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

Packages that use EntityReference

org.biopax.paxtools.controller
org.biopax.paxtools.impl.level3
org.biopax.paxtools.model.level3

Uses of EntityReference in org.biopax.paxtools.controller

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

static boolean

FeatureUtils.checkERFeatureSet(EntityReference er, boolean fix)

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

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

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

EntityReference	EntityFeatureImpl.getEntityFeatureOf()
protected EntityReference	EntityFeatureImpl.getEntityFeatureXOf()
EntityReference	SimplePhysicalEntityImpl.getEntityReference()
protected EntityReference	SimplePhysicalEntityImpl.getEntityReferenceX()

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

java.util.Set<EntityReference>	SimplePhysicalEntityImpl.getGenericEntityReferences()
java.util.Set<EntityReference>	EntityReferenceImpl.getMemberEntityReference()
java.util.Set<EntityReference>	EntityReferenceImpl.getMemberEntityReferenceOf()
java.util.Set<EntityReference>	ComplexImpl.getMemberReferences()
java.lang.Class<? extends EntityReference>	EntityReferenceImpl.getModelInterface()

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

void	EntityReferenceImpl.addMemberEntityReference(EntityReference memberEntity)
void	EntityReferenceImpl.removeMemberEntityReference(EntityReference memberEntity)
protected void	EntityFeatureImpl.setEntityFeatureOf(EntityReference newEntityReference) This method sets the EntityReference for this feature.
protected void	EntityFeatureImpl.setEntityFeatureXOf(EntityReference entityReference)
void	SimplePhysicalEntityImpl.setEntityReference(EntityReference entityReference)
protected void	SimplePhysicalEntityImpl.setEntityReferenceX(EntityReference entityReference)

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

protected void	EntityReferenceImpl.setMemberEntity(java.util.Set<EntityReference> memberEntity)
void	EntityReferenceImpl.setMemberEntityReference(java.util.Set<EntityReference> memberEntity)
protected void	EntityReferenceImpl.setMemberEntityReferenceOf(java.util.Set<EntityReference> newOwnerEntityReferenceSet)

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

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

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

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

java.util.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
java.util.Set<EntityReference>	EntityReference.getMemberEntityReference()
java.util.Set<EntityReference>	EntityReference.getMemberEntityReferenceOf() Reverse of getMemberEntityReference()
java.util.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

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.