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

Packages that use EntityReference

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 EntityReference in org.biopax.paxtools.controller

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

Modifier and Type	Method and Description
static boolean	ModelUtils.checkERFeatureSet(EntityReference er, boolean fix) Finds and adds all (missing) entity features to given entity reference from all its owner simple physical entities ('feature' and 'notFeature' properties).

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

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

Modifier and Type	Class and Description
class	DnaReferenceImpl
class	DnaRegionReferenceImpl
class	EntityReferenceImpl
class	NucleicAcidReferenceImpl
class	NucleicAcidRegionReferenceImpl
class	ProteinReferenceImpl
class	RnaReferenceImpl
class	RnaRegionReferenceImpl
class	SequenceEntityReferenceImpl
class	SmallMoleculeReferenceImpl

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

Modifier and Type	Method and Description
EntityReference	EntityFeatureImpl.getEntityFeatureOf()
EntityReference	SimplePhysicalEntityImpl.getEntityReference()

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

Modifier and Type	Method and Description
Set<EntityReference>	SimplePhysicalEntityImpl.getGenericEntityReferences()
Set<EntityReference>	EntityReferenceImpl.getMemberEntityReference()
Set<EntityReference>	EntityReferenceImpl.getMemberEntityReferenceOf()
Set<EntityReference>	ComplexImpl.getMemberReferences()
Class<? extends EntityReference>	EntityReferenceImpl.getModelInterface()

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

Modifier and Type	Method and Description
void	EntityReferenceImpl.addMemberEntityReference(EntityReference memberEntity)
void	EntityReferenceImpl.removeMemberEntityReference(EntityReference memberEntity)
void	EntityFeatureImpl.setEntityFeatureOf(EntityReference entityReference)
void	DnaRegionImpl.setEntityReference(EntityReference entityReference)
void	DnaImpl.setEntityReference(EntityReference entityReference)
void	RnaImpl.setEntityReference(EntityReference entityReference)
void	SimplePhysicalEntityImpl.setEntityReference(EntityReference entityReference)
void	ProteinImpl.setEntityReference(EntityReference entityReference)
void	RnaRegionImpl.setEntityReference(EntityReference entityReference)
void	SmallMoleculeImpl.setEntityReference(EntityReference entityReference)

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

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

Modifier and Type	Interface and Description
interface	DnaReference A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.
interface	DnaRegionReference Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.
interface	NucleicAcidReference Role interface for NucleicAcidReferences, namely DNA and RNA.
interface	NucleicAcidRegionReference
interface	ProteinReference Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence.
interface	RnaReference
interface	RnaRegionReference A RNA region reference
interface	SequenceEntityReference Tagger interface for protein, dna and rna entities
interface	SmallMoleculeReference

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

Modifier and Type	Method and Description
EntityReference	EntityFeature.getEntityFeatureOf() Inverse of getEntityFeature()
EntityReference	SimplePhysicalEntity.getEntityReference() Reference entity for this physical entity.

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

Modifier and Type	Method and Description
Set<EntityReference>	SimplePhysicalEntity.getGenericEntityReferences() This method returns: The entity reference of this PhysicalEntity plus If this PhysicalEntity has member PhysicalEntities their generic EntityReferences iteratively plus If the EntityReference of this PhysicalEntity has member EntityReferences their members iteratively
Set<EntityReference>	EntityReference.getMemberEntityReference()
Set<EntityReference>	EntityReference.getMemberEntityReferenceOf() Reverse of getMemberEntityReference()
Set<EntityReference>	Complex.getMemberReferences() Gets the EntityReferences of the member simple physical entities.

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

Modifier and Type	Method and Description
void	EntityReference.addMemberEntityReference(EntityReference entityReference) Adds the given entityReference to the member list
void	EntityReference.removeMemberEntityReference(EntityReference entityReference) Removes the given entityReference from the member list
void	SimplePhysicalEntity.setEntityReference(EntityReference entityReference) Reference entity for this physical entity.