org.biopax.paxtools.io.sif.level3

Class ComponentRule

java.lang.Object

org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

org.biopax.paxtools.io.sif.level3.ComponentRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL3

public class ComponentRule
extends InteractionRuleL3Adaptor

This rule class mines complex membership relations. It mines two types of relations. COMPONENT_OF: A is a member of the Complex B, membership relation can be multi step. IN_SAME_COMPONENT: A and B are members of the same complex, and this same complex can be in different level of nesting.

Author:

Emek Demir

Constructor Summary

Constructors

Constructor and Description
ComponentRule()

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets supported interaction types.
void	inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) Infer interactions where A = the given PhysicalEntity.
void	initOptionsNotNull(Map options) Initializes options.

Methods inherited from class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor

checkOption, collectEntities, createAndAdd, createClique, inferInteractions, initOptions

Methods inherited from class java.lang.Object

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

Constructor Detail

ComponentRule

public ComponentRule()

Method Detail

inferInteractionsFromPE

public void inferInteractionsFromPE(InteractionSetL3 interactionSet,
                                    PhysicalEntity pe,
                                    Model model)

Infer interactions where A = the given PhysicalEntity.

Parameters:

interactionSet - to be populated

pe - PhysicalEntity that will be the seed of the inference

model - BioPAX model

initOptionsNotNull

public void initOptionsNotNull(Map options)

Initializes options.

Overrides:

initOptionsNotNull in class InteractionRuleL3Adaptor

Parameters:

options - options map

getRuleTypes

public List<BinaryInteractionType> getRuleTypes()

Gets supported interaction types.

Returns:

interaction types supported