001/* 
002 * Copyright (c) 2012, Regents of the University of Colorado 
003 * All rights reserved.
004 * 
005 * Redistribution and use in source and binary forms, with or without
006 * modification, are permitted provided that the following conditions are met:
007 * 
008 * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 
009 * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 
010 * Neither the name of the University of Colorado at Boulder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 
011 * 
012 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
013 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
014 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
015 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
016 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
017 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
018 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
019 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
020 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
021 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
022 * POSSIBILITY OF SUCH DAMAGE. 
023 */
024package org.cleartk.ml.chunking;
025
026import java.util.HashMap;
027import java.util.List;
028import java.util.Map;
029
030import org.apache.uima.cas.Feature;
031import org.apache.uima.jcas.JCas;
032import org.apache.uima.jcas.tcas.Annotation;
033import org.apache.uima.fit.util.JCasUtil;
034
035/**
036 * Chunking with Begin-Inside-Outside labels
037 * 
038 * <br>
039 * Copyright (c) 2012, Regents of the University of Colorado <br>
040 * All rights reserved.
041 * 
042 * @author Steven Bethard
043 */
044public class BioChunking<SUB_CHUNK_TYPE extends Annotation, CHUNK_TYPE extends Annotation> extends
045    Chunking_ImplBase<SUB_CHUNK_TYPE, CHUNK_TYPE> {
046
047  public BioChunking(
048      Class<? extends SUB_CHUNK_TYPE> subChunkClass,
049      Class<? extends CHUNK_TYPE> chunkClass) {
050    super(subChunkClass, chunkClass, null);
051  }
052
053  public BioChunking(
054      Class<? extends SUB_CHUNK_TYPE> subChunkClass,
055      Class<? extends CHUNK_TYPE> chunkClass,
056      String featureName) {
057    super(subChunkClass, chunkClass, featureName);
058  }
059
060  @Override
061  protected Map<SUB_CHUNK_TYPE, String> getSubChunkToOutcomeMap(
062      JCas jCas,
063      List<SUB_CHUNK_TYPE> chunkComponents,
064      List<CHUNK_TYPE> chunks) {
065    Feature feature = this.getFeature(jCas);
066    Map<SUB_CHUNK_TYPE, String> subChunkToOutcome = new HashMap<SUB_CHUNK_TYPE, String>();
067    for (CHUNK_TYPE chunk : chunks) {
068      String suffix = this.getOutcomeSuffix(chunk, feature);
069      boolean isBegin = true;
070      for (SUB_CHUNK_TYPE chunkComponent : JCasUtil.selectCovered(this.subChunkClass, chunk)) {
071        if (isBegin) {
072          subChunkToOutcome.put(chunkComponent, "B" + suffix);
073          isBegin = false;
074        } else {
075          subChunkToOutcome.put(chunkComponent, "I" + suffix);
076        }
077      }
078    }
079    return subChunkToOutcome;
080  }
081
082  @Override
083  protected boolean isEndOfChunk(
084      char currPrefix,
085      String currLabel,
086      char nextPrefix,
087      String nextLabel) {
088    return nextPrefix == 'O' || nextPrefix == 'B' || !nextLabel.equals(currLabel);
089  }
090
091}