#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.

{
 
}

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.

{
    mc_registerPlasmid = RotateTo< molecular::Protein* >("RegisterPlasmid");
    mc_fetchPlasmid = RotateTo< molecular::Protein* >("FetchPlasmid");
    mc_registrationSite = mc_registerPlasmid->GetIdWithoutCreation("Plasmid Binding Site");
    mc_nameSite = mc_fetchPlasmid->GetIdWithoutCreation("Name Binding Site");
    mc_idSite = mc_fetchPlasmid->GetIdWithoutCreation("Id Binding Site");
    mc_fetchSite = mc_fetchPlasmid->GetIdWithoutCreation("Return Site");
}

◆ 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.

{
    Plasmid* ret = NULL;
    LockThread();
    mc_fetchPlasmid->RotateTo(mc_nameSite)->Bind(plasmidName);
    mc_fetchPlasmid->Activate();
    ret = mc_fetchPlasmid->RotateTo< Plasmid* >(mc_fetchSite);
    UnlockThread();
    return ret;
}

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.

{
    Plasmid* ret = NULL;
    LockThread();
    mc_fetchPlasmid->RotateTo(mc_idSite)->Bind(plasmidId);
    mc_fetchPlasmid->Activate();
    ret = mc_fetchPlasmid->RotateTo< Plasmid* >(mc_fetchSite);
    UnlockThread();
    return ret;
 
}

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.

{
    BIO_SANITIZE(toRegister, ,
        return PlasmidPerspective::InvalidId())
    StandardDimension ret = PlasmidPerspective::InvalidId();
    LockThread();
    mc_registerPlasmid->RotateTo(mc_registrationSite)->Bind(ChemicalCast< chemical::Substance* >(toRegister));
    if (mc_registerPlasmid->Activate() == code::Success())
    {
        ret = toRegister->GetId();
    }
    UnlockThread();
    return ret;
}

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:

/home/eons/git/biology/lib_bio/inc/bio/genetic/Genome.h
/home/eons/git/biology/lib_bio/src/genetic/Genome.cpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~GenomeImplementation()

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

◆ CacheProteins()

◆ FetchPlasmid() [1/2]

◆ FetchPlasmid() [2/2]

◆ RegisterPlasmid()

Member Data Documentation

◆ mc_fetchPlasmid

◆ mc_fetchSite

◆ mc_idSite

◆ mc_nameSite

◆ mc_registerPlasmid

◆ mc_registrationSite