#include <Solute.h>

Inheritance diagram for bio::chemical::Solute:

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Collaboration diagram for bio::chemical::Solute:

[legend]

Public Member Functions
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (chemical, Solute, filter::Chemical()) Solute(const Solute &other)

	Solute (Pointer< Substance > dissolvedSubstance, const DiffusionTime &diffusionTime=diffusion::time::Destruction(), const DiffusionEffort &diffusionEffort=diffusion::effort::Active())

virtual	~Solute ()

Solute &	operator= (const Solute &other)

	operator Pointer< Substance > ()

	operator Pointer< const Substance > () const

Pointer< Substance >	GetDissolvedSubstance ()

Pointer< const Substance >	GetDissolvedSubstance () const

virtual Concentration	GetConcentration () const

virtual void	Diffuse () const

virtual Code	Crest ()

virtual Code	MixWith (const Solute &other)

virtual Code	MixWith (Pointer< const Substance > other)

virtual void	SetEnvironment (Pointer< Solution > environment)

virtual Index	GetIndexInParentSolution () const

virtual void	SetIndexInParentSolution (Index indexInParentSolution)

virtual void	SetDiffusionTime (const DiffusionTime &diffusionTime)

virtual DiffusionTime	GetDiffusionTime () const

virtual void	SetDiffusionEffort (const DiffusionEffort &diffusionEffort)

virtual DiffusionEffort	GetDiffusionEffort () const

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

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

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

	Class (const Class &other)

virtual	~Class ()

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

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

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)

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

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

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::EnvironmentDependent< Solution >
	EnvironmentDependent (EnvironmentPointer environment=NULL)

virtual	~EnvironmentDependent ()

virtual EnvironmentPointer	GetEnvironment ()

virtual const EnvironmentPointer	GetEnvironment () const

virtual void	SetEnvironment (EnvironmentPointer environment)

Public Member Functions inherited from bio::physical::Periodic
	Periodic (Milliseconds interval=GetDefaultInterval())

virtual	~Periodic ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual bool	CheckIn ()

virtual Code	SetInterval (Milliseconds interval)

Milliseconds	GetInterval () const

Timestamp	GetTimeLastCrested () const

float	GetIntervalInSeconds () const

virtual void	SetLastCrestTimestamp (Timestamp lastCrest)

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

virtual Properties	GetProperties () const

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

	Class (Pointer< Periodic > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual	~Class ()

virtual Pointer< Periodic >	GetWaveObject ()

virtual Pointer< const Periodic >	GetWaveObject () const

virtual	operator Periodic & ()

virtual	operator const Periodic & () const

virtual Pointer< Wave >	Clone () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions
virtual void	Destructor ()

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

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

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)

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

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

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 Attributes
Pointer< Substance >	mDissolvedSubstance

Pointer< Solute >	mParentSolute

Index	mIndexInParent

DiffusionTime	mDiffusionTime

DiffusionEffort	mDiffusionEffort

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::chemical::EnvironmentDependent< Solution >
EnvironmentPointer	mEnvironment

Protected Attributes inherited from bio::physical::Periodic
Milliseconds	mInterval

Timestamp	mLastCrestTimestamp

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

Friends
class	Solution

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)

Public Types inherited from bio::chemical::EnvironmentDependent< Solution >
typedef type::RemovePointer< Solution >::Type	EnvironmentType

typedef Pointer< EnvironmentType >	EnvironmentPointer

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::physical::Periodic
static Milliseconds	GetDefaultInterval ()

static Properties	GetClassProperties ()

static Symmetry *	MakePeriodicSymmetry ()

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

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)

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)

Detailed Description

Solutes are used to implement shared-pointer style garbage collection.
The idea is that Solutes have a "Concentration" representing their overall abundance. Once the Concentration of a Solute drops to 0, it is destroyed.
The Concentration of a Solute is increased when it becomes available to a novel context (i.e. Solution) through Solution::Efflux (e.g. passed to a function).

Solute is very similar to physical::Linear. However, it is intended to be more user-facing and feature-rich. Where Linear is used to implement shared pointers for Structures, Solute implements shared pointer logic for Solutions. See Solution.h for more info, including the definition of Efflux and Influx.

Solutes can be accessed (Effluxed) in 2 distinct manners. Both manners of Effluxing increase the Concentration of the desired Solute.

When const (read-only) Effluxing, Solutes use a parent-child relationship: only the parent will contain a valid pointer to the Dissolved Substance, each child then points to the parent. This is slower across threads, as each read operation requires a lock, but is faster overall, since the Dissolved Substance doesn't need to be duplicated.
When non-const (read-write & mutable) Effluxing, the Dissolved Substance pointer is SHARED (not cloned) and a parent-child relationship is used to indicate the source Substance. Note: the original design intended for the mutable path to Clone the Dissolved Substance so that it could be modified without mutex locks, but the lock-free clone path is not yet implemented — the shipped code shares mDissolvedSubstance directly via the Solute copy constructor. As a result, concurrent mutable access across threads still requires external synchronisation. When you would like to merge the Solute back into the original Solution, you can Diffuse it, which will call Influx on the parent's Solution, Mixing the Solute with its parent.

DEFERRED (lock-free clone-on-mutable-Efflux): the implementation vehicle now exists — bio::CowPtr< Substance > (inc/bio/chemical/wrapper/CowPtr.h, RFC_COW_WRAPPER). The plan: hold mDissolvedSubstance behind a CowPtr< Substance >; const-Efflux Read()s (shares, as today), mutable-Efflux Write(SubstanceCloner)s (detaches a private clone so it is modified lock-free), and the existing Diffuse -> Influx -> Mix machinery merges the detached clone back into the parent. This is INTENTIONALLY NOT landed in the v7 batch: it CHANGES the mutable-Efflux contract (from "shared, externally synchronised" to "isolated until Diffuse"), which is downstream-visible concurrency semantics and warrants its own RFC + consumer coordination rather than riding the COW/arena ABI cascade. Until then, treat mutable Solutes as shared-pointer access, not copy-on-write.

For mutable Solutes, Diffusion happens automatically when the Solute is destroyed, unless you set SetDiffusionTime(diffusion::time::Never()). You may also set SetDiffusionTime(diffusion::time::Interval()) and SetInterval(...) to regularly Diffuse (this implies diffusion::time::Destruction() too).
The default diffusion::effort is Active(), whereby changes are pushed up the Concentration gradient, toward the source of the Dissolved Substance. However, parents of mutable Solutes can push changes to children using SetDiffusionEffort(diffusion::effort::Passive()) (or ActiveAndPassive()). Passive() Diffusion is only applicable to Solutes which have a diffusion::time::Interval().
You should prefer Active() Diffusion for Solutes with short lifetimes, as it is more efficient and requires less work. Inversely, you should prefer Passive() Diffusion for Solutes that you intend to keep around; this will help keep the system in sync.

When Solutes are Mixed, either through Diffusion or Solution::Influx, they are combined according to their Miscibilities.
See Types.h & Miscibility.h for more info on Mixing strategies.

To illustrate why parent Concentrations are increased when mutable Solutes are Effluxed, if function A uses Solute U1 from Solution V1 and function B also uses U1, even if each function exists in an isolated sub-Solution of V1, both functions will start with the same value. Furthermore, if B depends on modifications to U1 made by A, then having U1 be removed from V1 after A completes would break B.
Thus, by keeping Solutes around when they are not needed by the immediate context allows sub-contexts to depend on the assumption that other, isolated sub-contexts can reach the same values.

Constructor & Destructor Documentation

◆ Solute()

bio::chemical::Solute::Solute	(	Pointer< Substance >	dissolvedSubstance,
		const DiffusionTime &	diffusionTime = `diffusion::time::Destruction()`,
		const DiffusionEffort &	diffusionEffort = `diffusion::effort::Active()`
	)

Constructor for creating a Solute from a Substance.
This is used to create Solutes that are not yet in a Solution.
This is nearly identical to Solution::Dissolve(), except that it does not add the Solute to a Solution.

Parameters

dissolvedSubstance	the Substance to Dissolve.
diffusionTime	the time it takes for this Solute to diffuse.
diffusionEffort	the effort with which this Solute diffuses.

◆ ~Solute()

bio::chemical::Solute::~Solute ( )

virtual

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

bio::chemical::Solute::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR	(	chemical	,
		Solute	,
		filter::Chemical()
	)		const &

Ensure virtual methods point to Class implementations.
Copy constructor.
Adds the newly created Solute to the parent's Solution.
NOTE: const is a lie!

Parameters

other

◆ Crest()

Code bio::chemical::Solute::Crest ( )

virtual

physical::Periodic method.
Only does work if the DiffusionTime is Interval().

Returns: the result of diffusion

Reimplemented from bio::physical::Periodic.

◆ Destructor()

void bio::chemical::Solute::Destructor ( )

protectedvirtual

This is what happens when mConcentration = 0.
We use this instead of the proper destructor method to allow resolution of virtual methods.

◆ Diffuse()

void bio::chemical::Solute::Diffuse ( ) const

virtual

Influx() *this back into the parent Solution, if it exists.

◆ GetConcentration()

Concentration bio::chemical::Solute::GetConcentration ( ) const

virtual

Get the Concentration of *this (i.e. its reference count).

Returns: the mConcentration of *this.

◆ GetDiffusionEffort()

DiffusionEffort bio::chemical::Solute::GetDiffusionEffort ( ) const

virtual

Returns: the diffusion effort of *this.

◆ GetDiffusionTime()

DiffusionTime bio::chemical::Solute::GetDiffusionTime ( ) const

virtual

Returns: the diffusion time of *this.

◆ GetDissolvedSubstance() [1/2]

Pointer< Substance > bio::chemical::Solute::GetDissolvedSubstance ( )

Only applicable if *this is mutable.

Returns: the Substance that was Dissolved to form *this.

◆ GetDissolvedSubstance() [2/2]

Pointer< const Substance > bio::chemical::Solute::GetDissolvedSubstance ( ) const

Returns: the Substance that was Dissolved to form *this.

◆ GetIndexInParentSolution()

Index bio::chemical::Solute::GetIndexInParentSolution ( ) const

virtual

Returns: the Index of *this in its parent Solution.

◆ MixWith() [1/2]

Code bio::chemical::Solute::MixWith ( const Solute & other )

virtual

Combine *this with another Solute.
Uses the Mix Reaction to implement; see Mix.h for more info.
Only *this will be modified.

Parameters

other

Returns: the result of Mixing *this with other.

◆ MixWith() [2/2]

Code bio::chemical::Solute::MixWith ( Pointer< const Substance > other )

virtual

Combine *this with another Substance.
Uses the Mix Reaction to implement; see Mix.h for more info.
Only *this will be modified.

Parameters

other

Returns: the result of Mixing *this with other.

◆ operator Pointer< const Substance >()

bio::chemical::Solute::operator Pointer< const Substance > ( ) const

inline

Returns: the Dissolved Substance of *this.

◆ operator Pointer< Substance >()

bio::chemical::Solute::operator Pointer< Substance > ( )

inline

Only applicable if *this is mutable.

Returns: the Dissolved Substance of *this.

◆ operator=()

Solute & bio::chemical::Solute::operator= ( const Solute & other )

Same as copy ctor.
const is a lie!

Parameters

other

Returns: *this.

◆ SetDiffusionEffort()

void bio::chemical::Solute::SetDiffusionEffort ( const DiffusionEffort & diffusionEffort )

virtual

Set the diffusion effort of *this.
Setting the DiffusionEffort will control how *this is Diffused.
See Diffusion.h for some example values.

Parameters

diffusionEffort

◆ SetDiffusionTime()

void bio::chemical::Solute::SetDiffusionTime ( const DiffusionTime & diffusionTime )

virtual

Set the diffusion time of *this.
Setting the DiffusionTime will control when *this is Diffused.
See Diffusion.h for some example values.

Parameters

diffusionTime

◆ SetEnvironment()

void bio::chemical::Solute::SetEnvironment ( Pointer< Solution > environment )

virtual

Sets the Environment and the Perspective of *this.
Don't let the environment go out of scope or be deleted before *this!

Parameters

environment

◆ SetIndexInParentSolution()

void bio::chemical::Solute::SetIndexInParentSolution ( Index indexInParentSolution )

virtual

Set the Index of *this in its parent Solution.

Parameters

indexInParentSolution

Friends And Related Symbol Documentation

◆ Solution

friend class Solution

friend

Member Data Documentation

◆ mDiffusionEffort

DiffusionEffort bio::chemical::Solute::mDiffusionEffort

protected

◆ mDiffusionTime

DiffusionTime bio::chemical::Solute::mDiffusionTime

protected

◆ mDissolvedSubstance

Pointer< Substance > bio::chemical::Solute::mDissolvedSubstance

protected

The actual pointer to be shared.

◆ mIndexInParent

Index bio::chemical::Solute::mIndexInParent

mutableprotected

◆ mParentSolute

Pointer< Solute > bio::chemical::Solute::mParentSolute

mutableprotected

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

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Solute()

◆ ~Solute()

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR()

◆ Crest()

◆ Destructor()

◆ Diffuse()

◆ GetConcentration()

◆ GetDiffusionEffort()

◆ GetDiffusionTime()

◆ GetDissolvedSubstance() [1/2]

◆ GetDissolvedSubstance() [2/2]

◆ GetIndexInParentSolution()

◆ MixWith() [1/2]

◆ MixWith() [2/2]

◆ operator Pointer< const Substance >()

◆ operator Pointer< Substance >()

◆ operator=()

◆ SetDiffusionEffort()

◆ SetDiffusionTime()

◆ SetEnvironment()

◆ SetIndexInParentSolution()

Friends And Related Symbol Documentation

◆ Solution

Member Data Documentation

◆ mDiffusionEffort

◆ mDiffusionTime

◆ mDissolvedSubstance

◆ mIndexInParent

◆ mParentSolute