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

Packages that use SimplePhysicalEntity

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 SimplePhysicalEntity in org.biopax.paxtools.controller

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

Modifier and Type

Method and Description

static void

ModelUtils.addMissingEntityReference(Model model, SimplePhysicalEntity pe) For a non-generic simple physical entity (memberPhysicalEntity property is empty) that does not have entityReference property defined, this method generates and adds a new entity reference of proper type to both this entity and the model, and also copies names and xrefs from the source physical entity to the generated entity reference (UnificationXrefs are converted to RelationshipXref and then also deleted from the original entity.)

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

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

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

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

Modifier and Type	Method and Description
Set<SimplePhysicalEntity>	EntityReferenceImpl.getEntityReferenceOf()
Set<SimplePhysicalEntity>	ComplexImpl.getSimpleMembers()
protected Set<SimplePhysicalEntity>	ComplexImpl.getSimpleMembers(Set<SimplePhysicalEntity> set)

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

Modifier and Type	Method and Description
protected void	ComplexImpl.collectSimpleMembersRecursive(PhysicalEntity pe, Set<SimplePhysicalEntity> set)
protected Set<SimplePhysicalEntity>	ComplexImpl.getSimpleMembers(Set<SimplePhysicalEntity> set)

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

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

Modifier and Type	Interface and Description
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	SmallMolecule

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

Modifier and Type	Method and Description
Set<SimplePhysicalEntity>	EntityReference.getEntityReferenceOf() Inverse of getEntityReference()
Set<SimplePhysicalEntity>	Complex.getSimpleMembers() Gets the member physical entities which are not complex.