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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.wrapperL3;

import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.*;
import org.biopax.paxtools.query.model.AbstractGraph;
import org.biopax.paxtools.query.model.GraphObject;
import org.biopax.paxtools.query.model.Node;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.*;

/**
 * Wrapper for L3 Graphs.
 *
 * @author Ozgun Babur
 */
public class GraphL3 extends AbstractGraph 
{
	/**
	 * The model to be wrapped.
	 */
	protected Model model;

	protected List filters;

	/**
	 * Log for logging.
	 */
	protected final Logger log = LoggerFactory.getLogger(GraphL3.class);

	/**
	 * Constructor with the model and the IDs of the ubiquitous molecules. IDs can be null, meaning
	 * no labeling is desired.
	 * @param model Model to wrap
	 * @param filters for filtering graph elements
	 */
	public GraphL3(Model model, Filter... filters)
	{
		assert model.getLevel() == BioPAXLevel.L3;
		this.model = model;

		if (filters.length > 0)
		{
			this.filters = Arrays.asList(filters);
		}
	}

	/**
	 * There must be no filter opposing to traverse this object to traverse it.
	 * @param ele element to check
	 * @return true if ok to traverse
	 */
	private boolean passesFilters(Level3Element ele)
	{
		if (filters == null) return true;

		for (Filter filter : filters)
		{
			if (!filter.okToTraverse(ele)) return false;
		}
		return true;
	}

	/**
	 * This method creates a wrapper for every wrappable L3 element.
	 * @param obj Object to wrap
	 * @return The wrapper
	 */
	@Override
	public Node wrap(Object obj)
	{
		// Check if the object is level3
		if (!(obj instanceof Level3Element)) throw new IllegalArgumentException(
			"An object other than a Level3Element is trying to be wrapped: " + obj);

		// Check if the object passes the filter
		if (!passesFilters((Level3Element) obj)) return null;

		// Wrap if traversible

		if (obj instanceof PhysicalEntity)
		{
			return new PhysicalEntityWrapper((PhysicalEntity) obj, this);
		}
		else if (obj instanceof Conversion)
		{
			return new ConversionWrapper((Conversion) obj, this);
		}
		else if (obj instanceof TemplateReaction)
		{
			return new TemplateReactionWrapper((TemplateReaction) obj, this);
		}
		else if (obj instanceof Control)
		{
			return new ControlWrapper((Control) obj, this);
		}
		else
		{
			if (log.isWarnEnabled())
			{
				log.warn("Invalid BioPAX object to wrap as node. Ignoring: " + obj);
			}
			return null;
		}
	}

	/**
	 * RDF IDs of elements is used as key in the object map.
	 * @param wrapped Object to wrap
	 * @return Key
	 */
	@Override
	public String getKey(Object wrapped)
	{
		if (wrapped instanceof BioPAXElement)
		{
			return ((BioPAXElement) wrapped).getUri();
		}

		throw new IllegalArgumentException("Object cannot be wrapped: " + wrapped);
	}

	/**
	 * Gets wrappers of given elements
	 * @param objects Wrapped objects
	 * @return wrappers
	 */
	public Set getWrapperSet(Set objects)
	{
		Set wrapped = new HashSet();

		for (Object object : objects)
		{
			Node node = (Node) getGraphObject(object);
			if (node != null)
			{
				wrapped.add(node);
			}
		}
		return wrapped;
	}

	/**
	 * Gets an element-to-wrapper map for the given elements.
	 * @param objects Wrapped objects
	 * @return object-to-wrapper map
	 */
	public Map getWrapperMap(Set objects)
	{
		Map map = new HashMap();

		for (Object object : objects)
		{
			Node node = (Node) getGraphObject(object);
			if (node != null)
			{
				map.put(object, node);
			}
		}
		return map;
	}

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