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

Packages that use PhysicalEntity

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

Uses of PhysicalEntity in org.biopax.paxtools.controller

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

static boolean	FeatureUtils.checkMutuallyExclusiveSets(PhysicalEntity pe)
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 PhysicalEntity in org.biopax.paxtools.impl.level3

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

class	ComplexImpl
class	DnaImpl
class	DnaRegionImpl
class	NucleicAcidImpl
class	PhysicalEntityImpl
class	ProteinImpl
class	RnaImpl
class	RnaRegionImpl
class	SimplePhysicalEntityImpl
class	SmallMoleculeImpl

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

PhysicalEntity

StoichiometryImpl.getPhysicalEntity()

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

java.util.Set<PhysicalEntity>	CatalysisImpl.getCofactor()
java.util.Set<PhysicalEntity>	ComplexImpl.getComponent()
java.util.Set<PhysicalEntity>	EntityFeatureImpl.getFeatureOf()
java.util.Set<PhysicalEntity>	ConversionImpl.getLeft()
java.util.Set<PhysicalEntity>	PhysicalEntityImpl.getMemberPhysicalEntity()
java.util.Set<PhysicalEntity>	PhysicalEntityImpl.getMemberPhysicalEntityOf()
java.lang.Class<? extends PhysicalEntity>	SmallMoleculeImpl.getModelInterface()
java.lang.Class<? extends PhysicalEntity>	PhysicalEntityImpl.getModelInterface()
java.util.Set<PhysicalEntity>	EntityFeatureImpl.getNotFeatureOf()
protected java.util.Set<PhysicalEntity>	ControlImpl.getPeController()
java.lang.Class<? extends PhysicalEntity>	ComplexImpl.getPhysicalEntityClass()
java.util.Set<PhysicalEntity>	TemplateReactionImpl.getProduct()
java.util.Set<PhysicalEntity>	ConversionImpl.getRight()

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

void	CatalysisImpl.addCofactor(PhysicalEntity cofactor)
void	ComplexImpl.addComponent(PhysicalEntity component)
void	ConversionImpl.addLeft(PhysicalEntity left)
void	PhysicalEntityImpl.addMemberPhysicalEntity(PhysicalEntity newMember)
void	TemplateReactionImpl.addProduct(PhysicalEntity product)
void	ConversionImpl.addRight(PhysicalEntity right)
boolean	PhysicalEntityImpl.hasEquivalentCellularLocation(PhysicalEntity that)
boolean	PhysicalEntityImpl.hasEquivalentFeatures(PhysicalEntity that)
void	CatalysisImpl.removeCofactor(PhysicalEntity cofactor)
void	ComplexImpl.removeComponent(PhysicalEntity component)
void	ConversionImpl.removeLeft(PhysicalEntity left)
void	PhysicalEntityImpl.removeMemberPhysicalEntity(PhysicalEntity oldMember)
void	TemplateReactionImpl.removeProduct(PhysicalEntity product)
void	ConversionImpl.removeRight(PhysicalEntity right)
void	StoichiometryImpl.setPhysicalEntity(PhysicalEntity PhysicalEntity)

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

protected void	CatalysisImpl.setCofactor(java.util.Set<PhysicalEntity> cofactor)
protected void	ComplexImpl.setComponent(java.util.Set<PhysicalEntity> component)
protected void	EntityFeatureImpl.setFeatureOf(java.util.Set<PhysicalEntity> featureOf)
protected void	ConversionImpl.setLeft(java.util.Set<PhysicalEntity> left)
protected void	PhysicalEntityImpl.setMemberPhysicalEntity(java.util.Set<PhysicalEntity> memberPhysicalEntity)
protected void	PhysicalEntityImpl.setMemberPhysicalEntityOf(java.util.Set<PhysicalEntity> memberPhysicalEntityOf)
protected void	EntityFeatureImpl.setNotFeatureOf(java.util.Set<PhysicalEntity> notFeatureOf)
protected void	ControlImpl.setPeController(java.util.Set<PhysicalEntity> peController)
protected void	TemplateReactionImpl.setProduct(java.util.Set<PhysicalEntity> product)
protected void	ConversionImpl.setRight(java.util.Set<PhysicalEntity> right)

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

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

interface	Complex Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.
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	SimplePhysicalEntity Tagger interface for non-complex physical entities
interface	SmallMolecule

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

PhysicalEntity

Stoichiometry.getPhysicalEntity()

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

java.util.Set<PhysicalEntity>	Catalysis.getCofactor() Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
java.util.Set<PhysicalEntity>	Complex.getComponent() Defines the PhysicalEntity subunits of this complex.
java.util.Set<PhysicalEntity>	EntityFeature.getFeatureOf() Inverse of getFeature() Contents of this set is generated automatically and should not be modified.
java.util.Set<PhysicalEntity>	Conversion.getLeft() The participants on the left side of the conversion interaction.
java.util.Set<PhysicalEntity>	PhysicalEntity.getMemberPhysicalEntity()
java.util.Set<PhysicalEntity>	PhysicalEntity.getMemberPhysicalEntityOf()
java.lang.Class<? extends PhysicalEntity>	PhysicalEntity.getModelInterface() Overridden to provide better downcasting
java.util.Set<PhysicalEntity>	EntityFeature.getNotFeatureOf() Inverse of getNotFeature() Contents of this set is generated automatically and should not be modified.
java.util.Set<PhysicalEntity>	TemplateReaction.getProduct()
java.util.Set<PhysicalEntity>	Conversion.getRight() The participants on the right side of the conversion interaction.

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

void	Catalysis.addCofactor(PhysicalEntity cofactor) Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
void	Complex.addComponent(PhysicalEntity component) Defines the PhysicalEntity subunits of this complex.
void	Conversion.addLeft(PhysicalEntity left) Adds a participant to the left side of the conversion interaction.
void	PhysicalEntity.addMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity)
void	TemplateReaction.addProduct(PhysicalEntity product)
void	Conversion.addRight(PhysicalEntity right) Adds a participant to the right side of the conversion interaction.
boolean	PhysicalEntity.hasEquivalentCellularLocation(PhysicalEntity that)
boolean	PhysicalEntity.hasEquivalentFeatures(PhysicalEntity that)
void	Catalysis.removeCofactor(PhysicalEntity cofactor) Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
void	Complex.removeComponent(PhysicalEntity component) Defines the PhysicalEntity subunits of this complex.
void	Conversion.removeLeft(PhysicalEntity left) Removes a participant from the left side of the conversion interaction.
void	PhysicalEntity.removeMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity)
void	TemplateReaction.removeProduct(PhysicalEntity product)
void	Conversion.removeRight(PhysicalEntity right) Removes a participant from the right side of the conversion interaction.
void	Stoichiometry.setPhysicalEntity(PhysicalEntity physicalEntity)