org.biopax.paxtools.io.sif.level3

Class ExpressionRule

java.lang.Object

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

org.biopax.paxtools.io.sif.level3.ExpressionRule

All Implemented Interfaces:

InteractionRule, InteractionRuleL3

public class ExpressionRule
extends InteractionRuleL3Adaptor

This rule mines the transctivation and transinhibition relations between entities.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
ExpressionRule()

Method Summary

Modifier and Type	Method and Description
List<BinaryInteractionType>	getRuleTypes() Gets a list of the rule types that this class implements.
void	inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) Searches the transcriptional relations using the pattern, then decides the interaction type according to the type of the Control.

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

checkOption, collectEntities, createAndAdd, createClique, inferInteractions, initOptions, initOptionsNotNull

Methods inherited from class java.lang.Object

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

Constructor Detail

ExpressionRule

public ExpressionRule()

Method Detail

inferInteractionsFromPE

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

Searches the transcriptional relations using the pattern, then decides the interaction type according to the type of the Control.

Parameters:

interactionSet - to be populated

pe - PhysicalEntity that will be the seed of the inference

model - BioPAX model

getRuleTypes

public List<BinaryInteractionType> getRuleTypes()

Gets a list of the rule types that this class implements.

Returns:

supported rules