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BioPAX graph-theoretic querying - for finding paths between molecules, or identifying molecules that are reachable through specific paths, using the BioPAX pathway data model.

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package org.biopax.paxtools.query.model;

import java.util.Map;
import java.util.Set;

/**
 * This graph interface is used in graph algorithms.
 *
 * @author Ozgun Babur
 */
public interface Graph
{
	/**
	 * Gets the wrapper of the related object.
	 * @param obj The wrapped object
	 * @return Wrapper
	 */
	GraphObject getGraphObject(Object obj);

	/**
	 * Gets the set of wrappers for the given wrapped object set.
	 * @param objects Wrapped objects
	 * @return Related wrappers
	 */
	Set getWrapperSet(Set objects);

	/**
	 * Gets a map from objects to their wrappers.
	 * @param objects Wrapped objects
	 * @return Object-to-wrapper map
	 */
	Map getWrapperMap(Set objects);

	/**
	 * Gets the wrapped objects of the given wrapper set.
	 * @param wrappers Wrappers
	 * @return Wrapped objects
	 */
	Set