#include <Plasmid.h>

Inheritance diagram for bio::genetic::Plasmid:

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Collaboration diagram for bio::genetic::Plasmid:

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Public Member Functions
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (genetic, Plasmid, filter::Genetic()) virtual ~Plasmid()

virtual Pointer< molecular::Protein >	GetRNAPolymerase ()

virtual Pointer< const molecular::Protein >	GetRNAPolymerase () const

virtual Pointer< RNA >	TranscribeFor (Pointer< Expressor > expressor) const

Public Member Functions inherited from bio::genetic::Class< Plasmid >
	Class (Pointer< Plasmid > object, Filter filter=filter::Default())

	Class (Pointer< Plasmid > object, const Name &name, Filter filter=filter::Default())

	Class (Pointer< Plasmid > object, const Id &id, Filter filter=filter::Default())

virtual	~Class ()

Public Member Functions inherited from bio::molecular::Class< T >
	Class (Pointer< T > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< T > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< T > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

template<typename ENVIRONMENT >
void	SetEnvironment (Pointer< ENVIRONMENT > environment)

template<typename ENVIRONMENT >
Pointer< ENVIRONMENT >	GetEnvironment ()

template<typename ENVIRONMENT >
const Pointer< ENVIRONMENT >	GetEnvironment () const

Public Member Functions inherited from bio::chemical::Class< T >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< T > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< T > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< T > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

virtual Code	Attenuate (Pointer< const physical::Wave > other)

virtual Code	Disattenuate (Pointer< const physical::Wave > other)

Public Member Functions inherited from bio::physical::Class< T >
	Class (Pointer< T > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< T > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< T >	GetWaveObject ()

virtual Pointer< const T >	GetWaveObject () const

virtual	operator T& ()

virtual	operator const T & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::physical::Wave
	Wave (Pointer< Symmetry > symmetry=NULL)

	Wave (const Wave &other)

Wave &	operator= (const Wave &other)

virtual	~Wave ()

Pointer< const Symmetry >	GetSymmetry () const

virtual bool	Superpose (Pointer< const Wave > displacement, Pointer< Interference > pattern)

virtual Pointer< Wave >	Superpose (const ConstWaves &displacement, Pointer< Interference > pattern)

virtual Pointer< Wave >	Modulate (Pointer< Wave > signal)

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual void	operator\| (Pointer< Symmetry > symmetry)

virtual Pointer< Wave >	operator* (Pointer< Wave > signal)

virtual Pointer< Wave >	operator* ()

virtual Pointer< const Wave >	operator* () const

virtual void	operator+ (Pointer< const Wave > other)

virtual void	operator- (Pointer< const Wave > other)

uint16_t	GetTypeId () const

void	SetTypeId (uint16_t typeId)

Public Member Functions inherited from bio::physical::Identifiable< Id >
	Identifiable (Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Name &name, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (Identifier id, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Identifiable &other)

virtual	~Identifiable ()

virtual	operator Id () const

virtual bool	operator== (const Identifier id) const

virtual bool	operator== (const Name &name) const

virtual bool	operator== (const Identifiable< Id > &other) const

virtual Name	GetName () const

virtual Identifier	GetId () const

virtual bool	SetName (const Name &name)

virtual bool	SetId (Identifier id)

virtual bool	IsName (const Name &name) const

virtual bool	IsNameInsensitive (const Name &name) const

virtual bool	IsId (Identifier id) const

virtual void	SetPerspective (Pointer< Perspective< Id > > perspective)

Public Member Functions inherited from bio::physical::Observer< PERSPECTIVE >
	Observer (Pointer< Perspective > perspective=NULL)

	Observer (const Observer &other)

virtual	~Observer ()

virtual void	SetPerspective (Pointer< Perspective > perspective)

virtual Pointer< Perspective >	GetPerspective () const

Public Member Functions inherited from bio::log::Writer
	Writer ()

	Writer (Filter logFilter)

virtual	~Writer ()

virtual Pointer< const Writer >	AsLogWriter () const

bool	IsEnabled (LogLevel level) const

virtual void	Log (LogLevel level, const char *format, va_list args) const

Public Member Functions inherited from bio::physical::Class< Writer >
	Class (Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Writer > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Writer >	GetWaveObject ()

virtual Pointer< const Writer >	GetWaveObject () const

virtual	operator Writer & ()

virtual	operator const Writer & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::physical::Filterable
	Filterable ()

	Filterable (Filter filter)

virtual	~Filterable ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual void	SetFilter (Filter filter)

Filter	GetFilter () const

Public Member Functions inherited from bio::physical::Class< Filterable >
	Class (Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Filterable > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Filterable >	GetWaveObject ()

virtual Pointer< const Filterable >	GetWaveObject () const

virtual	operator Filterable & ()

virtual	operator const Filterable & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::chemical::Atom
	Atom ()

	Atom (const Atom &other)

virtual	~Atom ()

void	CloneBondsFrom (const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy)

Pointer< physical::Wave >	GetBonded (Valence position)

Pointer< const physical::Wave >	GetBonded (Valence position) const

Pointer< const physical::Wave >	ResolveBondedForReadById (AtomicNumber bondId) const

Pointer< physical::Wave >	ResolveBondedForWriteById (AtomicNumber bondId)

template<typename T >
Cow< T >	AsBonded () const

template<typename T >
Pointer< T >	AsBondedQuantum () const

template<typename T >
atom_detail::AsResultType< T, type::IsWaveImplementation< typenametype::RemovePointer< T >::Type >::sValue >::Type	As () const

template<typename T >
	operator T () const

template<typename T >
Valence	FormBond (T toBond, BondType type=bond_type::Unknown())

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (const Name &typeName) const

Valence	GetBondPositionLocked (AtomicNumber bondedId) const

template<typename T >
Valence	GetBondPosition () const

BondType	GetBondType (Valence position) const

template<typename T >
BondType	GetBondType () const

Pointer< Bonds >	GetAllBonds ()

Pointer< const Bonds >	GetAllBonds () const

void	ForEachBond (BondVisitor visitor, void *context=NULL) const

void	ForEachBondMutable (BondMutator mutator, void *context=NULL)

virtual Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type)

Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

Valence	FormBondImplementationLocked (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

virtual bool	BreakBondImplementation (AtomicNumber id, BondType type)

bool	BreakBondImplementationLocked (AtomicNumber id, BondType type)

Public Member Functions inherited from bio::physical::Class< Atom >
	Class (Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Atom > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Atom >	GetWaveObject ()

virtual Pointer< const Atom >	GetWaveObject () const

virtual	operator Atom & ()

virtual	operator const Atom & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

ThreadSafe &	operator= (const ThreadSafe &toCopy)

	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

void	LockMutexShared () const

void	UnlockMutexShared () const

Public Member Functions inherited from bio::chemical::Substance
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (chemical, Substance, filter::Chemical()) Substance(const UnorderedMotif< Property > &properties

virtual	~Substance ()

virtual void	Enable ()

virtual void	Disable ()

virtual bool	IsEnabled () const

Public Member Functions inherited from bio::chemical::Class< Substance >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< Substance > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Substance > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Substance > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

virtual Code	Attenuate (Pointer< const physical::Wave > other)

virtual Code	Disattenuate (Pointer< const physical::Wave > other)

Public Member Functions inherited from bio::Covalent< UnorderedMotif< Property > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< UnorderedMotif< Property > >	Object ()

Pointer< const UnorderedMotif< Property > >	Object () const

Public Member Functions inherited from bio::Covalent< UnorderedMotif< State > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< UnorderedMotif< State > >	Object ()

Pointer< const UnorderedMotif< State > >	Object () 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 >
Pointer< T >	Add (Pointer< T > t)

template<typename T >
Code	Remove (const T t)

template<typename T >
Code	Remove (Pointer< T > t)

template<typename T >
void	Import (Pointer< const UnorderedMotif< T > > other)

template<typename T >
void	Import (Pointer< const LinearMotif< T > > other)

template<typename T >
void	Import (const ::bio::Arrangement< T > &other)

Code	ImportAll (Pointer< const physical::Wave > other)

template<typename T >
Index	GetCount () const

template<typename T >
Pointer< Container >	GetAll ()

template<typename T >
Pointer< const Container >	GetAll () const

template<typename T >
bool	Has (T content) const

template<typename T >
bool	Has (Pointer< T > content) const

template<typename T >
unsigned int	GetNumMatching (Pointer< const Container > other) const

template<typename T >
bool	HasAll (Pointer< const Container > contents) const

template<typename T >
void	Clear ()

template<typename T >
std::string	GetStringFrom (std::string separator=", ")

template<typename T >
void	Log (const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId())

Public Member Functions inherited from bio::chemical::LinearStructureInterface
	LinearStructureInterface ()

virtual	~LinearStructureInterface ()

template<typename T >
Code	Insert (typename LinearStructureRequest< T >::PointerType toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false)

template<typename T >
LinearStructureRequest< T >::PointerType	GetById (const Id &id)

template<typename T >
const LinearStructureRequest< T >::PointerType	GetById (const Id &id) const

template<typename T >
LinearStructureRequest< T >::PointerType	GetByName (const Name &name)

template<typename T >
const LinearStructureRequest< T >::PointerType	GetByName (const Name &name) const

template<typename T >
LinearStructureRequest< T >::PointerType	GetOrCreateById (Id id)

template<typename T >
LinearStructureRequest< T >::PointerType	GetOrCreateByName (const Name &name)

template<typename T >
Code	RemoveById (const Id &id)

template<typename T >
Code	RemoveByName (const Name &name)

template<typename T >
LinearMotif< typenameLinearStructureRequest< T >::Pointee >::Contents	GetAllLike (Pointer< const Affinity > affinity) const

template<typename T >
Emission	ForEach (Pointer< ExcitationBase > excitation)

Public Member Functions inherited from bio::molecular::Molecule
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (molecular, Molecule, filter::Molecular()) Molecule(const Molecule &toCopy)

virtual	~Molecule ()

template<typename T >
Id	Use (const Name &varName, Pointer< T > varPtr)

template<typename T >
Id	Use (const Id &id, Pointer< T > varPtr)

Id	Define (const Name &varName)

Id	Define (const Id &id)

template<typename T >
Id	Define (const Name &varName)

template<typename T >
Id	Define (const Id &id)

template<typename T >
Id	Define (const Name &varName, const T &assignment)

template<typename T >
Id	Define (const Id &id, const T &assignment)

virtual Pointer< Surface >	RotateTo (const Id &surfaceId)

virtual Pointer< const Surface >	RotateTo (const Id &surfaceId) const

virtual Pointer< Surface >	RotateTo (const Name &surfaceName)

virtual Pointer< const Surface >	RotateTo (const Name &surfaceName) const

virtual Pointer< Surface >	RotateToOrDefine (const Id &surfaceId)

Pointer< Surface >	RotateToOrDefine (const Name &surfaceName)

template<typename T >
Pointer< Surface >	RotateToOrDefine (const Id &surfaceId, T &assignment)

template<typename T >
Pointer< Surface >	RotateToOrDefine (const Name &surfaceName, T &assignment)

virtual bool	DuplicateFrom (Pointer< Molecule > source, const Name &surface)

virtual bool	TransferFrom (Pointer< Molecule > source, const Name &surface)

virtual Pointer< const physical::Symmetry >	Spin () const

virtual Code	Reify (Pointer< const physical::Symmetry > symmetry)

virtual Pointer< Surface >	operator() (const Id &surfaceId)

virtual Pointer< const Surface >	operator() (const Id &surfaceId) const

template<typename T >
Pointer< Surface >	operator() (const Id &surfaceId)

virtual Pointer< Surface >	operator() (const Name &name)

virtual Pointer< const Surface >	operator() (const Name &name) const

template<typename T >
Pointer< Surface >	operator() (const Name &surfaceName)

virtual Pointer< Molecule >	operator<< (Pointer< Surface > source)

virtual Pointer< Surface >	operator>> (Pointer< Surface > target)

virtual Pointer< Molecule >	operator<< (Pointer< Molecule > source)

virtual Pointer< Molecule >	operator>> (Pointer< Molecule > target)

Public Member Functions inherited from bio::molecular::Class< Molecule >
	Class (Pointer< Molecule > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Molecule > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Molecule > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

void	SetEnvironment (Pointer< ENVIRONMENT > environment)

Pointer< ENVIRONMENT >	GetEnvironment ()

const Pointer< ENVIRONMENT >	GetEnvironment () const

Public Member Functions inherited from bio::Metallic< chemical::DependentMotif< Surface, Molecule > >
	Metallic ()

	Metallic (const Metallic &other)

virtual	~Metallic ()

Metallic &	operator= (const Metallic &other)

Pointer< chemical::DependentMotif< Surface, Molecule > >	Object ()

Pointer< const chemical::DependentMotif< Surface, Molecule > >	Object () const

Public Member Functions inherited from bio::Covalent< chemical::LinearMotif< Gene > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< chemical::LinearMotif< Gene > >	Object ()

Pointer< const chemical::LinearMotif< Gene > >	Object () const

Public Member Functions inherited from bio::molecular::DNA
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (molecular, DNA, filter::Molecular()) virtual ~DNA()

virtual Pointer< Protein >	GetProtein ()

virtual Pointer< const Protein >	GetProtein () const

virtual void	SetProtein (Pointer< Protein > protein)

virtual Id	GetProteinId () const

virtual Version	GetVersion ()

virtual void	SetVersion (Version newVersion)

Public Member Functions inherited from bio::molecular::Class< DNA >
	Class (Pointer< DNA > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< DNA > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< DNA > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

virtual	~Class ()

void	SetEnvironment (Pointer< ENVIRONMENT > environment)

Pointer< ENVIRONMENT >	GetEnvironment ()

const Pointer< ENVIRONMENT >	GetEnvironment () const

Additional Inherited Members
Public Types inherited from bio::physical::Identifiable< Id >
typedef Id	Identifier

typedef Arrangement< Identifier >	Ids

Public Types inherited from bio::physical::Observer< PERSPECTIVE >
typedef PERSPECTIVE	Perspective

Public Types inherited from bio::chemical::Atom
typedef BondCloneAction(*	BondClonePolicy) (const Bond &bond)

typedef void(*	BondVisitor) (const Bond &bond, void *context)

typedef BondCloneAction(*	BondMutator) (Bond &bond, void *context)

Static Public Member Functions inherited from bio::physical::Class< T >
static Pointer< T >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::physical::Wave
static Properties	GetResonanceBetween (ConstWaves waves)

static Properties	GetResonanceBetween (Pointer< const Wave > wave1, Pointer< const Wave > wave2)

static Properties	GetResonanceBetween (Pointer< const Wave > wave, const Properties &properties)

Static Public Member Functions inherited from bio::log::Writer
static void	Log (Pointer< const Writer > writer, LogLevel level, const char *format,...)

static bool	ShouldLog (Pointer< const Writer > writer, LogLevel level)

Static Public Member Functions inherited from bio::physical::Class< Writer >
static Pointer< Writer >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::physical::Class< Filterable >
static Pointer< Filterable >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::chemical::Atom
static BondCloneAction	DefaultBondClonePolicy (const Bond &bond)

template<typename T >
static AtomicNumber	GetBondId ()

Static Public Member Functions inherited from bio::physical::Class< Atom >
static Pointer< Atom >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::chemical::UnorderedStructureInterface
static void	ImportAllCollectVisitor (const chemical::Bond &bond, void *ctx)

Static Public Member Functions inherited from bio::Metallic< chemical::DependentMotif< Surface, Molecule > >
static void	DonateCollectVisitor (const chemical::Bond &bond, void *ctx)

static void	DonateBonds (Pointer< chemical::Atom > donor, Pointer< chemical::Atom > receiver)

static void	BreakDonatedCollectVisitor (const chemical::Bond &bond, void *ctx)

static void	BreakDonatedBonds (Pointer< chemical::Atom > receiver)

static BondType	GetBondType ()

Public Attributes inherited from bio::chemical::Substance
const UnorderedMotif< State > &	states

Protected Types inherited from bio::physical::Identifiable< Id >
typedef Id	Identifier

typedef Arrangement< Identifier >	Ids

Protected Types inherited from bio::physical::Observer< PERSPECTIVE >
typedef PERSPECTIVE	Perspective

Protected Types inherited from bio::chemical::Atom
typedef BondCloneAction(*	BondClonePolicy) (const Bond &bond)

typedef void(*	BondVisitor) (const Bond &bond, void *context)

typedef BondCloneAction(*	BondMutator) (Bond &bond, void *context)

Protected Member Functions inherited from bio::chemical::Elementary< T >
void	RegisterType ()

	Elementary (const Properties properties)

	Elementary ()

virtual	~Elementary ()

Protected Member Functions inherited from bio::physical::Identifiable< Id >
virtual void	InitializeImplementation (ByteStreams &args)

friend::std::ostream &	operator<< (std::ostream &out, const Identifiable< Id > &t)

	Identifiable (Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Name &name, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (Identifier id, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Identifiable &other)

virtual	~Identifiable ()

virtual	operator Id () const

virtual bool	operator== (const Identifier id) const

virtual bool	operator== (const Name &name) const

virtual bool	operator== (const Identifiable< Id > &other) const

virtual Name	GetName () const

virtual Identifier	GetId () const

virtual bool	SetName (const Name &name)

virtual bool	SetId (Identifier id)

virtual bool	IsName (const Name &name) const

virtual bool	IsNameInsensitive (const Name &name) const

virtual bool	IsId (Identifier id) const

virtual void	SetPerspective (Pointer< Perspective< Id > > perspective)

Protected Member Functions inherited from bio::physical::Observer< PERSPECTIVE >
	Observer (Pointer< Perspective > perspective=NULL)

	Observer (const Observer &other)

virtual	~Observer ()

virtual void	SetPerspective (Pointer< Perspective > perspective)

virtual Pointer< Perspective >	GetPerspective () const

Protected Member Functions inherited from bio::VirtualBase
	VirtualBase ()

virtual	~VirtualBase ()

void	Initialize (ByteStreams &args)

void	Initialize (ByteStream arg1)

void	Initialize (ByteStream arg1, ByteStream arg2)

void	Initialize (ByteStream arg1, ByteStream arg2, ByteStream arg3)

Protected Member Functions inherited from bio::log::Writer
	Writer ()

	Writer (Filter logFilter)

virtual	~Writer ()

virtual Pointer< const Writer >	AsLogWriter () const

bool	IsEnabled (LogLevel level) const

virtual void	Log (LogLevel level, const char *format, va_list args) const

Protected Member Functions inherited from bio::physical::Class< Writer >
	Class (Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Writer > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Writer >	GetWaveObject ()

virtual Pointer< const Writer >	GetWaveObject () const

virtual	operator Writer & ()

virtual	operator const Writer & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::physical::Filterable
	Filterable ()

	Filterable (Filter filter)

virtual	~Filterable ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual void	SetFilter (Filter filter)

Filter	GetFilter () const

Protected Member Functions inherited from bio::physical::Class< Filterable >
	Class (Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Filterable > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Filterable >	GetWaveObject ()

virtual Pointer< const Filterable >	GetWaveObject () const

virtual	operator Filterable & ()

virtual	operator const Filterable & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::chemical::Atom
void	IndexBond (AtomicNumber bondedId, Valence position)

void	UnindexBond (AtomicNumber bondedId)

	Atom ()

	Atom (const Atom &other)

virtual	~Atom ()

void	CloneBondsFrom (const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy)

Pointer< physical::Wave >	GetBonded (Valence position)

Pointer< const physical::Wave >	GetBonded (Valence position) const

Pointer< const physical::Wave >	ResolveBondedForReadById (AtomicNumber bondId) const

Pointer< physical::Wave >	ResolveBondedForWriteById (AtomicNumber bondId)

template<typename T >
Cow< T >	AsBonded () const

template<typename T >
Pointer< T >	AsBondedQuantum () const

template<typename T >
atom_detail::AsResultType< T, type::IsWaveImplementation< typenametype::RemovePointer< T >::Type >::sValue >::Type	As () const

template<typename T >
	operator T () const

template<typename T >
Valence	FormBond (T toBond, BondType type=bond_type::Unknown())

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (const Name &typeName) const

Valence	GetBondPositionLocked (AtomicNumber bondedId) const

template<typename T >
Valence	GetBondPosition () const

BondType	GetBondType (Valence position) const

template<typename T >
BondType	GetBondType () const

Pointer< Bonds >	GetAllBonds ()

Pointer< const Bonds >	GetAllBonds () const

void	ForEachBond (BondVisitor visitor, void *context=NULL) const

void	ForEachBondMutable (BondMutator mutator, void *context=NULL)

virtual Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type)

Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

Valence	FormBondImplementationLocked (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

virtual bool	BreakBondImplementation (AtomicNumber id, BondType type)

bool	BreakBondImplementationLocked (AtomicNumber id, BondType type)

Protected Member Functions inherited from bio::physical::Class< Atom >
	Class (Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Atom > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Atom >	GetWaveObject ()

virtual Pointer< const Atom >	GetWaveObject () const

virtual	operator Atom & ()

virtual	operator const Atom & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

ThreadSafe &	operator= (const ThreadSafe &toCopy)

	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

void	LockMutexShared () const

void	UnlockMutexShared () const

Protected Member Functions inherited from bio::chemical::LinearStructureInterface
template<typename T >
Pointer< LinearMotif< T > >	ResolveLinearMotif ()

template<typename T >
Pointer< const LinearMotif< T > >	ResolveLinearMotif () const

Static Protected Member Functions inherited from bio::log::Writer
static void	Log (Pointer< const Writer > writer, LogLevel level, const char *format,...)

static bool	ShouldLog (Pointer< const Writer > writer, LogLevel level)

Static Protected Member Functions inherited from bio::physical::Class< Writer >
static Pointer< Writer >	Convert (Pointer< Wave > wave)

Static Protected Member Functions inherited from bio::physical::Class< Filterable >
static Pointer< Filterable >	Convert (Pointer< Wave > wave)

Static Protected Member Functions inherited from bio::chemical::Atom
static BondCloneAction	DefaultBondClonePolicy (const Bond &bond)

template<typename T >
static AtomicNumber	GetBondId ()

Static Protected Member Functions inherited from bio::physical::Class< Atom >
static Pointer< Atom >	Convert (Pointer< Wave > wave)

Protected Attributes inherited from bio::physical::Class< T >
Pointer< T >	mObject

Protected Attributes inherited from bio::physical::Wave
LazyPointer< Symmetry >	mSymmetry

bool	mHasSignal

uint16_t	mTypeId

Protected Attributes inherited from bio::VirtualBase
bool	mHasBeenInitialized

Protected Attributes inherited from bio::physical::Class< Writer >
Pointer< Writer >	mObject

Protected Attributes inherited from bio::physical::Filterable
Filter	mFilter

Protected Attributes inherited from bio::physical::Class< Filterable >
Pointer< Filterable >	mObject

Protected Attributes inherited from bio::chemical::Atom
Bonds	mBonds

::std::map< AtomicNumber, Valence >	mBondIndex

Arrangement< Pointer< const physical::Wave > >	mBackflowPreventer

Protected Attributes inherited from bio::physical::Class< Atom >
Pointer< Atom >	mObject

Protected Attributes inherited from bio::Covalent< UnorderedMotif< Property > >
Pointer< UnorderedMotif< Property > >	mT

Protected Attributes inherited from bio::Covalent< UnorderedMotif< State > >
Pointer< UnorderedMotif< State > >	mT

Protected Attributes inherited from bio::Metallic< chemical::DependentMotif< Surface, Molecule > >
Pointer< chemical::DependentMotif< Surface, Molecule > >	mT

Protected Attributes inherited from bio::Covalent< chemical::LinearMotif< Gene > >
Pointer< chemical::LinearMotif< Gene > >	mT

Protected Attributes inherited from bio::molecular::DNA
Pointer< Protein >	mProtein

Version	mVersion

Detailed Description

The purpose of a Plasmid is to group logically similar Proteins into a single unit that can be easily distributed and applied to Biological projects.
Essentially, a Plasmid is a library; the code it stores is simply restricted to Proteins, Molecules, and other Biological classes for the purpose of integrating with the Biology framework.
You could create your own Plasmid that would make function calls to your own C++ library or other system. In that Plasmid, you would want to define a set of Proteins and Genes that would make such calls. Those Genes would then be Expressed in Cells and you would have bridged your framework and Biology.

Another benefit of modularizing code with through systems like this is that it allows updates, patches, and features to be rolled out incrementally, without disrupting service.
For example, if your friend creates their MyFavoritePlasmid, which contains your friend's MyFavoriteProtein and you would like the same behavior but done in a different way (e.g. a security patch or extra api call), you can create a stand-in replacement for your friend's MyFavoriteProtein and override just that one function while still using the rest of friend's MyFavoritePlasmid. You can then share your Plasmid with your friend and they can upgrade their systems by including it!

A brief bit of history: this whole framework was originally built when the sales lead wanted features to show investors that were in direct conflict with what the technical lead requested. Instead of forcing management to reconcile, Séon just developed a system to meet both needs simultaneously.

A lot happens on Plasmid creation. The first Protein *this will produce is RNATranscriptase, which is used for Transcribing the rest of the Genes in *this. This process will produce all Proteins used by the full system. If the log::Engine is supplied in the Plasmid constructor, any messages produced during the Protein creation process will be logged; otherwise, these messages will be ignored and the logEngine will be specified when the Proteins are Folded in their Cell.
Regarding Writer SetLogEngine, Plasmids do not forward any such calls onto their Genes, as they assume the Proteins will not use logs in their constructors and that the log engine will be set by the molecular::Protein or cellular::Cell they are added to (prior to initialization). This will be addressed in a future release.

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

bio::genetic::Plasmid::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR	(	genetic	,
		Plasmid	,
		filter::Genetic()
	)

Ensure virtual methods point to Class implementations.
Standard constructors.
These are easy to use but require setting member variables manually.

◆ GetRNAPolymerase() [1/2]

Pointer< molecular::Protein > bio::genetic::Plasmid::GetRNAPolymerase ( )

virtual

RNA polymerase is responsible for transcribing DNA into the mRNA that is then translated into protein.
Similarly, here, RNAPolymerase is responsible for Transcribing Genes.
If you would like your own custom unpacking system for your Plasmid, override this method.
If you don't need anything fancy, leave this as is.

Returns: A Protein that will carry out the Transcription of *this.

◆ GetRNAPolymerase() [2/2]

Pointer< const molecular::Protein > bio::genetic::Plasmid::GetRNAPolymerase ( ) const

virtual

◆ TranscribeFor()

Pointer< RNA > bio::genetic::Plasmid::TranscribeFor ( Pointer< Expressor > expressor ) const

virtual

Transcribes *this in the context of the given Expressor.
This does not alter either the expressor given nor *this but, instead creates an new RNA that can be added to the expressor's Transcriptome. Uses the RNAPolymerase from *this.

Parameters

expressor

Returns: a new RNA* to be Expressed.

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

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

◆ GetRNAPolymerase() [1/2]

◆ GetRNAPolymerase() [2/2]

◆ TranscribeFor()