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;
  
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.List;
  
  import uk.ac.cam.ch.wwmm.oscar.Oscar;
  import uk.ac.cam.ch.wwmm.oscar.document.NamedEntity;
  import uk.ac.cam.ch.wwmm.oscar.document.Token;
  import uk.ac.cam.ch.wwmm.oscar.document.TokenSequence;
  import uk.ac.cam.ch.wwmm.oscarMEMM.MEMMRecogniser;
  
  /*****************************************************
   * Runs the OSCAR tagger .
   * 
   * @author lh359, dmj30
   *****************************************************/
  
  public class OscarTagger implements Tagger {
  
  	protected Oscar oscar;
  
  	/*****************************
  	 * Default constructor method.
  	 * @param oscar (Oscar)
  	 ***************************/
  	public OscarTagger(Oscar oscar) {
  		this.oscar = oscar;
  		MEMMRecogniser recogniser = new MEMMRecogniser();
  		recogniser.setDeprioritiseOnts(true);
  		recogniser.setCprPseudoConfidence(0);
  		recogniser.setOntPseudoConfidence(0);
  		oscar.setRecogniser(recogniser);
  	}
  
  	/***********************************************
  	 * Runs OSCAR over a list of tokens and returns a list of tags
  	 * @param tokenList (List<Token>)
  	 * @return tagList (List<String>)
  	 ***********************************************/
  	public List<String> runTagger(List<Token> tokenList, String inputSentence) {
  		List<TokenSequence> tokenSequences = Arrays.asList(generateOscarTokenSequence(tokenList, inputSentence));
  		List<NamedEntity> neList = oscar.recogniseNamedEntities(tokenSequences);
          List<String> ignoreOscarList = Arrays.asList("cpr", "ont");
  		List<String> tagList = new ArrayList<String>();
  		String nilTag = "nil";
  		for (int i = 0; i < tokenList.size(); i++) {
  			tagList.add(nilTag);
  		}
  		for (NamedEntity ne : neList) {
  			if (!ignoreOscarList.contains(ne.getType().getName().toLowerCase())) {
  				List<Token> tokens = ne.getTokens();
                   
  				for (Token token : tokens) {
  					tagList.set(token.getIndex(), "OSCAR-"+ne.getType().getName());
  				}
  			}
  		}
  		return tagList;
  	}
  
  	public List<String> getIgnoredTags() {
  		return null;
  	}
  	
  	/*********************************************
  	 * Generates an OSCAR TokenSequence from a list of tokens
  	 * @param oscarTokens (List<Token>)
  	 * @param inputText (String)
  	 * @return tokenSequence (TokenSequence)
  	 ********************************************/
  	protected  TokenSequence generateOscarTokenSequence(List<Token> oscarTokens, String inputText) {
  		TokenSequence tokSeq = new TokenSequence(inputText, 0, null, oscarTokens);
  		int id = 0;
  		for (Token token : tokSeq.getTokens()) {
  			token.setTokenSequence(tokSeq);
  			token.setIndex(id++);
  		}
  		return tokSeq;
  	}
  }
  