuate (const Wave *other) |
| virtual Wave * | Clone () const |
| virtual Wave * | Demodulate () |
| virtual const Wave * | Demodulate () const |
| virtual Code | Disattenuate (const Wave *other) |
| virtual Properties | GetProperties () const |
| virtual Wave * | Modulate (Wave *signal) |
| virtual Wave * | operator* () |
| virtual const Wave * | operator* () const |
| virtual Wave * | operator* (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 Symmetry * | Spin () 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 Perspective * | GetPerspective () 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 Wave * | AsWave () |
| virtual const Wave * | AsWave () const |
| virtual Wave * | Clone () 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 |
| Engine * | GetLogEngine () |
| const Engine * | GetLogEngine () 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 Symmetry * | Spin () const |
| Public Member Functions inherited from bio::physical::Class< Filterable > | |
| Class (Filterable *object, Symmetry *symmetry=NULL) | |
| virtual | ~Class () |
| virtual Wave * | AsWave () |
| virtual const Wave * | AsWave () const |
| virtual Wave * | Clone () const |
| Filterable * | Convert (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 Wave * | AsWave () |
| virtual const Wave * | AsWave () const |
| virtual Wave * | Clone () 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 > | |
| T | As () |
| template<typename T > | |
| const T | As () const |
| template<typename T > | |
| T | AsBonded () |
| template<typename T > | |
| const T | AsBonded () const |
| template<typename T > | |
| 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()) |
| Bonds * | GetAllBonds () |
| const Bonds * | GetAllBonds () const |
| Wave * | GetBonded (Valence position) |
| const Wave * | GetBonded (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::Symmetry * | Spin () const |
| Public Member Functions inherited from bio::physical::Class< Atom > | |
| Class (Atom *object, Symmetry *symmetry=NULL) | |
| virtual | ~Class () |
| virtual Wave * | AsWave () |
| virtual const Wave * | AsWave () const |
| virtual Wave * | Clone () 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 > | |
| T | Add (const T t) |
| template<typename T > | |
| void | Clear () |
| template<typename T > | |
| Container * | GetAll () |
| template<typename T > | |
| const Container * | GetAll () 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 > | |
| 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 > | |
| T | GetById (StandardDimension id) |
| template<typename T > | |
| const T | GetById (StandardDimension id) const |
| template<typename T > | |
| T | GetByName (Name name) |
| template<typename T > | |
| const T | GetByName (Name name) const |
| template<typename T > | |
| T | GetOrCreateById (StandardDimension id) |
| template<typename T > | |
| 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 Container * | GetAllImplementation () |
| virtual const Container * | GetAllImplementation () 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 Molecule * | operator<< (Molecule *source) |
| virtual Molecule * | operator<< (Surface *source) |
| virtual Molecule * | operator>> (Molecule *target) |
| virtual Surface * | operator>> (Surface *target) |
| virtual Code | Reify (physical::Symmetry *symmetry) |
| virtual Surface * | RotateTo (Name surfaceName) |
| virtual const Surface * | RotateTo (Name surfaceName) const |
| template<typename T > | |
| T | RotateTo (Name surfaceName) const |
| virtual Surface * | RotateTo (StandardDimension surfaceId) |
| virtual const Surface * | RotateTo (StandardDimension surfaceId) const |
| template<typename T > | |
| T | RotateTo (StandardDimension surfaceId) const |
| virtual physical::Symmetry * | Spin () const |
| virtual bool | TransferFrom (Molecule *source, Name surface) |
| template<typename T > | |
| StandardDimension | Use (Name varName, T *varPtr) |
| virtual Surface * | operator() (StandardDimension surfaceId) |
| virtual const Surface * | operator() (StandardDimension surfaceId) const |
| template<typename T > | |
| Surface * | operator() (StandardDimension surfaceId) |
| virtual Surface * | operator() (Name name) |
| virtual const Surface * | operator() (Name name) const |
| template<typename T > | |
| Surface * | operator() (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 Wave * | GetNewObjectFromId (Id id) const |
| T | GetNewObjectFromIdAs (Id id) |
| virtual Wave * | GetNewObjectFromName (Name name) |
| T | GetNewObjectFromNameAs (Name name) |
| virtual Id | GetNumUsedIds () const |
| virtual const Wave * | GetTypeFromId (Id id) const |
| const T | GetTypeFromIdAs (Id id) const |
| virtual const Wave * | GetTypeFromName (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 Symmetry * | Spin () const |
| Public Member Functions inherited from bio::physical::Class< Periodic > | |
| Class (Periodic *object, Symmetry *symmetry=NULL) | |
| virtual | ~Class () |
| virtual Wave * | AsWave () |
| virtual const Wave * | AsWave () const |
| virtual Wave * | Clone () const |
| Periodic * | Convert (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 Vesicle * | operator<<= (Vesicle *source) |
| virtual Vesicle * | operator>>= (Vesicle *target) |
| & | VesiclePerspective::Instance () |
| virtual Molecule * | operator[] (StandardDimension moleculeId) |
| virtual const Molecule * | operator[] (StandardDimension moleculeId) const |
| template<typename T > | |
| Molecule * | operator[] (StandardDimension moleculeId) |
| virtual Molecule * | operator[] (Name moleculeName) |
| virtual const Molecule * | operator[] (Name moleculeName) const |
| template<typename T > | |
| Molecule * | operator[] (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::Plasmid * | AddImplementation (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::Plasmid * | CreateImplementation (StandardDimension id) |
| virtual Code | Disattenuate (const physical::Wave *other) |
| virtual Emission | ForEachImplementation (ExcitationBase *excitation) |
| virtual genetic::Plasmid * | GetByIdImplementation (StandardDimension id) |
| virtual const genetic::Plasmid * | GetByIdImplementation (StandardDimension id) const |
| virtual genetic::Plasmid * | GetByNameImplementation (Name name) |
| virtual const genetic::Plasmid * | GetByNameImplementation (Name name) const |
| virtual genetic::Plasmid * | GetOrCreateByIdImplementation (StandardDimension id) |
| virtual genetic::Plasmid * | GetOrCreateByNameImplementation (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::Plasmid * | AddImplementation (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::Plasmid * | RemoveImplementation (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) |
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.
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()
|
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
83 }
Code NotImplemented()
References bio::code::NotImplemented().
Referenced by bio::cellular::OrganSystem::Organogenesis().
◆ filter::Cellular()
| bio::cellular::Organ::filter::Cellular | ( | ) |
◆ GrowTissues()
|
inlinevirtual |
new all Tissues. Does NOT Differentiate them. See SpecializeTissues for that.
Definition at line 89 of file Organ.h.
References bio::code::NotImplemented().
Referenced by bio::cellular::OrganSystem::Organogenesis().
◆ OrganPerspective::Instance()
| & bio::cellular::Organ::OrganPerspective::Instance | ( | ) |
◆ 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;
48 {
49 ret = code::UnknownError();
50 }
51 }
52 return ret;
53}
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
The documentation for this class was generated from the following files:
