001package org.biopax.paxtools.io.sif.level3; 002 003import org.biopax.paxtools.io.sif.InteractionRule; 004import org.biopax.paxtools.model.Model; 005import org.biopax.paxtools.model.level3.PhysicalEntity; 006 007/** 008 * This interface defines a rule which can be run on BioPAX model L2 to derive 009 * simple interactions. All new rules should implement this interface. 010 * 011 * @author Emek Demir 012 * @author Ozgun Babur 013 */ 014public interface InteractionRuleL3 extends InteractionRule 015{ 016 /** 017 * This method populates the interactionSet with simple interactions that can 018 * be derived from the model based on this rule. 019 * @param interactionSet to be populated 020 * @param pe PhysicalEntity that will be the seed of the inference 021 * @param model BioPAX model 022 */ 023 void inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model); 024}