BIFHandler.java

/*
 * Encog(tm) Core v3.4 - Java Version
 * http://www.heatonresearch.com/encog/
 * https://github.com/encog/encog-java-core
 
 * Copyright 2008-2016 Heaton Research, Inc.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *   
 * For more information on Heaton Research copyrights, licenses 
 * and trademarks visit:
 * http://www.heatonresearch.com/copyright
 */
package org.encog.ml.bayesian.bif;

import java.util.ArrayList;
import java.util.List;

import org.encog.ml.bayesian.BayesianChoice;
import org.encog.ml.bayesian.BayesianEvent;
import org.encog.ml.bayesian.BayesianNetwork;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;

/**
 * Handler, used to parse the XML BIF files.
 */
public class BIFHandler extends DefaultHandler {
	/**
	 * The current section.
	 */
	private final List<FileSection> currentSection = new ArrayList<FileSection>();
	
	/**
	 * BIF variables.
	 */
	private final List<BIFVariable> bifVariables = new ArrayList<BIFVariable>();
	
	/**
	 * BIF definitions.
	 */
	private final List<BIFDefinition> bifDefinitions = new ArrayList<BIFDefinition>();
	
	/**
	 * The current variable.
	 */
	private BIFVariable currentVariable;
	
	/**
	 * The current definition.
	 */
	private BIFDefinition currentDefinition;
	
	/**
	 * THe current string.
	 */
	private String currentString;

	
	/**
	 * The network bing loaded.
	 */
	private BayesianNetwork network;

	/**
	 * Constructor.
	 */
	public BIFHandler() {
		this.network = new BayesianNetwork();
	}

	/**
	 * Handle the beginning of the BIF tag.
	 * @param qName The name of the tag.
	 * @param attributes The attributes.
	 */
	private void handleBeginBIF(String qName, Attributes attributes) {
		if (qName.equals("NETWORK")) {
			this.currentSection.add(FileSection.NETWORK);
		}
	}

	/**
	 * Handle the beginning of the BIF tag.
	 * @param qName The name of the tag.
	 * @param attributes The attributes.
	 */
	private void handleBeginNETWORK(String qName, Attributes attributes) {
		if (qName.equals("VARIABLE")) {
			this.currentSection.add(FileSection.VARIABLE);
			this.currentVariable = new BIFVariable();
			this.bifVariables.add(this.currentVariable);
		} else if (qName.equals("DEFINITION")) {
			this.currentSection.add(FileSection.DEFINITION);
			this.currentDefinition = new BIFDefinition();
			this.bifDefinitions.add(this.currentDefinition);
		}
	}

	/**
	 * Handle the beginning of the BIF tag.
	 * @param qName The name of the tag.
	 * @param attributes The attributes.
	 */
	private void handleBeginVARIABLE(String qName, Attributes attributes) {
		if (qName.equals("VARIABLE")) {
			this.currentVariable = new BIFVariable();
			this.bifVariables.add(this.currentVariable);
		}
	}

	/**
	 * Handle the beginning of the DEFINITION tag.
	 * @param qName The name of the tag.
	 */
	private void handleBeginDEFINITION(String qName, Attributes attributes) {
		if (qName.equals("DEFINITION")) {
			this.currentDefinition = new BIFDefinition();
			this.bifDefinitions.add(this.currentDefinition);
		}
	}

	/**
	 * Handle the end of the BIF tag.
	 * @param qName The name of the tag.
	 */
	private void handleEndBIF(String qName) {
		if (qName.equals("BIF")) {
			this.currentSection.remove(this.currentSection.size() - 1);
		}
	}

	/**
	 * Handle the end of the NETWORK tag.
	 * @param qName The name of the tag.
	 */
	private void handleEndNETWORK(String qName) {
		if (qName.equals("NETWORK")) {
			this.currentSection.remove(this.currentSection.size() - 1);
		}
	}

	/**
	 * Handle the end of the VARIABLE tag.
	 * @param qName The name of the tag.
	 */
	private void handleEndVARIABLE(String qName) {
		if (qName.equals("NAME")) {
			this.currentVariable.setName(this.currentString);
		} else if (qName.equals("OUTCOME")) {
			this.currentVariable.addOption(this.currentString);
		} else if( qName.equals("VARIABLE") ) {
			this.currentSection.remove(this.currentSection.size() - 1);
		}
	}

	/**
	 * Handle the end of the DEFINITION tag.
	 * @param qName The name of the tag.
	 */
	private void handleEndDEFINITION(String qName) {
		if (qName.equals("FOR")) {
			this.currentDefinition.setForDefinition(this.currentString);
		} else if (qName.equals("GIVEN")) {
			this.currentDefinition.addGiven(this.currentString);
		} else if (qName.equals("TABLE")) {
			this.currentDefinition.setTable(this.currentString);
		} else if( qName.equals("DEFINITION") ) {
			this.currentSection.remove(this.currentSection.size() - 1);
		}
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public void startElement(String uri, String localName, String qName,
			Attributes attributes) throws SAXException {
		super.startElement(uri, localName, qName, attributes);

		if (this.currentSection.size() == 0 && qName.equals("BIF")) {
			this.currentSection.add(FileSection.BIF);
		}

		else if (this.currentSection.size() > 0) {
			switch (this.currentSection.get(this.currentSection.size() - 1)) {
			case BIF:
				handleBeginBIF(qName, attributes);
				break;
			case DEFINITION:
				handleBeginDEFINITION(qName, attributes);
				break;
			case NETWORK:
				handleBeginNETWORK(qName, attributes);
				break;
			case VARIABLE:
				handleBeginVARIABLE(qName, attributes);
				break;
			}
		}
	}

	/**
	 * @return The network being parsed.
	 */
	public BayesianNetwork getNetwork() {
		return network;
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public void endElement(String uri, String localName, String qName)
			throws SAXException {
		super.endElement(uri, localName, qName);

		if (this.currentSection.size() > 0) {
			switch (this.currentSection.get(this.currentSection.size() - 1)) {
			case BIF:
				handleEndBIF(qName);
				break;
			case DEFINITION:
				handleEndDEFINITION(qName);
				break;
			case NETWORK:
				handleEndNETWORK(qName);
				break;
			case VARIABLE:
				handleEndVARIABLE(qName);
				break;
			}
		}
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public void endDocument() throws SAXException {
		super.endDocument();

		// define variables
		for (BIFVariable v : this.bifVariables) {
			List<BayesianChoice> c = new ArrayList<BayesianChoice>();
			int index = 0;
			for(String s : v.getOptions() ) {
				c.add(new BayesianChoice(s,index++));
			}
			
			this.network.createEvent(v.getName(), c);
		}

		// define relations 
		for (BIFDefinition d : this.bifDefinitions) {
			BayesianEvent childEvent = this.network.requireEvent(d
					.getForDefinition());
			for (String s : d.getGivenDefinitions()) {
				BayesianEvent parentEvent = this.network.requireEvent(s);
				this.network.createDependency(parentEvent, childEvent);
			}
		}

		this.network.finalizeStructure();
		
		// define probabilities
		
		for (BIFDefinition d : this.bifDefinitions) {
			double[] t = d.getTable();
			BayesianEvent childEvent = this.network.requireEvent(d.getForDefinition());
			
			int tableIndex = 0;
			int[] args = new int[childEvent.getParents().size()];
			do {
				for(int result = 0; result<childEvent.getChoices().size();result++) {
					childEvent.getTable().addLine(t[tableIndex++], result, args);	
				}
			} while(BIFUtil.rollArgs(childEvent,args));
		}
	}
	

	/**
	 * {@inheritDoc}
	 */
	@Override
	public void characters(char[] ch, int start, int length)
			throws SAXException {
		super.characters(ch, start, length);
		this.currentString = new String(ch, start, length);
	}
}