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From james-mas...@apache.org
Subject svn commit: r1403989 [7/28] - 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/parser...
Date Wed, 31 Oct 2012 05:26:55 GMT
Modified: incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java Wed Oct 31 05:26:43 2012
@@ -1,19 +1,12 @@
 package edu.mayo.bmi.nlp.parser.ae;
 /*
- * Copyright: (c) 2010   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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java Wed Oct 31 05:26:43 2012
@@ -1,19 +1,12 @@
 package edu.mayo.bmi.nlp.parser.ae;
 /*
- * Copyright: (c) 2010   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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java Wed Oct 31 05:26:43 2012
@@ -1,19 +1,12 @@
 package edu.mayo.bmi.nlp.parser.cr;
 /*
- * Copyright: (c) 2010   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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/util/Delim.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/util/Delim.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/util/Delim.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/util/Delim.java Wed Oct 31 05:26:43 2012
@@ -1,19 +1,12 @@
 /*
 
- * Copyright: (c) 2010   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
@@ -40,4 +33,4 @@ public class Delim {
 	public static String DN_ARC_B     = ">";
 	public static String TRIPLE_DELIM = ",";
 
-}
\ No newline at end of file
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/util/DependencyUtility.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/util/DependencyUtility.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/util/DependencyUtility.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/clearparser-wrapper/src/edu/mayo/bmi/nlp/parser/util/DependencyUtility.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
 /*
- * Copyright: (c) 2010   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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/clinical documents pipeline/src/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/clinical%20documents%20pipeline/src/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/clinical documents pipeline/src/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/clinical documents pipeline/src/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.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
@@ -21,8 +14,8 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.uima.cni.ae;
-
+package edu.mayo.bmi.uima.cni.ae;
+
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.Set;
@@ -44,168 +37,168 @@ import edu.mayo.bmi.uima.core.type.texts
 import edu.mayo.bmi.uima.core.type.textspan.Segment;
 import edu.mayo.bmi.uima.core.type.util.Pair;
 import edu.mayo.bmi.uima.core.type.util.Pairs;
-
-/**
- * UIMA annotator that prepares the CAS for output - performs
- * some (final) updates to the CAS
- * 
- * @author Mayo Clinic
- */
-public class ExtractionPrepAnnotator extends JCasAnnotator_ImplBase {
-	private String iv_annotVerPropKey;
-	private int iv_annotVer;
-
-	/**
-	 * Method invoked by UIMA framework to initialize this annotator
-	 */
-	public void initialize(UimaContext aCtx)
-			throws ResourceInitializationException {
-		
-		super.initialize(aCtx);
-
-		try {
-			iv_annotVer = ((Integer) aCtx.getConfigParameterValue("AnnotationVersion")).intValue();
-			iv_annotVerPropKey = (String) aCtx.getConfigParameterValue("AnnotationVersionPropKey");
-		} catch (Exception e) {
-			throw new ResourceInitializationException(e);
-		}
-	
-	}
-
-	/**
-	 * Method invoked by UIMA framework to process a document
-	 */
-	public void process(JCas jcas)
-			throws AnalysisEngineProcessException {
-		generateUidValues(jcas);
-		generateTokenNormForms(jcas);
-		assignNamedEntityFeats(jcas);
-		storeAnnotationVersion(jcas);
-	}
-
-	
-	/**
-	 * Stores annotation version as a property JCas object.
-	 * 
-	 * @param jcas
-	 */
-	private void storeAnnotationVersion(JCas jcas) {
-	 	FSIterator<TOP> itr = jcas.getJFSIndexRepository().getAllIndexedFS(Pairs.type);
-		if (itr == null || !itr.hasNext())
-			return;
-
-		Pairs props = (Pairs) itr.next(); 
-
-		// create a new property array that is one item bigger
-		FSArray propArr = props.getPairs();
-		FSArray newPropArr = new FSArray(jcas, propArr.size() + 1);
-		for (int i = 0; i < propArr.size(); i++) {
-			newPropArr.set(i, propArr.get(i));
-		}
-
-		Pair annotVerProp = new Pair(jcas);    		
-		annotVerProp.setAttribute(iv_annotVerPropKey);
-		annotVerProp.setValue(String.valueOf(iv_annotVer));
-
-		// add annotation version prop as last item in array
-		newPropArr.set(newPropArr.size() - 1, annotVerProp);
-		props.setPairs(newPropArr);
-	}
-
-	/**
-	 * Generates UID values for all IdentifiedAnnotation objects.
-	 * This is just a numeric identifier, assigned sequentially.
-	 */
-	private void generateUidValues(JCas jcas) {
-		int uid = 0;
-		Iterator itr = jcas.getJFSIndexRepository().getAnnotationIndex(
-				IdentifiedAnnotation.type).iterator();
-		while (itr.hasNext()) {
-			IdentifiedAnnotation idAnnot = (IdentifiedAnnotation) itr.next();
-			idAnnot.setId(uid);
-			uid++;
-		}
-	}
-
-	/**
-	 * Generates normalized form for each token annotation.
-	 * Considers whether it is a <code>WordToken</code> with a canonical form
-	 */
-	private void generateTokenNormForms(JCas jcas) {
-		JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-
-		// Determine and set the normalized form for each <code>BaseToken</code>
-		Iterator btaItr = indexes.getAnnotationIndex(BaseToken.type).iterator();
-		while (btaItr.hasNext()) {
-			BaseToken bta = (BaseToken) btaItr.next();
-			String normForm = null;
-			if (!(bta instanceof WordToken)) {
-				normForm = bta.getCoveredText();
-			} else {
-				WordToken wta = (WordToken) bta;
-				String canonicalForm = wta.getCanonicalForm();
-
-
-				// The norm form is the canonical form, if there is one
-				// Otherwise the norm form is the token's text.
-				if ((canonicalForm != null)	&& (canonicalForm.length() > 0)) {
-					normForm = canonicalForm;
-				} else {
-					normForm = wta.getCoveredText();
-				}
-			}
-			bta.setNormalizedForm(normForm);
-		}
-	}
-
-	/**
-	 * Assigns OID and segmentID values to NamedEntities
-	 */
-	private void assignNamedEntityFeats(JCas jcas) {
-		JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-		// Set keySet = new HashSet();
-		// List dupList = new ArrayList();
-
-		Set segmentSet = new HashSet();
-		Iterator segmentItr = indexes.getAnnotationIndex(Segment.type).iterator();
-		while (segmentItr.hasNext()) {
-			segmentSet.add(segmentItr.next());
-		}
-
-		// For each NE, assign segment ID and assign ontology concept OIDs if applicable
-		Iterator neItr = indexes.getAnnotationIndex(IdentifiedAnnotation.type).iterator();
-		while (neItr.hasNext()) {
-			
-			IdentifiedAnnotation neAnnot = (IdentifiedAnnotation) neItr.next();
-
-			// assign segment ID
-			Iterator segItr = segmentSet.iterator();
-			while (segItr.hasNext()) {
-				Segment seg = (Segment) segItr.next();
-				// see if NE is inside this segment
-				if ((neAnnot.getBegin() >= seg.getBegin())
-						&& (neAnnot.getEnd() <= seg.getEnd())) {
-					// found segment for this NE
-					neAnnot.setSegmentID(seg.getId());
-					break;
-				}
-			}
-
-			// assign ontology concept OID values
-			FSArray ocArr = neAnnot.getOntologyConceptArr();
-			if (ocArr != null) {
-				for (int i = 0; i < ocArr.size(); i++) {
-					OntologyConcept oc = (OntologyConcept) ocArr.get(i);
-					String code = oc.getCode();
-					String scheme = oc.getCodingScheme();
-
-					StringBuffer oid = new StringBuffer();
-					oid.append(code);
-					oid.append("#");
-					oid.append(scheme);
-					oc.setOid(oid.toString());
-				}
-			}
-		}
-	}
-}
\ No newline at end of file
+
+/**
+ * UIMA annotator that prepares the CAS for output - performs
+ * some (final) updates to the CAS
+ * 
+ * @author Mayo Clinic
+ */
+public class ExtractionPrepAnnotator extends JCasAnnotator_ImplBase {
+	private String iv_annotVerPropKey;
+	private int iv_annotVer;
+
+	/**
+	 * Method invoked by UIMA framework to initialize this annotator
+	 */
+	public void initialize(UimaContext aCtx)
+			throws ResourceInitializationException {
+		
+		super.initialize(aCtx);
+
+		try {
+			iv_annotVer = ((Integer) aCtx.getConfigParameterValue("AnnotationVersion")).intValue();
+			iv_annotVerPropKey = (String) aCtx.getConfigParameterValue("AnnotationVersionPropKey");
+		} catch (Exception e) {
+			throw new ResourceInitializationException(e);
+		}
+	
+	}
+
+	/**
+	 * Method invoked by UIMA framework to process a document
+	 */
+	public void process(JCas jcas)
+			throws AnalysisEngineProcessException {
+		generateUidValues(jcas);
+		generateTokenNormForms(jcas);
+		assignNamedEntityFeats(jcas);
+		storeAnnotationVersion(jcas);
+	}
+
+	
+	/**
+	 * Stores annotation version as a property JCas object.
+	 * 
+	 * @param jcas
+	 */
+	private void storeAnnotationVersion(JCas jcas) {
+	 	FSIterator<TOP> itr = jcas.getJFSIndexRepository().getAllIndexedFS(Pairs.type);
+		if (itr == null || !itr.hasNext())
+			return;
+
+		Pairs props = (Pairs) itr.next(); 
+
+		// create a new property array that is one item bigger
+		FSArray propArr = props.getPairs();
+		FSArray newPropArr = new FSArray(jcas, propArr.size() + 1);
+		for (int i = 0; i < propArr.size(); i++) {
+			newPropArr.set(i, propArr.get(i));
+		}
+
+		Pair annotVerProp = new Pair(jcas);    		
+		annotVerProp.setAttribute(iv_annotVerPropKey);
+		annotVerProp.setValue(String.valueOf(iv_annotVer));
+
+		// add annotation version prop as last item in array
+		newPropArr.set(newPropArr.size() - 1, annotVerProp);
+		props.setPairs(newPropArr);
+	}
+
+	/**
+	 * Generates UID values for all IdentifiedAnnotation objects.
+	 * This is just a numeric identifier, assigned sequentially.
+	 */
+	private void generateUidValues(JCas jcas) {
+		int uid = 0;
+		Iterator itr = jcas.getJFSIndexRepository().getAnnotationIndex(
+				IdentifiedAnnotation.type).iterator();
+		while (itr.hasNext()) {
+			IdentifiedAnnotation idAnnot = (IdentifiedAnnotation) itr.next();
+			idAnnot.setId(uid);
+			uid++;
+		}
+	}
+
+	/**
+	 * Generates normalized form for each token annotation.
+	 * Considers whether it is a <code>WordToken</code> with a canonical form
+	 */
+	private void generateTokenNormForms(JCas jcas) {
+		JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+
+		// Determine and set the normalized form for each <code>BaseToken</code>
+		Iterator btaItr = indexes.getAnnotationIndex(BaseToken.type).iterator();
+		while (btaItr.hasNext()) {
+			BaseToken bta = (BaseToken) btaItr.next();
+			String normForm = null;
+			if (!(bta instanceof WordToken)) {
+				normForm = bta.getCoveredText();
+			} else {
+				WordToken wta = (WordToken) bta;
+				String canonicalForm = wta.getCanonicalForm();
+
+
+				// The norm form is the canonical form, if there is one
+				// Otherwise the norm form is the token's text.
+				if ((canonicalForm != null)	&& (canonicalForm.length() > 0)) {
+					normForm = canonicalForm;
+				} else {
+					normForm = wta.getCoveredText();
+				}
+			}
+			bta.setNormalizedForm(normForm);
+		}
+	}
+
+	/**
+	 * Assigns OID and segmentID values to NamedEntities
+	 */
+	private void assignNamedEntityFeats(JCas jcas) {
+		JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+		// Set keySet = new HashSet();
+		// List dupList = new ArrayList();
+
+		Set segmentSet = new HashSet();
+		Iterator segmentItr = indexes.getAnnotationIndex(Segment.type).iterator();
+		while (segmentItr.hasNext()) {
+			segmentSet.add(segmentItr.next());
+		}
+
+		// For each NE, assign segment ID and assign ontology concept OIDs if applicable
+		Iterator neItr = indexes.getAnnotationIndex(IdentifiedAnnotation.type).iterator();
+		while (neItr.hasNext()) {
+			
+			IdentifiedAnnotation neAnnot = (IdentifiedAnnotation) neItr.next();
+
+			// assign segment ID
+			Iterator segItr = segmentSet.iterator();
+			while (segItr.hasNext()) {
+				Segment seg = (Segment) segItr.next();
+				// see if NE is inside this segment
+				if ((neAnnot.getBegin() >= seg.getBegin())
+						&& (neAnnot.getEnd() <= seg.getEnd())) {
+					// found segment for this NE
+					neAnnot.setSegmentID(seg.getId());
+					break;
+				}
+			}
+
+			// assign ontology concept OID values
+			FSArray ocArr = neAnnot.getOntologyConceptArr();
+			if (ocArr != null) {
+				for (int i = 0; i < ocArr.size(); i++) {
+					OntologyConcept oc = (OntologyConcept) ocArr.get(i);
+					String code = oc.getCode();
+					String scheme = oc.getCodingScheme();
+
+					StringBuffer oid = new StringBuffer();
+					oid.append(code);
+					oid.append("#");
+					oid.append(scheme);
+					oc.setOid(oid.toString());
+				}
+			}
+		}
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/common-type-system/src/edu/mayo/bmi/uima/core/type/constants/CONST.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/common-type-system/src/edu/mayo/bmi/uima/core/type/constants/CONST.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/common-type-system/src/edu/mayo/bmi/uima/core/type/constants/CONST.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/common-type-system/src/edu/mayo/bmi/uima/core/type/constants/CONST.java Wed Oct 31 05:26:43 2012
@@ -1,212 +1,205 @@
-/*
- * Copyright: (c) 2012   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
- * 
- * 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 edu.mayo.bmi.uima.core.type.constants;
-/**
- * Contains a set of constants for feature values.
- * 
- * @author Mayo
- */
-public class CONST {
-
-	public static final int NE_TYPE_ID_UNKNOWN = 0;
-	public static final int NE_TYPE_ID_DRUG = 1;
-	public static final int NE_TYPE_ID_DISORDER = 2;
-	public static final int NE_TYPE_ID_FINDING = 3;
-	public static final int NE_TYPE_ID_PROCEDURE = 5;
-	public static final int NE_TYPE_ID_ANATOMICAL_SITE = 6;
-	
-	public static final int MODIFIER_TYPE_ID_UNKNOWN = 0;
-	public static final int MODIFIER_TYPE_ID_COURSE_CLASS = 1;
-	public static final int MODIFIER_TYPE_ID_SEVERITY_CLASS = 2;
-	public static final int MODIFIER_TYPE_ID_LAB_INTERPRETATION_INDICATOR = 3;
-	
-	public static final int NE_DISCOVERY_TECH_DICT_LOOKUP = 1;
-	public static final int NE_DISCOVERY_TECH_GOLD_ANNOTATION = 2;
-	
-	public static final int NE_POLARITY_NEGATION_ABSENT = 1;
-	public static final int NE_POLARITY_NEGATION_PRESENT = -1;
-	
-	public static final int NE_UNCERTAINTY_PRESENT = 1;
-	public static final int NE_UNCERTAINTY_ABSENT = 0;
-	
-	public static final boolean NE_GENERIC_TRUE = true;
-	public static final boolean NE_GENERIC_FALSE = false;
-
-	public static final boolean NE_CONDITIONAL_TRUE = true;
-	public static final boolean NE_CONDITIONAL_FALSE = false;
-
-	public static final int NE_CERTAINTY_POSITIVE = NE_POLARITY_NEGATION_ABSENT; // TO BE DEPRECATED
-	public static final int NE_CERTAINTY_NEGATED = NE_POLARITY_NEGATION_PRESENT; // TO BE DEPRECATED
-	public static final int NE_DIAG_STATUS_CONFIRMED = 0; // TO BE DEPRECATED
-	public static final int NE_DIAG_STATUS_HISTORY_OF = 1; // TO BE DEPRECATED
-	public static final int NE_DIAG_STATUS_FAM_HISTORY_OF = 2; // TO BE DEPRECATED
-	public static final int NE_DIAG_STATUS_PROBABLE = 3; // TO BE DEPRECATED
-	
-	public static final String ATTR_SEVERITY_SEVERE = "severe";
-	public static final String ATTR_SEVERITY_MODERATE = "moderate";
-	public static final String ATTR_SEVERITY_SLIGHT = "slight";
-	public static final String ATTR_SEVERITY_UNMARKED = "unmarked";
-
-	public static final String ATTR_BODYSIDE_LEFT = "left";
-	public static final String ATTR_BODYSIDE_RIGHT = "right";
-	public static final String ATTR_BODYSIDE_BILATERAL = "bilateral";
-	public static final String ATTR_BODYSIDE_UNMARKED = "unmarked";
-
-	public static final String ATTR_BODYLATERALITY_SUPERIOR = "superior"; // Attribute name may change
-	public static final String ATTR_BODYLATERALITY_INFERIOR = "inferior"; // Attribute name may change
-	public static final String ATTR_BODYLATERALITY_DISTAL = "distal"; // Attribute name may change
-	public static final String ATTR_BODYLATERALITY_PROXIMAL = "proximal"; // Attribute name may change
-	public static final String ATTR_BODYLATERALITY_MEDIAL = "medial"; // Attribute name may change
-	public static final String ATTR_BODYLATERALITY_LATERAL = "lateral"; // Attribute name may change
-	public static final String ATTR_BODYLATERALITY_DORSAL = "dorsal"; // Attribute name may change
-	public static final String ATTR_BODYLATERALITY_VENTRAL = "ventral"; // Attribute name may change
-	public static final String ATTR_BODYLATERALITY_UNMARKED = "unmarked"; // Attribute name may change
-
-	public static final String ATTR_HISTORYOF_INDICATOR_PRESENT = "historyOf_present";
-	public static final String ATTR_HISTORYOF_INDICATOR_ABSENT = "historyOf_absent";	
-	
-	public static final String ATTR_SUBJECT_PATIENT = "patient";
-	public static final String ATTR_SUBJECT_FAMILY_MEMBER = "family_member";
-	public static final String ATTR_SUBJECT_DONOR_FAMILY_MEMBER = "donor_family_member";
-	public static final String ATTR_SUBJECT_DONOR_OTHER = "donor_other";
-	public static final String ATTR_SUBJECT_OTHER = "other";
-
-	// ATTR_PROCEDURE_DEVICE -- any string
-	// ATTR_PROCEDURE_METHOD -- any string
-	
-	// ATTR_LAB_VALUE_NUMBER -- any string
-	// ATTR_LAB_VALUE_UNIT -- any string
-	// ATTR_LAB_REFERENCE_RANGE -- any string
-	
-	public static final String ATTR_LAB_DELTAFLAG_CHANGEUP = "change_up";
-	public static final String ATTR_LAB_DELTAFLAG_CHANGEDOWN = "change_down";
-	public static final String ATTR_LAB_DELTAFLAG_NOCHANGE = "no_change";
-
-	public static final String ATTR_LAB_ABNORMAL_TRUE = "abnormal";
-	public static final String ATTR_LAB_ABNORMAL_VERYTRUE = "very_abnormal";
-
-	public static final String ATTR_LAB_ORDINAL_RESISTANT = "resistant";
-	public static final String ATTR_LAB_ORDINAL_POSITIVE = "positive";
-	public static final String ATTR_LAB_ORDINAL_REACTIVE = "reactive";
-	public static final String ATTR_LAB_ORDINAL_INTERMEDIATERESISTANCE = "intermediate_resistance";
-	public static final String ATTR_LAB_ORDINAL_INTERMEDIATE = "intermediate";
-	public static final String ATTR_LAB_ORDINAL_NEGATIVE = "negative";
-	public static final String ATTR_LAB_ORDINAL_NOTDETECTED = "not_detected";
-	public static final String ATTR_LAB_ORDINAL_DETECTED = "detected";
-	public static final String ATTR_LAB_ORDINAL_WEAKLY_REACTIVE = "weakly_reactive";
-	public static final String ATTR_LAB_ORDINAL_MODERATELYSUSCEPTIBLE = "moderately_susceptible";
-	public static final String ATTR_LAB_ORDINAL_VERYSUSCEPTIBLE = "very_susceptible";
-	public static final String ATTR_LAB_ORDINAL_SUSCEPTIBLE = "susceptible";
-	public static final String ATTR_LAB_ORDINAL_1ORMORE = "1+";
-	public static final String ATTR_LAB_ORDINAL_2ORMORE = "2+";
-	public static final String ATTR_LAB_ORDINAL_3ORMORE = "3+";
-	public static final String ATTR_LAB_ORDINAL_4ORMORE = "4+";
-	public static final String ATTR_LAB_ORDINAL_SMALL = "small";
-	public static final String ATTR_LAB_ORDINAL_TRACE = "trace";
-	public static final String ATTR_LAB_ORDINAL_NORMAL = "normal";
-	public static final String ATTR_LAB_ORDINAL_NO_OR_NA_RANGE = "no_range_or_normal_range_n/a";
-	public static final String ATTR_LAB_ORDINAL_ANTICOMPLEMENTARYPRESENT = "anti_complementary_substance_present";
-	public static final String ATTR_LAB_ORDINAL_CYTOTOXICPRESENT = "cytotoxic_substance_present";
-	public static final String ATTR_LAB_ORDINAL_QUALITYCONTROLFAIL = "quality_control_failure";
-
-	public static final boolean ATTR_LAB_ESTIMATED_FLAG_TRUE = true;
-	public static final boolean ATTR_LAB_ESTIMATED_FLAG_FALSE = false;
-	
-	public static final String ATTR_MEDICATION_DOSAGE_1 = "1";
-	public static final String ATTR_MEDICATION_DOSAGE_2 = "2";
-	public static final String ATTR_MEDICATION_DOSAGE_3 = "3";
-	public static final String ATTR_MEDICATION_DOSAGE_4 = "4";
-	public static final String ATTR_MEDICATION_DOSAGE_5 = "5";
-	public static final String ATTR_MEDICATION_DOSAGE_UNDETERMINED = "undetermined";
-	public static final String ATTR_MEDICATION_DOSAGE_OTHER = "other";
-	
-	public static final String ATTR_MEDICATION_ROUTE_TOPICAL = "topical";
-	public static final String ATTR_MEDICATION_ROUTE_ENTERAL_ORAL = "oral";
-	public static final String ATTR_MEDICATION_ROUTE_ENTERAL_GASTRIC = "gastric";
-	public static final String ATTR_MEDICATION_ROUTE_ENTERAL_RECTAL = "rectal";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAVENOUS = "intravenous";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAARTERIAL = "intra-arterial";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAMUSCULAR = "intramuscular";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRACARDIAC = "intracardiac";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_SUBCUTANEOUS = "subcutaneous";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRATHECAL = "intrathecal";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAPERIOTONEAL = "intraperiotoneal";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_TRANSDERMAL = "transdermal";
-	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_TRANSMUCOSAL = "transmucosal";
-	public static final String ATTR_MEDICATION_ROUTE_OTHER = "other";
-	public static final String ATTR_MEDICATION_ROUTE_UNDETERMINED = "undetermined";
-
-	public static final String ATTR_MEDICATION_FORM_AEROSOL = "aerosol";
-	public static final String ATTR_MEDICATION_FORM_CAPSULE = "capsule";
-	public static final String ATTR_MEDICATION_FORM_CREAM = "cream";
-	public static final String ATTR_MEDICATION_FORM_ELIXIR = "elixir";
-	public static final String ATTR_MEDICATION_FORM_EMULSION = "emulsion";
-	public static final String ATTR_MEDICATION_FORM_ENEMA = "enema";
-	public static final String ATTR_MEDICATION_FORM_GEL = "gel";
-	public static final String ATTR_MEDICATION_FORM_IMPLANT = "implant";
-	public static final String ATTR_MEDICATION_FORM_INHALANT = "inhalant";
-	public static final String ATTR_MEDICATION_FORM_INJECTION = "injection";
-	public static final String ATTR_MEDICATION_FORM_LIQUID = "liquid";
-	public static final String ATTR_MEDICATION_FORM_LOTION = "lotion";
-	public static final String ATTR_MEDICATION_FORM_LOZENGE = "lozenge";
-	public static final String ATTR_MEDICATION_FORM_OINTMENT = "ointment";
-	public static final String ATTR_MEDICATION_FORM_PATCH = "patch";
-	public static final String ATTR_MEDICATION_FORM_PELLET = "pellet";
-	public static final String ATTR_MEDICATION_FORM_PILL = "pill";
-	public static final String ATTR_MEDICATION_FORM_POWDER = "powder";
-	public static final String ATTR_MEDICATION_FORM_SHAMPOO = "shampoo";
-	public static final String ATTR_MEDICATION_FORM_SOAP = "soap";
-	public static final String ATTR_MEDICATION_FORM_SOLUTION = "solution";
-	public static final String ATTR_MEDICATION_FORM_SPRAY = "spray";
-	public static final String ATTR_MEDICATION_FORM_SUPPOSITORY = "suppository";
-	public static final String ATTR_MEDICATION_FORM_SYRUP = "syrup";
-	public static final String ATTR_MEDICATION_FORM_TABLET = "tablet";
-	public static final String ATTR_MEDICATION_FORM_OTHER = "other";
-	
-	public static final String ATTR_MEDICATION_STATUSCHANGE_START = "start";
-	public static final String ATTR_MEDICATION_STATUSCHANGE_STOP = "stop";
-	public static final String ATTR_MEDICATION_STATUSCHANGE_INCREASE = "increase";
-	public static final String ATTR_MEDICATION_STATUSCHANGE_DECREASE = "decrease";
-	public static final String ATTR_MEDICATION_STATUSCHANGE_NOCHANGE = "noChange";
-	
-	public static final String ATTR_MEDICATION_ALLERGY_INDICATOR_PRESENT = "allergy_present";
-	public static final String ATTR_MEDICATION_ALLERGY_INDICATOR_ABSENT = "allergy_absent";	
-
-	// ATTR_MEDICATION_STRENGTH is any number/unit pair
-	// ATTR_MEDICATION_DURATION is any string
-	// ATTR_MEDICATION_FREQUENCY is any number/unit pair
-	
-	public static final int REL_DISCOVERY_TECH_GOLD_ANNOTATION = 1;
-
-	public static final String MED_STATUS_CHANGE_START = ATTR_MEDICATION_STATUSCHANGE_START; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_STOP = ATTR_MEDICATION_STATUSCHANGE_STOP; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_INCREASEFROM = "increasefrom"; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_DECREASEFROM = "decreasefrom"; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_INCREASE = ATTR_MEDICATION_STATUSCHANGE_INCREASE; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_DECREASE = ATTR_MEDICATION_STATUSCHANGE_DECREASE; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_NOCHANGE = ATTR_MEDICATION_STATUSCHANGE_NOCHANGE; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_SUM = "add"; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_MAX = "maximum"; // TO BE DEPRECATED
-	public static final String MED_STATUS_CHANGE_OTHER = "change"; // TO BE DEPRECATED
-}
+/*
+ * 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
+ * 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 edu.mayo.bmi.uima.core.type.constants;
+/**
+ * Contains a set of constants for feature values.
+ * 
+ * @author Mayo
+ */
+public class CONST {
+
+	public static final int NE_TYPE_ID_UNKNOWN = 0;
+	public static final int NE_TYPE_ID_DRUG = 1;
+	public static final int NE_TYPE_ID_DISORDER = 2;
+	public static final int NE_TYPE_ID_FINDING = 3;
+	public static final int NE_TYPE_ID_PROCEDURE = 5;
+	public static final int NE_TYPE_ID_ANATOMICAL_SITE = 6;
+	
+	public static final int MODIFIER_TYPE_ID_UNKNOWN = 0;
+	public static final int MODIFIER_TYPE_ID_COURSE_CLASS = 1;
+	public static final int MODIFIER_TYPE_ID_SEVERITY_CLASS = 2;
+	public static final int MODIFIER_TYPE_ID_LAB_INTERPRETATION_INDICATOR = 3;
+	
+	public static final int NE_DISCOVERY_TECH_DICT_LOOKUP = 1;
+	public static final int NE_DISCOVERY_TECH_GOLD_ANNOTATION = 2;
+	
+	public static final int NE_POLARITY_NEGATION_ABSENT = 1;
+	public static final int NE_POLARITY_NEGATION_PRESENT = -1;
+	
+	public static final int NE_UNCERTAINTY_PRESENT = 1;
+	public static final int NE_UNCERTAINTY_ABSENT = 0;
+	
+	public static final boolean NE_GENERIC_TRUE = true;
+	public static final boolean NE_GENERIC_FALSE = false;
+
+	public static final boolean NE_CONDITIONAL_TRUE = true;
+	public static final boolean NE_CONDITIONAL_FALSE = false;
+
+	public static final int NE_CERTAINTY_POSITIVE = NE_POLARITY_NEGATION_ABSENT; // TO BE DEPRECATED
+	public static final int NE_CERTAINTY_NEGATED = NE_POLARITY_NEGATION_PRESENT; // TO BE DEPRECATED
+	public static final int NE_DIAG_STATUS_CONFIRMED = 0; // TO BE DEPRECATED
+	public static final int NE_DIAG_STATUS_HISTORY_OF = 1; // TO BE DEPRECATED
+	public static final int NE_DIAG_STATUS_FAM_HISTORY_OF = 2; // TO BE DEPRECATED
+	public static final int NE_DIAG_STATUS_PROBABLE = 3; // TO BE DEPRECATED
+	
+	public static final String ATTR_SEVERITY_SEVERE = "severe";
+	public static final String ATTR_SEVERITY_MODERATE = "moderate";
+	public static final String ATTR_SEVERITY_SLIGHT = "slight";
+	public static final String ATTR_SEVERITY_UNMARKED = "unmarked";
+
+	public static final String ATTR_BODYSIDE_LEFT = "left";
+	public static final String ATTR_BODYSIDE_RIGHT = "right";
+	public static final String ATTR_BODYSIDE_BILATERAL = "bilateral";
+	public static final String ATTR_BODYSIDE_UNMARKED = "unmarked";
+
+	public static final String ATTR_BODYLATERALITY_SUPERIOR = "superior"; // Attribute name may change
+	public static final String ATTR_BODYLATERALITY_INFERIOR = "inferior"; // Attribute name may change
+	public static final String ATTR_BODYLATERALITY_DISTAL = "distal"; // Attribute name may change
+	public static final String ATTR_BODYLATERALITY_PROXIMAL = "proximal"; // Attribute name may change
+	public static final String ATTR_BODYLATERALITY_MEDIAL = "medial"; // Attribute name may change
+	public static final String ATTR_BODYLATERALITY_LATERAL = "lateral"; // Attribute name may change
+	public static final String ATTR_BODYLATERALITY_DORSAL = "dorsal"; // Attribute name may change
+	public static final String ATTR_BODYLATERALITY_VENTRAL = "ventral"; // Attribute name may change
+	public static final String ATTR_BODYLATERALITY_UNMARKED = "unmarked"; // Attribute name may change
+
+	public static final String ATTR_HISTORYOF_INDICATOR_PRESENT = "historyOf_present";
+	public static final String ATTR_HISTORYOF_INDICATOR_ABSENT = "historyOf_absent";	
+	
+	public static final String ATTR_SUBJECT_PATIENT = "patient";
+	public static final String ATTR_SUBJECT_FAMILY_MEMBER = "family_member";
+	public static final String ATTR_SUBJECT_DONOR_FAMILY_MEMBER = "donor_family_member";
+	public static final String ATTR_SUBJECT_DONOR_OTHER = "donor_other";
+	public static final String ATTR_SUBJECT_OTHER = "other";
+
+	// ATTR_PROCEDURE_DEVICE -- any string
+	// ATTR_PROCEDURE_METHOD -- any string
+	
+	// ATTR_LAB_VALUE_NUMBER -- any string
+	// ATTR_LAB_VALUE_UNIT -- any string
+	// ATTR_LAB_REFERENCE_RANGE -- any string
+	
+	public static final String ATTR_LAB_DELTAFLAG_CHANGEUP = "change_up";
+	public static final String ATTR_LAB_DELTAFLAG_CHANGEDOWN = "change_down";
+	public static final String ATTR_LAB_DELTAFLAG_NOCHANGE = "no_change";
+
+	public static final String ATTR_LAB_ABNORMAL_TRUE = "abnormal";
+	public static final String ATTR_LAB_ABNORMAL_VERYTRUE = "very_abnormal";
+
+	public static final String ATTR_LAB_ORDINAL_RESISTANT = "resistant";
+	public static final String ATTR_LAB_ORDINAL_POSITIVE = "positive";
+	public static final String ATTR_LAB_ORDINAL_REACTIVE = "reactive";
+	public static final String ATTR_LAB_ORDINAL_INTERMEDIATERESISTANCE = "intermediate_resistance";
+	public static final String ATTR_LAB_ORDINAL_INTERMEDIATE = "intermediate";
+	public static final String ATTR_LAB_ORDINAL_NEGATIVE = "negative";
+	public static final String ATTR_LAB_ORDINAL_NOTDETECTED = "not_detected";
+	public static final String ATTR_LAB_ORDINAL_DETECTED = "detected";
+	public static final String ATTR_LAB_ORDINAL_WEAKLY_REACTIVE = "weakly_reactive";
+	public static final String ATTR_LAB_ORDINAL_MODERATELYSUSCEPTIBLE = "moderately_susceptible";
+	public static final String ATTR_LAB_ORDINAL_VERYSUSCEPTIBLE = "very_susceptible";
+	public static final String ATTR_LAB_ORDINAL_SUSCEPTIBLE = "susceptible";
+	public static final String ATTR_LAB_ORDINAL_1ORMORE = "1+";
+	public static final String ATTR_LAB_ORDINAL_2ORMORE = "2+";
+	public static final String ATTR_LAB_ORDINAL_3ORMORE = "3+";
+	public static final String ATTR_LAB_ORDINAL_4ORMORE = "4+";
+	public static final String ATTR_LAB_ORDINAL_SMALL = "small";
+	public static final String ATTR_LAB_ORDINAL_TRACE = "trace";
+	public static final String ATTR_LAB_ORDINAL_NORMAL = "normal";
+	public static final String ATTR_LAB_ORDINAL_NO_OR_NA_RANGE = "no_range_or_normal_range_n/a";
+	public static final String ATTR_LAB_ORDINAL_ANTICOMPLEMENTARYPRESENT = "anti_complementary_substance_present";
+	public static final String ATTR_LAB_ORDINAL_CYTOTOXICPRESENT = "cytotoxic_substance_present";
+	public static final String ATTR_LAB_ORDINAL_QUALITYCONTROLFAIL = "quality_control_failure";
+
+	public static final boolean ATTR_LAB_ESTIMATED_FLAG_TRUE = true;
+	public static final boolean ATTR_LAB_ESTIMATED_FLAG_FALSE = false;
+	
+	public static final String ATTR_MEDICATION_DOSAGE_1 = "1";
+	public static final String ATTR_MEDICATION_DOSAGE_2 = "2";
+	public static final String ATTR_MEDICATION_DOSAGE_3 = "3";
+	public static final String ATTR_MEDICATION_DOSAGE_4 = "4";
+	public static final String ATTR_MEDICATION_DOSAGE_5 = "5";
+	public static final String ATTR_MEDICATION_DOSAGE_UNDETERMINED = "undetermined";
+	public static final String ATTR_MEDICATION_DOSAGE_OTHER = "other";
+	
+	public static final String ATTR_MEDICATION_ROUTE_TOPICAL = "topical";
+	public static final String ATTR_MEDICATION_ROUTE_ENTERAL_ORAL = "oral";
+	public static final String ATTR_MEDICATION_ROUTE_ENTERAL_GASTRIC = "gastric";
+	public static final String ATTR_MEDICATION_ROUTE_ENTERAL_RECTAL = "rectal";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAVENOUS = "intravenous";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAARTERIAL = "intra-arterial";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAMUSCULAR = "intramuscular";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRACARDIAC = "intracardiac";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_SUBCUTANEOUS = "subcutaneous";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRATHECAL = "intrathecal";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAPERIOTONEAL = "intraperiotoneal";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_TRANSDERMAL = "transdermal";
+	public static final String ATTR_MEDICATION_ROUTE_PARENTERAL_TRANSMUCOSAL = "transmucosal";
+	public static final String ATTR_MEDICATION_ROUTE_OTHER = "other";
+	public static final String ATTR_MEDICATION_ROUTE_UNDETERMINED = "undetermined";
+
+	public static final String ATTR_MEDICATION_FORM_AEROSOL = "aerosol";
+	public static final String ATTR_MEDICATION_FORM_CAPSULE = "capsule";
+	public static final String ATTR_MEDICATION_FORM_CREAM = "cream";
+	public static final String ATTR_MEDICATION_FORM_ELIXIR = "elixir";
+	public static final String ATTR_MEDICATION_FORM_EMULSION = "emulsion";
+	public static final String ATTR_MEDICATION_FORM_ENEMA = "enema";
+	public static final String ATTR_MEDICATION_FORM_GEL = "gel";
+	public static final String ATTR_MEDICATION_FORM_IMPLANT = "implant";
+	public static final String ATTR_MEDICATION_FORM_INHALANT = "inhalant";
+	public static final String ATTR_MEDICATION_FORM_INJECTION = "injection";
+	public static final String ATTR_MEDICATION_FORM_LIQUID = "liquid";
+	public static final String ATTR_MEDICATION_FORM_LOTION = "lotion";
+	public static final String ATTR_MEDICATION_FORM_LOZENGE = "lozenge";
+	public static final String ATTR_MEDICATION_FORM_OINTMENT = "ointment";
+	public static final String ATTR_MEDICATION_FORM_PATCH = "patch";
+	public static final String ATTR_MEDICATION_FORM_PELLET = "pellet";
+	public static final String ATTR_MEDICATION_FORM_PILL = "pill";
+	public static final String ATTR_MEDICATION_FORM_POWDER = "powder";
+	public static final String ATTR_MEDICATION_FORM_SHAMPOO = "shampoo";
+	public static final String ATTR_MEDICATION_FORM_SOAP = "soap";
+	public static final String ATTR_MEDICATION_FORM_SOLUTION = "solution";
+	public static final String ATTR_MEDICATION_FORM_SPRAY = "spray";
+	public static final String ATTR_MEDICATION_FORM_SUPPOSITORY = "suppository";
+	public static final String ATTR_MEDICATION_FORM_SYRUP = "syrup";
+	public static final String ATTR_MEDICATION_FORM_TABLET = "tablet";
+	public static final String ATTR_MEDICATION_FORM_OTHER = "other";
+	
+	public static final String ATTR_MEDICATION_STATUSCHANGE_START = "start";
+	public static final String ATTR_MEDICATION_STATUSCHANGE_STOP = "stop";
+	public static final String ATTR_MEDICATION_STATUSCHANGE_INCREASE = "increase";
+	public static final String ATTR_MEDICATION_STATUSCHANGE_DECREASE = "decrease";
+	public static final String ATTR_MEDICATION_STATUSCHANGE_NOCHANGE = "noChange";
+	
+	public static final String ATTR_MEDICATION_ALLERGY_INDICATOR_PRESENT = "allergy_present";
+	public static final String ATTR_MEDICATION_ALLERGY_INDICATOR_ABSENT = "allergy_absent";	
+
+	// ATTR_MEDICATION_STRENGTH is any number/unit pair
+	// ATTR_MEDICATION_DURATION is any string
+	// ATTR_MEDICATION_FREQUENCY is any number/unit pair
+	
+	public static final int REL_DISCOVERY_TECH_GOLD_ANNOTATION = 1;
+
+	public static final String MED_STATUS_CHANGE_START = ATTR_MEDICATION_STATUSCHANGE_START; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_STOP = ATTR_MEDICATION_STATUSCHANGE_STOP; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_INCREASEFROM = "increasefrom"; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_DECREASEFROM = "decreasefrom"; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_INCREASE = ATTR_MEDICATION_STATUSCHANGE_INCREASE; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_DECREASE = ATTR_MEDICATION_STATUSCHANGE_DECREASE; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_NOCHANGE = ATTR_MEDICATION_STATUSCHANGE_NOCHANGE; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_SUM = "add"; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_MAX = "maximum"; // TO BE DEPRECATED
+	public static final String MED_STATUS_CHANGE_OTHER = "change"; // TO BE DEPRECATED
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/context dependent tokenizer/src/edu/mayo/bmi/uima/cdt/ae/ContextDependentTokenizerAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/context%20dependent%20tokenizer/src/edu/mayo/bmi/uima/cdt/ae/ContextDependentTokenizerAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/context dependent tokenizer/src/edu/mayo/bmi/uima/cdt/ae/ContextDependentTokenizerAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/context dependent tokenizer/src/edu/mayo/bmi/uima/cdt/ae/ContextDependentTokenizerAnnotator.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
@@ -21,8 +14,8 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.uima.cdt.ae;
-
+package edu.mayo.bmi.uima.cdt.ae;
+
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -75,163 +68,163 @@ import edu.mayo.bmi.uima.core.type.texts
 import edu.mayo.bmi.uima.core.type.textsem.RomanNumeralAnnotation;
 import edu.mayo.bmi.uima.core.type.textsem.TimeAnnotation;
 import edu.mayo.bmi.uima.core.type.textspan.Sentence;
-
-/**
- * Finds tokens based on context.
- * 
- * @author Mayo Clinic
- */
-public class ContextDependentTokenizerAnnotator extends JCasAnnotator_ImplBase {
-	// LOG4J logger based on class name
-	private Logger iv_logger = Logger.getLogger(getClass().getName());
-
-	private DateFSM iv_dateFSM;
-	private TimeFSM iv_timeFSM;
-	private FractionFSM iv_fractionFSM;
-	private RomanNumeralFSM iv_romanNumeralFSM;
-	private RangeFSM iv_rangeFSM;
-	private MeasurementFSM iv_measurementFSM;
-	private PersonTitleFSM iv_personTitleFSM;
-
-	public void initialize(UimaContext annotCtx) throws ResourceInitializationException {
-		super.initialize(annotCtx);
-
-		iv_dateFSM = new DateFSM();
-		iv_timeFSM = new TimeFSM();
-		iv_fractionFSM = new FractionFSM();
-		iv_romanNumeralFSM = new RomanNumeralFSM();
-		iv_rangeFSM = new RangeFSM();
-		iv_measurementFSM = new MeasurementFSM();
-		iv_personTitleFSM = new PersonTitleFSM();
-		iv_logger.info("Finite state machines loaded.");
-	}
-
-	public void process(JCas jcas) throws AnalysisEngineProcessException {
-
-		try {
-			
-	    	iv_logger.info("process(JCas)");
-
-			JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-			Iterator<?> sentItr = indexes.getAnnotationIndex(Sentence.type).iterator();
-			AnnotationIndex baseTokenIndex = jcas.getJFSIndexRepository().getAnnotationIndex(
-					edu.mayo.bmi.uima.core.type.syntax.BaseToken.type);
-			
-			while (sentItr.hasNext()) {
-				Sentence sentAnnot = (Sentence) sentItr.next();
-				FSIterator btaItr = baseTokenIndex.subiterator(sentAnnot);
-
-				// adapt JCas objects into objects expected by the Finite state
-				// machines
-				List<BaseToken> baseTokenList = new ArrayList<BaseToken>();
-				while (btaItr.hasNext()) {
-					edu.mayo.bmi.uima.core.type.syntax.BaseToken bta = (edu.mayo.bmi.uima.core.type.syntax.BaseToken) btaItr
-							.next();
-					baseTokenList.add(adaptToBaseToken(bta));
-				}
-
-				// execute FSM logic
-				executeFSMs(jcas, baseTokenList);
-			}
-		} catch (Exception e) {
-			throw new AnalysisEngineProcessException(e);
-		}
-	}
-
-	private void executeFSMs(JCas jcas, List<? extends BaseToken> baseTokenList) throws AnalysisEngineProcessException {
-		try {
-			Set<DateToken> dateTokenSet = iv_dateFSM.execute(baseTokenList);
-			Iterator<DateToken> dateTokenItr = dateTokenSet.iterator();
-			while (dateTokenItr.hasNext()) {
-				DateToken dt = dateTokenItr.next();
-				DateAnnotation dta = new DateAnnotation(jcas, dt.getStartOffset(), dt.getEndOffset());
-				dta.addToIndexes();
-			}
-
-			Set<TimeToken> timeTokenSet = iv_timeFSM.execute(baseTokenList);
-			Iterator<TimeToken> timeTokenItr = timeTokenSet.iterator();
-			while (timeTokenItr.hasNext()) {
-				TimeToken tt = timeTokenItr.next();
-				TimeAnnotation ta = new TimeAnnotation(jcas, tt.getStartOffset(), tt.getEndOffset());
-				ta.addToIndexes();
-			}
-
-			Set<RomanNumeralToken> romanNumeralTokenSet = iv_romanNumeralFSM.execute(baseTokenList);
-			Iterator<RomanNumeralToken> romanNumeralTokenItr = romanNumeralTokenSet.iterator();
-			while (romanNumeralTokenItr.hasNext()) {
-				RomanNumeralToken rnt = romanNumeralTokenItr.next();
-				RomanNumeralAnnotation rna = new RomanNumeralAnnotation(jcas, rnt.getStartOffset(), rnt.getEndOffset());
-				rna.addToIndexes();
-			}
-
-			Set<FractionToken> fractionTokenSet = iv_fractionFSM.execute(baseTokenList);
-			Iterator<FractionToken> fractionTokenItr = fractionTokenSet.iterator();
-			while (fractionTokenItr.hasNext()) {
-				FractionToken ft = fractionTokenItr.next();
-				FractionAnnotation fa = new FractionAnnotation(jcas, ft.getStartOffset(), ft.getEndOffset());
-				fa.addToIndexes();
-			}
-
-			Set<RangeToken> rangeTokenSet = iv_rangeFSM.execute(baseTokenList, romanNumeralTokenSet);
-			Iterator<RangeToken> rangeTokenItr = rangeTokenSet.iterator();
-			while (rangeTokenItr.hasNext()) {
-				RangeToken rt = rangeTokenItr.next();
-				RangeAnnotation ra = new RangeAnnotation(jcas, rt.getStartOffset(), rt.getEndOffset());
-				ra.addToIndexes();
-			}
-
-			Set<MeasurementToken> measurementTokenSet = iv_measurementFSM.execute(baseTokenList, rangeTokenSet);
-			Iterator<MeasurementToken> measurementTokenItr = measurementTokenSet.iterator();
-			while (measurementTokenItr.hasNext()) {
-				MeasurementToken mt = measurementTokenItr.next();
-				MeasurementAnnotation ma = new MeasurementAnnotation(jcas, mt.getStartOffset(), mt.getEndOffset());
-				ma.addToIndexes();
-			}
-
-			Set<PersonTitleToken> personTitleTokenSet = iv_personTitleFSM.execute(baseTokenList);
-			Iterator<PersonTitleToken> personTitleTokenItr = personTitleTokenSet.iterator();
-			while (personTitleTokenItr.hasNext()) {
-				PersonTitleToken ptt = personTitleTokenItr.next();
-				PersonTitleAnnotation pta = new PersonTitleAnnotation(jcas, ptt.getStartOffset(), ptt.getEndOffset());
-				pta.addToIndexes();
-			}
-		} catch (Exception e) {
-			throw new AnalysisEngineProcessException(e);
-		}
-	}
-
-	/**
-	 * Adapts JCas objects to BaseToken interfaces expected by the Finite State
-	 * Machines.
-	 * 
-	 * @param obj
-	 * @return
-	 */
-	private BaseToken adaptToBaseToken(edu.mayo.bmi.uima.core.type.syntax.BaseToken obj) throws Exception {
-		if (obj instanceof WordToken) {
-			WordToken wta = (WordToken) obj;
-			return new WordTokenAdapter(wta);
-		} else if (obj instanceof NumToken) {
-			NumToken nta = (NumToken) obj;
-			if (nta.getNumType() == TokenizerAnnotator.TOKEN_NUM_TYPE_INTEGER) {
-				return new IntegerTokenAdapter(nta);
-			} else {
-				return new DecimalTokenAdapter(nta);
-			}
-		} else if (obj instanceof PunctuationToken) {
-			PunctuationToken pta = (PunctuationToken) obj;
-			return new PunctuationTokenAdapter(pta);
-		} else if (obj instanceof NewlineToken) {
-			NewlineToken nta = (NewlineToken) obj;
-			return new NewlineTokenAdapter(nta);
-		} else if (obj instanceof ContractionToken) {
-			ContractionToken cta = (ContractionToken) obj;
-			return new ContractionTokenAdapter(cta);
-		} else if (obj instanceof SymbolToken) {
-			SymbolToken sta = (SymbolToken) obj;
-			return new SymbolTokenAdapter(sta);
-		}
-
-		throw new Exception("No Context Dependent Tokenizer adapter for class: " + obj.getClass());
-	}
-}
+
+/**
+ * Finds tokens based on context.
+ * 
+ * @author Mayo Clinic
+ */
+public class ContextDependentTokenizerAnnotator extends JCasAnnotator_ImplBase {
+	// LOG4J logger based on class name
+	private Logger iv_logger = Logger.getLogger(getClass().getName());
+
+	private DateFSM iv_dateFSM;
+	private TimeFSM iv_timeFSM;
+	private FractionFSM iv_fractionFSM;
+	private RomanNumeralFSM iv_romanNumeralFSM;
+	private RangeFSM iv_rangeFSM;
+	private MeasurementFSM iv_measurementFSM;
+	private PersonTitleFSM iv_personTitleFSM;
+
+	public void initialize(UimaContext annotCtx) throws ResourceInitializationException {
+		super.initialize(annotCtx);
+
+		iv_dateFSM = new DateFSM();
+		iv_timeFSM = new TimeFSM();
+		iv_fractionFSM = new FractionFSM();
+		iv_romanNumeralFSM = new RomanNumeralFSM();
+		iv_rangeFSM = new RangeFSM();
+		iv_measurementFSM = new MeasurementFSM();
+		iv_personTitleFSM = new PersonTitleFSM();
+		iv_logger.info("Finite state machines loaded.");
+	}
+
+	public void process(JCas jcas) throws AnalysisEngineProcessException {
+
+		try {
+			
+	    	iv_logger.info("process(JCas)");
+
+			JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+			Iterator<?> sentItr = indexes.getAnnotationIndex(Sentence.type).iterator();
+			AnnotationIndex baseTokenIndex = jcas.getJFSIndexRepository().getAnnotationIndex(
+					edu.mayo.bmi.uima.core.type.syntax.BaseToken.type);
+			
+			while (sentItr.hasNext()) {
+				Sentence sentAnnot = (Sentence) sentItr.next();
+				FSIterator btaItr = baseTokenIndex.subiterator(sentAnnot);
+
+				// adapt JCas objects into objects expected by the Finite state
+				// machines
+				List<BaseToken> baseTokenList = new ArrayList<BaseToken>();
+				while (btaItr.hasNext()) {
+					edu.mayo.bmi.uima.core.type.syntax.BaseToken bta = (edu.mayo.bmi.uima.core.type.syntax.BaseToken) btaItr
+							.next();
+					baseTokenList.add(adaptToBaseToken(bta));
+				}
+
+				// execute FSM logic
+				executeFSMs(jcas, baseTokenList);
+			}
+		} catch (Exception e) {
+			throw new AnalysisEngineProcessException(e);
+		}
+	}
+
+	private void executeFSMs(JCas jcas, List<? extends BaseToken> baseTokenList) throws AnalysisEngineProcessException {
+		try {
+			Set<DateToken> dateTokenSet = iv_dateFSM.execute(baseTokenList);
+			Iterator<DateToken> dateTokenItr = dateTokenSet.iterator();
+			while (dateTokenItr.hasNext()) {
+				DateToken dt = dateTokenItr.next();
+				DateAnnotation dta = new DateAnnotation(jcas, dt.getStartOffset(), dt.getEndOffset());
+				dta.addToIndexes();
+			}
+
+			Set<TimeToken> timeTokenSet = iv_timeFSM.execute(baseTokenList);
+			Iterator<TimeToken> timeTokenItr = timeTokenSet.iterator();
+			while (timeTokenItr.hasNext()) {
+				TimeToken tt = timeTokenItr.next();
+				TimeAnnotation ta = new TimeAnnotation(jcas, tt.getStartOffset(), tt.getEndOffset());
+				ta.addToIndexes();
+			}
+
+			Set<RomanNumeralToken> romanNumeralTokenSet = iv_romanNumeralFSM.execute(baseTokenList);
+			Iterator<RomanNumeralToken> romanNumeralTokenItr = romanNumeralTokenSet.iterator();
+			while (romanNumeralTokenItr.hasNext()) {
+				RomanNumeralToken rnt = romanNumeralTokenItr.next();
+				RomanNumeralAnnotation rna = new RomanNumeralAnnotation(jcas, rnt.getStartOffset(), rnt.getEndOffset());
+				rna.addToIndexes();
+			}
+
+			Set<FractionToken> fractionTokenSet = iv_fractionFSM.execute(baseTokenList);
+			Iterator<FractionToken> fractionTokenItr = fractionTokenSet.iterator();
+			while (fractionTokenItr.hasNext()) {
+				FractionToken ft = fractionTokenItr.next();
+				FractionAnnotation fa = new FractionAnnotation(jcas, ft.getStartOffset(), ft.getEndOffset());
+				fa.addToIndexes();
+			}
+
+			Set<RangeToken> rangeTokenSet = iv_rangeFSM.execute(baseTokenList, romanNumeralTokenSet);
+			Iterator<RangeToken> rangeTokenItr = rangeTokenSet.iterator();
+			while (rangeTokenItr.hasNext()) {
+				RangeToken rt = rangeTokenItr.next();
+				RangeAnnotation ra = new RangeAnnotation(jcas, rt.getStartOffset(), rt.getEndOffset());
+				ra.addToIndexes();
+			}
+
+			Set<MeasurementToken> measurementTokenSet = iv_measurementFSM.execute(baseTokenList, rangeTokenSet);
+			Iterator<MeasurementToken> measurementTokenItr = measurementTokenSet.iterator();
+			while (measurementTokenItr.hasNext()) {
+				MeasurementToken mt = measurementTokenItr.next();
+				MeasurementAnnotation ma = new MeasurementAnnotation(jcas, mt.getStartOffset(), mt.getEndOffset());
+				ma.addToIndexes();
+			}
+
+			Set<PersonTitleToken> personTitleTokenSet = iv_personTitleFSM.execute(baseTokenList);
+			Iterator<PersonTitleToken> personTitleTokenItr = personTitleTokenSet.iterator();
+			while (personTitleTokenItr.hasNext()) {
+				PersonTitleToken ptt = personTitleTokenItr.next();
+				PersonTitleAnnotation pta = new PersonTitleAnnotation(jcas, ptt.getStartOffset(), ptt.getEndOffset());
+				pta.addToIndexes();
+			}
+		} catch (Exception e) {
+			throw new AnalysisEngineProcessException(e);
+		}
+	}
+
+	/**
+	 * Adapts JCas objects to BaseToken interfaces expected by the Finite State
+	 * Machines.
+	 * 
+	 * @param obj
+	 * @return
+	 */
+	private BaseToken adaptToBaseToken(edu.mayo.bmi.uima.core.type.syntax.BaseToken obj) throws Exception {
+		if (obj instanceof WordToken) {
+			WordToken wta = (WordToken) obj;
+			return new WordTokenAdapter(wta);
+		} else if (obj instanceof NumToken) {
+			NumToken nta = (NumToken) obj;
+			if (nta.getNumType() == TokenizerAnnotator.TOKEN_NUM_TYPE_INTEGER) {
+				return new IntegerTokenAdapter(nta);
+			} else {
+				return new DecimalTokenAdapter(nta);
+			}
+		} else if (obj instanceof PunctuationToken) {
+			PunctuationToken pta = (PunctuationToken) obj;
+			return new PunctuationTokenAdapter(pta);
+		} else if (obj instanceof NewlineToken) {
+			NewlineToken nta = (NewlineToken) obj;
+			return new NewlineTokenAdapter(nta);
+		} else if (obj instanceof ContractionToken) {
+			ContractionToken cta = (ContractionToken) obj;
+			return new ContractionTokenAdapter(cta);
+		} else if (obj instanceof SymbolToken) {
+			SymbolToken sta = (SymbolToken) obj;
+			return new SymbolTokenAdapter(sta);
+		}
+
+		throw new Exception("No Context Dependent Tokenizer adapter for class: " + obj.getClass());
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/CombineCondition.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/CombineCondition.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/CombineCondition.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/CombineCondition.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
@@ -21,30 +14,30 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.fsm.condition;
-
-import net.openai.util.fsm.Condition;
-
-/**
- * 
- * @author Mayo Clinic
- */
-@SuppressWarnings("serial")
-public class CombineCondition extends Condition {
-	private Condition iv_condition1;
-	private Condition iv_condition2;
-
-	public CombineCondition(Condition c1, Condition c2) {
-		iv_condition1 = c1;
-		iv_condition2 = c2;
-	}
-
-	/**
-	 * Called to check if the conditional meets the criteria defined by this
-	 * state.
-	 */
-	public boolean satisfiedBy(Object conditional) {
-		return (iv_condition1.satisfiedBy(conditional) && iv_condition2
-				.satisfiedBy(conditional));
-	}
-}
+package edu.mayo.bmi.fsm.condition;
+
+import net.openai.util.fsm.Condition;
+
+/**
+ * 
+ * @author Mayo Clinic
+ */
+@SuppressWarnings("serial")
+public class CombineCondition extends Condition {
+	private Condition iv_condition1;
+	private Condition iv_condition2;
+
+	public CombineCondition(Condition c1, Condition c2) {
+		iv_condition1 = c1;
+		iv_condition2 = c2;
+	}
+
+	/**
+	 * Called to check if the conditional meets the criteria defined by this
+	 * state.
+	 */
+	public boolean satisfiedBy(Object conditional) {
+		return (iv_condition1.satisfiedBy(conditional) && iv_condition2
+				.satisfiedBy(conditional));
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DayNightWordCondition.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DayNightWordCondition.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DayNightWordCondition.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DayNightWordCondition.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.fsm.condition;
-
-import net.openai.util.fsm.Condition;
-import edu.mayo.bmi.fsm.token.WordToken;
-
-/**
- * Handles case of A.M. and P.M. The WordToken will actually be "A.M" or "P.M"
- * 
- * @author Mayo Clinic
- */
-@SuppressWarnings("serial")
-public class DayNightWordCondition extends Condition {
-	public boolean satisfiedBy(Object conditional) {
-		if (conditional instanceof WordToken) {
-			WordToken wt = (WordToken) conditional;
-			String text = wt.getText();
-			if (text.length() == 3) {
-				text = text.toUpperCase();
-				if ((text.charAt(2) == 'M') && (text.charAt(1) == '.')
-						&& ((text.charAt(0) == 'A') || (text.charAt(0) == 'P'))) {
-					return true;
-				}
-			}
-
-		}
-		return false;
-	}
-}
+package edu.mayo.bmi.fsm.condition;
+
+import net.openai.util.fsm.Condition;
+import edu.mayo.bmi.fsm.token.WordToken;
+
+/**
+ * Handles case of A.M. and P.M. The WordToken will actually be "A.M" or "P.M"
+ * 
+ * @author Mayo Clinic
+ */
+@SuppressWarnings("serial")
+public class DayNightWordCondition extends Condition {
+	public boolean satisfiedBy(Object conditional) {
+		if (conditional instanceof WordToken) {
+			WordToken wt = (WordToken) conditional;
+			String text = wt.getText();
+			if (text.length() == 3) {
+				text = text.toUpperCase();
+				if ((text.charAt(2) == 'M') && (text.charAt(1) == '.')
+						&& ((text.charAt(0) == 'A') || (text.charAt(0) == 'P'))) {
+					return true;
+				}
+			}
+
+		}
+		return false;
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalCondition.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalCondition.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalCondition.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalCondition.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
@@ -21,26 +14,26 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.fsm.condition;
-
-import net.openai.util.fsm.Condition;
-import edu.mayo.bmi.fsm.token.DecimalToken;
-
-/**
- * 
- * @author Mayo Clinic
- */
-@SuppressWarnings("serial")
-public class DecimalCondition extends Condition {
-	/**
-	 * Called to check if the conditional meets the criteria defined by this
-	 * state.
-	 */
-	public boolean satisfiedBy(Object conditional) {
-		if (conditional instanceof DecimalToken) {
-			return true;
-		}
-
-		return false;
-	}
-}
+package edu.mayo.bmi.fsm.condition;
+
+import net.openai.util.fsm.Condition;
+import edu.mayo.bmi.fsm.token.DecimalToken;
+
+/**
+ * 
+ * @author Mayo Clinic
+ */
+@SuppressWarnings("serial")
+public class DecimalCondition extends Condition {
+	/**
+	 * Called to check if the conditional meets the criteria defined by this
+	 * state.
+	 */
+	public boolean satisfiedBy(Object conditional) {
+		if (conditional instanceof DecimalToken) {
+			return true;
+		}
+
+		return false;
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalRangeCondition.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalRangeCondition.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalRangeCondition.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalRangeCondition.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
@@ -21,42 +14,42 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.fsm.condition;
-
-import net.openai.util.fsm.Condition;
-import edu.mayo.bmi.fsm.token.DecimalToken;
-
-/**
- * 
- * @author Mayo Clinic
- */
-@SuppressWarnings("serial")
-public class DecimalRangeCondition extends Condition {
-	private double iv_lowNum;
-	private double iv_highNum;
-
-	/**
-	 * Constructor
-	 * 
-	 * @param t
-	 */
-	public DecimalRangeCondition(double lowNumber, double highNumber) {
-		iv_lowNum = lowNumber;
-		iv_highNum = highNumber;
-	}
-
-	/**
-	 * Called to check if the conditional meets the criteria defined by this
-	 * state.
-	 */
-	public boolean satisfiedBy(Object conditional) {
-		if (conditional instanceof DecimalToken) {
-			DecimalToken t = (DecimalToken) conditional;
-			if ((t.getValue() >= iv_lowNum) && (t.getValue() <= iv_highNum)) {
-				return true;
-			}
-		}
-
-		return false;
-	}
-}
+package edu.mayo.bmi.fsm.condition;
+
+import net.openai.util.fsm.Condition;
+import edu.mayo.bmi.fsm.token.DecimalToken;
+
+/**
+ * 
+ * @author Mayo Clinic
+ */
+@SuppressWarnings("serial")
+public class DecimalRangeCondition extends Condition {
+	private double iv_lowNum;
+	private double iv_highNum;
+
+	/**
+	 * Constructor
+	 * 
+	 * @param t
+	 */
+	public DecimalRangeCondition(double lowNumber, double highNumber) {
+		iv_lowNum = lowNumber;
+		iv_highNum = highNumber;
+	}
+
+	/**
+	 * Called to check if the conditional meets the criteria defined by this
+	 * state.
+	 */
+	public boolean satisfiedBy(Object conditional) {
+		if (conditional instanceof DecimalToken) {
+			DecimalToken t = (DecimalToken) conditional;
+			if ((t.getValue() >= iv_lowNum) && (t.getValue() <= iv_highNum)) {
+				return true;
+			}
+		}
+
+		return false;
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalValueCondition.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalValueCondition.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalValueCondition.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DecimalValueCondition.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
@@ -21,40 +14,40 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.fsm.condition;
-
-import net.openai.util.fsm.Condition;
-import edu.mayo.bmi.fsm.token.DecimalToken;
-
-/**
- * 
- * @author Mayo Clinic
- */
-@SuppressWarnings("serial")
-public class DecimalValueCondition extends Condition {
-	private double iv_num;
-
-	/**
-	 * Constructor
-	 * 
-	 * @param t
-	 */
-	public DecimalValueCondition(double value) {
-		iv_num = value;
-	}
-
-	/**
-	 * Called to check if the conditional meets the criteria defined by this
-	 * state.
-	 */
-	public boolean satisfiedBy(Object conditional) {
-		if (conditional instanceof DecimalToken) {
-			DecimalToken t = (DecimalToken) conditional;
-			if (t.getValue() == iv_num) {
-				return true;
-			}
-		}
-
-		return false;
-	}
-}
+package edu.mayo.bmi.fsm.condition;
+
+import net.openai.util.fsm.Condition;
+import edu.mayo.bmi.fsm.token.DecimalToken;
+
+/**
+ * 
+ * @author Mayo Clinic
+ */
+@SuppressWarnings("serial")
+public class DecimalValueCondition extends Condition {
+	private double iv_num;
+
+	/**
+	 * Constructor
+	 * 
+	 * @param t
+	 */
+	public DecimalValueCondition(double value) {
+		iv_num = value;
+	}
+
+	/**
+	 * Called to check if the conditional meets the criteria defined by this
+	 * state.
+	 */
+	public boolean satisfiedBy(Object conditional) {
+		if (conditional instanceof DecimalToken) {
+			DecimalToken t = (DecimalToken) conditional;
+			if (t.getValue() == iv_num) {
+				return true;
+			}
+		}
+
+		return false;
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DisjoinCondition.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DisjoinCondition.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DisjoinCondition.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/fsm/condition/DisjoinCondition.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
@@ -21,30 +14,30 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.fsm.condition;
-
-import net.openai.util.fsm.Condition;
-
-/**
- * 
- * @author Mayo Clinic
- */
-@SuppressWarnings("serial")
-public class DisjoinCondition extends Condition {
-	private Condition iv_condition1;
-	private Condition iv_condition2;
-
-	public DisjoinCondition(Condition c1, Condition c2) {
-		iv_condition1 = c1;
-		iv_condition2 = c2;
-	}
-
-	/**
-	 * Called to check if the conditional meets the criteria defined by this
-	 * state.
-	 */
-	public boolean satisfiedBy(Object conditional) {
-		return (iv_condition1.satisfiedBy(conditional) || iv_condition2
-				.satisfiedBy(conditional));
-	}
-}
+package edu.mayo.bmi.fsm.condition;
+
+import net.openai.util.fsm.Condition;
+
+/**
+ * 
+ * @author Mayo Clinic
+ */
+@SuppressWarnings("serial")
+public class DisjoinCondition extends Condition {
+	private Condition iv_condition1;
+	private Condition iv_condition2;
+
+	public DisjoinCondition(Condition c1, Condition c2) {
+		iv_condition1 = c1;
+		iv_condition2 = c2;
+	}
+
+	/**
+	 * Called to check if the conditional meets the criteria defined by this
+	 * state.
+	 */
+	public boolean satisfiedBy(Object conditional) {
+		return (iv_condition1.satisfiedBy(conditional) || iv_condition2
+				.satisfiedBy(conditional));
+	}
+}



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