#include <GenomeDefault.h>

Inheritance diagram for bio::genetic::GenomeDefault:

Collaboration diagram for bio::genetic::GenomeDefault:

Public Member Functions
	GenomeDefault ()

virtual	~GenomeDefault ()

Public Member Functions inherited from bio::genetic::Plasmid
	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

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 ()

Public Attributes inherited from bio::genetic::Plasmid
	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

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

Definition at line 29 of file GenomeDefault.h.

Constructor & Destructor Documentation

◆ GenomeDefault()

bio::genetic::GenomeDefault::GenomeDefault ( )

Definition at line 31 of file GenomeDefault.cpp.

{
    Gene* registerPlasmid = new Gene("Register Plasmid Default");
    registerPlasmid->SetProtein(new RegisterPlasmid());
    registerPlasmid->Add< TranscriptionFactor >(transcription_factor::Genome());
    Add< Gene* >(registerPlasmid);
 
    Gene* fetchPlasmid = new Gene("Fetch Plasmid Default");
    fetchPlasmid->SetProtein(new FetchPlasmid());
    fetchPlasmid->Add< TranscriptionFactor >(transcription_factor::Genome());
    Add< Gene* >(fetchPlasmid);
}

References bio::chemical::UnorderedStructureInterface::Add(), bio::transcription_factor::Genome(), and bio::molecular::DNA::SetProtein().

◆ ~GenomeDefault()

bio::genetic::GenomeDefault::~GenomeDefault ( )

virtual

Definition at line 44 of file GenomeDefault.cpp.

{
    //Gene*s will be automatically deleted.
}

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GenomeDefault()

◆ ~GenomeDefault()