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bio::molecular::Class< T > Class Template Reference

#include <Class.h>

+ Inheritance diagram for bio::molecular::Class< T >:
+ Collaboration diagram for bio::molecular::Class< T >:

Public Member Functions

 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 Attributes

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
 

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
 
- 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 ()
 
- 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

template<typename T>
class bio::molecular::Class< T >

A molecular::Class extends chemical::Class Class in other namespaces will grow to include more complex, templated logic. This pattern prevents you from having to define virtual methods each of your child classes, so long as you always derive from the appropriate Class<T>.

Template Parameters
T

Definition at line 37 of file Class.h.

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

template<typename T >
bio::molecular::Class< T >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS ( chemical  ,
T   
)

Providing just the object should not Initialize anything. For default constructors of virtually inherited classes.

Parameters
object
perspective
filter
symmetryType

Member Data Documentation

◆ filter

template<typename T >
physical::Perspective< StandardDimension > Filter bio::molecular::Class< T >::filter = filter::Default()

Definition at line 57 of file Class.h.

◆ perspective

template<typename T >
physical::Perspective< StandardDimension >* bio::molecular::Class< T >::perspective = NULL

Definition at line 56 of file Class.h.

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