| UnorderedMotif< Property >::bio::Class< Plasmid >::AbstractMotif() | bio::chemical::AbstractMotif | |
| UnorderedMotif< State >::bio::Class< Plasmid >::AbstractMotif() | bio::chemical::AbstractMotif | |
| bio::molecular::Molecule::LinearMotif< Surface * >::Class< Plasmid >::AbstractMotif() | bio::chemical::AbstractMotif | |
| LinearMotif< Gene * >::AbstractMotif() | bio::chemical::AbstractMotif | |
| Add(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::AddImplementation(const Property content) | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::AddImplementation(const State content) | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::AddImplementation(Surface * content) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| Class< Plasmid >::UnorderedMotif< Surface * >::AddImplementation(const Surface * content) | bio::chemical::UnorderedMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::AddImplementation(Gene * content) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| UnorderedMotif< Gene * >::AddImplementation(const Gene * content) | bio::chemical::UnorderedMotif< Gene * > | inlinevirtual |
| As() | bio::chemical::Atom | inline |
| As() const | bio::chemical::Atom | inline |
| AsAtom() | bio::physical::Wave | inlinevirtual |
| AsAtom() const | bio::physical::Wave | inlinevirtual |
| AsBonded() | bio::chemical::Atom | inline |
| AsBonded() const | bio::chemical::Atom | inline |
| AsBondedQuantum() | bio::chemical::Atom | inline |
| AsBondedQuantum() const | bio::chemical::Atom | inline |
| AssociateType(Id id, Wave *type) | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| Class< Plasmid >::bio::AsWave() | bio::physical::Class< T > | inlinevirtual |
| Class< Plasmid >::bio::AsWave() const | bio::physical::Class< T > | inlinevirtual |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::AsWave() | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::AsWave() const | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Plasmid >::bio::log::Writer::bio::AsWave() | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Plasmid >::bio::log::Writer::AsWave() const | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Plasmid >::bio::log::Writer::Class< Writer >::AsWave() | bio::physical::Class< Writer > | inlinevirtual |
| Class< Plasmid >::bio::Class< Writer >::AsWave() const | bio::physical::Class< Writer > | inlinevirtual |
| bio::chemical::Atom::AsWave() | bio::physical::Class< Atom > | inlinevirtual |
| bio::chemical::Atom::AsWave() const | bio::physical::Class< Atom > | inlinevirtual |
| Atom(const Atom &other) | bio::chemical::Atom | explicit |
| Class< Plasmid >::bio::Attenuate(const Wave *other) | bio::physical::Wave | virtual |
| Class< Plasmid >::bio::chemical::Atom::Attenuate(const Wave *other) | bio::chemical::Atom | virtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::Attenuate(const physical::Wave *other) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::Attenuate(const physical::Wave *other) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(chemical, Substance, &SubstancePerspective::Instance(), filter::Chemical()) BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical | bio::chemical::Substance | |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS(genetic, Plasmid) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(genetic | bio::genetic::Plasmid | |
| Class< Plasmid >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(molecular, Plasmid) Class(Plasmid *object | bio::genetic::Class< Plasmid > | |
| Class< Plasmid >::bio::molecular::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, T) Class(T *object | bio::molecular::Class< T > | |
| Class< Plasmid >::bio::chemical::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, T) Class(T *object | bio::chemical::Class< T > | |
| Class< Plasmid >::Identifiable< StandardDimension >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspective | bio::physical::Identifiable< StandardDimension > | |
| Class< Plasmid >::bio::log::Writer::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Writer) Writer() | bio::log::Writer | |
| Class< Plasmid >::bio::physical::Filterable::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Filterable) Filterable() | bio::physical::Filterable | |
| Class< Plasmid >::bio::chemical::Atom::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Atom) explicit Atom() | bio::chemical::Atom | |
| Class< Plasmid >::bio::chemical::Substance::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Substance) Class(Substance *object | bio::chemical::Class< Substance > | |
| Class< Plasmid >::bio::chemical::Substance::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Property >) UnorderedMotif() | bio::chemical::UnorderedMotif< Property > | inline |
| Class< Plasmid >::Class< UnorderedMotif< Property > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Property >) Class(UnorderedMotif< Property > *object | bio::chemical::Class< UnorderedMotif< Property > > | |
| Class< Plasmid >::bio::chemical::Substance::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< State >) UnorderedMotif() | bio::chemical::UnorderedMotif< State > | inline |
| Class< Plasmid >::Class< UnorderedMotif< State > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< State >) Class(UnorderedMotif< State > *object | bio::chemical::Class< UnorderedMotif< State > > | |
| Class< Plasmid >::bio::molecular::Molecule::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(molecular, Molecule) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(molecular | bio::molecular::Molecule | |
| Class< Plasmid >::Class< Molecule >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, Molecule) Class(Molecule *object | bio::molecular::Class< Molecule > | |
| Class< Plasmid >::bio::chemical::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, T) Class(T *object | bio::chemical::Class< T > | |
| Class< Plasmid >::LinearMotif< Surface * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, LinearMotif< Surface * >) Class(LinearMotif< Surface * > *object | bio::chemical::Class< LinearMotif< Surface * > > | |
| Class< Plasmid >::LinearMotif< Surface * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Surface * >) UnorderedMotif() | bio::chemical::UnorderedMotif< Surface * > | inline |
| Class< Plasmid >::Class< UnorderedMotif< Surface * > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Surface * >) Class(UnorderedMotif< Surface * > *object | bio::chemical::Class< UnorderedMotif< Surface * > > | |
| LinearMotif< Gene * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, LinearMotif< Gene * >) Class(LinearMotif< Gene * > *object | bio::chemical::Class< LinearMotif< Gene * > > | |
| LinearMotif< Gene * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Gene * >) UnorderedMotif() | bio::chemical::UnorderedMotif< Gene * > | inline |
| LinearMotif< Gene * >::Class< UnorderedMotif< Gene * > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Gene * >) Class(UnorderedMotif< Gene * > *object | bio::chemical::Class< UnorderedMotif< Gene * > > | |
| bio::molecular::DNA::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(molecular, DNA) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(molecular | bio::molecular::DNA | |
| Class< DNA >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, DNA) Class(DNA *object | bio::molecular::Class< DNA > | |
| bio::chemical::Class::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, T) Class(T *object | bio::chemical::Class< T > | |
| Class< Plasmid >::BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS(chemical, LinearMotif< Surface * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical | bio::chemical::LinearMotif< Surface * > | |
| LinearMotif< Gene * >::BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS(chemical, LinearMotif< Gene * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical | bio::chemical::LinearMotif< Gene * > | |
| BreakBond(T toDisassociate, BondType type=bond_type::Unknown()) | bio::chemical::Atom | inline |
| BreakBondImplementation(Wave *toDisassociate, AtomicNumber id, BondType type) | bio::chemical::Atom | protectedvirtual |
| Class< Plasmid >::bio::Class< Plasmid >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::Class(Identifiable< StandardDimension > *object, Symmetry *symmetry=NULL) | bio::physical::Class< Identifiable< StandardDimension > > | inline |
| Class< Plasmid >::bio::log::Writer::bio::Class(Filterable *object, Symmetry *symmetry=NULL) | bio::physical::Class< Filterable > | inline |
| Class< Plasmid >::bio::log::Writer::Class< Writer >::Class(Writer *object, Symmetry *symmetry=NULL) | bio::physical::Class< Writer > | inline |
| Class< Plasmid >::bio::chemical::Atom::Class(Atom *object, Symmetry *symmetry=NULL) | bio::physical::Class< Atom > | inline |
| bio::chemical::Substance::Class< Substance >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| bio::chemical::Substance::UnorderedMotif< State >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| bio::molecular::Molecule::Class< Molecule >::bio::Class< Molecule >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| bio::molecular::Molecule::LinearMotif< Surface * >::Class< LinearMotif< Surface * > >::bio::Class< LinearMotif< Surface * > >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| LinearMotif< Gene * >::Class< LinearMotif< Gene * > >::bio::Class< LinearMotif< Gene * > >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| LinearMotif< Gene * >::UnorderedMotif< Gene * >::bio::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| bio::molecular::DNA::Class< DNA >::bio::Class< DNA >::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| Clear() | bio::chemical::UnorderedStructureInterface | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::ClearImplementation() | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::ClearImplementation() | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::ClearImplementation() | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::ClearImplementation() | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| Class< Plasmid >::bio::Clone() const | bio::physical::Class< T > | inlinevirtual |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::Clone() const | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Plasmid >::bio::log::Writer::bio::Clone() const | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Plasmid >::bio::log::Writer::Class< Writer >::Clone() const | bio::physical::Class< Writer > | inlinevirtual |
| bio::chemical::Atom::Clone() const | bio::physical::Class< Atom > | inlinevirtual |
| CloneIntoName(Name name) | bio::physical::Identifiable< StandardDimension > | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::Contents typedef | bio::chemical::UnorderedMotif< Property > | |
| Class< Plasmid >::bio::UnorderedMotif< State >::Contents typedef | bio::chemical::UnorderedMotif< State > | |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::Contents typedef | bio::chemical::LinearMotif< Surface * > | |
| LinearMotif< Gene * >::Contents typedef | bio::chemical::LinearMotif< Gene * > | |
| Class< Plasmid >::bio::Class< Plasmid >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::Convert(Wave *wave) | bio::physical::Class< Identifiable< StandardDimension > > | inline |
| Class< Plasmid >::bio::log::Writer::bio::Convert(Wave *wave) | bio::physical::Class< Filterable > | inline |
| Class< Plasmid >::bio::log::Writer::Class< Writer >::Convert(Wave *wave) | bio::physical::Class< Writer > | inline |
| Class< Plasmid >::bio::chemical::Atom::Convert(Wave *wave) | bio::physical::Class< Atom > | inline |
| bio::chemical::Substance::Class< Substance >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| bio::chemical::Substance::UnorderedMotif< State >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| bio::molecular::Molecule::Class< Molecule >::bio::Class< Molecule >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| bio::molecular::Molecule::LinearMotif< Surface * >::Class< LinearMotif< Surface * > >::bio::Class< LinearMotif< Surface * > >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| LinearMotif< Gene * >::Class< LinearMotif< Gene * > >::bio::Class< LinearMotif< Gene * > >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| LinearMotif< Gene * >::UnorderedMotif< Gene * >::bio::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| bio::molecular::DNA::Class< DNA >::bio::Class< DNA >::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| Class< Plasmid >::CreateImplementation(StandardDimension id) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::CreateImplementation(StandardDimension id) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| Define(Name varName) | bio::molecular::Molecule | inline |
| Define(Name varName) | bio::molecular::Molecule | inline |
| Define(Name varName, const T &assignment) | bio::molecular::Molecule | inline |
| Demodulate() | bio::physical::Wave | virtual |
| Demodulate() const | bio::physical::Wave | virtual |
| Disable() | bio::chemical::Substance | virtual |
| DisassociateType(Id id) | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| Class< Plasmid >::bio::Disattenuate(const Wave *other) | bio::physical::Wave | virtual |
| Class< Plasmid >::bio::chemical::Atom::Disattenuate(const Wave *other) | bio::chemical::Atom | virtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::Disattenuate(const physical::Wave *other) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::Disattenuate(const physical::Wave *other) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| DNA | bio::molecular::DNA | |
| DNAPerspective::Instance() | bio::molecular::DNA | |
| DuplicateFrom(Molecule *source, Name surface) | bio::molecular::Molecule | virtual |
| Class< Plasmid >::Elementary(const Properties properties) | bio::chemical::Elementary< LinearMotif< Surface * > > | inline |
| Class< Plasmid >::Elementary() | bio::chemical::Elementary< LinearMotif< Surface * > > | inline |
| LinearMotif< Gene * >::Elementary(const Properties properties) | bio::chemical::Elementary< LinearMotif< Gene * > > | inline |
| LinearMotif< Gene * >::Elementary() | bio::chemical::Elementary< LinearMotif< Gene * > > | inline |
| Enable() | bio::chemical::Substance | virtual |
| ExternalLog(Filter logFilter, Level level, const char *format,...) const | bio::log::Writer | |
| Class< Plasmid >::bio::filter | bio::molecular::Class< T > | |
| Class< Plasmid >::bio::molecular::Molecule::Class< Molecule >::filter | bio::molecular::Class< Molecule > | |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::Class< LinearMotif< Surface * > >::filter | bio::chemical::Class< LinearMotif< Surface * > > | |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::filter | bio::chemical::Class< UnorderedMotif< Surface * > > | |
| LinearMotif< Gene * >::Class< LinearMotif< Gene * > >::filter | bio::chemical::Class< LinearMotif< Gene * > > | |
| LinearMotif< Gene * >::UnorderedMotif< Gene * >::filter | bio::chemical::Class< UnorderedMotif< Gene * > > | |
| bio::molecular::DNA::Class< DNA >::filter | bio::molecular::Class< DNA > | |
| filter::Genetic()) virtual ~Plasmid() | bio::genetic::Plasmid | |
| Class< Plasmid >::filter::Molecular()) Molecule(const Molecule &toCopy) | bio::molecular::Molecule | |
| bio::molecular::DNA::filter::Molecular()) virtual ~DNA() | bio::molecular::DNA | |
| Filterable(Filter filter) | bio::physical::Filterable | |
| Find(Id id) | bio::physical::Perspective< StandardDimension > | inline |
| Find(Id id) const | bio::physical::Perspective< StandardDimension > | inline |
| ForEach(ExcitationBase *excitation) | bio::chemical::LinearStructureInterface | inline |
| Class< Plasmid >::ForEachImplementation(ExcitationBase *excitation) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::ForEachImplementation(ExcitationBase *excitation) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| FormBond(T toBond, BondType type=bond_type::Unknown()) | bio::chemical::Atom | inline |
| FormBondImplementation(Wave *toBond, AtomicNumber id, BondType type) | bio::chemical::Atom | protectedvirtual |
| GetAll() | bio::chemical::UnorderedStructureInterface | inline |
| GetAll() const | bio::chemical::UnorderedStructureInterface | inline |
| GetAllAsVector() | bio::chemical::UnorderedStructureInterface | inline |
| GetAllAsVector() const | bio::chemical::UnorderedStructureInterface | inline |
| GetAllBonds() | bio::chemical::Atom | |
| GetAllBonds() const | bio::chemical::Atom | |
| GetAllImplementation() | bio::chemical::AbstractMotif | virtual |
| GetAllImplementation() const | bio::chemical::AbstractMotif | virtual |
| GetBonded(Valence position) | bio::chemical::Atom | |
| GetBonded(Valence position) const | bio::chemical::Atom | |
| GetBondPosition(AtomicNumber bondedId) const | bio::chemical::Atom | |
| GetBondPosition(Name typeName) const | bio::chemical::Atom | |
| GetBondPosition() const | bio::chemical::Atom | inline |
| GetBondType(Valence position) const | bio::chemical::Atom | |
| GetBondType() const | bio::chemical::Atom | inline |
| GetById(StandardDimension id) | bio::chemical::LinearStructureInterface | inline |
| GetById(StandardDimension id) const | bio::chemical::LinearStructureInterface | inline |
| Class< Plasmid >::GetByIdImplementation(StandardDimension id) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| Class< Plasmid >::GetByIdImplementation(StandardDimension id) const | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::GetByIdImplementation(StandardDimension id) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| LinearMotif< Gene * >::GetByIdImplementation(StandardDimension id) const | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| GetByName(Name name) | bio::chemical::LinearStructureInterface | inline |
| GetByName(Name name) const | bio::chemical::LinearStructureInterface | inline |
| Class< Plasmid >::GetByNameImplementation(Name name) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| Class< Plasmid >::GetByNameImplementation(Name name) const | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::GetByNameImplementation(Name name) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| LinearMotif< Gene * >::GetByNameImplementation(Name name) const | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< Property >::GetClassProperties() | bio::chemical::AbstractMotif | static |
| Class< Plasmid >::bio::UnorderedMotif< State >::GetClassProperties() | bio::chemical::AbstractMotif | static |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::GetClassProperties() | bio::chemical::LinearMotif< Surface * > | inlinestatic |
| LinearMotif< Gene * >::GetClassProperties() | bio::chemical::LinearMotif< Gene * > | inlinestatic |
| GetCount() const | bio::chemical::UnorderedStructureInterface | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::GetCountImplementation() const | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::GetCountImplementation() const | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::GetCountImplementation() const | bio::chemical::UnorderedMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::GetCountImplementation() const | bio::chemical::UnorderedMotif< Gene * > | inlinevirtual |
| GetFilter() const | bio::physical::Filterable | |
| GetIdFromName(Name name) | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| GetIdWithoutCreation(Name name) const | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| GetLogEngine() | bio::log::Writer | |
| GetLogEngine() const | bio::log::Writer | |
| GetNameFromId(Id id) const | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| GetNewObjectFromId(Id id) const | bio::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) const | bio::chemical::UnorderedStructureInterface | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::GetNumMatchingImplementation(const Container *other) const | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::GetNumMatchingImplementation(const Container *other) const | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::GetNumMatchingImplementation(const Container *other) const | bio::chemical::UnorderedMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::GetNumMatchingImplementation(const Container *other) const | bio::chemical::UnorderedMotif< Gene * > | inlinevirtual |
| GetNumUsedIds() const | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| GetOrCreateById(StandardDimension id) | bio::chemical::LinearStructureInterface | inline |
| Class< Plasmid >::GetOrCreateByIdImplementation(StandardDimension id) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::GetOrCreateByIdImplementation(StandardDimension id) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| GetOrCreateByName(Name name) | bio::chemical::LinearStructureInterface | inline |
| Class< Plasmid >::GetOrCreateByNameImplementation(Name name) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::GetOrCreateByNameImplementation(Name name) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| GetPerspective() const | bio::physical::Observer< Perspective< StandardDimension > > | inlinevirtual |
| GetProperties() const | bio::physical::Wave | virtual |
| GetProtein() | bio::molecular::DNA | virtual |
| GetProtein() const | bio::molecular::DNA | virtual |
| GetProteinId() const | bio::molecular::DNA | virtual |
| bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| Class< Writer >::bio::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Class< Writer >::bio::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| Class< Writer >::bio::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| Class< Substance >::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Class< Substance >::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| Class< Substance >::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| UnorderedMotif< Property >::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| UnorderedMotif< Property >::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| UnorderedMotif< Property >::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| UnorderedMotif< State >::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| UnorderedMotif< State >::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| UnorderedMotif< State >::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| bio::molecular::Molecule::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::molecular::Molecule::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| bio::molecular::Molecule::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| LinearMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| LinearMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| LinearMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| UnorderedMotif< Surface * >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| UnorderedMotif< Surface * >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| UnorderedMotif< Surface * >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| LinearMotif< Gene * >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| LinearMotif< Gene * >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| LinearMotif< Gene * >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| UnorderedMotif< Gene * >::LinearMotif< Gene * >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| UnorderedMotif< Gene * >::LinearMotif< Gene * >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| UnorderedMotif< Gene * >::LinearMotif< Gene * >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| bio::molecular::DNA::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::molecular::DNA::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| bio::molecular::DNA::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| GetRNAPolymerase() | bio::genetic::Plasmid | virtual |
| GetRNAPolymerase() const | bio::genetic::Plasmid | virtual |
| GetStringFrom(std::string separator=", ") | bio::chemical::UnorderedStructureInterface | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::GetStringFromImplementation(std::string separator=", ") | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::GetStringFromImplementation(std::string separator=", ") | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::GetStringFromImplementation(std::string separator=", ") | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::GetStringFromImplementation(std::string separator=", ") | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| Class< Plasmid >::GetStructuralPerspective() | bio::chemical::LinearMotif< Surface * > | inline |
| Class< Plasmid >::GetStructuralPerspective() const | bio::chemical::LinearMotif< Surface * > | inline |
| LinearMotif< Gene * >::GetStructuralPerspective() | bio::chemical::LinearMotif< Gene * > | inline |
| LinearMotif< Gene * >::GetStructuralPerspective() const | bio::chemical::LinearMotif< Gene * > | inline |
| GetTypeFromId(Id id) const | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| GetTypeFromIdAs(Id id) const | bio::physical::Perspective< StandardDimension > | inline |
| GetTypeFromName(Name name) const | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| GetTypeFromNameAs(Name name) const | bio::physical::Perspective< StandardDimension > | inline |
| GetUniqueIdFor(Name name) | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| GetVersion() | bio::molecular::DNA | virtual |
| Hadits typedef | bio::physical::Perspective< StandardDimension > | |
| Has(T content) const | bio::chemical::UnorderedStructureInterface | inline |
| HasAll(const Container *contents) const | bio::chemical::UnorderedStructureInterface | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::HasAllImplementation(const Container *contents) const | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::HasAllImplementation(const Container *contents) const | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::HasAllImplementation(const Container *contents) const | bio::chemical::UnorderedMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::HasAllImplementation(const Container *contents) const | bio::chemical::UnorderedMotif< Gene * > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< Property >::HasImplementation(const Property content) const | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::HasImplementation(const State content) const | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::HasImplementation(const Surface * &content) const | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| Class< Plasmid >::UnorderedMotif< Surface * >::HasImplementation(const Surface * content) const | bio::chemical::UnorderedMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::HasImplementation(const Gene * &content) const | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| UnorderedMotif< Gene * >::HasImplementation(const Gene * content) const | bio::chemical::UnorderedMotif< Gene * > | inlinevirtual |
| HasLogEngine() const | bio::log::Writer | |
| Class< Plasmid >::hasRegistered | bio::chemical::Elementary< LinearMotif< Surface * > > | static |
| LinearMotif< Gene * >::hasRegistered | bio::chemical::Elementary< LinearMotif< Gene * > > | static |
| Class< Plasmid >::bio::Id typedef | bio::physical::Identifiable< StandardDimension > | |
| bio::molecular::Molecule::Perspective< StandardDimension >::Id typedef | bio::physical::Perspective< StandardDimension > | |
| Class< Plasmid >::bio::Ids typedef | bio::physical::Identifiable< StandardDimension > | |
| bio::molecular::Molecule::Perspective< StandardDimension >::Ids typedef | bio::physical::Perspective< StandardDimension > | |
| Import(const UnorderedMotif< T > *other) | bio::chemical::UnorderedStructureInterface | inline |
| Import(const std::vector< T > &other) | bio::chemical::UnorderedStructureInterface | inline |
| ImportAll(const physical::Wave *other) | bio::chemical::UnorderedStructureInterface | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::ImportImplementation(const UnorderedMotif< Property > *other) | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< Property >::bio::chemical::AbstractMotif::ImportImplementation(const void *other) | bio::chemical::AbstractMotif | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::ImportImplementation(const UnorderedMotif< State > *other) | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::ImportImplementation(const LinearMotif< Surface * > *other) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| Class< Plasmid >::UnorderedMotif< Surface * >::ImportImplementation(const UnorderedMotif< Surface * > *other) | bio::chemical::UnorderedMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::ImportImplementation(const LinearMotif< Gene * > *other) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| UnorderedMotif< Gene * >::ImportImplementation(const UnorderedMotif< Gene * > *other) | bio::chemical::UnorderedMotif< Gene * > | inlinevirtual |
| Initialize(ByteStreams args) | bio::VirtualBase | protected |
| Initialize(ByteStream arg1) | bio::VirtualBase | protected |
| Initialize(ByteStream arg1, ByteStream arg2) | bio::VirtualBase | protected |
| Initialize(ByteStream arg1, ByteStream arg2, ByteStream arg3) | bio::VirtualBase | protected |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::InitializeImplementation(ByteStreams args) | bio::physical::Observer< Perspective< StandardDimension > > | inlineprotectedvirtual |
| bio::log::Writer::InitializeImplementation(ByteStreams args) | bio::log::Writer | protectedvirtual |
| Insert(T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false) | bio::chemical::LinearStructureInterface | inline |
| Class< Plasmid >::InsertImplementation(Surface * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false) | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::InsertImplementation(Gene * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false) | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| InvalidId() | bio::physical::Perspective< StandardDimension > | inlinestatic |
| InvalidName() | bio::physical::Perspective< StandardDimension > | inlinestatic |
| IsEnabled() const | bio::chemical::Substance | virtual |
| Class< Plasmid >::LinearMotif(physical::Perspective< StandardDimension > *perspective=NULL) | bio::chemical::LinearMotif< Surface * > | inlineexplicit |
| Class< Plasmid >::LinearMotif(const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL) | bio::chemical::LinearMotif< Surface * > | inlineexplicit |
| Class< Plasmid >::LinearMotif(const LinearMotif< Surface * > &toCopy) | bio::chemical::LinearMotif< Surface * > | inline |
| LinearMotif< Gene * >::LinearMotif(physical::Perspective< StandardDimension > *perspective=NULL) | bio::chemical::LinearMotif< Gene * > | inlineexplicit |
| LinearMotif< Gene * >::LinearMotif(const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL) | bio::chemical::LinearMotif< Gene * > | inlineexplicit |
| LinearMotif< Gene * >::LinearMotif(const LinearMotif< Gene * > &toCopy) | bio::chemical::LinearMotif< Gene * > | inline |
| LinearStructureInterface() | bio::chemical::LinearStructureInterface | inline |
| Class< Plasmid >::LockThread() const | bio::ThreadSafe | |
| bio::ThreadSafe::LockThread() const | bio::ThreadSafe | |
| Log(Level level, const char *format,...) const | bio::log::Writer | protected |
| m_bonds | bio::chemical::Atom | protected |
| UnorderedMotif< Property >::bio::Class< Plasmid >::m_contents | bio::chemical::AbstractMotif | mutableprotected |
| UnorderedMotif< State >::bio::Class< Plasmid >::m_contents | bio::chemical::AbstractMotif | mutableprotected |
| bio::molecular::Molecule::LinearMotif< Surface * >::Class< Plasmid >::m_contents | bio::chemical::AbstractMotif | mutableprotected |
| LinearMotif< Gene * >::m_contents | bio::chemical::AbstractMotif | mutableprotected |
| m_filter | bio::physical::Filterable | protected |
| m_hadits | bio::physical::Perspective< StandardDimension > | protected |
| m_hasBeenInitialized | bio::VirtualBase | protected |
| m_id | bio::physical::Identifiable< StandardDimension > | |
| m_nextId | bio::physical::Perspective< StandardDimension > | protected |
| Class< Plasmid >::bio::Class< Plasmid >::m_object | bio::physical::Class< T > | protected |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::m_object | bio::physical::Class< Identifiable< StandardDimension > > | protected |
| Class< Plasmid >::bio::log::Writer::bio::m_object | bio::physical::Class< Filterable > | protected |
| Class< Plasmid >::bio::log::Writer::Class< Writer >::m_object | bio::physical::Class< Writer > | protected |
| Class< Plasmid >::bio::chemical::Atom::m_object | bio::physical::Class< Atom > | protected |
| bio::chemical::Substance::Class< Substance >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_object | bio::physical::Class< T > | protected |
| bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_object | bio::physical::Class< T > | protected |
| bio::chemical::Substance::UnorderedMotif< State >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_object | bio::physical::Class< T > | protected |
| bio::molecular::Molecule::Class< Molecule >::bio::Class< Molecule >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_object | bio::physical::Class< T > | protected |
| bio::molecular::Molecule::LinearMotif< Surface * >::Class< LinearMotif< Surface * > >::bio::Class< LinearMotif< Surface * > >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_object | bio::physical::Class< T > | protected |
| bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_object | bio::physical::Class< T > | protected |
| LinearMotif< Gene * >::Class< LinearMotif< Gene * > >::bio::Class< LinearMotif< Gene * > >::m_object | bio::physical::Class< T > | protected |
| LinearMotif< Gene * >::UnorderedMotif< Gene * >::bio::m_object | bio::physical::Class< T > | protected |
| bio::molecular::DNA::Class< DNA >::bio::Class< DNA >::m_object | bio::physical::Class< T > | protected |
| Class< Plasmid >::m_perspective | bio::chemical::LinearMotif< Surface * > | |
| LinearMotif< Gene * >::m_perspective | bio::chemical::LinearMotif< Gene * > | |
| m_protein | bio::molecular::DNA | protected |
| bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| bio::chemical::Atom::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| bio::chemical::Substance::Class< Substance >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| bio::chemical::Substance::UnorderedMotif< State >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| bio::molecular::Molecule::bio::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| bio::molecular::Molecule::LinearMotif< Surface * >::bio::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_signal | bio::physical::Wave | protected |
| LinearMotif< Gene * >::bio::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::m_signal | bio::physical::Wave | protected |
| LinearMotif< Gene * >::UnorderedMotif< Gene * >::bio::m_signal | bio::physical::Wave | protected |
| bio::molecular::DNA::bio::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::m_signal | bio::physical::Wave | protected |
| bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| bio::chemical::Atom::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| bio::chemical::Substance::Class< Substance >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| bio::chemical::Substance::UnorderedMotif< State >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| bio::molecular::Molecule::bio::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| bio::molecular::Molecule::LinearMotif< Surface * >::bio::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< LinearMotif< Surface * > >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::m_symmetry | bio::physical::Wave | protected |
| LinearMotif< Gene * >::bio::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::m_symmetry | bio::physical::Wave | protected |
| LinearMotif< Gene * >::UnorderedMotif< Gene * >::bio::m_symmetry | bio::physical::Wave | protected |
| bio::molecular::DNA::bio::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::m_symmetry | bio::physical::Wave | protected |
| m_version | bio::molecular::DNA | protected |
| Modulate(Wave *signal) | bio::physical::Wave | virtual |
| Molecule | bio::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::Atom | inline |
| operator T*() | bio::physical::Class< T > | inlinevirtual |
| Class< Plasmid >::bio::operator Wave *() | bio::physical::Class< T > | inlinevirtual |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::operator Wave *() | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Plasmid >::bio::log::Writer::bio::operator Wave *() | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Plasmid >::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::Molecule | virtual |
| operator()(StandardDimension surfaceId) const | bio::molecular::Molecule | virtual |
| operator()(StandardDimension surfaceId) | bio::molecular::Molecule | inline |
| operator()(Name name) | bio::molecular::Molecule | virtual |
| operator()(Name name) const | bio::molecular::Molecule | virtual |
| operator()(Name surfaceName) | bio::molecular::Molecule | inline |
| operator*(Wave *signal) | bio::physical::Wave | virtual |
| operator*() | bio::physical::Wave | virtual |
| operator*() const | bio::physical::Wave | virtual |
| operator+(const Wave *other) | bio::physical::Wave | virtual |
| operator-(const Wave *other) | bio::physical::Wave | virtual |
| operator<<(Surface *source) | bio::molecular::Molecule | virtual |
| operator<<(Molecule *source) | bio::molecular::Molecule | virtual |
| operator>>(Surface *target) | bio::molecular::Molecule | virtual |
| operator>>(Molecule *target) | bio::molecular::Molecule | virtual |
| operator|(Symmetry *symmetry) | bio::physical::Wave | virtual |
| Class< Plasmid >::bio::Perspective typedef | bio::physical::Observer< Perspective< StandardDimension > > | |
| bio::molecular::Molecule::Perspective< StandardDimension >::Perspective() | bio::physical::Perspective< StandardDimension > | inline |
| Class< Plasmid >::perspective | bio::genetic::Class< Plasmid > | |
| LinearMotif< Gene * >::Class< LinearMotif< Gene * > >::perspective | bio::chemical::Class< LinearMotif< Gene * > > | |
| LinearMotif< Gene * >::UnorderedMotif< Gene * >::perspective | bio::chemical::Class< UnorderedMotif< Gene * > > | |
| bio::molecular::DNA::Class< DNA >::perspective | bio::molecular::Class< DNA > | |
| Plasmid | bio::genetic::Plasmid | |
| PlasmidPerspective::Instance() | bio::genetic::Plasmid | |
| Class< Plasmid >::RegisterProperties(const Properties properties) | bio::chemical::Elementary< LinearMotif< Surface * > > | inline |
| LinearMotif< Gene * >::RegisterProperties(const Properties properties) | bio::chemical::Elementary< LinearMotif< Gene * > > | inline |
| Class< Plasmid >::bio::Reify(Symmetry *symmetry) | bio::physical::Wave | virtual |
| Class< Plasmid >::bio::log::Writer::Reify(Symmetry *symmetry) | bio::physical::Filterable | virtual |
| Class< Plasmid >::bio::chemical::Atom::Reify(physical::Symmetry *symmetry) | bio::chemical::Atom | virtual |
| bio::molecular::Molecule::Reify(physical::Symmetry *symmetry) | bio::molecular::Molecule | virtual |
| Remove(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::RemoveImplementation(const Property content) | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::RemoveImplementation(const State content) | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::RemoveImplementation(const Surface * content) | bio::chemical::UnorderedMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::RemoveImplementation(const Gene * content) | bio::chemical::UnorderedMotif< Gene * > | inlinevirtual |
| RotateTo(StandardDimension surfaceId) | bio::molecular::Molecule | virtual |
| RotateTo(StandardDimension surfaceId) const | bio::molecular::Molecule | virtual |
| RotateTo(StandardDimension surfaceId) const | bio::molecular::Molecule | inline |
| RotateTo(Name surfaceName) | bio::molecular::Molecule | virtual |
| RotateTo(Name surfaceName) const | bio::molecular::Molecule | virtual |
| RotateTo(Name surfaceName) const | bio::molecular::Molecule | inline |
| SetFilter(Filter filter) | bio::physical::Filterable | virtual |
| SetLogEngine(Engine *logEngine) | bio::log::Writer | virtual |
| SetPerspective(Perspective *perspective) | bio::physical::Observer< Perspective< StandardDimension > > | inlinevirtual |
| SetProtein(Protein *protein) | bio::molecular::DNA | virtual |
| SetVersion(Version newVersion) | bio::molecular::DNA | virtual |
| Class< Plasmid >::bio::Spin() const | bio::physical::Wave | virtual |
| Class< Plasmid >::bio::log::Writer::Spin() const | bio::physical::Filterable | virtual |
| Class< Plasmid >::bio::chemical::Atom::Spin() const | bio::chemical::Atom | virtual |
| bio::molecular::Molecule::Spin() const | bio::molecular::Molecule | virtual |
| Structure() | bio::chemical::Structure | |
| Substance(const typename UnorderedMotif< Property >::Contents *properties, const typename UnorderedMotif< State >::Contents *states) | bio::chemical::Substance | |
| Class< Plasmid >::ThreadSafe() | bio::ThreadSafe | |
| Class< Plasmid >::ThreadSafe(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| bio::ThreadSafe::ThreadSafe() | bio::ThreadSafe | |
| bio::ThreadSafe::ThreadSafe(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| TranscribeFor(Expressor *expressor) const | bio::genetic::Plasmid | virtual |
| TransferFrom(Molecule *source, Name surface) | bio::molecular::Molecule | virtual |
| Class< Plasmid >::UnlockThread() const | bio::ThreadSafe | |
| bio::ThreadSafe::UnlockThread() const | bio::ThreadSafe | |
| Class< Plasmid >::bio::UnorderedMotif< Property >::UnorderedMotif(const Contents *contents) | bio::chemical::UnorderedMotif< Property > | inline |
| Class< Plasmid >::bio::UnorderedMotif< Property >::UnorderedMotif(const UnorderedMotif< Property > *toCopy) | bio::chemical::UnorderedMotif< Property > | inline |
| Class< Plasmid >::bio::UnorderedMotif< State >::UnorderedMotif(const Contents *contents) | bio::chemical::UnorderedMotif< State > | inline |
| Class< Plasmid >::bio::UnorderedMotif< State >::UnorderedMotif(const UnorderedMotif< State > *toCopy) | bio::chemical::UnorderedMotif< State > | inline |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif(const Contents *contents) | bio::chemical::UnorderedMotif< Surface * > | inline |
| Class< Plasmid >::LinearMotif< Surface * >::UnorderedMotif(const UnorderedMotif< Surface * > *toCopy) | bio::chemical::UnorderedMotif< Surface * > | inline |
| LinearMotif< Gene * >::UnorderedMotif(const Contents *contents) | bio::chemical::UnorderedMotif< Gene * > | inline |
| LinearMotif< Gene * >::UnorderedMotif(const UnorderedMotif< Gene * > *toCopy) | bio::chemical::UnorderedMotif< Gene * > | inline |
| UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inline |
| Use(Name varName, T *varPtr) | bio::molecular::Molecule | inline |
| VirtualBase() | bio::VirtualBase | protected |
| bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| Identifiable< StandardDimension >::bio::bio::bio::bio::bio::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::log::Writer::Class< Writer >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Atom::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Substance::Class< Substance >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Substance::UnorderedMotif< Property >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Substance::UnorderedMotif< State >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::molecular::Molecule::bio::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Molecule >::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::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< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::molecular::Molecule::LinearMotif< Surface * >::UnorderedMotif< Surface * >::bio::Class< Plasmid >::Class< Plasmid >::Class< Plasmid >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| LinearMotif< Gene * >::bio::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::Class< LinearMotif< Gene * > >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| LinearMotif< Gene * >::UnorderedMotif< Gene * >::bio::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::molecular::DNA::bio::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Class< DNA >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| Writer(Engine *logEngine, Filter logFilter) | bio::log::Writer | |
| ~AbstractMotif() | bio::chemical::AbstractMotif | virtual |
| ~Atom() | bio::chemical::Atom | virtual |
| Class< Plasmid >::bio::~Class() | bio::physical::Class< T > | inlinevirtual |
| Class< Plasmid >::bio::Identifiable< StandardDimension >::~Class() | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Plasmid >::bio::log::Writer::bio::~Class() | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Plasmid >::bio::log::Writer::Class< Writer >::~Class() | bio::physical::Class< Writer > | inlinevirtual |
| bio::chemical::Atom::~Class() | bio::physical::Class< Atom > | inlinevirtual |
| Class< Plasmid >::~Elementary() | bio::chemical::Elementary< LinearMotif< Surface * > > | inlinevirtual |
| LinearMotif< Gene * >::~Elementary() | bio::chemical::Elementary< LinearMotif< Gene * > > | inlinevirtual |
| ~Filterable() | bio::physical::Filterable | virtual |
| Class< Plasmid >::~LinearMotif() | bio::chemical::LinearMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::~LinearMotif() | bio::chemical::LinearMotif< Gene * > | inlinevirtual |
| ~LinearStructureInterface() | bio::chemical::LinearStructureInterface | inlinevirtual |
| ~Molecule() | bio::molecular::Molecule | virtual |
| ~Observer() | bio::physical::Observer< Perspective< StandardDimension > > | inlinevirtual |
| ~Perspective() | bio::physical::Perspective< StandardDimension > | inlinevirtual |
| ~Structure() | bio::chemical::Structure | virtual |
| ~Substance() | bio::chemical::Substance | virtual |
| ~ThreadSafe() | bio::ThreadSafe | virtual |
| Class< Plasmid >::bio::UnorderedMotif< Property >::~UnorderedMotif() | bio::chemical::UnorderedMotif< Property > | inlinevirtual |
| Class< Plasmid >::bio::UnorderedMotif< State >::~UnorderedMotif() | bio::chemical::UnorderedMotif< State > | inlinevirtual |
| Class< Plasmid >::bio::molecular::Molecule::LinearMotif< Surface * >::~UnorderedMotif() | bio::chemical::UnorderedMotif< Surface * > | inlinevirtual |
| LinearMotif< Gene * >::~UnorderedMotif() | bio::chemical::UnorderedMotif< Gene * > | inlinevirtual |
| ~UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inlinevirtual |
| ~VirtualBase() | bio::VirtualBase | protectedvirtual |
| ~Wave() | bio::physical::Wave | virtual |
| ~Writer() | bio::log::Writer | virtual |
1.9.4