bio::cellular::Cell Class Reference
#include <Cell.h>
Inheritance diagram for bio::cellular::Cell: Collaboration diagram for bio::cellular::Cell:Public Member Functions | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (cellular, Cell) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(cellular | |
| & | CellPerspective::Instance () |
| filter::Cellular ()) virtual ~Cell() | |
| virtual Code | Peak () |
| Public Member Functions inherited from bio::cellular::Class< Cell > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (genetic, Cell) Class(Cell *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< Organelle * > | |
| LinearMotif (const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL) | |
| LinearMotif (const LinearMotif< Organelle * > &toCopy) | |
| LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL) | |
| virtual | ~LinearMotif () |
| virtual Organelle * | AddImplementation (Organelle * content) |
| virtual Code | Attenuate (const physical::Wave *other) |
| BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Organelle * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical | |
| virtual void | ClearImplementation () |
| virtual Organelle * | CreateImplementation (StandardDimension id) |
| virtual Code | Disattenuate (const physical::Wave *other) |
| virtual Emission | ForEachImplementation (ExcitationBase *excitation) |
| virtual Organelle * | GetByIdImplementation (StandardDimension id) |
| virtual const Organelle * | GetByIdImplementation (StandardDimension id) const |
| virtual Organelle * | GetByNameImplementation (Name name) |
| virtual const Organelle * | GetByNameImplementation (Name name) const |
| virtual Organelle * | GetOrCreateByIdImplementation (StandardDimension id) |
| virtual Organelle * | GetOrCreateByNameImplementation (Name name) |
| virtual std::string | GetStringFromImplementation (std::string separator=", ") |
| physical::Perspective< StandardDimension > * | GetStructuralPerspective () |
| const physical::Perspective< StandardDimension > * | GetStructuralPerspective () const |
| virtual bool | HasImplementation (const Organelle * &content) const |
| virtual void | ImportImplementation (const LinearMotif< Organelle * > *other) |
| virtual Code | InsertImplementation (Organelle * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false) |
| Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< Organelle * > > | |
| Elementary () | |
| Elementary (const Properties properties) | |
| virtual | ~Elementary () |
| void | RegisterProperties (const Properties properties) |
| Public Member Functions inherited from bio::chemical::Class< LinearMotif< Organelle * > > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Organelle * >) Class(LinearMotif< Organelle * > *object | |
| Public Member Functions inherited from bio::chemical::UnorderedMotif< Organelle * > | |
| UnorderedMotif (const Contents *contents) | |
| UnorderedMotif (const UnorderedMotif< Organelle * > *toCopy) | |
| virtual | ~UnorderedMotif () |
| virtual Organelle * | AddImplementation (const Organelle * content) |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Organelle * >) 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 Organelle * content) const |
| virtual void | ImportImplementation (const UnorderedMotif< Organelle * > *other) |
| virtual Organelle * | RemoveImplementation (const Organelle * content) |
| Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Organelle * > > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Organelle * >) Class(UnorderedMotif< Organelle * > *object | |
| Public Member Functions inherited from bio::molecular::EnvironmentDependent< cellular::Tissue > | |
| EnvironmentDependent (cellular::Tissue *environment=NULL) | |
| virtual | ~EnvironmentDependent () |
| virtual cellular::Tissue * | GetEnvironment () |
| virtual const cellular::Tissue * | GetEnvironment () const |
| virtual void | SetEnvironment (cellular::Tissue *environment) |
| Public Member Functions inherited from bio::genetic::Expressor | |
| template<typename T > | |
| Code | Activate () |
| Code | Activate (Name proteinName) |
| Code | Activate (StandardDimension proteinId) |
| virtual Code | AddToTranscriptome (const RNA *toExpress) |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (genetic, Expressor) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(genetic | |
| virtual void | CacheProteins () |
| virtual Code | ExpressGenes () |
| filter::Genetic ()) virtual ~Expressor() | |
| & | molecular::VesiclePerspective::Instance () |
| virtual Code | Translate (const RNA *mRNA) |
| Public Member Functions inherited from bio::genetic::Class< Expressor > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, Expressor) Class(Expressor *object | |
| Public Member Functions inherited from bio::chemical::UnorderedMotif< TranscriptionFactor > | |
| UnorderedMotif (const Contents *contents) | |
| UnorderedMotif (const UnorderedMotif< TranscriptionFactor > *toCopy) | |
| virtual | ~UnorderedMotif () |
| virtual TranscriptionFactor | AddImplementation (const TranscriptionFactor content) |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< TranscriptionFactor >) 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 TranscriptionFactor content) const |
| virtual void | ImportImplementation (const UnorderedMotif< TranscriptionFactor > *other) |
| virtual TranscriptionFactor | RemoveImplementation (const TranscriptionFactor content) |
| Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< TranscriptionFactor > > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< TranscriptionFactor >) Class(UnorderedMotif< TranscriptionFactor > *object | |
| Public Member Functions inherited from bio::chemical::LinearMotif< Plasmid * > | |
| LinearMotif (const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL) | |
| LinearMotif (const LinearMotif< Plasmid * > &toCopy) | |
| LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL) | |
| virtual | ~LinearMotif () |
| virtual Plasmid * | AddImplementation (Plasmid * content) |
| virtual Code | Attenuate (const physical::Wave *other) |
| BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Plasmid * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical | |
| virtual void | ClearImplementation () |
| virtual Plasmid * | CreateImplementation (StandardDimension id) |
| virtual Code | Disattenuate (const physical::Wave *other) |
| virtual Emission | ForEachImplementation (ExcitationBase *excitation) |
| virtual Plasmid * | GetByIdImplementation (StandardDimension id) |
| virtual const Plasmid * | GetByIdImplementation (StandardDimension id) const |
| virtual Plasmid * | GetByNameImplementation (Name name) |
| virtual const Plasmid * | GetByNameImplementation (Name name) const |
| virtual Plasmid * | GetOrCreateByIdImplementation (StandardDimension id) |
| virtual 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 Plasmid * &content) const |
| virtual void | ImportImplementation (const LinearMotif< Plasmid * > *other) |
| virtual Code | InsertImplementation (Plasmid * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false) |
| Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< Plasmid * > > | |
| Elementary () | |
| Elementary (const Properties properties) | |
| virtual | ~Elementary () |
| void | RegisterProperties (const Properties properties) |
| Public Member Functions inherited from bio::chemical::Class< LinearMotif< Plasmid * > > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Plasmid * >) Class(LinearMotif< Plasmid * > *object | |
| Public Member Functions inherited from bio::chemical::UnorderedMotif< Plasmid * > | |
| UnorderedMotif (const Contents *contents) | |
| UnorderedMotif (const UnorderedMotif< Plasmid * > *toCopy) | |
| virtual | ~UnorderedMotif () |
| virtual Plasmid * | AddImplementation (const Plasmid * content) |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< 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 Plasmid * content) const |
| virtual void | ImportImplementation (const UnorderedMotif< Plasmid * > *other) |
| virtual Plasmid * | RemoveImplementation (const Plasmid * content) |
| Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Plasmid * > > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Plasmid * >) Class(UnorderedMotif< Plasmid * > *object | |
| Public Member Functions inherited from bio::chemical::LinearMotif< molecular::Protein * > | |
| LinearMotif (const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL) | |
| LinearMotif (const LinearMotif< molecular::Protein * > &toCopy) | |
| LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL) | |
| virtual | ~LinearMotif () |
| virtual molecular::Protein * | AddImplementation (molecular::Protein * content) |
| virtual Code | Attenuate (const physical::Wave *other) |
| BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< molecular::Protein * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical | |
| virtual void | ClearImplementation () |
| virtual molecular::Protein * | CreateImplementation (StandardDimension id) |
| virtual Code | Disattenuate (const physical::Wave *other) |
| virtual Emission | ForEachImplementation (ExcitationBase *excitation) |
| virtual molecular::Protein * | GetByIdImplementation (StandardDimension id) |
| virtual const molecular::Protein * | GetByIdImplementation (StandardDimension id) const |
| virtual molecular::Protein * | GetByNameImplementation (Name name) |
| virtual const molecular::Protein * | GetByNameImplementation (Name name) const |
| virtual molecular::Protein * | GetOrCreateByIdImplementation (StandardDimension id) |
| virtual molecular::Protein * | GetOrCreateByNameImplementation (Name name) |
| virtual std::string | GetStringFromImplementation (std::string separator=", ") |
| physical::Perspective< StandardDimension > * | GetStructuralPerspective () |
| const physical::Perspective< StandardDimension > * | GetStructuralPerspective () const |
| virtual bool | HasImplementation (const molecular::Protein * &content) const |
| virtual void | ImportImplementation (const LinearMotif< molecular::Protein * > *other) |
| virtual Code | InsertImplementation (molecular::Protein * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false) |
| Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< molecular::Protein * > > | |
| Elementary () | |
| Elementary (const Properties properties) | |
| virtual | ~Elementary () |
| void | RegisterProperties (const Properties properties) |
| Public Member Functions inherited from bio::chemical::Class< LinearMotif< molecular::Protein * > > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< molecular::Protein * >) Class(LinearMotif< molecular::Protein * > *object | |
| Public Member Functions inherited from bio::chemical::UnorderedMotif< molecular::Protein * > | |
| UnorderedMotif (const Contents *contents) | |
| UnorderedMotif (const UnorderedMotif< molecular::Protein * > *toCopy) | |
| virtual | ~UnorderedMotif () |
| virtual molecular::Protein * | AddImplementation (const molecular::Protein * content) |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< molecular::Protein * >) 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 molecular::Protein * content) const |
| virtual void | ImportImplementation (const UnorderedMotif< molecular::Protein * > *other) |
| virtual molecular::Protein * | RemoveImplementation (const molecular::Protein * content) |
| Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< molecular::Protein * > > | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< molecular::Protein * >) Class(UnorderedMotif< molecular::Protein * > *object | |
Detailed Description
A Cell is the basic unit of function-driven organization within Biology. Cells use Proteins & Organelles to accomplish tasks. You can think of each Protein as a stand-in for a class method except, instead of hard-coding your classes, you instead code in (hard or soft) the TranscriptionFactors and Plasmids present in a Cell. The Cell then determines its functionality at runtime.
In order to simplify the arbitrarily complex behavior that a Cell can perform, Cells are made to Peak, allowing their main function to be called on a clock at a regular interval. Programming a Cell this way is similar to programming an Arduino with a main loop. Of course, you are allowed to modify this behavior in any way you'd like ;)
Member Function Documentation
◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()
| bio::cellular::Cell::BIO_DISAMBIGUATE_ALL_CLASS_METHODS | ( | cellular | , |
| Cell | |||
| ) |
Ensure virtual methods point to Class implementations. Standard ctors.
◆ CellPerspective::Instance()
| & bio::cellular::Cell::CellPerspective::Instance | ( | ) |
◆ filter::Cellular()
| bio::cellular::Cell::filter::Cellular | ( | ) |
◆ Peak()
|
inlinevirtual |
Peak()s occur at Periodic::m_intervals. Define your main Periodic logic here. This method must be fast:
- do not read slow hardware here
- do not block for a long time
- do not sleep If derived classes must do slow work to oscillate, that slow logic MUST BE placed in a separate thread. This method would then get the data stored by that thread and returns the data quickly. MAKE SURE that the thread never causes a long mutex wait as a side-effect in this Peak method. Please call this method when you're done :)
Reimplemented from bio::physical::Periodic.
Definition at line 86 of file Cell.h.
87 {
88
89 // YOUR CODE GOES HERE!
90
92 }
References bio::physical::Periodic::Peak().
Member Data Documentation
◆ Cell
The documentation for this class was generated from the following file:
- /home/eons/git/biology/lib_bio/inc/bio/cellular/Cell.h
