001package org.biopax.paxtools.pattern.miner; 002 003import org.biopax.paxtools.pattern.Match; 004import org.biopax.paxtools.pattern.util.Blacklist; 005 006import java.util.Set; 007 008/** 009 * This interface tells that the miner supports SIF output. 010 * @author Ozgun Babur 011 */ 012public interface SIFMiner extends Miner 013{ 014 /** 015 * Gets the label of the source node. 016 * @return source label 017 */ 018 public String getSourceLabel(); 019 020 /** 021 * Gets the label of the target node. 022 * @return target label 023 */ 024 public String getTargetLabel(); 025 026 /** 027 * Gets the type of the interaction. 028 * @return interaction type 029 */ 030 public SIFType getSIFType(); 031 032 /** 033 * Creates SIF interactions for the given match. 034 * @param m match to use for SIF creation 035 * @param fetcher ID generator from BioPAX object 036 * @return SIF interaction 037 */ 038 public Set<SIFInteraction> createSIFInteraction(Match m, IDFetcher fetcher); 039 040 /** 041 * Sets the blacklist that can be used during the search. 042 * @param blacklist the blacklist 043 */ 044 public void setBlacklist(Blacklist blacklist); 045 046 /** 047 * Sets the idFetcher that helps to fasten the search. 048 * @param idFetcher ID generator from BioPAX object 049 */ 050 public void setIDFetcher(IDFetcher idFetcher); 051}