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

Packages that use EntityFeature

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

Uses of EntityFeature in org.biopax.paxtools.controller

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

static java.util.Set<EntityFeature>	FeatureUtils.findFeaturesAddedToSecond(PhysicalEntity first, PhysicalEntity second, boolean fix)
static java.util.Set<EntityFeature>	FeatureUtils.getFeatureIntersection(PhysicalEntity first, int firstClass, PhysicalEntity second, int secondClass)
static java.util.Set<EntityFeature>	FeatureUtils.getFeatureSetByType(PhysicalEntity pe, int type)

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

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

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

java.util.Set<EntityFeature>	EntityReferenceImpl.getEntityFeature() The contents of this set should NOT be modified.
java.util.Set<EntityFeature>	ExperimentalFormImpl.getExperimentalFeature()
java.util.Set<EntityFeature>	PhysicalEntityImpl.getFeature()
java.util.Set<EntityFeature>	EntityFeatureImpl.getMemberFeature()
java.util.Set<EntityFeature>	EntityFeatureImpl.getMemberFeatureOf()
java.lang.Class<? extends EntityFeature>	EntityFeatureImpl.getModelInterface()
java.util.Set<EntityFeature>	PhysicalEntityImpl.getNotFeature()

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

void	EntityReferenceImpl.addEntityFeature(EntityFeature entityFeature)
void	ExperimentalFormImpl.addExperimentalFeature(EntityFeature experimentalFeature)
void	PhysicalEntityImpl.addFeature(EntityFeature feature)
void	EntityFeatureImpl.addMemberFeature(EntityFeature feature)
void	PhysicalEntityImpl.addNotFeature(EntityFeature feature)
boolean	EntityFeatureImpl.atEquivalentLocation(EntityFeature that)
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)

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

protected void	EntityReferenceImpl.setEntityFeature(java.util.Set<EntityFeature> entityFeature)
void	ExperimentalFormImpl.setExperimentalFeature(java.util.Set<EntityFeature> experimentalFeature)
protected void	PhysicalEntityImpl.setFeature(java.util.Set<EntityFeature> feature)
protected void	EntityFeatureImpl.setMemberFeature(java.util.Set<EntityFeature> memberFeature)
protected void	EntityFeatureImpl.setMemberFeatureOf(java.util.Set<EntityFeature> memberFeatureOf)
protected void	PhysicalEntityImpl.setNotFeature(java.util.Set<EntityFeature> featureSet)

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

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

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

java.util.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.
java.util.Set<EntityFeature>	ExperimentalForm.getExperimentalFeature() Contents of this set should not be modified.
java.util.Set<EntityFeature>	PhysicalEntity.getFeature()
java.util.Set<EntityFeature>	EntityFeature.getMemberFeature() An entity feature that belongs to this homology grouping.
java.util.Set<EntityFeature>	EntityFeature.getMemberFeatureOf() Reverse of getMemberFeature()
java.util.Set<EntityFeature>	PhysicalEntity.getNotFeature()

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

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)