001package org.biopax.paxtools.io.sif.level2; 002 003import org.biopax.paxtools.io.sif.InteractionRule; 004import org.biopax.paxtools.io.sif.InteractionSet; 005import org.biopax.paxtools.model.Model; 006import org.biopax.paxtools.model.level2.physicalEntity; 007 008/** 009 * This interface defines a rule which can be run on BioPAX model L2 to derive 010 * simple interactions. All new rules should implement this interface. 011 * 012 * @author Emek Demir 013 * @author Ozgun Babur 014 */ 015public interface InteractionRuleL2 extends InteractionRule 016{ 017 /** 018 * This method populates the interactionSet with simple interactions that can 019 * be derived from the model based on this rule. 020 * @param interactionSet to be populated 021 * @param entity first physicalEntity 022 * @param model BioPAX model 023 */ 024 void inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity entity, Model model); 025}