#include <OrganSystem.h>

Inheritance diagram for bio::cellular::OrganSystem:

Collaboration diagram for bio::cellular::OrganSystem:

Public Member Functions
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (cellular, OrganSystem) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(cellular

	filter::Cellular ()) virtual ~OrganSystem()

virtual Code	Organogenesis ()

&	OrganSystemPerspective::Instance ()

Public Member Functions inherited from bio::chemical::LinearMotif< Organ * >
	LinearMotif (const Contents contents, physical::Perspective< StandardDimension > perspective=NULL)

	LinearMotif (const LinearMotif< Organ * > &toCopy)

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

virtual	~LinearMotif ()

virtual Organ *	AddImplementation (Organ * content)

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

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

virtual void	ClearImplementation ()

virtual Organ *	CreateImplementation (StandardDimension id)

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

virtual Emission	ForEachImplementation (ExcitationBase *excitation)

virtual Organ *	GetByIdImplementation (StandardDimension id)

virtual const Organ *	GetByIdImplementation (StandardDimension id) const

virtual Organ *	GetByNameImplementation (Name name)

virtual const Organ *	GetByNameImplementation (Name name) const

virtual Organ *	GetOrCreateByIdImplementation (StandardDimension id)

virtual Organ *	GetOrCreateByNameImplementation (Name name)

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

physical::Perspective< StandardDimension > *	GetStructuralPerspective ()

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

virtual bool	HasImplementation (const Organ * &content) const

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

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

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

	Elementary (const Properties properties)

virtual	~Elementary ()

void	RegisterProperties (const Properties properties)

Public Member Functions inherited from bio::chemical::Class< LinearMotif< Organ * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Organ * >) Class(LinearMotif< Organ * > *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::UnorderedMotif< Organ * >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< Organ * > *toCopy)

virtual	~UnorderedMotif ()

virtual Organ *	AddImplementation (const Organ * content)

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

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

virtual Organ *	RemoveImplementation (const Organ * content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Organ * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Organ * >) Class(UnorderedMotif< Organ * > *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 Attributes
	OrganSystem

Public Attributes inherited from bio::chemical::LinearMotif< Organ * >
physical::Perspective< StandardDimension > *	m_perspective

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

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::physical::Identifiable< StandardDimension >
Id	m_id

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

physical::Perspective< StandardDimension > *	perspective

Additional Inherited Members
Public Types inherited from bio::chemical::LinearMotif< Organ * >
typedef physical::Line	Contents

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< Organ * >
typedef physical::Arrangement< Organ * >	Contents

Static Public Member Functions inherited from bio::chemical::LinearMotif< Organ * >
static LinearMotif< Organ * > Properties	GetClassProperties ()

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 Attributes inherited from bio::chemical::Elementary< LinearMotif< Organ * > >
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

Detailed Description

OrganSystems are very similar to Organs. The only difference is that they contain logic for combining multiple Organs. For example, the heart relies on vasculature to move blood around the body. This requires a Heart Organ as well as integrations into all other Tissues in order to supply the BloodStream. In order to accommodate this functionality, we must invasively add functionality to other Organs. Because the modification of existing Organs can lead to more errors and make debugging more difficult, it is not recommended that you take advantage of OrganSystem machinery unless you absolutely need to. However, if you do need to make system-wide modifications, these methods are available to you.

Definition at line 42 of file OrganSystem.h.

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::cellular::OrganSystem::BIO_DISAMBIGUATE_ALL_CLASS_METHODS	(	cellular	,
		OrganSystem
	)

Ensure virtual methods point to Class implementations. Standard ctors.

◆ filter::Cellular()

bio::cellular::OrganSystem::filter::Cellular ( )

◆ Organogenesis()

Code bio::cellular::OrganSystem::Organogenesis ( )

virtual

Create all Organs and, if necessary, link them. Call the parent method (OrganSystem::Organogenesis()) when done to initialize all Organs (calls Organ::BuildMobilome() and Organ::SpecializeTissues()).

Definition at line 34 of file OrganSystem.cpp.

{
    Code ret = code::Success();
    Container* organs = GetAll< Organ* >();
    BIO_SANITIZE(organs, ,
        return code::CouldNotFindValue1())
    Organ* organBuffer;
    for (
        SmartIterator org = organs->Begin();
        !org.IsAtEnd();
        ++org
        )
    {
        organBuffer = org;
        organBuffer->SetEnvironment(this);
        if (organBuffer->BuildMobilome() != code::Success() && ret == code::Success())
        {
            ret = code::UnknownError();
        }
        if (organBuffer->GrowTissues() != code::Success() && ret == code::Success())
        {
            ret = code::UnknownError();
        }
        if (organBuffer->SpecializeTissues() != code::Success() && ret == code::Success())
        {
            ret = code::UnknownError();
        }
    }
    return ret;
}

References bio::Container::Begin(), BIO_SANITIZE, bio::cellular::Organ::BuildMobilome(), bio::code::CouldNotFindValue1(), bio::cellular::Organ::GrowTissues(), bio::SmartIterator::IsAtEnd(), bio::molecular::EnvironmentDependent< T >::SetEnvironment(), bio::cellular::Organ::SpecializeTissues(), bio::code::Success(), and bio::code::UnknownError().

Referenced by bio::organic::Organism::Morphogenesis().

◆ OrganSystemPerspective::Instance()

& bio::cellular::OrganSystem::OrganSystemPerspective::Instance ( )

Member Data Documentation

◆ OrganSystem

bio::cellular::OrganSystem::OrganSystem

Definition at line 57 of file OrganSystem.h.

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

/home/eons/git/biology/lib_bio/inc/bio/cellular/OrganSystem.h
/home/eons/git/biology/lib_bio/src/cellular/OrganSystem.cpp

Public Member Functions

Public Attributes

Additional Inherited Members