org.biopax.paxtools.io.sif.level3

Class ParticipatesRule

java.lang.Object

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

org.biopax.paxtools.io.sif.level3.ParticipatesRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL3

public class ParticipatesRule
extends InteractionRuleL3Adaptor

Finds pairs of molecules that are participants of the same interaction for the INTERACTS_WITH type, and participants of the same Conversion for the REACTS_WITH type.

Author:

Emek Demir, Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
ParticipatesRule()

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets supported interaction types.
void	inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) Infers interactions starting from 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

ParticipatesRule

public ParticipatesRule()

Method Detail

initOptionsNotNull

public void initOptionsNotNull(Map options)

Initializes options.

Overrides:

initOptionsNotNull in class InteractionRuleL3Adaptor

Parameters:

options - options map

inferInteractionsFromPE

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

Infers interactions starting from the given PhysicalEntity.

Parameters:

interactionSet - to be populated

pe - PhysicalEntity that will be the seed of the inference

model - BioPAX model

getRuleTypes

public List<BinaryInteractionType> getRuleTypes()

Gets supported interaction types.

Returns:

supported interaction types