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AIMA-Java Core Algorithms from the book Artificial Intelligence a Modern Approach 3rd Ed.
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package aima.core.probability.bayes.impl;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import aima.core.probability.RandomVariable;
import aima.core.probability.bayes.BayesianNetwork;
import aima.core.probability.bayes.Node;

/**
 * Default implementation of the BayesianNetwork interface.
 * 
 * @author Ciaran O'Reilly
 * @author Ravi Mohan
 */
public class BayesNet implements BayesianNetwork {
	protected Set rootNodes = new LinkedHashSet();
	protected List variables = new ArrayList();
	protected Map varToNodeMap = new HashMap();

	public BayesNet(Node... rootNodes) {
		if (null == rootNodes) {
			throw new IllegalArgumentException(
					"Root Nodes need to be specified.");
		}
		for (Node n : rootNodes) {
			this.rootNodes.add(n);
		}
		if (this.rootNodes.size() != rootNodes.length) {
			throw new IllegalArgumentException(
					"Duplicate Root Nodes Passed in.");
		}
		// Ensure is a DAG
		checkIsDAGAndCollectVariablesInTopologicalOrder();
		variables = Collections.unmodifiableList(variables);
	}

	//
	// START-BayesianNetwork
	@Override
	public List getVariablesInTopologicalOrder() {
		return variables;
	}

	@Override
	public Node getNode(RandomVariable rv) {
		return varToNodeMap.get(rv);
	}

	// END-BayesianNetwork
	//

	//
	// PRIVATE METHODS
	//
	private void checkIsDAGAndCollectVariablesInTopologicalOrder() {

		// Topological sort based on logic described at:
		// http://en.wikipedia.org/wiki/Topoligical_sorting
		Set seenAlready = new HashSet();
		Map> incomingEdges = new HashMap>();
		Set s = new LinkedHashSet();
		for (Node n : this.rootNodes) {
			walkNode(n, seenAlready, incomingEdges, s);
		}
		while (!s.isEmpty()) {
			Node n = s.iterator().next();
			s.remove(n);
			variables.add(n.getRandomVariable());
			varToNodeMap.put(n.getRandomVariable(), n);
			for (Node m : n.getChildren()) {
				List edges = incomingEdges.get(m);
				edges.remove(n);
				if (edges.isEmpty()) {
					s.add(m);
				}
			}
		}

		for (List edges : incomingEdges.values()) {
			if (!edges.isEmpty()) {
				throw new IllegalArgumentException(
						"Network contains at least one cycle in it, must be a DAG.");
			}
		}
	}

	private void walkNode(Node n, Set seenAlready,
			Map> incomingEdges, Set rootNodes) {
		if (!seenAlready.contains(n)) {
			seenAlready.add(n);
			// Check if has no incoming edges
			if (n.isRoot()) {
				rootNodes.add(n);
			}
			incomingEdges.put(n, new ArrayList(n.getParents()));
			for (Node c : n.getChildren()) {
				walkNode(c, seenAlready, incomingEdges, rootNodes);
			}
		}
	}
}