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From james-mas...@apache.org
Subject svn commit: r1403989 [21/28] - in /incubator/ctakes/branches/SHARPn-cTAKES: Constituency Parser/src/org/chboston/cnlp/ctakes/parser/ Constituency Parser/src/org/chboston/cnlp/ctakes/parser/uima/ae/ Constituency Parser/src/org/chboston/cnlp/ctakes/parse...
Date Wed, 31 Oct 2012 05:26:55 GMT
Modified: incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/FirstTokenPermutationImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/dictionary%20lookup/src/edu/mayo/bmi/lookup/algorithms/FirstTokenPermutationImpl.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/FirstTokenPermutationImpl.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/FirstTokenPermutationImpl.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
 /*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * 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
- * 
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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
@@ -21,690 +14,690 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.lookup.algorithms;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import edu.mayo.bmi.dictionary.DictionaryEngine;
-import edu.mayo.bmi.dictionary.MetaDataHit;
-import edu.mayo.bmi.lookup.phrasebuilder.PhraseBuilder;
-import edu.mayo.bmi.lookup.vo.LookupAnnotation;
-import edu.mayo.bmi.lookup.vo.LookupHit;
-import edu.mayo.bmi.lookup.vo.LookupToken;
-
-/**
- * <b>OVERVIEW: </b> Each LookupToken is fed into a "first token" Dictionary. A
- * hit indicates an anchor and the window around this anchor is based on
- * context. This hit also contains all the presentations from the Dictionary
- * where the "first token" is contained.
- * 
- * The window is determined by finding the largest overlapping context window
- * annotation. Permutations of LookupTokens found within this window are used to
- * match against the presentations found earlier. If context window annotations
- * are not provided, a fixed window is used based on the specified max
- * permutation level.
- * 
- * <b>OPTIONAL CONTEXT: </b> context window annotations
- * 
- * @author Mayo Clinic
- */
-public class FirstTokenPermutationImpl implements LookupAlgorithm
-{
-    // LOG4J logger based on class name
-    private Logger iv_logger = Logger.getLogger(getClass().getName());
-
-    /**
-     * Key value for context map. Value is expected to be a List of
-     * LookupAnnotation objects in sorted order.
-     */
-    public static final String CTX_KEY_WINDOW_ANNOTATIONS = "WINDOW_ANNOTATIONS";
-
-    /**
-     * Key value for LookupToken attribute. Value is expected to be either TRUE
-     * or FALSE. This indicates whether to use this token for a "first token"
-     * lookup or not. This is optional.
-     */
-    public static final String LT_KEY_USE_FOR_LOOKUP = "USE_FOR_LOOKUP";
-
-    private DictionaryEngine iv_firstTokenDictEngine;
-    private PhraseBuilder iv_phrBuilder;
-
-    private int iv_maxPermutationLevel;
-    // key = level Integer, value = Permutation list
-    private Map iv_permCacheMap = new HashMap();
-
-    private String[] iv_textMetaFieldNames;
-
-    /**
-     * Constructor
-     * 
-     * @param firstTokenDictEngine
-     *            Dictionary that is indexed against first tokens.
-     * @param phraseBuilder
-     *            Builds phrases to match against Dictionary.
-     * @param textMetaFieldNames
-     *            MetaFieldNames used to extract presentations.
-     * @param maxPermutationLevel
-     *            Max permutation Level allowed.
-     */
-    public FirstTokenPermutationImpl(DictionaryEngine firstTokenDictEngine,
-            PhraseBuilder phraseBuilder, String textMetaFieldNames[],
-            int maxPermutationLevel)
-    {
-        iv_firstTokenDictEngine = firstTokenDictEngine;
-        iv_phrBuilder = phraseBuilder;
-        iv_textMetaFieldNames = textMetaFieldNames;
-
-        iv_maxPermutationLevel = maxPermutationLevel;
-        for (int i = 0; i <= maxPermutationLevel; i++)
-        {
-            Integer level = new Integer(i);
-            List permList = PermutationUtil.getPermutationList(i);
-            iv_permCacheMap.put(level, permList);
-        }
-    }
-
-    /**
-     * Implementation of algorithm.
-     */
-    public Collection lookup(List ltList, Map ctxMap) throws Exception
-    {
-        // setup optional window context data
-        boolean useWindowAnnots = false;
-        List wAnnotList = getWindowAnnotations(ctxMap);
-        if (wAnnotList.size() > 0)
-        {
-            useWindowAnnots = true;
-        }
-        Map wStartOffsetMap = getStartOffsetMap(wAnnotList, true);
-        Map wEndOffsetMap = getEndOffsetMap(wAnnotList, true);
-
-        Map ltListIndexMap = getListIndexMap(ltList);
-        Map ltStartOffsetMap = getStartOffsetMap(ltList, true);
-        Map ltEndOffsetMap = getEndOffsetMap(ltList, true);
-
-        List lhList = new ArrayList();
-        for (int ltIdx = 0; ltIdx < ltList.size(); ltIdx++)
-        {
-            LookupToken lt = (LookupToken) ltList.get(ltIdx);
-
-            Boolean useForLookup = Boolean.valueOf(lt.getStringAttribute(LT_KEY_USE_FOR_LOOKUP));
-
-            if ((useForLookup == null) || (useForLookup.booleanValue()))
-            {
-                Collection mdhCol = getFirstTokenHits(lt);
-
-                if ((mdhCol != null) && (mdhCol.size() > 0))
-                {
-                    int wEndOffset = -1;
-                    if (useWindowAnnots)
-                    {
-                        // get the largest overlapping window annotation
-                        LookupAnnotation wAnnot = getLargestWindowAnnotation(
-                                ltIdx,
-                                lt,
-                                ltStartOffsetMap,
-                                ltEndOffsetMap,
-                                ltListIndexMap,
-                                wStartOffsetMap,
-                                wEndOffsetMap);
-                        if (wAnnot != null)
-                        {
-                            wEndOffset = wAnnot.getEndOffset();
-                        }
-                    }
-                    if (wEndOffset == -1)
-                    {
-                        iv_logger.debug("Window size set to max perm level.");
-                        wEndOffset = getFixedWindowEndOffset(ltIdx, lt, ltList);
-                    }
-
-                    List endLookupTokenList = getLookupTokenList(
-                            wEndOffset,
-                            ltEndOffsetMap,
-                            false);
-                    LookupToken endLookupToken = (LookupToken) endLookupTokenList.get(endLookupTokenList.size() - 1);
-
-                    int startTokenIdx = ltIdx;
-                    int endTokenIdx = ((Integer) ltListIndexMap.get(endLookupToken)).intValue();
-
-                    // list of LookupToken objects bound by the window
-                    List wLookupTokenList = ltList.subList(
-                            startTokenIdx,
-                            endTokenIdx + 1);
-
-                    // use permutation algorithm to find any hits inside the window
-                    Collection lhCol = getLookupHits(
-                            mdhCol,
-                            wLookupTokenList,
-                            new Integer(ltIdx - startTokenIdx));
-
-                    lhList.addAll(lhCol);
-                }
-            }
-        }
-
-        return lhList;
-    }
-
-    private Collection getLookupHits(
-            Collection mdhCol,
-            List wLookupTokenList,
-            Integer firstTokenIndex) throws Exception
-    {
-        if ((wLookupTokenList.size() - 1) > iv_maxPermutationLevel)
-        {
-            iv_logger.debug("Beyond permutation cache size.");
-            return new ArrayList();
-        }
-
-        // build a list of index values (excludes index of first token)
-        List idxList = new ArrayList();
-        for (int i = 0; i < wLookupTokenList.size(); i++)
-        {
-            if (i != firstTokenIndex.intValue())
-            {
-                idxList.add(new Integer(i));
-            }
-        }
-
-        Collection permCol = (Collection) iv_permCacheMap.get(new Integer(
-                idxList.size()));
-
-        List lhList = new ArrayList();
-
-        Map mdhMap = new HashMap();
-        Iterator mdhItr = mdhCol.iterator();
-        while (mdhItr.hasNext())
-        {
-            MetaDataHit mdh = (MetaDataHit) mdhItr.next();
-            for (int i = 0; i < iv_textMetaFieldNames.length; i++)
-            {
-                String text = mdh.getMetaFieldValue(iv_textMetaFieldNames[i]);
-                if (text != null)
-                {
-                    text = text.toLowerCase();
-                    Set mdhSet = (Set) mdhMap.get(text);
-                    if (mdhSet == null)
-                    {
-                        mdhSet = new HashSet();
-                    }
-                    mdhSet.add(mdh);
-                    mdhMap.put(text, mdhSet);
-                }
-                else
-                {
-                    if (iv_logger.isDebugEnabled())
-                    {
-                        iv_logger.debug("MetaField "
-                                + iv_textMetaFieldNames[i]
-                                + " contains no data.");
-                    }
-                }
-            }
-        }
-
-        LookupToken firstWordLookupToken = (LookupToken) wLookupTokenList.get(firstTokenIndex.intValue());
-
-        Iterator permItr = permCol.iterator();
-        while (permItr.hasNext())
-        {
-            // convert permutation idx back into LookupTokens
-            List tempList = new ArrayList();
-            List permutation = (List) permItr.next();
-            Iterator idxItr = permutation.iterator();
-            while (idxItr.hasNext())
-            {
-                int idx = ((Integer) idxItr.next()).intValue();
-                if (idx <= firstTokenIndex.intValue())
-                {
-                    idx--;
-                }
-                LookupToken lt = (LookupToken) wLookupTokenList.get(idx);
-                tempList.add(lt);
-            }
-
-            List singleTokenList = new ArrayList();
-            singleTokenList.add(firstWordLookupToken);
-            String[] fwPerms = iv_phrBuilder.getPhrases(singleTokenList);
-
-            String[] phrArr = iv_phrBuilder.getPhrases(tempList);
-            for (int i = 0; i < phrArr.length; i++)
-            {
-                for (int fwPermIdx = 0; fwPermIdx < fwPerms.length; fwPermIdx++)
-                {
-                    StringBuffer phraseSB = new StringBuffer();
-                    phraseSB.append(fwPerms[fwPermIdx]);
-                    phraseSB.append(' ');
-                    phraseSB.append(phrArr[i]);
-                    String phrase = phraseSB.toString().trim().toLowerCase();
-                    Set mdhSet = (Set) mdhMap.get(phrase);
-                    if (mdhSet != null)
-                    {
-                        Iterator mdhIterator = mdhSet.iterator();
-                        while (mdhIterator.hasNext())
-                        {
-                            MetaDataHit mdh = (MetaDataHit) mdhIterator.next();
-                            // figure out start and end offsets
-                            Collections.sort(permutation);
-
-                            int startOffset;
-                            if (permutation.size() > 0)
-                            {
-                                int firstIdx = ((Integer) permutation.get(0)).intValue();
-                                if (firstIdx <= firstTokenIndex.intValue())
-                                {
-                                    firstIdx--;
-                                }
-                                LookupToken lt = (LookupToken) wLookupTokenList.get(firstIdx);
-                                if (lt.getStartOffset() < firstWordLookupToken.getStartOffset())
-                                {
-                                    startOffset = lt.getStartOffset();
-                                }
-                                else
-                                {
-                                    startOffset = firstWordLookupToken.getStartOffset();
-                                }
-                            }
-                            else
-                            {
-                                startOffset = firstWordLookupToken.getStartOffset();
-                            }
-
-                            int endOffset;
-                            if (permutation.size() > 0)
-                            {
-                                int lastIdx = ((Integer) permutation.get(permutation.size() - 1)).intValue();
-                                if (lastIdx <= firstTokenIndex.intValue())
-                                {
-                                    lastIdx--;
-                                }
-                                LookupToken lt = (LookupToken) wLookupTokenList.get(lastIdx);
-                                if (lt.getEndOffset() > firstWordLookupToken.getEndOffset())
-                                {
-                                    endOffset = lt.getEndOffset();
-                                }
-                                else
-                                {
-                                    endOffset = firstWordLookupToken.getEndOffset();
-                                }
-                            }
-                            else
-                            {
-                                endOffset = firstWordLookupToken.getEndOffset();
-                            }
-
-                            LookupHit lh = new LookupHit(
-                                    mdh,
-                                    startOffset,
-                                    endOffset);
-
-                            lhList.add(lh);
-                        }
-                    }
-                }
-            }
-        }
-        return lhList;
-    }
-
-    /**
-     * Extracts the list of LookupAnnotation objects representing noun phrases
-     * from the context map.
-     * 
-     * @param contextMap
-     * @return
-     */
-    private List getWindowAnnotations(Map contextMap)
-    {
-        List list = (List) contextMap.get(CTX_KEY_WINDOW_ANNOTATIONS);
-        if ((list == null) || (list.size() == 0))
-        {
-            iv_logger.debug("No context window annotations.");
-            return new ArrayList();
-        }
-        return list;
-    }
-
-    /**
-     * Determines the number of ListTokens are contained within the specified
-     * start and end offsets;
-     * 
-     * @param ltStartOffsetMap
-     * @param ltEndOffsetMap
-     * @param ltListIndexMap
-     * @param startOffset
-     * @param endOffset
-     * @return
-     */
-    private int getNumberOfListTokens(
-            Map ltStartOffsetMap,
-            Map ltEndOffsetMap,
-            Map ltListIndexMap,
-            int startOffset,
-            int endOffset)
-    {
-        List startLookupTokenList = getLookupTokenList(
-                startOffset,
-                ltStartOffsetMap,
-                true);
-        List endLookupTokenList = getLookupTokenList(
-                endOffset,
-                ltEndOffsetMap,
-                false);
-
-        if ((startLookupTokenList == null) || (endLookupTokenList == null))
-        {
-            iv_logger.debug("Invalid window:" + startOffset + "," + endOffset);
-            return -1;
-        }
-        LookupToken startLookupToken = (LookupToken) startLookupTokenList.get(0);
-        Integer startIdx = (Integer) ltListIndexMap.get(startLookupToken);
-
-        LookupToken endLookupToken = (LookupToken) endLookupTokenList.get(endLookupTokenList.size() - 1);
-        Integer endIdx = (Integer) ltListIndexMap.get(endLookupToken);
-
-        return endIdx.intValue() - startIdx.intValue() + 1;
-    }
-
-    /**
-     * Attempts to get a list of LookupToken objects at the specified offset. If
-     * there are none, this method attempts to try nearby offsets based on the
-     * traversal direction.
-     * 
-     * @param offset
-     * @param ltOffsetMap
-     * @param traverseRight
-     * @return
-     */
-    private List getLookupTokenList(
-            int offset,
-            Map ltOffsetMap,
-            boolean traverseRight)
-    {
-        // first attempt the original offset, which will be the case most of the
-        // time
-        List lookupTokenList = (List) ltOffsetMap.get(new Integer(offset));
-        if (lookupTokenList != null)
-        {
-            return lookupTokenList;
-        }
-        else
-        {
-            // otherwise traverse some nearby offsets and attempt to find a
-            // token
-
-            // TODO hardcoded max offset window is 10 char
-            final int offsetWindow = 10;
-
-            // build list of offsets to try
-            List offsetList = new ArrayList();
-            if (traverseRight)
-            {
-                int max = offset + offsetWindow;
-                for (int i = offset; i <= max; i++)
-                {
-                    offsetList.add(new Integer(i));
-                }
-            }
-            else
-            {
-                int min = offset - offsetWindow;
-                for (int i = offset; i >= min; i--)
-                {
-                    offsetList.add(new Integer(i));
-                }
-            }
-
-            Iterator offsetItr = offsetList.iterator();
-            while (offsetItr.hasNext())
-            {
-                Integer tempOffset = (Integer) offsetItr.next();
-                lookupTokenList = (List) ltOffsetMap.get(tempOffset);
-                if (lookupTokenList != null)
-                {
-                    return lookupTokenList;
-                }
-            }
-        }
-        // no tokens in window
-        return null;
-    }
-
-    /**
-     * Determines the largest overlapping window annotation for the specified
-     * LookupToken.
-     * 
-     * @param lt
-     * @param wStartOffsetMap
-     * @param wEndOffsetMap
-     * @return
-     */
-    private LookupAnnotation getLargestWindowAnnotation(
-            int tokenIdx,
-            LookupToken lt,
-            Map ltStartOffsetMap,
-            Map ltEndOffsetMap,
-            Map ltListIndexMap,
-            Map wStartOffsetMap,
-            Map wEndOffsetMap)
-    {
-        Set startCandidateSet = new HashSet();
-        Set endCandidateSet = new HashSet();
-
-        Iterator startItr = wStartOffsetMap.keySet().iterator();
-        while (startItr.hasNext())
-        {
-            Integer startOffset = (Integer) startItr.next();
-            if (startOffset.intValue() <= lt.getStartOffset())
-            {
-                List wAnnotList = (List) wStartOffsetMap.get(startOffset);
-                startCandidateSet.addAll(wAnnotList);
-            }
-        }
-
-        Iterator endItr = wEndOffsetMap.keySet().iterator();
-        while (endItr.hasNext())
-        {
-            Integer endOffset = (Integer) endItr.next();
-            if (endOffset.intValue() >= lt.getEndOffset())
-            {
-                List wAnnotList = (List) wEndOffsetMap.get(endOffset);
-                endCandidateSet.addAll(wAnnotList);
-            }
-        }
-
-        // union to get window annotations that are overlapping with LookupToken
-        startCandidateSet.retainAll(endCandidateSet);
-
-        // find largest overlapping window annotation
-        LookupAnnotation largestWindowAnnot = null;
-        Iterator laItr = startCandidateSet.iterator();
-        while (laItr.hasNext())
-        {
-            LookupAnnotation tempLookupAnnot = (LookupAnnotation) laItr.next();
-            if ((largestWindowAnnot == null)
-                    || (tempLookupAnnot.getLength() > largestWindowAnnot.getLength()))
-            {
-                // now see if we can handle the size of this window (permutation
-                // wise)
-                int ltCount = getNumberOfListTokens(
-                        ltStartOffsetMap,
-                        ltEndOffsetMap,
-                        ltListIndexMap,
-                        tempLookupAnnot.getStartOffset(),
-                        tempLookupAnnot.getEndOffset());
-
-                if ((ltCount <= iv_maxPermutationLevel) && (ltCount > 0))
-                {
-                    largestWindowAnnot = tempLookupAnnot;
-                }
-                else
-                {
-                    if (iv_logger.isDebugEnabled())
-                    {
-                        iv_logger.debug("Window size of "
-                                + ltCount
-                                + " exceeds the max permutation level of "
-                                + iv_maxPermutationLevel
-                                + ".");
-                    }
-                }
-            }
-        }
-
-        return largestWindowAnnot;
-    }
-
-    private int getFixedWindowEndOffset(
-            int tokenIdx,
-            LookupToken lt,
-            List ltList)
-    {
-        int fixedEndOffset = 0;
-
-        for (int i = tokenIdx; (i < tokenIdx + iv_maxPermutationLevel)
-                && (i < ltList.size()); i++)
-        {
-            LookupToken tempLookupToken = (LookupToken) ltList.get(i);
-            if (tempLookupToken != null)
-            {
-                fixedEndOffset = tempLookupToken.getEndOffset();
-            }
-        }
-        return fixedEndOffset;
-    }
-
-    /**
-     * Creates a map that binds an object from a list to its index position.
-     * 
-     * @param list
-     * @return
-     */
-    private Map getListIndexMap(List list)
-    {
-        Map m = new HashMap();
-
-        for (int i = 0; i < list.size(); i++)
-        {
-            Integer index = new Integer(i);
-            m.put(list.get(i), index);
-        }
-
-        return m;
-    }
-
-    /**
-     * Creates a map that uses the start offset to index the LookupAnnotation
-     * objects. If multiple LookupAnnotations can exist at the same start
-     * offset, then hasMultiples=true and the values with be a List of
-     * LookupAnnotation objects at that offset.
-     * 
-     * @param lookupAnnotList
-     * @param hasMultiples
-     * @return
-     */
-    private Map getStartOffsetMap(List lookupAnnotList, boolean hasMultiples)
-    {
-        Map m = new HashMap();
-
-        Iterator laItr = lookupAnnotList.iterator();
-        while (laItr.hasNext())
-        {
-            LookupAnnotation la = (LookupAnnotation) laItr.next();
-            Integer key = new Integer(la.getStartOffset());
-            if (hasMultiples)
-            {
-                List list = (List) m.get(key);
-                if (list == null)
-                {
-                    list = new ArrayList();
-                }
-                list.add(la);
-                m.put(key, list);
-            }
-            else
-            {
-                m.put(key, la);
-            }
-        }
-
-        return m;
-    }
-
-    /**
-     * Creates a map that uses the end offset to index the LookupAnnotation
-     * objects. If multiple LookupAnnotations can exist at the end start offset,
-     * then hasMultiples=true and the values with be a List of LookupAnnotation
-     * objects at that offset.
-     * 
-     * @param lookupAnnotList
-     * @param hasMultiples
-     * @return
-     */
-    private Map getEndOffsetMap(List lookupAnnotList, boolean hasMultiples)
-    {
-        Map m = new HashMap();
-
-        Iterator laItr = lookupAnnotList.iterator();
-        while (laItr.hasNext())
-        {
-            LookupAnnotation la = (LookupAnnotation) laItr.next();
-            Integer key = new Integer(la.getEndOffset());
-            if (hasMultiples)
-            {
-                List list = (List) m.get(key);
-                if (list == null)
-                {
-                    list = new ArrayList();
-                }
-                list.add(la);
-                m.put(key, list);
-            }
-            else
-            {
-                m.put(key, la);
-            }
-        }
-
-        return m;
-    }
-
-    /**
-     * Gets the hits for the specified LookupToken. This uses the first token Dictionary.
-     * 
-     * @param firstLookupToken
-     * @return
-     * @throws Exception
-     */
-    private Collection getFirstTokenHits(LookupToken firstLookupToken)
-            throws Exception
-    {
-        List singleLtList = new ArrayList();
-        singleLtList.add(firstLookupToken);
-
-        String[] phrases = iv_phrBuilder.getPhrases(singleLtList);
-
-        Collection mdhCol = new ArrayList();
-        for (int i = 0; i < phrases.length; i++)
-        {
-            Collection curMdhCol = iv_firstTokenDictEngine.metaLookup(phrases[i]);
-
-            if (curMdhCol.size() > 0)
-            {
-                mdhCol.addAll(curMdhCol);
-            }
-        }
-        return mdhCol;
-    }
-}
\ No newline at end of file
+package edu.mayo.bmi.lookup.algorithms;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import edu.mayo.bmi.dictionary.DictionaryEngine;
+import edu.mayo.bmi.dictionary.MetaDataHit;
+import edu.mayo.bmi.lookup.phrasebuilder.PhraseBuilder;
+import edu.mayo.bmi.lookup.vo.LookupAnnotation;
+import edu.mayo.bmi.lookup.vo.LookupHit;
+import edu.mayo.bmi.lookup.vo.LookupToken;
+
+/**
+ * <b>OVERVIEW: </b> Each LookupToken is fed into a "first token" Dictionary. A
+ * hit indicates an anchor and the window around this anchor is based on
+ * context. This hit also contains all the presentations from the Dictionary
+ * where the "first token" is contained.
+ * 
+ * The window is determined by finding the largest overlapping context window
+ * annotation. Permutations of LookupTokens found within this window are used to
+ * match against the presentations found earlier. If context window annotations
+ * are not provided, a fixed window is used based on the specified max
+ * permutation level.
+ * 
+ * <b>OPTIONAL CONTEXT: </b> context window annotations
+ * 
+ * @author Mayo Clinic
+ */
+public class FirstTokenPermutationImpl implements LookupAlgorithm
+{
+    // LOG4J logger based on class name
+    private Logger iv_logger = Logger.getLogger(getClass().getName());
+
+    /**
+     * Key value for context map. Value is expected to be a List of
+     * LookupAnnotation objects in sorted order.
+     */
+    public static final String CTX_KEY_WINDOW_ANNOTATIONS = "WINDOW_ANNOTATIONS";
+
+    /**
+     * Key value for LookupToken attribute. Value is expected to be either TRUE
+     * or FALSE. This indicates whether to use this token for a "first token"
+     * lookup or not. This is optional.
+     */
+    public static final String LT_KEY_USE_FOR_LOOKUP = "USE_FOR_LOOKUP";
+
+    private DictionaryEngine iv_firstTokenDictEngine;
+    private PhraseBuilder iv_phrBuilder;
+
+    private int iv_maxPermutationLevel;
+    // key = level Integer, value = Permutation list
+    private Map iv_permCacheMap = new HashMap();
+
+    private String[] iv_textMetaFieldNames;
+
+    /**
+     * Constructor
+     * 
+     * @param firstTokenDictEngine
+     *            Dictionary that is indexed against first tokens.
+     * @param phraseBuilder
+     *            Builds phrases to match against Dictionary.
+     * @param textMetaFieldNames
+     *            MetaFieldNames used to extract presentations.
+     * @param maxPermutationLevel
+     *            Max permutation Level allowed.
+     */
+    public FirstTokenPermutationImpl(DictionaryEngine firstTokenDictEngine,
+            PhraseBuilder phraseBuilder, String textMetaFieldNames[],
+            int maxPermutationLevel)
+    {
+        iv_firstTokenDictEngine = firstTokenDictEngine;
+        iv_phrBuilder = phraseBuilder;
+        iv_textMetaFieldNames = textMetaFieldNames;
+
+        iv_maxPermutationLevel = maxPermutationLevel;
+        for (int i = 0; i <= maxPermutationLevel; i++)
+        {
+            Integer level = new Integer(i);
+            List permList = PermutationUtil.getPermutationList(i);
+            iv_permCacheMap.put(level, permList);
+        }
+    }
+
+    /**
+     * Implementation of algorithm.
+     */
+    public Collection lookup(List ltList, Map ctxMap) throws Exception
+    {
+        // setup optional window context data
+        boolean useWindowAnnots = false;
+        List wAnnotList = getWindowAnnotations(ctxMap);
+        if (wAnnotList.size() > 0)
+        {
+            useWindowAnnots = true;
+        }
+        Map wStartOffsetMap = getStartOffsetMap(wAnnotList, true);
+        Map wEndOffsetMap = getEndOffsetMap(wAnnotList, true);
+
+        Map ltListIndexMap = getListIndexMap(ltList);
+        Map ltStartOffsetMap = getStartOffsetMap(ltList, true);
+        Map ltEndOffsetMap = getEndOffsetMap(ltList, true);
+
+        List lhList = new ArrayList();
+        for (int ltIdx = 0; ltIdx < ltList.size(); ltIdx++)
+        {
+            LookupToken lt = (LookupToken) ltList.get(ltIdx);
+
+            Boolean useForLookup = Boolean.valueOf(lt.getStringAttribute(LT_KEY_USE_FOR_LOOKUP));
+
+            if ((useForLookup == null) || (useForLookup.booleanValue()))
+            {
+                Collection mdhCol = getFirstTokenHits(lt);
+
+                if ((mdhCol != null) && (mdhCol.size() > 0))
+                {
+                    int wEndOffset = -1;
+                    if (useWindowAnnots)
+                    {
+                        // get the largest overlapping window annotation
+                        LookupAnnotation wAnnot = getLargestWindowAnnotation(
+                                ltIdx,
+                                lt,
+                                ltStartOffsetMap,
+                                ltEndOffsetMap,
+                                ltListIndexMap,
+                                wStartOffsetMap,
+                                wEndOffsetMap);
+                        if (wAnnot != null)
+                        {
+                            wEndOffset = wAnnot.getEndOffset();
+                        }
+                    }
+                    if (wEndOffset == -1)
+                    {
+                        iv_logger.debug("Window size set to max perm level.");
+                        wEndOffset = getFixedWindowEndOffset(ltIdx, lt, ltList);
+                    }
+
+                    List endLookupTokenList = getLookupTokenList(
+                            wEndOffset,
+                            ltEndOffsetMap,
+                            false);
+                    LookupToken endLookupToken = (LookupToken) endLookupTokenList.get(endLookupTokenList.size() - 1);
+
+                    int startTokenIdx = ltIdx;
+                    int endTokenIdx = ((Integer) ltListIndexMap.get(endLookupToken)).intValue();
+
+                    // list of LookupToken objects bound by the window
+                    List wLookupTokenList = ltList.subList(
+                            startTokenIdx,
+                            endTokenIdx + 1);
+
+                    // use permutation algorithm to find any hits inside the window
+                    Collection lhCol = getLookupHits(
+                            mdhCol,
+                            wLookupTokenList,
+                            new Integer(ltIdx - startTokenIdx));
+
+                    lhList.addAll(lhCol);
+                }
+            }
+        }
+
+        return lhList;
+    }
+
+    private Collection getLookupHits(
+            Collection mdhCol,
+            List wLookupTokenList,
+            Integer firstTokenIndex) throws Exception
+    {
+        if ((wLookupTokenList.size() - 1) > iv_maxPermutationLevel)
+        {
+            iv_logger.debug("Beyond permutation cache size.");
+            return new ArrayList();
+        }
+
+        // build a list of index values (excludes index of first token)
+        List idxList = new ArrayList();
+        for (int i = 0; i < wLookupTokenList.size(); i++)
+        {
+            if (i != firstTokenIndex.intValue())
+            {
+                idxList.add(new Integer(i));
+            }
+        }
+
+        Collection permCol = (Collection) iv_permCacheMap.get(new Integer(
+                idxList.size()));
+
+        List lhList = new ArrayList();
+
+        Map mdhMap = new HashMap();
+        Iterator mdhItr = mdhCol.iterator();
+        while (mdhItr.hasNext())
+        {
+            MetaDataHit mdh = (MetaDataHit) mdhItr.next();
+            for (int i = 0; i < iv_textMetaFieldNames.length; i++)
+            {
+                String text = mdh.getMetaFieldValue(iv_textMetaFieldNames[i]);
+                if (text != null)
+                {
+                    text = text.toLowerCase();
+                    Set mdhSet = (Set) mdhMap.get(text);
+                    if (mdhSet == null)
+                    {
+                        mdhSet = new HashSet();
+                    }
+                    mdhSet.add(mdh);
+                    mdhMap.put(text, mdhSet);
+                }
+                else
+                {
+                    if (iv_logger.isDebugEnabled())
+                    {
+                        iv_logger.debug("MetaField "
+                                + iv_textMetaFieldNames[i]
+                                + " contains no data.");
+                    }
+                }
+            }
+        }
+
+        LookupToken firstWordLookupToken = (LookupToken) wLookupTokenList.get(firstTokenIndex.intValue());
+
+        Iterator permItr = permCol.iterator();
+        while (permItr.hasNext())
+        {
+            // convert permutation idx back into LookupTokens
+            List tempList = new ArrayList();
+            List permutation = (List) permItr.next();
+            Iterator idxItr = permutation.iterator();
+            while (idxItr.hasNext())
+            {
+                int idx = ((Integer) idxItr.next()).intValue();
+                if (idx <= firstTokenIndex.intValue())
+                {
+                    idx--;
+                }
+                LookupToken lt = (LookupToken) wLookupTokenList.get(idx);
+                tempList.add(lt);
+            }
+
+            List singleTokenList = new ArrayList();
+            singleTokenList.add(firstWordLookupToken);
+            String[] fwPerms = iv_phrBuilder.getPhrases(singleTokenList);
+
+            String[] phrArr = iv_phrBuilder.getPhrases(tempList);
+            for (int i = 0; i < phrArr.length; i++)
+            {
+                for (int fwPermIdx = 0; fwPermIdx < fwPerms.length; fwPermIdx++)
+                {
+                    StringBuffer phraseSB = new StringBuffer();
+                    phraseSB.append(fwPerms[fwPermIdx]);
+                    phraseSB.append(' ');
+                    phraseSB.append(phrArr[i]);
+                    String phrase = phraseSB.toString().trim().toLowerCase();
+                    Set mdhSet = (Set) mdhMap.get(phrase);
+                    if (mdhSet != null)
+                    {
+                        Iterator mdhIterator = mdhSet.iterator();
+                        while (mdhIterator.hasNext())
+                        {
+                            MetaDataHit mdh = (MetaDataHit) mdhIterator.next();
+                            // figure out start and end offsets
+                            Collections.sort(permutation);
+
+                            int startOffset;
+                            if (permutation.size() > 0)
+                            {
+                                int firstIdx = ((Integer) permutation.get(0)).intValue();
+                                if (firstIdx <= firstTokenIndex.intValue())
+                                {
+                                    firstIdx--;
+                                }
+                                LookupToken lt = (LookupToken) wLookupTokenList.get(firstIdx);
+                                if (lt.getStartOffset() < firstWordLookupToken.getStartOffset())
+                                {
+                                    startOffset = lt.getStartOffset();
+                                }
+                                else
+                                {
+                                    startOffset = firstWordLookupToken.getStartOffset();
+                                }
+                            }
+                            else
+                            {
+                                startOffset = firstWordLookupToken.getStartOffset();
+                            }
+
+                            int endOffset;
+                            if (permutation.size() > 0)
+                            {
+                                int lastIdx = ((Integer) permutation.get(permutation.size() - 1)).intValue();
+                                if (lastIdx <= firstTokenIndex.intValue())
+                                {
+                                    lastIdx--;
+                                }
+                                LookupToken lt = (LookupToken) wLookupTokenList.get(lastIdx);
+                                if (lt.getEndOffset() > firstWordLookupToken.getEndOffset())
+                                {
+                                    endOffset = lt.getEndOffset();
+                                }
+                                else
+                                {
+                                    endOffset = firstWordLookupToken.getEndOffset();
+                                }
+                            }
+                            else
+                            {
+                                endOffset = firstWordLookupToken.getEndOffset();
+                            }
+
+                            LookupHit lh = new LookupHit(
+                                    mdh,
+                                    startOffset,
+                                    endOffset);
+
+                            lhList.add(lh);
+                        }
+                    }
+                }
+            }
+        }
+        return lhList;
+    }
+
+    /**
+     * Extracts the list of LookupAnnotation objects representing noun phrases
+     * from the context map.
+     * 
+     * @param contextMap
+     * @return
+     */
+    private List getWindowAnnotations(Map contextMap)
+    {
+        List list = (List) contextMap.get(CTX_KEY_WINDOW_ANNOTATIONS);
+        if ((list == null) || (list.size() == 0))
+        {
+            iv_logger.debug("No context window annotations.");
+            return new ArrayList();
+        }
+        return list;
+    }
+
+    /**
+     * Determines the number of ListTokens are contained within the specified
+     * start and end offsets;
+     * 
+     * @param ltStartOffsetMap
+     * @param ltEndOffsetMap
+     * @param ltListIndexMap
+     * @param startOffset
+     * @param endOffset
+     * @return
+     */
+    private int getNumberOfListTokens(
+            Map ltStartOffsetMap,
+            Map ltEndOffsetMap,
+            Map ltListIndexMap,
+            int startOffset,
+            int endOffset)
+    {
+        List startLookupTokenList = getLookupTokenList(
+                startOffset,
+                ltStartOffsetMap,
+                true);
+        List endLookupTokenList = getLookupTokenList(
+                endOffset,
+                ltEndOffsetMap,
+                false);
+
+        if ((startLookupTokenList == null) || (endLookupTokenList == null))
+        {
+            iv_logger.debug("Invalid window:" + startOffset + "," + endOffset);
+            return -1;
+        }
+        LookupToken startLookupToken = (LookupToken) startLookupTokenList.get(0);
+        Integer startIdx = (Integer) ltListIndexMap.get(startLookupToken);
+
+        LookupToken endLookupToken = (LookupToken) endLookupTokenList.get(endLookupTokenList.size() - 1);
+        Integer endIdx = (Integer) ltListIndexMap.get(endLookupToken);
+
+        return endIdx.intValue() - startIdx.intValue() + 1;
+    }
+
+    /**
+     * Attempts to get a list of LookupToken objects at the specified offset. If
+     * there are none, this method attempts to try nearby offsets based on the
+     * traversal direction.
+     * 
+     * @param offset
+     * @param ltOffsetMap
+     * @param traverseRight
+     * @return
+     */
+    private List getLookupTokenList(
+            int offset,
+            Map ltOffsetMap,
+            boolean traverseRight)
+    {
+        // first attempt the original offset, which will be the case most of the
+        // time
+        List lookupTokenList = (List) ltOffsetMap.get(new Integer(offset));
+        if (lookupTokenList != null)
+        {
+            return lookupTokenList;
+        }
+        else
+        {
+            // otherwise traverse some nearby offsets and attempt to find a
+            // token
+
+            // TODO hardcoded max offset window is 10 char
+            final int offsetWindow = 10;
+
+            // build list of offsets to try
+            List offsetList = new ArrayList();
+            if (traverseRight)
+            {
+                int max = offset + offsetWindow;
+                for (int i = offset; i <= max; i++)
+                {
+                    offsetList.add(new Integer(i));
+                }
+            }
+            else
+            {
+                int min = offset - offsetWindow;
+                for (int i = offset; i >= min; i--)
+                {
+                    offsetList.add(new Integer(i));
+                }
+            }
+
+            Iterator offsetItr = offsetList.iterator();
+            while (offsetItr.hasNext())
+            {
+                Integer tempOffset = (Integer) offsetItr.next();
+                lookupTokenList = (List) ltOffsetMap.get(tempOffset);
+                if (lookupTokenList != null)
+                {
+                    return lookupTokenList;
+                }
+            }
+        }
+        // no tokens in window
+        return null;
+    }
+
+    /**
+     * Determines the largest overlapping window annotation for the specified
+     * LookupToken.
+     * 
+     * @param lt
+     * @param wStartOffsetMap
+     * @param wEndOffsetMap
+     * @return
+     */
+    private LookupAnnotation getLargestWindowAnnotation(
+            int tokenIdx,
+            LookupToken lt,
+            Map ltStartOffsetMap,
+            Map ltEndOffsetMap,
+            Map ltListIndexMap,
+            Map wStartOffsetMap,
+            Map wEndOffsetMap)
+    {
+        Set startCandidateSet = new HashSet();
+        Set endCandidateSet = new HashSet();
+
+        Iterator startItr = wStartOffsetMap.keySet().iterator();
+        while (startItr.hasNext())
+        {
+            Integer startOffset = (Integer) startItr.next();
+            if (startOffset.intValue() <= lt.getStartOffset())
+            {
+                List wAnnotList = (List) wStartOffsetMap.get(startOffset);
+                startCandidateSet.addAll(wAnnotList);
+            }
+        }
+
+        Iterator endItr = wEndOffsetMap.keySet().iterator();
+        while (endItr.hasNext())
+        {
+            Integer endOffset = (Integer) endItr.next();
+            if (endOffset.intValue() >= lt.getEndOffset())
+            {
+                List wAnnotList = (List) wEndOffsetMap.get(endOffset);
+                endCandidateSet.addAll(wAnnotList);
+            }
+        }
+
+        // union to get window annotations that are overlapping with LookupToken
+        startCandidateSet.retainAll(endCandidateSet);
+
+        // find largest overlapping window annotation
+        LookupAnnotation largestWindowAnnot = null;
+        Iterator laItr = startCandidateSet.iterator();
+        while (laItr.hasNext())
+        {
+            LookupAnnotation tempLookupAnnot = (LookupAnnotation) laItr.next();
+            if ((largestWindowAnnot == null)
+                    || (tempLookupAnnot.getLength() > largestWindowAnnot.getLength()))
+            {
+                // now see if we can handle the size of this window (permutation
+                // wise)
+                int ltCount = getNumberOfListTokens(
+                        ltStartOffsetMap,
+                        ltEndOffsetMap,
+                        ltListIndexMap,
+                        tempLookupAnnot.getStartOffset(),
+                        tempLookupAnnot.getEndOffset());
+
+                if ((ltCount <= iv_maxPermutationLevel) && (ltCount > 0))
+                {
+                    largestWindowAnnot = tempLookupAnnot;
+                }
+                else
+                {
+                    if (iv_logger.isDebugEnabled())
+                    {
+                        iv_logger.debug("Window size of "
+                                + ltCount
+                                + " exceeds the max permutation level of "
+                                + iv_maxPermutationLevel
+                                + ".");
+                    }
+                }
+            }
+        }
+
+        return largestWindowAnnot;
+    }
+
+    private int getFixedWindowEndOffset(
+            int tokenIdx,
+            LookupToken lt,
+            List ltList)
+    {
+        int fixedEndOffset = 0;
+
+        for (int i = tokenIdx; (i < tokenIdx + iv_maxPermutationLevel)
+                && (i < ltList.size()); i++)
+        {
+            LookupToken tempLookupToken = (LookupToken) ltList.get(i);
+            if (tempLookupToken != null)
+            {
+                fixedEndOffset = tempLookupToken.getEndOffset();
+            }
+        }
+        return fixedEndOffset;
+    }
+
+    /**
+     * Creates a map that binds an object from a list to its index position.
+     * 
+     * @param list
+     * @return
+     */
+    private Map getListIndexMap(List list)
+    {
+        Map m = new HashMap();
+
+        for (int i = 0; i < list.size(); i++)
+        {
+            Integer index = new Integer(i);
+            m.put(list.get(i), index);
+        }
+
+        return m;
+    }
+
+    /**
+     * Creates a map that uses the start offset to index the LookupAnnotation
+     * objects. If multiple LookupAnnotations can exist at the same start
+     * offset, then hasMultiples=true and the values with be a List of
+     * LookupAnnotation objects at that offset.
+     * 
+     * @param lookupAnnotList
+     * @param hasMultiples
+     * @return
+     */
+    private Map getStartOffsetMap(List lookupAnnotList, boolean hasMultiples)
+    {
+        Map m = new HashMap();
+
+        Iterator laItr = lookupAnnotList.iterator();
+        while (laItr.hasNext())
+        {
+            LookupAnnotation la = (LookupAnnotation) laItr.next();
+            Integer key = new Integer(la.getStartOffset());
+            if (hasMultiples)
+            {
+                List list = (List) m.get(key);
+                if (list == null)
+                {
+                    list = new ArrayList();
+                }
+                list.add(la);
+                m.put(key, list);
+            }
+            else
+            {
+                m.put(key, la);
+            }
+        }
+
+        return m;
+    }
+
+    /**
+     * Creates a map that uses the end offset to index the LookupAnnotation
+     * objects. If multiple LookupAnnotations can exist at the end start offset,
+     * then hasMultiples=true and the values with be a List of LookupAnnotation
+     * objects at that offset.
+     * 
+     * @param lookupAnnotList
+     * @param hasMultiples
+     * @return
+     */
+    private Map getEndOffsetMap(List lookupAnnotList, boolean hasMultiples)
+    {
+        Map m = new HashMap();
+
+        Iterator laItr = lookupAnnotList.iterator();
+        while (laItr.hasNext())
+        {
+            LookupAnnotation la = (LookupAnnotation) laItr.next();
+            Integer key = new Integer(la.getEndOffset());
+            if (hasMultiples)
+            {
+                List list = (List) m.get(key);
+                if (list == null)
+                {
+                    list = new ArrayList();
+                }
+                list.add(la);
+                m.put(key, list);
+            }
+            else
+            {
+                m.put(key, la);
+            }
+        }
+
+        return m;
+    }
+
+    /**
+     * Gets the hits for the specified LookupToken. This uses the first token Dictionary.
+     * 
+     * @param firstLookupToken
+     * @return
+     * @throws Exception
+     */
+    private Collection getFirstTokenHits(LookupToken firstLookupToken)
+            throws Exception
+    {
+        List singleLtList = new ArrayList();
+        singleLtList.add(firstLookupToken);
+
+        String[] phrases = iv_phrBuilder.getPhrases(singleLtList);
+
+        Collection mdhCol = new ArrayList();
+        for (int i = 0; i < phrases.length; i++)
+        {
+            Collection curMdhCol = iv_firstTokenDictEngine.metaLookup(phrases[i]);
+
+            if (curMdhCol.size() > 0)
+            {
+                mdhCol.addAll(curMdhCol);
+            }
+        }
+        return mdhCol;
+    }
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/LookupAlgorithm.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/dictionary%20lookup/src/edu/mayo/bmi/lookup/algorithms/LookupAlgorithm.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/LookupAlgorithm.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/LookupAlgorithm.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
 /*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * 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
- * 
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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
@@ -21,31 +14,31 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.lookup.algorithms;
-
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
-/**
- * Generic interface to specific lookup algorithm implementations.
- * 
- * @author Mayo Clinic
- */
-public interface LookupAlgorithm
-{
-    /**
-     * Lookup the given text specified via LookupToken objects. Any hits will be
-     * returned as a collection of LookupHit objects.
-     * 
-     * @param lookupTokenList
-     *            List of LookupTokens, must be sorted.
-     * @param contextMap
-     *            Map where key=Impl specific String object and value=List of
-     *            LookupAnnotation objects
-     * @return Collection of LookupHits.
-     * @throws Exception
-     */
-    public Collection lookup(List lookupTokenList, Map contextMap)
-            throws Exception;
-}
+package edu.mayo.bmi.lookup.algorithms;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Generic interface to specific lookup algorithm implementations.
+ * 
+ * @author Mayo Clinic
+ */
+public interface LookupAlgorithm
+{
+    /**
+     * Lookup the given text specified via LookupToken objects. Any hits will be
+     * returned as a collection of LookupHit objects.
+     * 
+     * @param lookupTokenList
+     *            List of LookupTokens, must be sorted.
+     * @param contextMap
+     *            Map where key=Impl specific String object and value=List of
+     *            LookupAnnotation objects
+     * @return Collection of LookupHits.
+     * @throws Exception
+     */
+    public Collection lookup(List lookupTokenList, Map contextMap)
+            throws Exception;
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/PermutationUtil.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/dictionary%20lookup/src/edu/mayo/bmi/lookup/algorithms/PermutationUtil.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/PermutationUtil.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/algorithms/PermutationUtil.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
 /*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * 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
- * 
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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
@@ -21,220 +14,220 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.lookup.algorithms;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-
-/**
- * @author Mayo Clinic
- */
-public class PermutationUtil
-{
-    /**
-     * Gets all permutations for the given level and all sub-levels.
-     * 
-     * @param maxLevel
-     */
-    public static List getPermutationList(int maxLevel)
-    {
-        List permList = new ArrayList();
-        for (int levelIdx = maxLevel; levelIdx >= 0; levelIdx--)
-        {
-            // contains ALL index values
-            List baseNumList = new ArrayList();
-            for (int j = 1; j <= levelIdx; j++)
-            {
-                baseNumList.add(new Integer(j));
-            }
-
-            Collection numListCol = new ArrayList();
-            if (levelIdx != maxLevel)
-            {
-                numListCol.addAll(getNumLists(maxLevel, baseNumList));
-            }
-            else
-            {
-                numListCol.add(baseNumList);
-            }
-
-            Iterator numListItr = numListCol.iterator();
-            while (numListItr.hasNext())
-            {
-                List numList = (List) numListItr.next();
-                Collection pCol = PermutationUtil
-                        .getLinearPermutations(numList);
-                Iterator pItr = pCol.iterator();
-                while (pItr.hasNext())
-                {
-                    List permutation = (List) pItr.next();
-                    permList.add(permutation);
-                }
-            }
-
-            if (levelIdx == 0)
-            {
-                permList.add(new ArrayList());
-            }
-        }
-
-        return permList;
-    }
-
-    private static Collection getNumLists(int maxLevel, List baseNumList)
-    {
-        Collection numListCol = new ArrayList();
-        buildPermutations(maxLevel, baseNumList, numListCol, new ArrayList(), 0);
-        filterNonIncreasingLists(numListCol);
-        return numListCol;
-    }
-
-    /**
-     * Filters the number lists such that only lists with increasing numbers are
-     * kept.
-     * 
-     * @param numListCol
-     */
-    private static void filterNonIncreasingLists(Collection numListCol)
-    {
-        Set removalSet = new HashSet();
-
-        Iterator numListItr = numListCol.iterator();
-        while (numListItr.hasNext())
-        {
-            List numList = (List) numListItr.next();
-            Integer largestNum = null;
-            Iterator numItr = numList.iterator();
-            while (numItr.hasNext())
-            {
-                Integer num = (Integer) numItr.next();
-                if (largestNum == null)
-                {
-                    largestNum = num;
-                }
-                else
-                {
-                    int comparison = largestNum.compareTo(num);
-                    if (comparison == 1)
-                    {
-                        removalSet.add(numList);
-                    }
-                    else
-                    {
-                        largestNum = num;
-                    }
-                }
-            }
-        }
-        numListCol.removeAll(removalSet);
-    }
-
-    /**
-     * Recursively builds permutations of numbers specified by the base num
-     * list. This includes permutations of these numbers with few items than the
-     * original list.
-     * 
-     * @param maxLevel
-     * @param baseNumList
-     * @param numListCol
-     * @param residualList
-     * @param residualCount
-     */
-    private static void buildPermutations(
-            int maxLevel,
-            List baseNumList,
-            Collection numListCol,
-            List residualList,
-            int residualCount)
-    {
-        if (residualCount > baseNumList.size())
-        {
-            return;
-        }
-        else if (residualCount == baseNumList.size())
-        {
-            numListCol.add(new ArrayList(residualList));
-            return;
-        }
-        else
-        {
-            int num = ((Integer) baseNumList.get(residualCount)).intValue();
-            residualCount++;
-            for (int i = num; i <= maxLevel; i++)
-            {
-                List tempList = new ArrayList(residualList);
-                if (!tempList.contains(new Integer(i)))
-                {
-                    tempList.add(new Integer(i));
-                    buildPermutations(
-                            maxLevel,
-                            baseNumList,
-                            numListCol,
-                            tempList,
-                            residualCount);
-                }
-            }
-        }
-    }
-
-    /**
-     * Gets a collection of lists, each list represents a single permutation.
-     * This permutation is composed of Integer objects in defined order.
-     * 
-     * @param level
-     * @return
-     */
-    public static Collection getLinearPermutations(List numList)
-    {
-        Collection permutations = new ArrayList();
-        getLinearPermutations(permutations, new ArrayList(), numList);
-        return permutations;
-    }
-
-    /**
-     * Recurisvely builds permutations from the number list. The size of the
-     * permutations remains constant.
-     * 
-     * @param permutations
-     * @param plusList
-     * @param numList
-     */
-    private static void getLinearPermutations(
-            Collection permutations,
-            List plusList,
-            List numList)
-    {
-        Iterator numItr = numList.iterator();
-        while (numItr.hasNext())
-        {
-            Integer num = (Integer) numItr.next();
-
-            List subList = new ArrayList();
-            subList.addAll(numList);
-            subList.remove(num);
-
-            plusList.add(num);
-
-            if (subList.size() > 0)
-            {
-                getLinearPermutations(permutations, plusList, subList);
-            }
-            else
-            {
-                List permutation = new ArrayList();
-                for (int i = 0; i < plusList.size(); i++)
-                {
-                    Integer n = (Integer) plusList.get(i);
-                    permutation.add(n);
-                }
-                permutations.add(permutation);
-            }
-
-            plusList.remove(num);
-        }
-    }
-}
\ No newline at end of file
+package edu.mayo.bmi.lookup.algorithms;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * @author Mayo Clinic
+ */
+public class PermutationUtil
+{
+    /**
+     * Gets all permutations for the given level and all sub-levels.
+     * 
+     * @param maxLevel
+     */
+    public static List getPermutationList(int maxLevel)
+    {
+        List permList = new ArrayList();
+        for (int levelIdx = maxLevel; levelIdx >= 0; levelIdx--)
+        {
+            // contains ALL index values
+            List baseNumList = new ArrayList();
+            for (int j = 1; j <= levelIdx; j++)
+            {
+                baseNumList.add(new Integer(j));
+            }
+
+            Collection numListCol = new ArrayList();
+            if (levelIdx != maxLevel)
+            {
+                numListCol.addAll(getNumLists(maxLevel, baseNumList));
+            }
+            else
+            {
+                numListCol.add(baseNumList);
+            }
+
+            Iterator numListItr = numListCol.iterator();
+            while (numListItr.hasNext())
+            {
+                List numList = (List) numListItr.next();
+                Collection pCol = PermutationUtil
+                        .getLinearPermutations(numList);
+                Iterator pItr = pCol.iterator();
+                while (pItr.hasNext())
+                {
+                    List permutation = (List) pItr.next();
+                    permList.add(permutation);
+                }
+            }
+
+            if (levelIdx == 0)
+            {
+                permList.add(new ArrayList());
+            }
+        }
+
+        return permList;
+    }
+
+    private static Collection getNumLists(int maxLevel, List baseNumList)
+    {
+        Collection numListCol = new ArrayList();
+        buildPermutations(maxLevel, baseNumList, numListCol, new ArrayList(), 0);
+        filterNonIncreasingLists(numListCol);
+        return numListCol;
+    }
+
+    /**
+     * Filters the number lists such that only lists with increasing numbers are
+     * kept.
+     * 
+     * @param numListCol
+     */
+    private static void filterNonIncreasingLists(Collection numListCol)
+    {
+        Set removalSet = new HashSet();
+
+        Iterator numListItr = numListCol.iterator();
+        while (numListItr.hasNext())
+        {
+            List numList = (List) numListItr.next();
+            Integer largestNum = null;
+            Iterator numItr = numList.iterator();
+            while (numItr.hasNext())
+            {
+                Integer num = (Integer) numItr.next();
+                if (largestNum == null)
+                {
+                    largestNum = num;
+                }
+                else
+                {
+                    int comparison = largestNum.compareTo(num);
+                    if (comparison == 1)
+                    {
+                        removalSet.add(numList);
+                    }
+                    else
+                    {
+                        largestNum = num;
+                    }
+                }
+            }
+        }
+        numListCol.removeAll(removalSet);
+    }
+
+    /**
+     * Recursively builds permutations of numbers specified by the base num
+     * list. This includes permutations of these numbers with few items than the
+     * original list.
+     * 
+     * @param maxLevel
+     * @param baseNumList
+     * @param numListCol
+     * @param residualList
+     * @param residualCount
+     */
+    private static void buildPermutations(
+            int maxLevel,
+            List baseNumList,
+            Collection numListCol,
+            List residualList,
+            int residualCount)
+    {
+        if (residualCount > baseNumList.size())
+        {
+            return;
+        }
+        else if (residualCount == baseNumList.size())
+        {
+            numListCol.add(new ArrayList(residualList));
+            return;
+        }
+        else
+        {
+            int num = ((Integer) baseNumList.get(residualCount)).intValue();
+            residualCount++;
+            for (int i = num; i <= maxLevel; i++)
+            {
+                List tempList = new ArrayList(residualList);
+                if (!tempList.contains(new Integer(i)))
+                {
+                    tempList.add(new Integer(i));
+                    buildPermutations(
+                            maxLevel,
+                            baseNumList,
+                            numListCol,
+                            tempList,
+                            residualCount);
+                }
+            }
+        }
+    }
+
+    /**
+     * Gets a collection of lists, each list represents a single permutation.
+     * This permutation is composed of Integer objects in defined order.
+     * 
+     * @param level
+     * @return
+     */
+    public static Collection getLinearPermutations(List numList)
+    {
+        Collection permutations = new ArrayList();
+        getLinearPermutations(permutations, new ArrayList(), numList);
+        return permutations;
+    }
+
+    /**
+     * Recurisvely builds permutations from the number list. The size of the
+     * permutations remains constant.
+     * 
+     * @param permutations
+     * @param plusList
+     * @param numList
+     */
+    private static void getLinearPermutations(
+            Collection permutations,
+            List plusList,
+            List numList)
+    {
+        Iterator numItr = numList.iterator();
+        while (numItr.hasNext())
+        {
+            Integer num = (Integer) numItr.next();
+
+            List subList = new ArrayList();
+            subList.addAll(numList);
+            subList.remove(num);
+
+            plusList.add(num);
+
+            if (subList.size() > 0)
+            {
+                getLinearPermutations(permutations, plusList, subList);
+            }
+            else
+            {
+                List permutation = new ArrayList();
+                for (int i = 0; i < plusList.size(); i++)
+                {
+                    Integer n = (Integer) plusList.get(i);
+                    permutation.add(n);
+                }
+                permutations.add(permutation);
+            }
+
+            plusList.remove(num);
+        }
+    }
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/phrasebuilder/PhraseBuilder.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/dictionary%20lookup/src/edu/mayo/bmi/lookup/phrasebuilder/PhraseBuilder.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/phrasebuilder/PhraseBuilder.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/phrasebuilder/PhraseBuilder.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
 /*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * 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
- * 
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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
@@ -21,22 +14,22 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.lookup.phrasebuilder;
-
-import java.util.List;
-
-/**
- * Interface for building phrases from LookupToken objects.
- * 
- * @author Mayo Clinic
- */
-public interface PhraseBuilder
-{
-    /**
-     * Given a list of LookupTokens, one or more phrases are built.
-     * 
-     * @param lookupTokenList List of LookupTokens.
-     * @return One or more String phrases.
-     */
-    public String[] getPhrases(List lookupTokenList);
-}
+package edu.mayo.bmi.lookup.phrasebuilder;
+
+import java.util.List;
+
+/**
+ * Interface for building phrases from LookupToken objects.
+ * 
+ * @author Mayo Clinic
+ */
+public interface PhraseBuilder
+{
+    /**
+     * Given a list of LookupTokens, one or more phrases are built.
+     * 
+     * @param lookupTokenList List of LookupTokens.
+     * @return One or more String phrases.
+     */
+    public String[] getPhrases(List lookupTokenList);
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/phrasebuilder/VariantPhraseBuilderImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/dictionary%20lookup/src/edu/mayo/bmi/lookup/phrasebuilder/VariantPhraseBuilderImpl.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/phrasebuilder/VariantPhraseBuilderImpl.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/phrasebuilder/VariantPhraseBuilderImpl.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
 /*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * 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
- * 
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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
@@ -21,146 +14,146 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.lookup.phrasebuilder;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-
-import edu.mayo.bmi.lookup.vo.LookupToken;
-
-/**
- * Builds phrases based on various variants of a LookupToken. For instance, a
- * single LookupToken may have a spell corrected variant, abbreviation expansion
- * variant, etc...
- * 
- * @author Mayo Clinic
- */
-public class VariantPhraseBuilderImpl implements PhraseBuilder
-{
-    private List iv_textExtractorList;
-
-    /**
-     * Constructor
-     * 
-     * @param variantAttrNames
-     *            Key names of the variant attributes attached to the
-     *            LookupToken objects.
-     * @param useOriginalText
-     *            flag that determines whether to use the original text or not.
-     */
-    public VariantPhraseBuilderImpl(String[] variantAttrNames,
-            boolean useOriginalText)
-    {
-        iv_textExtractorList = new ArrayList();
-
-        if (useOriginalText)
-        {
-            // use original text as a variant
-            iv_textExtractorList.add(new OriginalTextImpl());
-        }
-
-        // add variants
-        for (int i = 0; i < variantAttrNames.length; i++)
-        {
-            iv_textExtractorList.add(new AttributeTextImpl(variantAttrNames[i]));
-        }
-    }
-
-    public String[] getPhrases(List lookupTokenList)
-    {
-        Set phraseSet = new HashSet();
-        Iterator teItr = iv_textExtractorList.iterator();
-        while (teItr.hasNext())
-        {
-            TextExtractor te = (TextExtractor) teItr.next();
-
-            StringBuffer sb = new StringBuffer();
-            LookupToken previousLt = null;
-            Iterator ltItr = lookupTokenList.iterator();
-            while (ltItr.hasNext())
-            {
-                LookupToken lt = (LookupToken) ltItr.next();
-                String variant = te.getText(lt);
-
-                if (variant == null)
-                {
-                    variant = lt.getText();
-                }
-
-                if (previousLt != null)
-                {
-                    // check delta between previous token and current token
-                    // this delta represents whitespace between tokens
-                    if (previousLt.getEndOffset() != lt.getStartOffset())
-                    {
-                        // insert whitespace
-                        sb.append(' ');
-                    }
-                }
-
-                sb.append(variant);
-
-                previousLt = lt;
-            }
-            String phrase = sb.toString().trim();
-            phraseSet.add(phrase);
-        }
-
-        String[] phraseArr = new String[phraseSet.size()];
-        phraseSet.toArray(phraseArr);
-
-        return phraseArr;
-    }
-
-    /**
-     * Common interface to extract text from a LookupToken.
-     * 
-     * @author Mayo Clinic
-     */
-    private interface TextExtractor
-    {
-        public String getText(LookupToken lt);
-    }
-
-    /**
-     * Implementation that extracts text from the original text of a
-     * LookupToken.
-     * 
-     * @author Mayo Clinic
-     */
-    class OriginalTextImpl implements TextExtractor
-    {
-        public String getText(LookupToken lt)
-        {
-            return lt.getText();
-        }
-    }
-
-    /**
-     * Implementation that extracts text from an attribute of a LookupToken.
-     * 
-     * @author Mayo Clinic
-     */
-    class AttributeTextImpl implements TextExtractor
-    {
-        private String iv_varAttrName;
-
-        /**
-         * Constructor
-         * 
-         * @param varAttrName
-         */
-        public AttributeTextImpl(String varAttrName)
-        {
-            iv_varAttrName = varAttrName;
-        }
-
-        public String getText(LookupToken lt)
-        {
-            return lt.getStringAttribute(iv_varAttrName);
-        }
-    }
-}
\ No newline at end of file
+package edu.mayo.bmi.lookup.phrasebuilder;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+import edu.mayo.bmi.lookup.vo.LookupToken;
+
+/**
+ * Builds phrases based on various variants of a LookupToken. For instance, a
+ * single LookupToken may have a spell corrected variant, abbreviation expansion
+ * variant, etc...
+ * 
+ * @author Mayo Clinic
+ */
+public class VariantPhraseBuilderImpl implements PhraseBuilder
+{
+    private List iv_textExtractorList;
+
+    /**
+     * Constructor
+     * 
+     * @param variantAttrNames
+     *            Key names of the variant attributes attached to the
+     *            LookupToken objects.
+     * @param useOriginalText
+     *            flag that determines whether to use the original text or not.
+     */
+    public VariantPhraseBuilderImpl(String[] variantAttrNames,
+            boolean useOriginalText)
+    {
+        iv_textExtractorList = new ArrayList();
+
+        if (useOriginalText)
+        {
+            // use original text as a variant
+            iv_textExtractorList.add(new OriginalTextImpl());
+        }
+
+        // add variants
+        for (int i = 0; i < variantAttrNames.length; i++)
+        {
+            iv_textExtractorList.add(new AttributeTextImpl(variantAttrNames[i]));
+        }
+    }
+
+    public String[] getPhrases(List lookupTokenList)
+    {
+        Set phraseSet = new HashSet();
+        Iterator teItr = iv_textExtractorList.iterator();
+        while (teItr.hasNext())
+        {
+            TextExtractor te = (TextExtractor) teItr.next();
+
+            StringBuffer sb = new StringBuffer();
+            LookupToken previousLt = null;
+            Iterator ltItr = lookupTokenList.iterator();
+            while (ltItr.hasNext())
+            {
+                LookupToken lt = (LookupToken) ltItr.next();
+                String variant = te.getText(lt);
+
+                if (variant == null)
+                {
+                    variant = lt.getText();
+                }
+
+                if (previousLt != null)
+                {
+                    // check delta between previous token and current token
+                    // this delta represents whitespace between tokens
+                    if (previousLt.getEndOffset() != lt.getStartOffset())
+                    {
+                        // insert whitespace
+                        sb.append(' ');
+                    }
+                }
+
+                sb.append(variant);
+
+                previousLt = lt;
+            }
+            String phrase = sb.toString().trim();
+            phraseSet.add(phrase);
+        }
+
+        String[] phraseArr = new String[phraseSet.size()];
+        phraseSet.toArray(phraseArr);
+
+        return phraseArr;
+    }
+
+    /**
+     * Common interface to extract text from a LookupToken.
+     * 
+     * @author Mayo Clinic
+     */
+    private interface TextExtractor
+    {
+        public String getText(LookupToken lt);
+    }
+
+    /**
+     * Implementation that extracts text from the original text of a
+     * LookupToken.
+     * 
+     * @author Mayo Clinic
+     */
+    class OriginalTextImpl implements TextExtractor
+    {
+        public String getText(LookupToken lt)
+        {
+            return lt.getText();
+        }
+    }
+
+    /**
+     * Implementation that extracts text from an attribute of a LookupToken.
+     * 
+     * @author Mayo Clinic
+     */
+    class AttributeTextImpl implements TextExtractor
+    {
+        private String iv_varAttrName;
+
+        /**
+         * Constructor
+         * 
+         * @param varAttrName
+         */
+        public AttributeTextImpl(String varAttrName)
+        {
+            iv_varAttrName = varAttrName;
+        }
+
+        public String getText(LookupToken lt)
+        {
+            return lt.getStringAttribute(iv_varAttrName);
+        }
+    }
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/vo/LookupAnnotation.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/dictionary%20lookup/src/edu/mayo/bmi/lookup/vo/LookupAnnotation.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/vo/LookupAnnotation.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/dictionary lookup/src/edu/mayo/bmi/lookup/vo/LookupAnnotation.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
 /*
- * Copyright: (c) 2009   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * 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
- * 
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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
@@ -21,56 +14,56 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.lookup.vo;
-
-/**
- * Value object that models a text annotation.
- * 
- * @author Mayo Clinic
- */
-public interface LookupAnnotation
-{
-    /**
-     * Gets the start offset.
-     * 
-     * @return
-     */
-    public int getStartOffset();
-
-    /**
-     * Gets the end offset.
-     * 
-     * @return
-     */
-    public int getEndOffset();
-
-    /**
-     * Gets the length of this annotation based on offsets.
-     * 
-     * @return
-     */
-    public int getLength();
-
-    /**
-     * Gets the text.
-     * 
-     * @return
-     */
-    public String getText();
-    
-    /**
-     * Adds an attribute that may be used for filtering.
-     * 
-     * @param attrKey
-     * @param attrVal
-     */
-    public void addStringAttribute(String attrKey, String attrVal);
-
-    /**
-     * Gets an attribute.
-     * 
-     * @param attrKey
-     * @return
-     */
-    public String getStringAttribute(String attrKey);    
-}
\ No newline at end of file
+package edu.mayo.bmi.lookup.vo;
+
+/**
+ * Value object that models a text annotation.
+ * 
+ * @author Mayo Clinic
+ */
+public interface LookupAnnotation
+{
+    /**
+     * Gets the start offset.
+     * 
+     * @return
+     */
+    public int getStartOffset();
+
+    /**
+     * Gets the end offset.
+     * 
+     * @return
+     */
+    public int getEndOffset();
+
+    /**
+     * Gets the length of this annotation based on offsets.
+     * 
+     * @return
+     */
+    public int getLength();
+
+    /**
+     * Gets the text.
+     * 
+     * @return
+     */
+    public String getText();
+    
+    /**
+     * Adds an attribute that may be used for filtering.
+     * 
+     * @param attrKey
+     * @param attrVal
+     */
+    public void addStringAttribute(String attrKey, String attrVal);
+
+    /**
+     * Gets an attribute.
+     * 
+     * @param attrKey
+     * @return
+     */
+    public String getStringAttribute(String attrKey);    
+}



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