Class BioPAXModel

java.lang.Object

org.episteme.natural.biology.loaders.biopax.BioPAXModel

public class BioPAXModel
extends Object

BioPAX model containing pathways, entities, and interactions.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Constructor Summary

Constructors

Constructor	Description
BioPAXModel()

Method Summary

Modifier and Type	Method	Description
void	addEntity(BioPAXPhysicalEntity e)
void	addInteraction(BioPAXInteraction i)
void	addPathway(BioPAXPathway p)
Collection<BioPAXPhysicalEntity>	getEntities()
BioPAXPhysicalEntity	getEntity(String id)
List<BioPAXInteraction>	getInteractions()
List<BioPAXPathway>	getPathways()
List<BioPAXPhysicalEntity>	getProteins()
List<BioPAXInteraction>	getReactions()
String	toString()

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

BioPAXModel

public BioPAXModel()

Method Details

addPathway

public void addPathway(BioPAXPathway p)

getPathways

public List<BioPAXPathway> getPathways()

addEntity

public void addEntity(BioPAXPhysicalEntity e)

getEntities

public Collection<BioPAXPhysicalEntity> getEntities()

getEntity

public BioPAXPhysicalEntity getEntity(String id)

addInteraction

public void addInteraction(BioPAXInteraction i)

getInteractions

public List<BioPAXInteraction> getInteractions()

getProteins

public List<BioPAXPhysicalEntity> getProteins()

getReactions

public List<BioPAXInteraction> getReactions()

toString

public String toString()

Overrides:

toString in class Object