Uses of Class
org.episteme.natural.biology.loaders.biopax.BioPAXPhysicalEntity

Packages that use BioPAXPhysicalEntity

Package	Description
org.episteme.natural.biology.loaders.biopax	BioPAX loader for biological pathways and networks.

Uses of BioPAXPhysicalEntity in org.episteme.natural.biology.loaders.biopax

Methods in org.episteme.natural.biology.loaders.biopax that return BioPAXPhysicalEntity

Modifier and Type	Method	Description
BioPAXPhysicalEntity	BioPAXCatalysis.getController()
BioPAXPhysicalEntity	BioPAXModel.getEntity(String id)

Methods in org.episteme.natural.biology.loaders.biopax that return types with arguments of type BioPAXPhysicalEntity

Modifier and Type	Method	Description
Collection<BioPAXPhysicalEntity>	BioPAXModel.getEntities()
List<BioPAXPhysicalEntity>	BioPAXBiochemicalReaction.getLeft()
List<BioPAXPhysicalEntity>	BioPAXModel.getProteins()
List<BioPAXPhysicalEntity>	BioPAXBiochemicalReaction.getRight()

Methods in org.episteme.natural.biology.loaders.biopax with parameters of type BioPAXPhysicalEntity

Modifier and Type	Method	Description
void	BioPAXModel.addEntity(BioPAXPhysicalEntity e)
void	BioPAXBiochemicalReaction.addLeft(BioPAXPhysicalEntity e)
void	BioPAXBiochemicalReaction.addRight(BioPAXPhysicalEntity e)
Protein	BioPAXBridge.convertProtein(BioPAXPhysicalEntity entity)	Converts BioPAX protein to Episteme Protein.
Molecule	BioPAXBridge.convertSmallMolecule(BioPAXPhysicalEntity entity)	Converts BioPAX small molecule to Episteme Molecule.
void	BioPAXCatalysis.setController(BioPAXPhysicalEntity c)