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bio::genetic::GenomeImplementation Class Reference

#include <Genome.h>

+ Inheritance diagram for bio::genetic::GenomeImplementation:
+ Collaboration diagram for bio::genetic::GenomeImplementation:

Public Member Functions

virtual ~GenomeImplementation ()
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (genetic, GenomeImplementation) GenomeImplementation()
 
virtual void CacheProteins ()
 
virtual Plasmid * FetchPlasmid (Name plasmidName)
 
virtual Plasmid * FetchPlasmid (StandardDimension plasmidId)
 
virtual StandardDimension RegisterPlasmid (Plasmid *toRegister)
 
- Public Member Functions inherited from bio::genetic::Class< GenomeImplementation >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, GenomeImplementation) Class(GenomeImplementation *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::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
 
- 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
 

Protected Attributes

molecular::Protein * mc_fetchPlasmid
 
StandardDimension mc_fetchSite
 
StandardDimension mc_idSite
 
StandardDimension mc_nameSite
 
molecular::Protein * mc_registerPlasmid
 
StandardDimension mc_registrationSite
 
- Protected Attributes inherited from bio::physical::Class< T >
T * m_object
 
- Protected Attributes inherited from bio::physical::Wave
Wave * m_signal
 
Symmetry * m_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 >
Filterable * m_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
Container * m_contents
 
- Protected Attributes inherited from bio::physical::Perspective< StandardDimension >
Hadits m_hadits
 
Id m_nextId
 
- Protected Attributes inherited from bio::genetic::Expressor
Transcriptome m_transcriptome
 

Additional Inherited Members

- Public Types inherited from bio::physical::Identifiable< StandardDimension >
typedef StandardDimension Id
 
typedef std::vector< Id > Ids
 
- 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< Id > Ids
 
- 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::UnorderedMotif< TranscriptionFactor >
typedef physical::Arrangement< TranscriptionFactor > Contents
 
- Public Types inherited from bio::chemical::LinearMotif< Plasmid * >
typedef physical::Line Contents
 
- Public Types inherited from bio::chemical::UnorderedMotif< Plasmid * >
typedef physical::Arrangement< Plasmid * > Contents
 
- Public Types inherited from bio::chemical::LinearMotif< molecular::Protein * >
typedef physical::Line Contents
 
- Public Types inherited from bio::chemical::UnorderedMotif< molecular::Protein * >
typedef physical::Arrangement< molecular::Protein * > 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
 
- 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::chemical::LinearMotif< Plasmid * >
static LinearMotif< Plasmid * > Properties GetClassProperties ()
 
- Static Public Member Functions inherited from bio::chemical::LinearMotif< molecular::Protein * >
static LinearMotif< molecular::Protein * > Properties GetClassProperties ()
 
- Static Public Member Functions inherited from bio::chemical::LinearMotif< Molecule * >
static LinearMotif< Molecule * > Properties GetClassProperties ()
 
- Public Attributes inherited from bio::genetic::Class< GenomeImplementation >
physical::Perspective< StandardDimension > * perspective
 
- 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::genetic::Expressor
 Expressor
 
- Public Attributes inherited from bio::genetic::Class< Expressor >
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< TranscriptionFactor > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::LinearMotif< Plasmid * >
physical::Perspective< StandardDimension > * m_perspective
 
- Public Attributes inherited from bio::chemical::Class< LinearMotif< Plasmid * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Plasmid * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::LinearMotif< molecular::Protein * >
physical::Perspective< StandardDimension > * m_perspective
 
- Public Attributes inherited from bio::chemical::Class< LinearMotif< molecular::Protein * > >
physical::Perspective< StandardDimension > Filter filter
 
physical::Perspective< StandardDimension > * perspective
 
- Public Attributes inherited from bio::chemical::Class< UnorderedMotif< molecular::Protein * > >
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
 
- Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Surface * > >
static bool hasRegistered
 
- Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Plasmid * > >
static bool hasRegistered
 
- Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< molecular::Protein * > >
static bool hasRegistered
 
- Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Molecule * > >
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)
 

Detailed Description

The Genome is a system for managing Plasmids. This is the Biology package manager. While not implemented here, there is an official Plasmid that adds online repository integration to the Genome, which allows you to specify Plasmids by Name and at run time. See: [TODO: TO BE DETERMINED]

The Genome is a singleton to match the PlasmidPerspective it manages.

Definition at line 37 of file Genome.h.

Constructor & Destructor Documentation

◆ ~GenomeImplementation()

bio::genetic::GenomeImplementation::~GenomeImplementation ( )
virtual

Definition at line 40 of file Genome.cpp.

41{
42
43}

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::genetic::GenomeImplementation::BIO_DISAMBIGUATE_ALL_CLASS_METHODS ( genetic  ,
GenomeImplementation   
)

Ensure virtual methods point to Class implementations.

◆ CacheProteins()

void bio::genetic::GenomeImplementation::CacheProteins ( )
virtual

Adds caching for Protein-backed methods. See Expressor for docs.

Reimplemented from bio::genetic::Expressor.

Definition at line 45 of file Genome.cpp.

46{
47 mc_registerPlasmid = RotateTo< molecular::Protein* >("RegisterPlasmid");
48 mc_fetchPlasmid = RotateTo< molecular::Protein* >("FetchPlasmid");
49 mc_registrationSite = mc_registerPlasmid->GetIdWithoutCreation("Plasmid Binding Site");
50 mc_nameSite = mc_fetchPlasmid->GetIdWithoutCreation("Name Binding Site");
51 mc_idSite = mc_fetchPlasmid->GetIdWithoutCreation("Id Binding Site");
52 mc_fetchSite = mc_fetchPlasmid->GetIdWithoutCreation("Return Site");
53}
bio::genetic::GenomeImplementation::mc_nameSite
StandardDimension mc_nameSite
Definition: Genome.h:84
bio::genetic::GenomeImplementation::mc_fetchSite
StandardDimension mc_fetchSite
Definition: Genome.h:86
bio::genetic::GenomeImplementation::mc_registerPlasmid
molecular::Protein * mc_registerPlasmid
Definition: Genome.h:81
bio::genetic::GenomeImplementation::mc_fetchPlasmid
molecular::Protein * mc_fetchPlasmid
Definition: Genome.h:82
bio::genetic::GenomeImplementation::mc_idSite
StandardDimension mc_idSite
Definition: Genome.h:85
bio::genetic::GenomeImplementation::mc_registrationSite
StandardDimension mc_registrationSite
Definition: Genome.h:83
bio::physical::Perspective::GetIdWithoutCreation
virtual Id GetIdWithoutCreation(Name name) const
Definition: Perspective.h:310

◆ FetchPlasmid() [1/2]

Plasmid * bio::genetic::GenomeImplementation::FetchPlasmid ( Name  plasmidName)
virtual

Get a Plasmid!

Parameters
plasmidName
Returns
a shared Plasmid*. Should become const in a future release.

Definition at line 82 of file Genome.cpp.

83{
84 Plasmid* ret = NULL;
85 LockThread();
86 mc_fetchPlasmid->RotateTo(mc_nameSite)->Bind(plasmidName);
87 mc_fetchPlasmid->Activate();
88 ret = mc_fetchPlasmid->RotateTo< Plasmid* >(mc_fetchSite);
89 UnlockThread();
90 return ret;
91}
bio::ThreadSafe::LockThread
void LockThread() const
Definition: ThreadSafe.cpp:84
bio::ThreadSafe::UnlockThread
void UnlockThread() const
Definition: ThreadSafe.cpp:97
bio::molecular::Molecule::RotateTo
virtual Surface * RotateTo(StandardDimension surfaceId)
Definition: Molecule.cpp:48
bio::molecular::Protein::Activate
virtual Code Activate()
Definition: Protein.cpp:58
bio::molecular::Surface::Bind
T Bind(T toBind, BondType bondType=bond_type::Temporary())
Definition: Surface.h:129

References bio::molecular::Molecule::RotateTo().

◆ FetchPlasmid() [2/2]

Plasmid * bio::genetic::GenomeImplementation::FetchPlasmid ( StandardDimension  plasmidId)
virtual

Get a Plasmid!

Parameters
plasmidId
Returns
a shared Plasmid*. Should become const in a future release.

Definition at line 70 of file Genome.cpp.

71{
72 Plasmid* ret = NULL;
73 LockThread();
74 mc_fetchPlasmid->RotateTo(mc_idSite)->Bind(plasmidId);
75 mc_fetchPlasmid->Activate();
76 ret = mc_fetchPlasmid->RotateTo< Plasmid* >(mc_fetchSite);
77 UnlockThread();
78 return ret;
79
80}

References bio::molecular::Molecule::RotateTo().

◆ RegisterPlasmid()

StandardDimension bio::genetic::GenomeImplementation::RegisterPlasmid ( Plasmid *  toRegister)
virtual

Adds a Plasmid to the PlasmidPerspective.

Parameters
toRegister
Returns
the Id of the Registered Plasmid.

Definition at line 55 of file Genome.cpp.

56{
57 BIO_SANITIZE(toRegister, ,
58 return PlasmidPerspective::InvalidId())
59 StandardDimension ret = PlasmidPerspective::InvalidId();
60 LockThread();
61 mc_registerPlasmid->RotateTo(mc_registrationSite)->Bind(ChemicalCast< chemical::Substance* >(toRegister));
62 if (mc_registerPlasmid->Activate() == code::Success())
63 {
64 ret = toRegister->GetId();
65 }
66 UnlockThread();
67 return ret;
68}
BIO_SANITIZE
#define BIO_SANITIZE(test, success, failure)
Definition: SanitizeMacros.h:70
bio::chemical::Substance::Substance
Substance Substance(const typename UnorderedMotif< Property >::Contents *properties, const typename UnorderedMotif< State >::Contents *states)
Definition: Substance.cpp:27
bio::code::Success
Code Success()
bio::ChemicalCast
TO ChemicalCast(FROM toCast)
Definition: Cast.h:31

References BIO_SANITIZE, and bio::code::Success().

Member Data Documentation

◆ mc_fetchPlasmid

molecular::Protein* bio::genetic::GenomeImplementation::mc_fetchPlasmid
protected

Definition at line 82 of file Genome.h.

◆ mc_fetchSite

StandardDimension bio::genetic::GenomeImplementation::mc_fetchSite
protected

Definition at line 86 of file Genome.h.

◆ mc_idSite

StandardDimension bio::genetic::GenomeImplementation::mc_idSite
protected

Definition at line 85 of file Genome.h.

◆ mc_nameSite

StandardDimension bio::genetic::GenomeImplementation::mc_nameSite
protected

Definition at line 84 of file Genome.h.

◆ mc_registerPlasmid

molecular::Protein* bio::genetic::GenomeImplementation::mc_registerPlasmid
protected

Definition at line 81 of file Genome.h.

◆ mc_registrationSite

StandardDimension bio::genetic::GenomeImplementation::mc_registrationSite
protected

Definition at line 83 of file Genome.h.

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