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bio::genetic::GenomeImplementation Member List

This is the complete list of members for bio::genetic::GenomeImplementation, including all inherited members.

UnorderedMotif< Property >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::AbstractMotif()bio::chemical::AbstractMotif
UnorderedMotif< State >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::AbstractMotif()bio::chemical::AbstractMotif
bio::molecular::Molecule::LinearMotif< Surface * >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::AbstractMotif()bio::chemical::AbstractMotif
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::AbstractMotif()bio::chemical::AbstractMotif
bio::genetic::Expressor::LinearMotif< Plasmid * >::AbstractMotif()bio::chemical::AbstractMotif
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::AbstractMotif()bio::chemical::AbstractMotif
Activate(StandardDimension proteinId)bio::genetic::Expressor
Activate(Name proteinName)bio::genetic::Expressor
Activate()bio::genetic::Expressorinline
Add(const T t)bio::chemical::UnorderedStructureInterfaceinline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::AddImplementation(const Property content)bio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::AddImplementation(const State content)bio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::AddImplementation(Surface * content)bio::chemical::LinearMotif< Surface * >inlinevirtual
Class< GenomeImplementation >::UnorderedMotif< Surface * >::AddImplementation(const Surface * content)bio::chemical::UnorderedMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::AddImplementation(const TranscriptionFactor content)bio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::AddImplementation(Plasmid * content)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::UnorderedMotif< Plasmid * >::AddImplementation(const Plasmid * content)bio::chemical::UnorderedMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::AddImplementation(molecular::Protein * content)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::UnorderedMotif< molecular::Protein * >::AddImplementation(const molecular::Protein * content)bio::chemical::UnorderedMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::AddImplementation(Molecule * content)bio::chemical::LinearMotif< Molecule * >inlinevirtual
UnorderedMotif< Molecule * >::AddImplementation(const Molecule * content)bio::chemical::UnorderedMotif< Molecule * >inlinevirtual
AddToTranscriptome(const RNA *toExpress)bio::genetic::Expressorvirtual
As()bio::chemical::Atominline
As() constbio::chemical::Atominline
AsAtom()bio::physical::Waveinlinevirtual
AsAtom() constbio::physical::Waveinlinevirtual
AsBonded()bio::chemical::Atominline
AsBonded() constbio::chemical::Atominline
AsBondedQuantum()bio::chemical::Atominline
AsBondedQuantum() constbio::chemical::Atominline
AssociateType(Id id, Wave *type)bio::physical::Perspective< StandardDimension >inlinevirtual
Class< GenomeImplementation >::bio::AsWave()bio::physical::Class< T >inlinevirtual
Class< GenomeImplementation >::bio::AsWave() constbio::physical::Class< T >inlinevirtual
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::AsWave()bio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::AsWave() constbio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::bio::AsWave()bio::physical::Class< Filterable >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::AsWave() constbio::physical::Class< Filterable >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::Class< Writer >::AsWave()bio::physical::Class< Writer >inlinevirtual
Class< GenomeImplementation >::bio::Class< Writer >::AsWave() constbio::physical::Class< Writer >inlinevirtual
bio::chemical::Atom::AsWave()bio::physical::Class< Atom >inlinevirtual
bio::chemical::Atom::AsWave() constbio::physical::Class< Atom >inlinevirtual
Atom(const Atom &other)bio::chemical::Atomexplicit
Class< GenomeImplementation >::bio::Attenuate(const Wave *other)bio::physical::Wavevirtual
Class< GenomeImplementation >::bio::chemical::Atom::Attenuate(const Wave *other)bio::chemical::Atomvirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::Attenuate(const physical::Wave *other)bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::Attenuate(const physical::Wave *other)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Attenuate(const physical::Wave *other)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::Attenuate(const physical::Wave *other)bio::chemical::LinearMotif< Molecule * >inlinevirtual
BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(chemical, Substance, &SubstancePerspective::Instance(), filter::Chemical()) BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemicalbio::chemical::Substance
BIO_DISAMBIGUATE_ALL_CLASS_METHODS(genetic, GenomeImplementation) GenomeImplementation()bio::genetic::GenomeImplementation
Class< GenomeImplementation >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(molecular, GenomeImplementation) Class(GenomeImplementation *objectbio::genetic::Class< GenomeImplementation >
Class< GenomeImplementation >::bio::molecular::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, T) Class(T *objectbio::molecular::Class< T >
Class< GenomeImplementation >::bio::chemical::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, T) Class(T *objectbio::chemical::Class< T >
Class< GenomeImplementation >::Identifiable< StandardDimension >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspectivebio::physical::Identifiable< StandardDimension >
Class< GenomeImplementation >::bio::log::Writer::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Writer) Writer()bio::log::Writer
Class< GenomeImplementation >::bio::physical::Filterable::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Filterable) Filterable()bio::physical::Filterable
Class< GenomeImplementation >::bio::chemical::Atom::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Atom) explicit Atom()bio::chemical::Atom
Class< GenomeImplementation >::bio::chemical::Substance::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Substance) Class(Substance *objectbio::chemical::Class< Substance >
Class< GenomeImplementation >::bio::chemical::Substance::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Property >) UnorderedMotif()bio::chemical::UnorderedMotif< Property >inline
Class< GenomeImplementation >::Class< UnorderedMotif< Property > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Property >) Class(UnorderedMotif< Property > *objectbio::chemical::Class< UnorderedMotif< Property > >
Class< GenomeImplementation >::bio::chemical::Substance::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< State >) UnorderedMotif()bio::chemical::UnorderedMotif< State >inline
Class< GenomeImplementation >::Class< UnorderedMotif< State > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< State >) Class(UnorderedMotif< State > *objectbio::chemical::Class< UnorderedMotif< State > >
Class< GenomeImplementation >::bio::molecular::Molecule::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(molecular, Molecule) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(molecularbio::molecular::Molecule
Class< GenomeImplementation >::Class< Molecule >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, Molecule) Class(Molecule *objectbio::molecular::Class< Molecule >
Class< GenomeImplementation >::bio::chemical::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, T) Class(T *objectbio::chemical::Class< T >
Class< GenomeImplementation >::LinearMotif< Surface * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, LinearMotif< Surface * >) Class(LinearMotif< Surface * > *objectbio::chemical::Class< LinearMotif< Surface * > >
Class< GenomeImplementation >::LinearMotif< Surface * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Surface * >) UnorderedMotif()bio::chemical::UnorderedMotif< Surface * >inline
Class< GenomeImplementation >::Class< UnorderedMotif< Surface * > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Surface * >) Class(UnorderedMotif< Surface * > *objectbio::chemical::Class< UnorderedMotif< Surface * > >
bio::genetic::Expressor::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(genetic, Expressor) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(geneticbio::genetic::Expressor
bio::Class< Expressor >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(molecular, Expressor) Class(Expressor *objectbio::genetic::Class< Expressor >
bio::molecular::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, T) Class(T *objectbio::molecular::Class< T >
bio::chemical::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, T) Class(T *objectbio::chemical::Class< T >
bio::UnorderedMotif< TranscriptionFactor >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< TranscriptionFactor >) UnorderedMotif()bio::chemical::UnorderedMotif< TranscriptionFactor >inline
bio::Class< UnorderedMotif< TranscriptionFactor > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< TranscriptionFactor >) Class(UnorderedMotif< TranscriptionFactor > *objectbio::chemical::Class< UnorderedMotif< TranscriptionFactor > >
bio::LinearMotif< Plasmid * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, LinearMotif< Plasmid * >) Class(LinearMotif< Plasmid * > *objectbio::chemical::Class< LinearMotif< Plasmid * > >
bio::LinearMotif< Plasmid * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Plasmid * >) UnorderedMotif()bio::chemical::UnorderedMotif< Plasmid * >inline
bio::Class< UnorderedMotif< Plasmid * > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Plasmid * >) Class(UnorderedMotif< Plasmid * > *objectbio::chemical::Class< UnorderedMotif< Plasmid * > >
bio::LinearMotif< molecular::Protein * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, LinearMotif< molecular::Protein * >) Class(LinearMotif< molecular::Protein * > *objectbio::chemical::Class< LinearMotif< molecular::Protein * > >
bio::LinearMotif< molecular::Protein * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< molecular::Protein * >) UnorderedMotif()bio::chemical::UnorderedMotif< molecular::Protein * >inline
bio::Class< UnorderedMotif< molecular::Protein * > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< molecular::Protein * >) Class(UnorderedMotif< molecular::Protein * > *objectbio::chemical::Class< UnorderedMotif< molecular::Protein * > >
bio::molecular::Vesicle::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(molecular, Vesicle) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(molecularbio::molecular::Vesicle
bio::Class< Vesicle >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, Vesicle) Class(Vesicle *objectbio::molecular::Class< Vesicle >
bio::LinearMotif< Molecule * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, LinearMotif< Molecule * >) Class(LinearMotif< Molecule * > *objectbio::chemical::Class< LinearMotif< Molecule * > >
LinearMotif< Molecule * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Molecule * >) UnorderedMotif()bio::chemical::UnorderedMotif< Molecule * >inline
Class< UnorderedMotif< Molecule * > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Molecule * >) Class(UnorderedMotif< Molecule * > *objectbio::chemical::Class< UnorderedMotif< Molecule * > >
Class< GenomeImplementation >::BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS(chemical, LinearMotif< Surface * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physicalbio::chemical::LinearMotif< Surface * >
bio::genetic::Expressor::LinearMotif< Plasmid * >::BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS(chemical, LinearMotif< Plasmid * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physicalbio::chemical::LinearMotif< Plasmid * >
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS(chemical, LinearMotif< molecular::Protein * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physicalbio::chemical::LinearMotif< molecular::Protein * >
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS(chemical, LinearMotif< Molecule * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physicalbio::chemical::LinearMotif< Molecule * >
BreakBond(T toDisassociate, BondType type=bond_type::Unknown())bio::chemical::Atominline
BreakBondImplementation(Wave *toDisassociate, AtomicNumber id, BondType type)bio::chemical::Atomprotectedvirtual
CacheProteins()bio::genetic::GenomeImplementationvirtual
Class< GenomeImplementation >::bio::Class< GenomeImplementation >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::Class(Identifiable< StandardDimension > *object, Symmetry *symmetry=NULL)bio::physical::Class< Identifiable< StandardDimension > >inline
Class< GenomeImplementation >::bio::log::Writer::bio::Class(Filterable *object, Symmetry *symmetry=NULL)bio::physical::Class< Filterable >inline
Class< GenomeImplementation >::bio::log::Writer::Class< Writer >::Class(Writer *object, Symmetry *symmetry=NULL)bio::physical::Class< Writer >inline
Class< GenomeImplementation >::bio::chemical::Atom::Class(Atom *object, Symmetry *symmetry=NULL)bio::physical::Class< Atom >inline
bio::chemical::Substance::Class< Substance >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::chemical::Substance::UnorderedMotif< State >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::molecular::Molecule::Class< Molecule >::bio::Class< Molecule >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::molecular::Molecule::LinearMotif< Surface * >::Class< LinearMotif< Surface * > >::bio::Class< LinearMotif< Surface * > >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::genetic::Expressor::Class< Expressor >::bio::Class< Expressor >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::Class< LinearMotif< Plasmid * > >::bio::Class< LinearMotif< Plasmid * > >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif< Plasmid * >::bio::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Class< LinearMotif< molecular::bio::Class< LinearMotif< molecular::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif< molecular::Protein * >::bio::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
Clear()bio::chemical::UnorderedStructureInterfaceinline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::ClearImplementation()bio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::ClearImplementation()bio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::ClearImplementation()bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::ClearImplementation()bio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::ClearImplementation()bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::ClearImplementation()bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::ClearImplementation()bio::chemical::LinearMotif< Molecule * >inlinevirtual
Class< GenomeImplementation >::bio::Clone() constbio::physical::Class< T >inlinevirtual
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::Clone() constbio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::bio::Clone() constbio::physical::Class< Filterable >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::Class< Writer >::Clone() constbio::physical::Class< Writer >inlinevirtual
bio::chemical::Atom::Clone() constbio::physical::Class< Atom >inlinevirtual
CloneIntoName(Name name)bio::physical::Identifiable< StandardDimension >inline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::Contents typedefbio::chemical::UnorderedMotif< Property >
Class< GenomeImplementation >::bio::UnorderedMotif< State >::Contents typedefbio::chemical::UnorderedMotif< State >
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::Contents typedefbio::chemical::LinearMotif< Surface * >
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::Contents typedefbio::chemical::UnorderedMotif< TranscriptionFactor >
bio::genetic::Expressor::LinearMotif< Plasmid * >::Contents typedefbio::chemical::LinearMotif< Plasmid * >
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Contents typedefbio::chemical::LinearMotif< molecular::Protein * >
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::Contents typedefbio::chemical::LinearMotif< Molecule * >
Class< GenomeImplementation >::bio::Class< GenomeImplementation >::Convert(Wave *wave)bio::physical::Class< T >inline
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::Convert(Wave *wave)bio::physical::Class< Identifiable< StandardDimension > >inline
Class< GenomeImplementation >::bio::log::Writer::bio::Convert(Wave *wave)bio::physical::Class< Filterable >inline
Class< GenomeImplementation >::bio::log::Writer::Class< Writer >::Convert(Wave *wave)bio::physical::Class< Writer >inline
Class< GenomeImplementation >::bio::chemical::Atom::Convert(Wave *wave)bio::physical::Class< Atom >inline
bio::chemical::Substance::Class< Substance >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Convert(Wave *wave)bio::physical::Class< T >inline
bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Convert(Wave *wave)bio::physical::Class< T >inline
bio::chemical::Substance::UnorderedMotif< State >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Convert(Wave *wave)bio::physical::Class< T >inline
bio::molecular::Molecule::Class< Molecule >::bio::Class< Molecule >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Convert(Wave *wave)bio::physical::Class< T >inline
bio::molecular::Molecule::LinearMotif< Surface * >::Class< LinearMotif< Surface * > >::bio::Class< LinearMotif< Surface * > >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Convert(Wave *wave)bio::physical::Class< T >inline
bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Convert(Wave *wave)bio::physical::Class< T >inline
bio::genetic::Expressor::Class< Expressor >::bio::Class< Expressor >::Convert(Wave *wave)bio::physical::Class< T >inline
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::Convert(Wave *wave)bio::physical::Class< T >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::Class< LinearMotif< Plasmid * > >::bio::Class< LinearMotif< Plasmid * > >::Convert(Wave *wave)bio::physical::Class< T >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif< Plasmid * >::bio::Convert(Wave *wave)bio::physical::Class< T >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Class< LinearMotif< molecular::bio::Class< LinearMotif< molecular::Convert(Wave *wave)bio::physical::Class< T >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif< molecular::Protein * >::bio::Convert(Wave *wave)bio::physical::Class< T >inline
Class< GenomeImplementation >::CreateImplementation(StandardDimension id)bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::CreateImplementation(StandardDimension id)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::CreateImplementation(StandardDimension id)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::CreateImplementation(StandardDimension id)bio::chemical::LinearMotif< Molecule * >inlinevirtual
Define(Name varName)bio::molecular::Moleculeinline
Define(Name varName)bio::molecular::Moleculeinline
Define(Name varName, const T &assignment)bio::molecular::Moleculeinline
Demodulate()bio::physical::Wavevirtual
Demodulate() constbio::physical::Wavevirtual
Disable()bio::chemical::Substancevirtual
DisassociateType(Id id)bio::physical::Perspective< StandardDimension >inlinevirtual
Class< GenomeImplementation >::bio::Disattenuate(const Wave *other)bio::physical::Wavevirtual
Class< GenomeImplementation >::bio::chemical::Atom::Disattenuate(const Wave *other)bio::chemical::Atomvirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::Disattenuate(const physical::Wave *other)bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::Disattenuate(const physical::Wave *other)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Disattenuate(const physical::Wave *other)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::Disattenuate(const physical::Wave *other)bio::chemical::LinearMotif< Molecule * >inlinevirtual
DuplicateFrom(Molecule *source, Name surface)bio::molecular::Moleculevirtual
Class< GenomeImplementation >::Elementary(const Properties properties)bio::chemical::Elementary< LinearMotif< Surface * > >inline
Class< GenomeImplementation >::Elementary()bio::chemical::Elementary< LinearMotif< Surface * > >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::Elementary(const Properties properties)bio::chemical::Elementary< LinearMotif< Plasmid * > >inline
bio::LinearMotif< Plasmid * >::Elementary()bio::chemical::Elementary< LinearMotif< Plasmid * > >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Elementary(const Properties properties)bio::chemical::Elementary< LinearMotif< molecular::Protein * > >inline
bio::LinearMotif< molecular::Protein * >::Elementary()bio::chemical::Elementary< LinearMotif< molecular::Protein * > >inline
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::Elementary(const Properties properties)bio::chemical::Elementary< LinearMotif< Molecule * > >inline
LinearMotif< Molecule * >::Elementary()bio::chemical::Elementary< LinearMotif< Molecule * > >inline
Enable()bio::chemical::Substancevirtual
ExpressGenes()bio::genetic::Expressorvirtual
Expressorbio::genetic::Expressor
ExternalLog(Filter logFilter, Level level, const char *format,...) constbio::log::Writer
FetchPlasmid(StandardDimension plasmidId)bio::genetic::GenomeImplementationvirtual
FetchPlasmid(Name plasmidName)bio::genetic::GenomeImplementationvirtual
Class< GenomeImplementation >::bio::Class< GenomeImplementation >::filterbio::molecular::Class< T >
Class< GenomeImplementation >::bio::molecular::Molecule::Class< Molecule >::filterbio::molecular::Class< Molecule >
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::Class< LinearMotif< Surface * > >::filterbio::chemical::Class< LinearMotif< Surface * > >
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::filterbio::chemical::Class< UnorderedMotif< Surface * > >
bio::genetic::Expressor::Class< Expressor >::bio::filterbio::molecular::Class< T >
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::filterbio::chemical::Class< UnorderedMotif< TranscriptionFactor > >
bio::genetic::Expressor::LinearMotif< Plasmid * >::Class< LinearMotif< Plasmid * > >::filterbio::chemical::Class< LinearMotif< Plasmid * > >
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif< Plasmid * >::filterbio::chemical::Class< UnorderedMotif< Plasmid * > >
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Class< LinearMotif< molecular::filterbio::chemical::Class< LinearMotif< molecular::Protein * > >
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif< molecular::Protein * >::filterbio::chemical::Class< UnorderedMotif< molecular::Protein * > >
bio::genetic::Expressor::bio::molecular::Vesicle::Class< Vesicle >::filterbio::molecular::Class< Vesicle >
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::Class< LinearMotif< Molecule * > >::filterbio::chemical::Class< LinearMotif< Molecule * > >
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::UnorderedMotif< Molecule * >::filterbio::chemical::Class< UnorderedMotif< Molecule * > >
filter::Genetic()) virtual ~Expressor()bio::genetic::Expressor
Class< GenomeImplementation >::filter::Molecular()) Molecule(const Molecule &toCopy)bio::molecular::Molecule
bio::genetic::Expressor::bio::molecular::Vesicle::filter::Molecular()) Vesicle(const Vesicle &toCopy)bio::molecular::Vesicle
Filterable(Filter filter)bio::physical::Filterable
Find(Id id)bio::physical::Perspective< StandardDimension >inline
Find(Id id) constbio::physical::Perspective< StandardDimension >inline
ForEach(ExcitationBase *excitation)bio::chemical::LinearStructureInterfaceinline
Class< GenomeImplementation >::ForEachImplementation(ExcitationBase *excitation)bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::ForEachImplementation(ExcitationBase *excitation)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::ForEachImplementation(ExcitationBase *excitation)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::ForEachImplementation(ExcitationBase *excitation)bio::chemical::LinearMotif< Molecule * >inlinevirtual
FormBond(T toBond, BondType type=bond_type::Unknown())bio::chemical::Atominline
FormBondImplementation(Wave *toBond, AtomicNumber id, BondType type)bio::chemical::Atomprotectedvirtual
GetAll()bio::chemical::UnorderedStructureInterfaceinline
GetAll() constbio::chemical::UnorderedStructureInterfaceinline
GetAllAsVector()bio::chemical::UnorderedStructureInterfaceinline
GetAllAsVector() constbio::chemical::UnorderedStructureInterfaceinline
GetAllBonds()bio::chemical::Atom
GetAllBonds() constbio::chemical::Atom
GetAllImplementation()bio::chemical::AbstractMotifvirtual
GetAllImplementation() constbio::chemical::AbstractMotifvirtual
GetBonded(Valence position)bio::chemical::Atom
GetBonded(Valence position) constbio::chemical::Atom
GetBondPosition(AtomicNumber bondedId) constbio::chemical::Atom
GetBondPosition(Name typeName) constbio::chemical::Atom
GetBondPosition() constbio::chemical::Atominline
GetBondType(Valence position) constbio::chemical::Atom
GetBondType() constbio::chemical::Atominline
GetById(StandardDimension id)bio::chemical::LinearStructureInterfaceinline
GetById(StandardDimension id) constbio::chemical::LinearStructureInterfaceinline
Class< GenomeImplementation >::GetByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< Surface * >inlinevirtual
Class< GenomeImplementation >::GetByIdImplementation(StandardDimension id) constbio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::LinearMotif< Plasmid * >::GetByIdImplementation(StandardDimension id) constbio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::LinearMotif< molecular::Protein * >::GetByIdImplementation(StandardDimension id) constbio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< Molecule * >inlinevirtual
LinearMotif< Molecule * >::GetByIdImplementation(StandardDimension id) constbio::chemical::LinearMotif< Molecule * >inlinevirtual
GetByName(Name name)bio::chemical::LinearStructureInterfaceinline
GetByName(Name name) constbio::chemical::LinearStructureInterfaceinline
Class< GenomeImplementation >::GetByNameImplementation(Name name)bio::chemical::LinearMotif< Surface * >inlinevirtual
Class< GenomeImplementation >::GetByNameImplementation(Name name) constbio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetByNameImplementation(Name name)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::LinearMotif< Plasmid * >::GetByNameImplementation(Name name) constbio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetByNameImplementation(Name name)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::LinearMotif< molecular::Protein * >::GetByNameImplementation(Name name) constbio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetByNameImplementation(Name name)bio::chemical::LinearMotif< Molecule * >inlinevirtual
LinearMotif< Molecule * >::GetByNameImplementation(Name name) constbio::chemical::LinearMotif< Molecule * >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::GetClassProperties()bio::chemical::AbstractMotifstatic
Class< GenomeImplementation >::bio::UnorderedMotif< State >::GetClassProperties()bio::chemical::AbstractMotifstatic
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::GetClassProperties()bio::chemical::LinearMotif< Surface * >inlinestatic
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetClassProperties()bio::chemical::LinearMotif< Plasmid * >inlinestatic
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetClassProperties()bio::chemical::LinearMotif< molecular::Protein * >inlinestatic
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetClassProperties()bio::chemical::LinearMotif< Molecule * >inlinestatic
GetCount() constbio::chemical::UnorderedStructureInterfaceinline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::GetCountImplementation() constbio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::GetCountImplementation() constbio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::GetCountImplementation() constbio::chemical::UnorderedMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::GetCountImplementation() constbio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetCountImplementation() constbio::chemical::UnorderedMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetCountImplementation() constbio::chemical::UnorderedMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetCountImplementation() constbio::chemical::UnorderedMotif< Molecule * >inlinevirtual
GetFilter() constbio::physical::Filterable
GetIdFromName(Name name)bio::physical::Perspective< StandardDimension >inlinevirtual
GetIdWithoutCreation(Name name) constbio::physical::Perspective< StandardDimension >inlinevirtual
GetLogEngine()bio::log::Writer
GetLogEngine() constbio::log::Writer
GetNameFromId(Id id) constbio::physical::Perspective< StandardDimension >inlinevirtual
GetNewObjectFromId(Id id) constbio::physical::Perspective< StandardDimension >inlinevirtual
GetNewObjectFromIdAs(Id id)bio::physical::Perspective< StandardDimension >inline
GetNewObjectFromName(Name name)bio::physical::Perspective< StandardDimension >inlinevirtual
GetNewObjectFromNameAs(Name name)bio::physical::Perspective< StandardDimension >inline
GetNumMatching(const Container *other) constbio::chemical::UnorderedStructureInterfaceinline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::GetNumMatchingImplementation(const Container *other) constbio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::GetNumMatchingImplementation(const Container *other) constbio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::GetNumMatchingImplementation(const Container *other) constbio::chemical::UnorderedMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::GetNumMatchingImplementation(const Container *other) constbio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetNumMatchingImplementation(const Container *other) constbio::chemical::UnorderedMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetNumMatchingImplementation(const Container *other) constbio::chemical::UnorderedMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetNumMatchingImplementation(const Container *other) constbio::chemical::UnorderedMotif< Molecule * >inlinevirtual
GetNumUsedIds() constbio::physical::Perspective< StandardDimension >inlinevirtual
GetOrCreateById(StandardDimension id)bio::chemical::LinearStructureInterfaceinline
Class< GenomeImplementation >::GetOrCreateByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetOrCreateByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetOrCreateByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetOrCreateByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< Molecule * >inlinevirtual
GetOrCreateByName(Name name)bio::chemical::LinearStructureInterfaceinline
Class< GenomeImplementation >::GetOrCreateByNameImplementation(Name name)bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetOrCreateByNameImplementation(Name name)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetOrCreateByNameImplementation(Name name)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetOrCreateByNameImplementation(Name name)bio::chemical::LinearMotif< Molecule * >inlinevirtual
GetPerspective() constbio::physical::Observer< Perspective< StandardDimension > >inlinevirtual
GetProperties() constbio::physical::Wavevirtual
bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
Class< Writer >::bio::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
Class< Writer >::bio::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
Class< Writer >::bio::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
bio::chemical::Atom::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
bio::chemical::Atom::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
bio::chemical::Atom::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
Class< Substance >::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
Class< Substance >::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
Class< Substance >::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
UnorderedMotif< Property >::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
UnorderedMotif< Property >::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
UnorderedMotif< Property >::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
UnorderedMotif< State >::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
UnorderedMotif< State >::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
UnorderedMotif< State >::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
bio::molecular::Molecule::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
bio::molecular::Molecule::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
bio::molecular::Molecule::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
LinearMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
LinearMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
LinearMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
UnorderedMotif< Surface * >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
UnorderedMotif< Surface * >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
UnorderedMotif< Surface * >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
bio::genetic::Expressor::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
bio::genetic::Expressor::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
bio::genetic::Expressor::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
UnorderedMotif< TranscriptionFactor >::bio::bio::bio::bio::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
UnorderedMotif< TranscriptionFactor >::bio::bio::bio::bio::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
UnorderedMotif< TranscriptionFactor >::bio::bio::bio::bio::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
LinearMotif< Plasmid * >::bio::bio::bio::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
LinearMotif< Plasmid * >::bio::bio::bio::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
LinearMotif< Plasmid * >::bio::bio::bio::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
UnorderedMotif< Plasmid * >::bio::bio::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
UnorderedMotif< Plasmid * >::bio::bio::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
UnorderedMotif< Plasmid * >::bio::bio::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
LinearMotif< molecular::Protein * >::bio::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
LinearMotif< molecular::Protein * >::bio::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
LinearMotif< molecular::Protein * >::bio::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
UnorderedMotif< molecular::Protein * >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
UnorderedMotif< molecular::Protein * >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
UnorderedMotif< molecular::Protein * >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
GetStringFrom(std::string separator=", ")bio::chemical::UnorderedStructureInterfaceinline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::GetStringFromImplementation(std::string separator=", ")bio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::GetStringFromImplementation(std::string separator=", ")bio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::GetStringFromImplementation(std::string separator=", ")bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::GetStringFromImplementation(std::string separator=", ")bio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetStringFromImplementation(std::string separator=", ")bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetStringFromImplementation(std::string separator=", ")bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetStringFromImplementation(std::string separator=", ")bio::chemical::LinearMotif< Molecule * >inlinevirtual
Class< GenomeImplementation >::GetStructuralPerspective()bio::chemical::LinearMotif< Surface * >inline
Class< GenomeImplementation >::GetStructuralPerspective() constbio::chemical::LinearMotif< Surface * >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::GetStructuralPerspective()bio::chemical::LinearMotif< Plasmid * >inline
bio::LinearMotif< Plasmid * >::GetStructuralPerspective() constbio::chemical::LinearMotif< Plasmid * >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::GetStructuralPerspective()bio::chemical::LinearMotif< molecular::Protein * >inline
bio::LinearMotif< molecular::Protein * >::GetStructuralPerspective() constbio::chemical::LinearMotif< molecular::Protein * >inline
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::GetStructuralPerspective()bio::chemical::LinearMotif< Molecule * >inline
LinearMotif< Molecule * >::GetStructuralPerspective() constbio::chemical::LinearMotif< Molecule * >inline
GetTypeFromId(Id id) constbio::physical::Perspective< StandardDimension >inlinevirtual
GetTypeFromIdAs(Id id) constbio::physical::Perspective< StandardDimension >inline
GetTypeFromName(Name name) constbio::physical::Perspective< StandardDimension >inlinevirtual
GetTypeFromNameAs(Name name) constbio::physical::Perspective< StandardDimension >inline
GetUniqueIdFor(Name name)bio::physical::Perspective< StandardDimension >inlinevirtual
Hadits typedefbio::physical::Perspective< StandardDimension >
Has(T content) constbio::chemical::UnorderedStructureInterfaceinline
HasAll(const Container *contents) constbio::chemical::UnorderedStructureInterfaceinline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::HasAllImplementation(const Container *contents) constbio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::HasAllImplementation(const Container *contents) constbio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::HasAllImplementation(const Container *contents) constbio::chemical::UnorderedMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::HasAllImplementation(const Container *contents) constbio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::HasAllImplementation(const Container *contents) constbio::chemical::UnorderedMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::HasAllImplementation(const Container *contents) constbio::chemical::UnorderedMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::HasAllImplementation(const Container *contents) constbio::chemical::UnorderedMotif< Molecule * >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::HasImplementation(const Property content) constbio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::HasImplementation(const State content) constbio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::HasImplementation(const Surface * &content) constbio::chemical::LinearMotif< Surface * >inlinevirtual
Class< GenomeImplementation >::UnorderedMotif< Surface * >::HasImplementation(const Surface * content) constbio::chemical::UnorderedMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::HasImplementation(const TranscriptionFactor content) constbio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::HasImplementation(const Plasmid * &content) constbio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::UnorderedMotif< Plasmid * >::HasImplementation(const Plasmid * content) constbio::chemical::UnorderedMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::HasImplementation(const molecular::Protein * &content) constbio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::UnorderedMotif< molecular::Protein * >::HasImplementation(const molecular::Protein * content) constbio::chemical::UnorderedMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::HasImplementation(const Molecule * &content) constbio::chemical::LinearMotif< Molecule * >inlinevirtual
UnorderedMotif< Molecule * >::HasImplementation(const Molecule * content) constbio::chemical::UnorderedMotif< Molecule * >inlinevirtual
HasLogEngine() constbio::log::Writer
Class< GenomeImplementation >::hasRegisteredbio::chemical::Elementary< LinearMotif< Surface * > >static
bio::genetic::Expressor::LinearMotif< Plasmid * >::hasRegisteredbio::chemical::Elementary< LinearMotif< Plasmid * > >static
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::hasRegisteredbio::chemical::Elementary< LinearMotif< molecular::Protein * > >static
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::hasRegisteredbio::chemical::Elementary< LinearMotif< Molecule * > >static
Class< GenomeImplementation >::bio::Id typedefbio::physical::Identifiable< StandardDimension >
bio::molecular::Molecule::Perspective< StandardDimension >::Id typedefbio::physical::Perspective< StandardDimension >
Class< GenomeImplementation >::bio::Ids typedefbio::physical::Identifiable< StandardDimension >
bio::molecular::Molecule::Perspective< StandardDimension >::Ids typedefbio::physical::Perspective< StandardDimension >
Import(const UnorderedMotif< T > *other)bio::chemical::UnorderedStructureInterfaceinline
Import(const std::vector< T > &other)bio::chemical::UnorderedStructureInterfaceinline
ImportAll(const physical::Wave *other)bio::chemical::UnorderedStructureInterfaceinline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::ImportImplementation(const UnorderedMotif< Property > *other)bio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::bio::chemical::AbstractMotif::ImportImplementation(const void *other)bio::chemical::AbstractMotifinlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::ImportImplementation(const UnorderedMotif< State > *other)bio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::ImportImplementation(const LinearMotif< Surface * > *other)bio::chemical::LinearMotif< Surface * >inlinevirtual
Class< GenomeImplementation >::UnorderedMotif< Surface * >::ImportImplementation(const UnorderedMotif< Surface * > *other)bio::chemical::UnorderedMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::ImportImplementation(const UnorderedMotif< TranscriptionFactor > *other)bio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::ImportImplementation(const LinearMotif< Plasmid * > *other)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::UnorderedMotif< Plasmid * >::ImportImplementation(const UnorderedMotif< Plasmid * > *other)bio::chemical::UnorderedMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::ImportImplementation(const LinearMotif< molecular::Protein * > *other)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::UnorderedMotif< molecular::Protein * >::ImportImplementation(const UnorderedMotif< molecular::Protein * > *other)bio::chemical::UnorderedMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::ImportImplementation(const LinearMotif< Molecule * > *other)bio::chemical::LinearMotif< Molecule * >inlinevirtual
UnorderedMotif< Molecule * >::ImportImplementation(const UnorderedMotif< Molecule * > *other)bio::chemical::UnorderedMotif< Molecule * >inlinevirtual
Initialize(ByteStreams args)bio::VirtualBaseprotected
Initialize(ByteStream arg1)bio::VirtualBaseprotected
Initialize(ByteStream arg1, ByteStream arg2)bio::VirtualBaseprotected
Initialize(ByteStream arg1, ByteStream arg2, ByteStream arg3)bio::VirtualBaseprotected
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::InitializeImplementation(ByteStreams args)bio::physical::Observer< Perspective< StandardDimension > >inlineprotectedvirtual
bio::log::Writer::InitializeImplementation(ByteStreams args)bio::log::Writerprotectedvirtual
Insert(T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)bio::chemical::LinearStructureInterfaceinline
Class< GenomeImplementation >::InsertImplementation(Surface * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::InsertImplementation(Plasmid * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::InsertImplementation(molecular::Protein * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::InsertImplementation(Molecule * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)bio::chemical::LinearMotif< Molecule * >inlinevirtual
InvalidId()bio::physical::Perspective< StandardDimension >inlinestatic
InvalidName()bio::physical::Perspective< StandardDimension >inlinestatic
IsEnabled() constbio::chemical::Substancevirtual
Class< GenomeImplementation >::LinearMotif(physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< Surface * >inlineexplicit
Class< GenomeImplementation >::LinearMotif(const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< Surface * >inlineexplicit
Class< GenomeImplementation >::LinearMotif(const LinearMotif< Surface * > &toCopy)bio::chemical::LinearMotif< Surface * >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::LinearMotif(physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< Plasmid * >inlineexplicit
bio::LinearMotif< Plasmid * >::LinearMotif(const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< Plasmid * >inlineexplicit
bio::LinearMotif< Plasmid * >::LinearMotif(const LinearMotif< Plasmid * > &toCopy)bio::chemical::LinearMotif< Plasmid * >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::LinearMotif(physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< molecular::Protein * >inlineexplicit
bio::LinearMotif< molecular::Protein * >::LinearMotif(const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< molecular::Protein * >inlineexplicit
bio::LinearMotif< molecular::Protein * >::LinearMotif(const LinearMotif< molecular::Protein * > &toCopy)bio::chemical::LinearMotif< molecular::Protein * >inline
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::LinearMotif(physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< Molecule * >inlineexplicit
LinearMotif< Molecule * >::LinearMotif(const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< Molecule * >inlineexplicit
LinearMotif< Molecule * >::LinearMotif(const LinearMotif< Molecule * > &toCopy)bio::chemical::LinearMotif< Molecule * >inline
LinearStructureInterface()bio::chemical::LinearStructureInterfaceinline
Class< GenomeImplementation >::LockThread() constbio::ThreadSafe
bio::ThreadSafe::LockThread() constbio::ThreadSafe
Log(Level level, const char *format,...) constbio::log::Writerprotected
m_bondsbio::chemical::Atomprotected
UnorderedMotif< Property >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_contentsbio::chemical::AbstractMotifmutableprotected
UnorderedMotif< State >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_contentsbio::chemical::AbstractMotifmutableprotected
bio::molecular::Molecule::LinearMotif< Surface * >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_contentsbio::chemical::AbstractMotifmutableprotected
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::m_contentsbio::chemical::AbstractMotifmutableprotected
bio::genetic::Expressor::LinearMotif< Plasmid * >::m_contentsbio::chemical::AbstractMotifmutableprotected
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::m_contentsbio::chemical::AbstractMotifmutableprotected
m_filterbio::physical::Filterableprotected
m_haditsbio::physical::Perspective< StandardDimension >protected
m_hasBeenInitializedbio::VirtualBaseprotected
m_idbio::physical::Identifiable< StandardDimension >
m_nextIdbio::physical::Perspective< StandardDimension >protected
Class< GenomeImplementation >::bio::Class< GenomeImplementation >::m_objectbio::physical::Class< T >protected
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::m_objectbio::physical::Class< Identifiable< StandardDimension > >protected
Class< GenomeImplementation >::bio::log::Writer::bio::m_objectbio::physical::Class< Filterable >protected
Class< GenomeImplementation >::bio::log::Writer::Class< Writer >::m_objectbio::physical::Class< Writer >protected
Class< GenomeImplementation >::bio::chemical::Atom::m_objectbio::physical::Class< Atom >protected
bio::chemical::Substance::Class< Substance >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_objectbio::physical::Class< T >protected
bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_objectbio::physical::Class< T >protected
bio::chemical::Substance::UnorderedMotif< State >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_objectbio::physical::Class< T >protected
bio::molecular::Molecule::Class< Molecule >::bio::Class< Molecule >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_objectbio::physical::Class< T >protected
bio::molecular::Molecule::LinearMotif< Surface * >::Class< LinearMotif< Surface * > >::bio::Class< LinearMotif< Surface * > >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_objectbio::physical::Class< T >protected
bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_objectbio::physical::Class< T >protected
bio::genetic::Expressor::Class< Expressor >::bio::Class< Expressor >::m_objectbio::physical::Class< T >protected
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::m_objectbio::physical::Class< T >protected
bio::genetic::Expressor::LinearMotif< Plasmid * >::Class< LinearMotif< Plasmid * > >::bio::Class< LinearMotif< Plasmid * > >::m_objectbio::physical::Class< T >protected
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif< Plasmid * >::bio::m_objectbio::physical::Class< T >protected
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Class< LinearMotif< molecular::bio::Class< LinearMotif< molecular::m_objectbio::physical::Class< T >protected
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif< molecular::Protein * >::bio::m_objectbio::physical::Class< T >protected
Class< GenomeImplementation >::m_perspectivebio::chemical::LinearMotif< Surface * >
bio::genetic::Expressor::LinearMotif< Plasmid * >::m_perspectivebio::chemical::LinearMotif< Plasmid * >
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::m_perspectivebio::chemical::LinearMotif< molecular::Protein * >
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::m_perspectivebio::chemical::LinearMotif< Molecule * >
bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::log::Writer::Class< Writer >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::chemical::Atom::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::chemical::Substance::Class< Substance >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::chemical::Substance::UnorderedMotif< State >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::molecular::Molecule::bio::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::molecular::Molecule::LinearMotif< Surface * >::bio::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_signalbio::physical::Waveprotected
bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::m_signalbio::physical::Waveprotected
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::m_signalbio::physical::Waveprotected
bio::genetic::Expressor::LinearMotif< Plasmid * >::bio::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::m_signalbio::physical::Waveprotected
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif< Plasmid * >::bio::m_signalbio::physical::Waveprotected
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::bio::Class< LinearMotif< molecular::Class< LinearMotif< molecular::Class< LinearMotif< molecular::Class< LinearMotif< molecular::m_signalbio::physical::Waveprotected
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif< molecular::Protein * >::bio::m_signalbio::physical::Waveprotected
bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::log::Writer::Class< Writer >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::chemical::Atom::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::chemical::Substance::Class< Substance >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::chemical::Substance::UnorderedMotif< State >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::molecular::Molecule::bio::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::molecular::Molecule::LinearMotif< Surface * >::bio::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::m_symmetrybio::physical::Waveprotected
bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::m_symmetrybio::physical::Waveprotected
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::m_symmetrybio::physical::Waveprotected
bio::genetic::Expressor::LinearMotif< Plasmid * >::bio::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::m_symmetrybio::physical::Waveprotected
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif< Plasmid * >::bio::m_symmetrybio::physical::Waveprotected
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::bio::Class< LinearMotif< molecular::Class< LinearMotif< molecular::Class< LinearMotif< molecular::Class< LinearMotif< molecular::m_symmetrybio::physical::Waveprotected
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif< molecular::Protein * >::bio::m_symmetrybio::physical::Waveprotected
m_transcriptomebio::genetic::Expressorprotected
mc_fetchPlasmidbio::genetic::GenomeImplementationprotected
mc_fetchSitebio::genetic::GenomeImplementationprotected
mc_idSitebio::genetic::GenomeImplementationprotected
mc_nameSitebio::genetic::GenomeImplementationprotected
mc_registerPlasmidbio::genetic::GenomeImplementationprotected
mc_registrationSitebio::genetic::GenomeImplementationprotected
Modulate(Wave *signal)bio::physical::Wavevirtual
molecular::VesiclePerspective::Instance()bio::genetic::Expressor
Moleculebio::molecular::Molecule
MoleculePerspective::Instance()bio::molecular::Molecule
Observer(Perspective *perspective=NULL)bio::physical::Observer< Perspective< StandardDimension > >inlineexplicit
Observer(const Observer &other)bio::physical::Observer< Perspective< StandardDimension > >inline
operator Atom *()bio::physical::Class< Atom >inlinevirtual
operator Filterable *()bio::physical::Class< Filterable >inlinevirtual
operator Identifiable< StandardDimension > *()bio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
operator T()bio::chemical::Atominline
operator T*()bio::physical::Class< T >inlinevirtual
Class< GenomeImplementation >::bio::operator Wave *()bio::physical::Class< T >inlinevirtual
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::operator Wave *()bio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::bio::operator Wave *()bio::physical::Class< Filterable >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::Class< Writer >::operator Wave *()bio::physical::Class< Writer >inlinevirtual
bio::chemical::Atom::operator Wave *()bio::physical::Class< Atom >inlinevirtual
operator Writer *()bio::physical::Class< Writer >inlinevirtual
operator()(StandardDimension surfaceId)bio::molecular::Moleculevirtual
operator()(StandardDimension surfaceId) constbio::molecular::Moleculevirtual
operator()(StandardDimension surfaceId)bio::molecular::Moleculeinline
operator()(Name name)bio::molecular::Moleculevirtual
operator()(Name name) constbio::molecular::Moleculevirtual
operator()(Name surfaceName)bio::molecular::Moleculeinline
operator*(Wave *signal)bio::physical::Wavevirtual
operator*()bio::physical::Wavevirtual
operator*() constbio::physical::Wavevirtual
operator+(const Wave *other)bio::physical::Wavevirtual
operator-(const Wave *other)bio::physical::Wavevirtual
operator<<(Surface *source)bio::molecular::Moleculevirtual
operator<<(Molecule *source)bio::molecular::Moleculevirtual
operator<<=(Vesicle *source)bio::molecular::Vesiclevirtual
operator>>(Surface *target)bio::molecular::Moleculevirtual
operator>>(Molecule *target)bio::molecular::Moleculevirtual
operator>>=(Vesicle *target)bio::molecular::Vesiclevirtual
operator[](StandardDimension moleculeId)bio::molecular::Vesiclevirtual
operator[](StandardDimension moleculeId) constbio::molecular::Vesiclevirtual
operator[](StandardDimension moleculeId)bio::molecular::Vesicleinline
operator[](Name moleculeName)bio::molecular::Vesiclevirtual
operator[](Name moleculeName) constbio::molecular::Vesiclevirtual
operator[](Name moleculeName)bio::molecular::Vesicleinline
operator|(Symmetry *symmetry)bio::physical::Wavevirtual
Class< GenomeImplementation >::bio::Perspective typedefbio::physical::Observer< Perspective< StandardDimension > >
bio::molecular::Molecule::Perspective< StandardDimension >::Perspective()bio::physical::Perspective< StandardDimension >inline
Class< GenomeImplementation >::perspectivebio::genetic::Class< GenomeImplementation >
bio::genetic::Expressor::Class< Expressor >::perspectivebio::genetic::Class< Expressor >
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::perspectivebio::chemical::Class< UnorderedMotif< TranscriptionFactor > >
bio::genetic::Expressor::LinearMotif< Plasmid * >::Class< LinearMotif< Plasmid * > >::perspectivebio::chemical::Class< LinearMotif< Plasmid * > >
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif< Plasmid * >::perspectivebio::chemical::Class< UnorderedMotif< Plasmid * > >
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::Class< LinearMotif< molecular::perspectivebio::chemical::Class< LinearMotif< molecular::Protein * > >
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif< molecular::Protein * >::perspectivebio::chemical::Class< UnorderedMotif< molecular::Protein * > >
bio::genetic::Expressor::bio::molecular::Vesicle::Class< Vesicle >::perspectivebio::molecular::Class< Vesicle >
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::Class< LinearMotif< Molecule * > >::perspectivebio::chemical::Class< LinearMotif< Molecule * > >
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::UnorderedMotif< Molecule * >::perspectivebio::chemical::Class< UnorderedMotif< Molecule * > >
RegisterPlasmid(Plasmid *toRegister)bio::genetic::GenomeImplementationvirtual
Class< GenomeImplementation >::RegisterProperties(const Properties properties)bio::chemical::Elementary< LinearMotif< Surface * > >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::RegisterProperties(const Properties properties)bio::chemical::Elementary< LinearMotif< Plasmid * > >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::RegisterProperties(const Properties properties)bio::chemical::Elementary< LinearMotif< molecular::Protein * > >inline
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::RegisterProperties(const Properties properties)bio::chemical::Elementary< LinearMotif< Molecule * > >inline
Class< GenomeImplementation >::bio::Reify(Symmetry *symmetry)bio::physical::Wavevirtual
Class< GenomeImplementation >::bio::log::Writer::Reify(Symmetry *symmetry)bio::physical::Filterablevirtual
Class< GenomeImplementation >::bio::chemical::Atom::Reify(physical::Symmetry *symmetry)bio::chemical::Atomvirtual
bio::molecular::Molecule::Reify(physical::Symmetry *symmetry)bio::molecular::Moleculevirtual
Remove(const T t)bio::chemical::UnorderedStructureInterfaceinline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::RemoveImplementation(const Property content)bio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::RemoveImplementation(const State content)bio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::RemoveImplementation(const Surface * content)bio::chemical::UnorderedMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::RemoveImplementation(const TranscriptionFactor content)bio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::RemoveImplementation(const Plasmid * content)bio::chemical::UnorderedMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::RemoveImplementation(const molecular::Protein * content)bio::chemical::UnorderedMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::RemoveImplementation(const Molecule * content)bio::chemical::UnorderedMotif< Molecule * >inlinevirtual
RotateTo(StandardDimension surfaceId)bio::molecular::Moleculevirtual
RotateTo(StandardDimension surfaceId) constbio::molecular::Moleculevirtual
RotateTo(StandardDimension surfaceId) constbio::molecular::Moleculeinline
RotateTo(Name surfaceName)bio::molecular::Moleculevirtual
RotateTo(Name surfaceName) constbio::molecular::Moleculevirtual
RotateTo(Name surfaceName) constbio::molecular::Moleculeinline
SetFilter(Filter filter)bio::physical::Filterablevirtual
SetLogEngine(Engine *logEngine)bio::log::Writervirtual
SetPerspective(Perspective *perspective)bio::physical::Observer< Perspective< StandardDimension > >inlinevirtual
Class< GenomeImplementation >::bio::Spin() constbio::physical::Wavevirtual
Class< GenomeImplementation >::bio::log::Writer::Spin() constbio::physical::Filterablevirtual
Class< GenomeImplementation >::bio::chemical::Atom::Spin() constbio::chemical::Atomvirtual
bio::molecular::Molecule::Spin() constbio::molecular::Moleculevirtual
Structure()bio::chemical::Structure
Substance(const typename UnorderedMotif< Property >::Contents *properties, const typename UnorderedMotif< State >::Contents *states)bio::chemical::Substance
Class< GenomeImplementation >::ThreadSafe()bio::ThreadSafe
Class< GenomeImplementation >::ThreadSafe(const ThreadSafe &toCopy)bio::ThreadSafe
bio::ThreadSafe::ThreadSafe()bio::ThreadSafe
bio::ThreadSafe::ThreadSafe(const ThreadSafe &toCopy)bio::ThreadSafe
TransferFrom(Molecule *source, Name surface)bio::molecular::Moleculevirtual
Translate(const RNA *mRNA)bio::genetic::Expressorvirtual
Class< GenomeImplementation >::UnlockThread() constbio::ThreadSafe
bio::ThreadSafe::UnlockThread() constbio::ThreadSafe
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::UnorderedMotif(const Contents *contents)bio::chemical::UnorderedMotif< Property >inline
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::UnorderedMotif(const UnorderedMotif< Property > *toCopy)bio::chemical::UnorderedMotif< Property >inline
Class< GenomeImplementation >::bio::UnorderedMotif< State >::UnorderedMotif(const Contents *contents)bio::chemical::UnorderedMotif< State >inline
Class< GenomeImplementation >::bio::UnorderedMotif< State >::UnorderedMotif(const UnorderedMotif< State > *toCopy)bio::chemical::UnorderedMotif< State >inline
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif(const Contents *contents)bio::chemical::UnorderedMotif< Surface * >inline
Class< GenomeImplementation >::LinearMotif< Surface * >::UnorderedMotif(const UnorderedMotif< Surface * > *toCopy)bio::chemical::UnorderedMotif< Surface * >inline
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::UnorderedMotif(const Contents *contents)bio::chemical::UnorderedMotif< TranscriptionFactor >inline
bio::UnorderedMotif< TranscriptionFactor >::UnorderedMotif(const UnorderedMotif< TranscriptionFactor > *toCopy)bio::chemical::UnorderedMotif< TranscriptionFactor >inline
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif(const Contents *contents)bio::chemical::UnorderedMotif< Plasmid * >inline
bio::LinearMotif< Plasmid * >::UnorderedMotif(const UnorderedMotif< Plasmid * > *toCopy)bio::chemical::UnorderedMotif< Plasmid * >inline
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif(const Contents *contents)bio::chemical::UnorderedMotif< molecular::Protein * >inline
bio::LinearMotif< molecular::Protein * >::UnorderedMotif(const UnorderedMotif< molecular::Protein * > *toCopy)bio::chemical::UnorderedMotif< molecular::Protein * >inline
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::UnorderedMotif(const Contents *contents)bio::chemical::UnorderedMotif< Molecule * >inline
LinearMotif< Molecule * >::UnorderedMotif(const UnorderedMotif< Molecule * > *toCopy)bio::chemical::UnorderedMotif< Molecule * >inline
UnorderedStructureInterface()bio::chemical::UnorderedStructureInterfaceinline
Use(Name varName, T *varPtr)bio::molecular::Moleculeinline
Vesiclebio::molecular::Vesicle
VesiclePerspective::Instance()bio::molecular::Vesicle
VirtualBase()bio::VirtualBaseprotected
bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::log::Writer::Class< Writer >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::chemical::Atom::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::chemical::Substance::Class< Substance >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::chemical::Substance::UnorderedMotif< State >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::molecular::Molecule::bio::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::molecular::Molecule::LinearMotif< Surface * >::bio::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Class< GenomeImplementation >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::genetic::Expressor::LinearMotif< Plasmid * >::bio::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::Class< LinearMotif< Plasmid * > >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::genetic::Expressor::LinearMotif< Plasmid * >::UnorderedMotif< Plasmid * >::bio::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::bio::Class< LinearMotif< molecular::Class< LinearMotif< molecular::Class< LinearMotif< molecular::Class< LinearMotif< molecular::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::UnorderedMotif< molecular::Protein * >::bio::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
Writer(Engine *logEngine, Filter logFilter)bio::log::Writer
~AbstractMotif()bio::chemical::AbstractMotifvirtual
~Atom()bio::chemical::Atomvirtual
Class< GenomeImplementation >::bio::~Class()bio::physical::Class< T >inlinevirtual
Class< GenomeImplementation >::bio::Identifiable< StandardDimension >::~Class()bio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::bio::~Class()bio::physical::Class< Filterable >inlinevirtual
Class< GenomeImplementation >::bio::log::Writer::Class< Writer >::~Class()bio::physical::Class< Writer >inlinevirtual
bio::chemical::Atom::~Class()bio::physical::Class< Atom >inlinevirtual
Class< GenomeImplementation >::~Elementary()bio::chemical::Elementary< LinearMotif< Surface * > >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::~Elementary()bio::chemical::Elementary< LinearMotif< Plasmid * > >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::~Elementary()bio::chemical::Elementary< LinearMotif< molecular::Protein * > >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::~Elementary()bio::chemical::Elementary< LinearMotif< Molecule * > >inlinevirtual
~Filterable()bio::physical::Filterablevirtual
~GenomeImplementation()bio::genetic::GenomeImplementationvirtual
Class< GenomeImplementation >::~LinearMotif()bio::chemical::LinearMotif< Surface * >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::~LinearMotif()bio::chemical::LinearMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::~LinearMotif()bio::chemical::LinearMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::~LinearMotif()bio::chemical::LinearMotif< Molecule * >inlinevirtual
~LinearStructureInterface()bio::chemical::LinearStructureInterfaceinlinevirtual
~Molecule()bio::molecular::Moleculevirtual
~Observer()bio::physical::Observer< Perspective< StandardDimension > >inlinevirtual
~Perspective()bio::physical::Perspective< StandardDimension >inlinevirtual
~Structure()bio::chemical::Structurevirtual
~Substance()bio::chemical::Substancevirtual
~ThreadSafe()bio::ThreadSafevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< Property >::~UnorderedMotif()bio::chemical::UnorderedMotif< Property >inlinevirtual
Class< GenomeImplementation >::bio::UnorderedMotif< State >::~UnorderedMotif()bio::chemical::UnorderedMotif< State >inlinevirtual
Class< GenomeImplementation >::bio::molecular::Molecule::LinearMotif< Surface * >::~UnorderedMotif()bio::chemical::UnorderedMotif< Surface * >inlinevirtual
bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::~UnorderedMotif()bio::chemical::UnorderedMotif< TranscriptionFactor >inlinevirtual
bio::genetic::Expressor::LinearMotif< Plasmid * >::~UnorderedMotif()bio::chemical::UnorderedMotif< Plasmid * >inlinevirtual
bio::genetic::Expressor::LinearMotif< molecular::Protein * >::~UnorderedMotif()bio::chemical::UnorderedMotif< molecular::Protein * >inlinevirtual
bio::genetic::Expressor::bio::molecular::Vesicle::LinearMotif< Molecule * >::~UnorderedMotif()bio::chemical::UnorderedMotif< Molecule * >inlinevirtual
~UnorderedStructureInterface()bio::chemical::UnorderedStructureInterfaceinlinevirtual
~Vesicle()bio::molecular::Vesiclevirtual
~VirtualBase()bio::VirtualBaseprotectedvirtual
~Wave()bio::physical::Wavevirtual
~Writer()bio::log::Writervirtual