Uses of Interface
org.biopax.paxtools.model.level3.PhysicalEntity

Packages that use PhysicalEntity

Package	Description
org.biopax.paxtools.controller	This package contains various methods and algorithms for traversing and manipulating the model.
org.biopax.paxtools.impl.level3	This package contains the default implementation for BioPAX Level 3.
org.biopax.paxtools.model.level3	This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.

Uses of PhysicalEntity in org.biopax.paxtools.controller

Methods in org.biopax.paxtools.controller with parameters of type PhysicalEntity

Modifier and Type	Method	Description
static Set<EntityFeature>	ModelUtils.findFeaturesAddedToSecond(PhysicalEntity first, PhysicalEntity second, boolean fix)
static Set<EntityFeature>	ModelUtils.getFeatureIntersection(PhysicalEntity first, org.biopax.paxtools.controller.ModelUtils.FeatureType firstClass, PhysicalEntity second, org.biopax.paxtools.controller.ModelUtils.FeatureType secondClass)
static Set<EntityFeature>	ModelUtils.getFeatureSetByType(PhysicalEntity pe, org.biopax.paxtools.controller.ModelUtils.FeatureType type)
static void	ModelUtils.normalizeGeneric(Model model, PhysicalEntity generic)	In all interactions and complexes, replace generic physical entities (having members) with their corresponding members; clone the parent object, if needed, for each member.

Uses of PhysicalEntity in org.biopax.paxtools.impl.level3

Classes in org.biopax.paxtools.impl.level3 that implement PhysicalEntity

Modifier and Type	Class	Description
class	ComplexImpl
class	DnaImpl
class	DnaRegionImpl
class	NucleicAcidImpl
class	PhysicalEntityImpl
class	ProteinImpl
class	RnaImpl
class	RnaRegionImpl
class	SimplePhysicalEntityImpl
class	SmallMoleculeImpl

Methods in org.biopax.paxtools.impl.level3 that return PhysicalEntity

Modifier and Type	Method	Description
PhysicalEntity	StoichiometryImpl.getPhysicalEntity()

Methods in org.biopax.paxtools.impl.level3 that return types with arguments of type PhysicalEntity

Modifier and Type	Method	Description
Set<PhysicalEntity>	CatalysisImpl.getCofactor()
Set<PhysicalEntity>	ComplexImpl.getComponent()
Set<PhysicalEntity>	EntityFeatureImpl.getFeatureOf()
Set<PhysicalEntity>	ConversionImpl.getLeft()
Set<PhysicalEntity>	PhysicalEntityImpl.getMemberPhysicalEntity()
Set<PhysicalEntity>	PhysicalEntityImpl.getMemberPhysicalEntityOf()
Class<? extends PhysicalEntity>	PhysicalEntityImpl.getModelInterface()
Class<? extends PhysicalEntity>	SmallMoleculeImpl.getModelInterface()
Set<PhysicalEntity>	EntityFeatureImpl.getNotFeatureOf()
protected Set<PhysicalEntity>	ControlImpl.getPeController()
Set<PhysicalEntity>	TemplateReactionImpl.getProduct()
Set<PhysicalEntity>	ConversionImpl.getRight()

Methods in org.biopax.paxtools.impl.level3 with parameters of type PhysicalEntity

Modifier and Type	Method	Description
void	CatalysisImpl.addCofactor(PhysicalEntity cofactor)
void	ComplexImpl.addComponent(PhysicalEntity component)
void	ConversionImpl.addLeft(PhysicalEntity left)
void	PhysicalEntityImpl.addMemberPhysicalEntity(PhysicalEntity mpe)
void	TemplateReactionImpl.addProduct(PhysicalEntity product)
void	ConversionImpl.addRight(PhysicalEntity right)
protected void	ComplexImpl.collectSimpleMembersRecursive(PhysicalEntity pe, Set<SimplePhysicalEntity> set)
boolean	PhysicalEntityImpl.hasEquivalentCellularLocation(PhysicalEntity that)
boolean	PhysicalEntityImpl.hasEquivalentFeatures(PhysicalEntity that)
void	CatalysisImpl.removeCofactor(PhysicalEntity cofactor)
void	ComplexImpl.removeComponent(PhysicalEntity component)
void	ConversionImpl.removeLeft(PhysicalEntity left)
void	PhysicalEntityImpl.removeMemberPhysicalEntity(PhysicalEntity oldMember)
void	TemplateReactionImpl.removeProduct(PhysicalEntity product)
void	ConversionImpl.removeRight(PhysicalEntity right)
void	StoichiometryImpl.setPhysicalEntity(PhysicalEntity PhysicalEntity)

Method parameters in org.biopax.paxtools.impl.level3 with type arguments of type PhysicalEntity

Modifier and Type	Method	Description
protected void	ComplexImpl.setComponent(Set<PhysicalEntity> component)
protected void	TemplateReactionImpl.setProduct(Set<PhysicalEntity> product)

Uses of PhysicalEntity in org.biopax.paxtools.model.level3

Subinterfaces of PhysicalEntity in org.biopax.paxtools.model.level3

Modifier and Type	Interface	Description
interface	Complex	Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.
interface	Dna	Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
interface	DnaRegion	Definition: A region on a DNA molecule.
interface	NucleicAcid	Tagger interface for DNA and RNA
interface	Protein
interface	Rna
interface	RnaRegion	Definition: A region on a RNA molecule.
interface	SequenceEntity	Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
interface	SimplePhysicalEntity	Tagger interface for non-complex physical entities
interface	SmallMolecule

Methods in org.biopax.paxtools.model.level3 that return PhysicalEntity

Modifier and Type	Method	Description
PhysicalEntity	Stoichiometry.getPhysicalEntity()

Methods in org.biopax.paxtools.model.level3 that return types with arguments of type PhysicalEntity

Modifier and Type	Method	Description
Set<PhysicalEntity>	Catalysis.getCofactor()	Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
Set<PhysicalEntity>	Complex.getComponent()	Defines the PhysicalEntity subunits of this complex.
Set<PhysicalEntity>	EntityFeature.getFeatureOf()	Inverse of getFeature() Contents of this set is generated automatically and should not be modified.
Set<PhysicalEntity>	Conversion.getLeft()	The participants on the left side of the conversion interaction.
Set<PhysicalEntity>	PhysicalEntity.getMemberPhysicalEntity()	Please avoid using this property in your BioPAX L3 models unless absolutely sure/required, for there is an alternative way (using PhysicalEntity/entityReference/memberEntityReference), and this will probably be deprecated in the future BioPAX releases.
Set<PhysicalEntity>	PhysicalEntity.getMemberPhysicalEntityOf()
Class<? extends PhysicalEntity>	PhysicalEntity.getModelInterface()	Overridden to provide better downcasting
Set<PhysicalEntity>	EntityFeature.getNotFeatureOf()	Inverse of getNotFeature() Contents of this set is generated automatically and should not be modified.
Set<PhysicalEntity>	TemplateReaction.getProduct()
Set<PhysicalEntity>	Conversion.getRight()	The participants on the right side of the conversion interaction.

Methods in org.biopax.paxtools.model.level3 with parameters of type PhysicalEntity

Modifier and Type	Method	Description
void	Catalysis.addCofactor(PhysicalEntity cofactor)	Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
void	Complex.addComponent(PhysicalEntity component)	Defines the PhysicalEntity subunits of this complex.
void	Conversion.addLeft(PhysicalEntity left)	Adds a participant to the left side of the conversion interaction.
void	PhysicalEntity.addMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity)
void	TemplateReaction.addProduct(PhysicalEntity product)
void	Conversion.addRight(PhysicalEntity right)	Adds a participant to the right side of the conversion interaction.
boolean	PhysicalEntity.hasEquivalentCellularLocation(PhysicalEntity that)
boolean	PhysicalEntity.hasEquivalentFeatures(PhysicalEntity that)
void	Catalysis.removeCofactor(PhysicalEntity cofactor)	Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
void	Complex.removeComponent(PhysicalEntity component)	Defines the PhysicalEntity subunits of this complex.
void	Conversion.removeLeft(PhysicalEntity left)	Removes a participant from the left side of the conversion interaction.
void	PhysicalEntity.removeMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity)
void	TemplateReaction.removeProduct(PhysicalEntity product)
void	Conversion.removeRight(PhysicalEntity right)	Removes a participant from the right side of the conversion interaction.
void	Stoichiometry.setPhysicalEntity(PhysicalEntity physicalEntity)