#include <Plasmid.h>

Inheritance diagram for bio::genetic::Plasmid:

Collaboration diagram for bio::genetic::Plasmid:

Public Member Functions
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (genetic, Plasmid) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(genetic

	filter::Genetic ()) virtual ~Plasmid()

virtual molecular::Protein *	GetRNAPolymerase ()

virtual const molecular::Protein *	GetRNAPolymerase () const

&	PlasmidPerspective::Instance ()

virtual RNA *	TranscribeFor (Expressor *expressor) const

Public Member Functions inherited from bio::genetic::Class< Plasmid >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, Plasmid) Class(Plasmid *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::chemical::LinearMotif< Gene * >
	LinearMotif (const Contents contents, physical::Perspective< StandardDimension > perspective=NULL)

	LinearMotif (const LinearMotif< Gene * > &toCopy)

	LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)

virtual	~LinearMotif ()

virtual Gene *	AddImplementation (Gene * content)

virtual Code	Attenuate (const physical::Wave *other)

	BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Gene * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical

virtual void	ClearImplementation ()

virtual Gene *	CreateImplementation (StandardDimension id)

virtual Code	Disattenuate (const physical::Wave *other)

virtual Emission	ForEachImplementation (ExcitationBase *excitation)

virtual Gene *	GetByIdImplementation (StandardDimension id)

virtual const Gene *	GetByIdImplementation (StandardDimension id) const

virtual Gene *	GetByNameImplementation (Name name)

virtual const Gene *	GetByNameImplementation (Name name) const

virtual Gene *	GetOrCreateByIdImplementation (StandardDimension id)

virtual Gene *	GetOrCreateByNameImplementation (Name name)

virtual std::string	GetStringFromImplementation (std::string separator=", ")

physical::Perspective< StandardDimension > *	GetStructuralPerspective ()

const physical::Perspective< StandardDimension > *	GetStructuralPerspective () const

virtual bool	HasImplementation (const Gene * &content) const

virtual void	ImportImplementation (const LinearMotif< Gene * > *other)

virtual Code	InsertImplementation (Gene * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)

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

	Elementary (const Properties properties)

virtual	~Elementary ()

void	RegisterProperties (const Properties properties)

Public Member Functions inherited from bio::chemical::Class< LinearMotif< Gene * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Gene * >) Class(LinearMotif< Gene * > *object

Public Member Functions inherited from bio::chemical::UnorderedMotif< Gene * >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< Gene * > *toCopy)

virtual	~UnorderedMotif ()

virtual Gene *	AddImplementation (const Gene * content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Gene * >) 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 Gene * content) const

virtual void	ImportImplementation (const UnorderedMotif< Gene * > *other)

virtual Gene *	RemoveImplementation (const Gene * content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Gene * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Gene * >) Class(UnorderedMotif< Gene * > *object

Public Member Functions inherited from bio::molecular::DNA
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, DNA) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(molecular

&	DNAPerspective::Instance ()

	filter::Molecular ()) virtual ~DNA()

virtual Protein *	GetProtein ()

virtual const Protein *	GetProtein () const

virtual StandardDimension	GetProteinId () const

virtual Version	GetVersion ()

virtual void	SetProtein (Protein *protein)

virtual void	SetVersion (Version newVersion)

Public Member Functions inherited from bio::molecular::Class< DNA >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, DNA) Class(DNA *object

Public Attributes
	Plasmid

Public Attributes inherited from bio::genetic::Class< Plasmid >
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::chemical::LinearMotif< Gene * >
physical::Perspective< StandardDimension > *	m_perspective

Public Attributes inherited from bio::chemical::Class< LinearMotif< Gene * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Gene * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::molecular::DNA
	DNA

Public Attributes inherited from bio::molecular::Class< DNA >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

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::LinearMotif< Gene * >
typedef physical::Line	Contents

Public Types inherited from bio::chemical::UnorderedMotif< Gene * >
typedef physical::Arrangement< Gene * >	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< Gene * >
static LinearMotif< Gene * > Properties	GetClassProperties ()

Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Surface * > >
static bool	hasRegistered

Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Gene * > >
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)

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::molecular::DNA
Protein *	m_protein

Version	m_version

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, Seon 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 cellular::Protein or cellular::Cell they are added to (prior to initialization). This will be addressed in a future release.

Definition at line 48 of file Plasmid.h.

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::genetic::Plasmid::BIO_DISAMBIGUATE_ALL_CLASS_METHODS	(	genetic	,
		Plasmid
	)

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

◆ filter::Genetic()

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

◆ GetRNAPolymerase() [1/2]

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.

Definition at line 34 of file Plasmid.cpp.

{
    return GetProtein();
}

References bio::molecular::DNA::GetProtein().

Referenced by TranscribeFor().

◆ GetRNAPolymerase() [2/2]

const molecular::Protein * bio::genetic::Plasmid::GetRNAPolymerase ( ) const

virtual

Definition at line 39 of file Plasmid.cpp.

{
    return GetProtein();
}

References bio::molecular::DNA::GetProtein().

◆ PlasmidPerspective::Instance()

& bio::genetic::Plasmid::PlasmidPerspective::Instance ( )

◆ TranscribeFor()

RNA * bio::genetic::Plasmid::TranscribeFor ( 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.

Definition at line 49 of file Plasmid.cpp.

{
    std::string rnaName = "mRNA_";
    rnaName += GetName();
    RNA* ret = new RNA(rnaName.c_str());
    molecular::Protein* polymerase = ForceCast< molecular::Protein* >(GetRNAPolymerase()->Clone());
    StandardDimension bindingSite = polymerase->GetIdFromName("RNA Binding Site");
    polymerase->RecruitChaperones(expressor);
    polymerase->Fold();
    polymerase->RotateTo(bindingSite)->Bind(ret);
    polymerase->Activate();
    polymerase->RotateTo(bindingSite)->ReleaseAll();
    delete polymerase;
    return ret;
}

References bio::molecular::Protein::Activate(), bio::molecular::Surface::Bind(), bio::physical::Class< T >::Clone(), bio::molecular::Protein::Fold(), bio::physical::Perspective< DIMENSION >::GetIdFromName(), GetRNAPolymerase(), bio::molecular::Protein::RecruitChaperones(), bio::molecular::Surface::ReleaseAll(), and bio::molecular::Molecule::RotateTo().

Referenced by bio::genetic::Expressor::ExpressGenes().

Member Data Documentation

◆ Plasmid

bio::genetic::Plasmid::Plasmid

Definition at line 66 of file Plasmid.h.

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

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

◆ filter::Genetic()

◆ GetRNAPolymerase() [1/2]

◆ GetRNAPolymerase() [2/2]

◆ PlasmidPerspective::Instance()

◆ TranscribeFor()

Member Data Documentation

◆ Plasmid