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libGPML is a library for reading, writing, manipulation, and conversion of files and data streams in the GPML (Graphical Pathway Markup Language) format.
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/*******************************************************************************
 * PathVisio, a tool for data visualization and analysis using biological pathways
 * Copyright 2006-2022 BiGCaT Bioinformatics, WikiPathways
 * 
 * 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.
 ******************************************************************************/
package org.pathvisio.libgpml.util;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;

import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.XMLReader;
import org.xml.sax.helpers.DefaultHandler;
import org.xml.sax.helpers.XMLReaderFactory;

/**
 * This is similar to com.sun.xml.internal.ws.message.RootElementSniffer,
 * perhaps can be re-used.
 * 
 * @author unknown
 */
public class RootElementFinder {

	/**
	 * Root element handler class. 
	 * 
	 * @author unknown
	 */
	static class RootElementHandler extends DefaultHandler {

		private String rootQName = null;
		private String rootUri = null;

		/**
		 *
		 */
		@Override
		public void startElement(String uri, String localName, String qName, Attributes attributes)
				throws SAXException {
			if (rootQName == null && rootUri == null) {
				rootQName = qName;
				rootUri = uri;
			}
			// TODO: stop parsing here...
		}

		public String getRootQName() {
			return rootQName;
		}

		public String getRootUri() {
			return rootUri;
		}
	};

	/**
	 * Special reader that works around problem with UTF-BOM
	 * 
	 * @param xin
	 * @return
	 * @throws IOException
	 */
	private static Reader inputStreamToReader(InputStream xin) throws IOException {
		BufferedInputStream in = new BufferedInputStream(xin);
		in.mark(3);
		int byte1 = in.read();
		int byte2 = in.read();
		if (byte1 == 0xFF && byte2 == 0xFE) {
			return new InputStreamReader(in, "UTF-16LE");
		} else if (byte1 == 0xFF && byte2 == 0xFF) {
			return new InputStreamReader(in, "UTF-16BE");
		} else {
			int byte3 = in.read();
			if (byte1 == 0xEF && byte2 == 0xBB && byte3 == 0xBF) {
				return new InputStreamReader(in, "UTF-8");
			} else {
				in.reset();
				return new InputStreamReader(in);
			}
		}
	}

	/**
	 * Handles root element.
	 * 
	 * @param file
	 * @return
	 * @throws FileNotFoundException
	 * @throws IOException
	 * @throws SAXException
	 */
	private static RootElementHandler parse(File file) throws FileNotFoundException, IOException, SAXException {
		XMLReader xr;
		xr = XMLReaderFactory.createXMLReader();

		RootElementHandler rootElementHandler = new RootElementHandler();

		xr.setEntityResolver(null);
		xr.setContentHandler(rootElementHandler);
		xr.setErrorHandler(rootElementHandler);
		xr.parse(new InputSource(inputStreamToReader(new FileInputStream(file))));

		return rootElementHandler;
	}

	/**
	 * Returns root URI.
	 * 
	 * @param file
	 * @return
	 * @throws SAXException
	 * @throws FileNotFoundException
	 * @throws IOException
	 */
	public static String getRootUri(File file) throws SAXException, FileNotFoundException, IOException {
		RootElementHandler handler = parse(file);
		return handler.getRootUri();
	}

}