org.biopax.paxtools.io.sif.level3

Interface InteractionRuleL3

All Superinterfaces:

InteractionRule

All Known Implementing Classes:

ComponentRule, ConsecutiveCatalysisRule, ControlRule, ControlsTogetherRule, ExpressionRule, InteractionRuleL3Adaptor, ParticipatesRule

public interface InteractionRuleL3
extends InteractionRule

This interface defines a rule which can be run on BioPAX model L2 to derive simple interactions. All new rules should implement this interface.

Author:

Emek Demir, Ozgun Babur

Method Summary

Modifier and Type	Method and Description
void	inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.

Methods inherited from interface org.biopax.paxtools.io.sif.InteractionRule

getRuleTypes, inferInteractions, initOptions

Method Detail

inferInteractionsFromPE

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

This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.

Parameters:

interactionSet - to be populated

pe - PhysicalEntity that will be the seed of the inference

model - BioPAX model