org.biopax.paxtools.io.sif.level2

Class AffectsRule

java.lang.Object

org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor

org.biopax.paxtools.io.sif.level2.AffectsRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL2

public class AffectsRule
extends InteractionRuleL2Adaptor

This is an experimental rule that mines ACTIVATES and INHIBITS relations between molecules.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
AffectsRule()

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets supported interactions types.
void	inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity pe, Model model) Infers interactions using the given physicalEntity as seed.

Methods inherited from class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor

inferInteractions, initOptions, initOptionsNotNull

Methods inherited from class java.lang.Object

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

Constructor Detail

AffectsRule

public AffectsRule()

Method Detail

inferInteractionsFromPE

public void inferInteractionsFromPE(InteractionSet interactionSet,
                                    physicalEntity pe,
                                    Model model)

Infers interactions using the given physicalEntity as seed.

Parameters:

interactionSet - to be populated

pe - first physicalEntity

model - BioPAX model

getRuleTypes

public List<BinaryInteractionType> getRuleTypes()

Gets supported interactions types.

Returns:

supported interactions types