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bio::molecular::DNA Class Reference

#include <DNA.h>

+ Inheritance diagram for bio::molecular::DNA:
+ Collaboration diagram for bio::molecular::DNA:

Public Member Functions

 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, DNA) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(molecular
 
& DNAPerspective::Instance ()
 
 filter::Molecular ()) virtual ~DNA()
 
virtual Protein * GetProtein ()
 
virtual const Protein * GetProtein () const
 
virtual StandardDimension GetProteinId () const
 
virtual Version GetVersion ()
 
virtual void SetProtein (Protein *protein)
 
virtual void SetVersion (Version newVersion)
 
- Public Member Functions inherited from bio::molecular::Class< DNA >
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, DNA) Class(DNA *object
 
- Public 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 Attributes

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

Protected Attributes

Protein * m_protein
 
Version m_version
 
- 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
 

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
 
- 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 Attributes inherited from bio::chemical::Elementary< LinearMotif< Surface * > >
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)
 

Detailed Description

DNA allows Proteins to be stored as variables and be Transcribed and Translated later. In order to improve debugging, Proteins store a pointer to their encoding DNA (similar to how a RISC-like mechanism might identify similar mRNA to that with produced the Protein in order to down-regulate its production; for more info, look into RNA Interference). Because Proteins will point back to their parent DNA, we also provide a name and version for each DNA Molecule. This helps to identify Proteins that might be otherwise indistinguishable. NOTE: genetic/Gene.h has most of the DNA interface.

Also note that, in reality, a single allele (Protein*) may result in the production of multiple proteins. That is true here as well; however, that logic is abstracted to a Protein's sub-proteins. In other words if you want 1 DNA Molecule to produce several Proteins, you must Add<Protein*>() those to the Protein in *this.

Definition at line 42 of file DNA.h.

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::molecular::DNA::BIO_DISAMBIGUATE_ALL_CLASS_METHODS ( molecular  ,
DNA   
)

Ensure virtual methods point to Class implementations. Standard ctors. These are easy to use but require setting the Version after instantiation. For example: DNA myAllele = DNA("MyGene"); myAllele.SetVersion(1.0);

◆ DNAPerspective::Instance()

& bio::molecular::DNA::DNAPerspective::Instance ( )

◆ filter::Molecular()

bio::molecular::DNA::filter::Molecular ( )

◆ GetProtein() [1/2]

Protein * bio::molecular::DNA::GetProtein ( )
virtual

See classes in the genetic namespace for proper Translation of Protein.

Returns
the Protein in *this.

Definition at line 46 of file DNA.cpp.

47{
48 return m_protein;
49}
bio::molecular::DNA::m_protein
Protein * m_protein
Definition: DNA.h:105

References m_protein.

Referenced by bio::genetic::Plasmid::GetRNAPolymerase().

◆ GetProtein() [2/2]

const Protein * bio::molecular::DNA::GetProtein ( ) const
virtual

See classes in the genetic namespace for proper Translation of Protein.

Returns
the Protein in *this.

Definition at line 51 of file DNA.cpp.

52{
53 return m_protein;
54}

References m_protein.

◆ GetProteinId()

StandardDimension bio::molecular::DNA::GetProteinId ( ) const
virtual
Returns
the Id of the Protein *this encodes.

Definition at line 56 of file DNA.cpp.

57{
58 BIO_SANITIZE(m_protein, ,
59 return ProteinPerspective::InvalidId());
60 return m_protein->GetId();
61}
BIO_SANITIZE
#define BIO_SANITIZE(test, success, failure)
Definition: SanitizeMacros.h:70

References BIO_SANITIZE, and m_protein.

◆ GetVersion()

Version bio::molecular::DNA::GetVersion ( )
virtual
Returns
the m_version of *this.

Definition at line 63 of file DNA.cpp.

64{
65 return m_version;
66}
bio::molecular::DNA::m_version
Version m_version
Definition: DNA.h:106

References m_version.

◆ SetProtein()

void bio::molecular::DNA::SetProtein ( Protein *  protein)
virtual

Change what *this encodes.

Parameters
protein

Definition at line 73 of file DNA.cpp.

74{
75 m_protein = protein;
76}

References m_protein.

Referenced by bio::genetic::GenomeDefault::GenomeDefault().

◆ SetVersion()

void bio::molecular::DNA::SetVersion ( Version  newVersion)
virtual

Set the Version of *this.

Parameters
newVersion

Definition at line 68 of file DNA.cpp.

69{
70 m_version = newVersion;
71}

References m_version.

Member Data Documentation

◆ DNA

bio::molecular::DNA::DNA

Definition at line 61 of file DNA.h.

◆ m_protein

Protein* bio::molecular::DNA::m_protein
protected

Definition at line 105 of file DNA.h.

Referenced by GetProtein(), GetProteinId(), and SetProtein().

◆ m_version

Version bio::molecular::DNA::m_version
protected

Definition at line 106 of file DNA.h.

Referenced by GetVersion(), and SetVersion().

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