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

Packages that use EntityFeature

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 EntityFeature in org.biopax.paxtools.controller

Methods in org.biopax.paxtools.controller that return types with arguments of type EntityFeature

Modifier and Type	Method and 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)

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

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

Modifier and Type	Class and Description
class	BindingFeatureImpl
class	CovalentBindingFeatureImpl
class	EntityFeatureImpl
class	FragmentFeatureImpl
class	ModificationFeatureImpl

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

Modifier and Type	Method and Description
Set<EntityFeature>	EntityReferenceImpl.getEntityFeature()
Set<EntityFeature>	ExperimentalFormImpl.getExperimentalFeature()
Set<EntityFeature>	PhysicalEntityImpl.getFeature()
Set<EntityFeature>	EntityFeatureImpl.getMemberFeature()
Set<EntityFeature>	EntityFeatureImpl.getMemberFeatureOf()
Class<? extends EntityFeature>	EntityFeatureImpl.getModelInterface()
Set<EntityFeature>	PhysicalEntityImpl.getNotFeature()

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

Modifier and Type	Method and Description
void	EntityReferenceImpl.addEntityFeature(EntityFeature entityFeature)
void	ExperimentalFormImpl.addExperimentalFeature(EntityFeature experimentalFeature)
void	PhysicalEntityImpl.addFeature(EntityFeature feature)
void	SmallMoleculeImpl.addFeature(EntityFeature feature)
void	EntityFeatureImpl.addMemberFeature(EntityFeature feature)
void	PhysicalEntityImpl.addNotFeature(EntityFeature feature)
void	SmallMoleculeImpl.addNotFeature(EntityFeature feature)
boolean	EntityFeatureImpl.atEquivalentLocation(EntityFeature that) This method returns true if and only if two entity features are on the same known location on a known ER.
void	EntityReferenceImpl.removeEntityFeature(EntityFeature entityFeature)
void	ExperimentalFormImpl.removeExperimentalFeature(EntityFeature experimentalFeature)
void	PhysicalEntityImpl.removeFeature(EntityFeature feature)
void	EntityFeatureImpl.removeMemberFeature(EntityFeature feature)
void	PhysicalEntityImpl.removeNotFeature(EntityFeature feature)

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

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

Modifier and Type	Interface and Description
interface	BindingFeature
interface	CovalentBindingFeature Definition: An entity feature that represent the covalently bound state of a physical entity.
interface	FragmentFeature Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.
interface	ModificationFeature Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.

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

Modifier and Type	Method and Description
Set<EntityFeature>	EntityReference.getEntityFeature() Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.
Set<EntityFeature>	ExperimentalForm.getExperimentalFeature() Contents of this set should not be modified.
Set<EntityFeature>	PhysicalEntity.getFeature()
Set<EntityFeature>	EntityFeature.getMemberFeature() An entity feature that belongs to this homology grouping.
Set<EntityFeature>	EntityFeature.getMemberFeatureOf() Reverse of getMemberFeature()
Set<EntityFeature>	PhysicalEntity.getNotFeature()

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

Modifier and Type	Method and Description
void	EntityReference.addEntityFeature(EntityFeature feature) Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.
void	ExperimentalForm.addExperimentalFeature(EntityFeature experimentalFeature) This method adds an experimental feature
void	PhysicalEntity.addFeature(EntityFeature feature)
void	EntityFeature.addMemberFeature(EntityFeature entityFeature) An entity feature that belongs to this homology grouping.
void	PhysicalEntity.addNotFeature(EntityFeature feature)
boolean	EntityFeature.atEquivalentLocation(EntityFeature that)
void	EntityReference.removeEntityFeature(EntityFeature feature) Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.
void	ExperimentalForm.removeExperimentalFeature(EntityFeature experimentalFeature) This method removes an experimental feature
void	PhysicalEntity.removeFeature(EntityFeature feature)
void	EntityFeature.removeMemberFeature(EntityFeature entityFeature) An entity feature that belongs to this homology grouping.
void	PhysicalEntity.removeNotFeature(EntityFeature feature)