code: /**
   * Copyright 2012 Lezan Hawizy, David M. Jessop, Daniel Lowe and Peter Murray-Rust
   *
   * 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 uk.ac.cam.ch.wwmm.chemicaltagger.modelParser;
  
  import java.io.IOException;
  import java.io.InputStream;
  
  import nu.xom.Document;
  import opennlp.tools.cmdline.parser.ParserTool;
  import opennlp.tools.parser.Parse;
  import opennlp.tools.parser.Parser;
  import opennlp.tools.parser.ParserFactory;
  import opennlp.tools.parser.ParserModel;
  import uk.ac.cam.ch.wwmm.chemicaltagger.Utils;
  
  /************************************************
   *
   * Runs the ChemicalParser model against text.
   * 
   * @author lh359
   ************************************************/
  public class ChemistryModelParser {
  
  	private Parser parser;
  
  	public ChemistryModelParser() {
  		InputStream modelIn = null;
  		ParserModel model = null;
  		try {
  			modelIn = Utils
  					.getInputStream(getClass(),
  							"/uk/ac/cam/ch/wwmm/chemicaltagger/modelParser/chem-parser-chunking.bin");
  			model = new ParserModel(modelIn);
  
  		} catch (IOException e) {
  			e.printStackTrace();
  		} 
  		if (model != null)
  			parser = ParserFactory.create(model);
  		else
  			throw new NullPointerException();
  	}
  
  	public void parseSentence(String sentence) {
  		Parse[] topParses = ParserTool.parseLine(sentence, parser, 1);
  		ParseTreetoXML parseToXML = new ParseTreetoXML();
  		
  		for (Parse parse : topParses) {
  			Document doc = parseToXML.convert(parse);
  			Utils.writeXMLToFile(doc,"target/testParse.xml");
  			
  		}
  	}
  }
  