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From james-mas...@apache.org
Subject svn commit: r1403989 [17/28] - 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/core/src/edu/mayo/bmi/uima/core/util/DocumentIDAnnotationUtil.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/DocumentIDAnnotationUtil.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/DocumentIDAnnotationUtil.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/DocumentIDAnnotationUtil.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
@@ -21,28 +14,28 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.uima.core.util;
-
+package edu.mayo.bmi.uima.core.util;
+
 import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.jcas.cas.TOP;
 
 import edu.mayo.bmi.uima.core.type.structured.DocumentID;
-
-public class DocumentIDAnnotationUtil 
-{
-	public static String getDocumentID(JCas jcas)
-	{
-		try
-		{
-		 	JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-		 	FSIterator<TOP> documentIDIterator = indexes.getAllIndexedFS(DocumentID.type);
-		 	DocumentID documentIDAnnotation = (DocumentID) documentIDIterator.next();
-		 	String documentID = documentIDAnnotation.getDocumentID();
-		 	return documentID;
-		}
-		catch(Exception e) { return null;}
-	}
-
-}
+
+public class DocumentIDAnnotationUtil 
+{
+	public static String getDocumentID(JCas jcas)
+	{
+		try
+		{
+		 	JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+		 	FSIterator<TOP> documentIDIterator = indexes.getAllIndexedFS(DocumentID.type);
+		 	DocumentID documentIDAnnotation = (DocumentID) documentIDIterator.next();
+		 	String documentID = documentIDAnnotation.getDocumentID();
+		 	return documentID;
+		}
+		catch(Exception e) { return null;}
+	}
+
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/FSUtil.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/FSUtil.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/FSUtil.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/FSUtil.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.core.util;
-
+package edu.mayo.bmi.uima.core.util;
+
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -41,35 +34,35 @@ import org.apache.uima.jcas.JFSIndexRepo
 import org.apache.uima.jcas.tcas.Annotation;
 
 import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-
-public class FSUtil {
-	
-	@Deprecated
-	public static FSIterator getAnnotationsInSpanIterator(JCas jcas, int type, int beginSpan, int endSpan)
-	{
-		ConstraintFactory constraintFactory = jcas.getConstraintFactory();
-	    FSIntConstraint windowConstraint = constraintFactory.createIntConstraint();
-	    windowConstraint.gt(beginSpan-1);
-	    windowConstraint.lt(endSpan);
-	    
-	    Type annotType = jcas.getCasType(type);
-	    Feature beginSpanFeature = annotType.getFeatureByBaseName("begin");
-	    Feature endSpanFeature = annotType.getFeatureByBaseName("end");
-	    
-	    FeaturePath beginFeaturePath = jcas.createFeaturePath();
-	    beginFeaturePath.addFeature(beginSpanFeature);
-	    FSMatchConstraint beginSpanConstraint = constraintFactory.embedConstraint(beginFeaturePath, windowConstraint);
-	    
-	    FeaturePath endFeaturePath = jcas.createFeaturePath();
-	    endFeaturePath.addFeature(endSpanFeature);
-	    FSMatchConstraint endSpanConstraint = constraintFactory.embedConstraint(endFeaturePath, windowConstraint);
-	    
-	    FSMatchConstraint spanConstraint = constraintFactory.and(beginSpanConstraint, endSpanConstraint);
-	    
-	    JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-	    FSIndex annotIndex = indexes.getAnnotationIndex(type);
-	    FSIterator annotsInSpanItr = jcas.createFilteredIterator(annotIndex.iterator(), spanConstraint);
-	    return annotsInSpanItr;
+
+public class FSUtil {
+	
+	@Deprecated
+	public static FSIterator getAnnotationsInSpanIterator(JCas jcas, int type, int beginSpan, int endSpan)
+	{
+		ConstraintFactory constraintFactory = jcas.getConstraintFactory();
+	    FSIntConstraint windowConstraint = constraintFactory.createIntConstraint();
+	    windowConstraint.gt(beginSpan-1);
+	    windowConstraint.lt(endSpan);
+	    
+	    Type annotType = jcas.getCasType(type);
+	    Feature beginSpanFeature = annotType.getFeatureByBaseName("begin");
+	    Feature endSpanFeature = annotType.getFeatureByBaseName("end");
+	    
+	    FeaturePath beginFeaturePath = jcas.createFeaturePath();
+	    beginFeaturePath.addFeature(beginSpanFeature);
+	    FSMatchConstraint beginSpanConstraint = constraintFactory.embedConstraint(beginFeaturePath, windowConstraint);
+	    
+	    FeaturePath endFeaturePath = jcas.createFeaturePath();
+	    endFeaturePath.addFeature(endSpanFeature);
+	    FSMatchConstraint endSpanConstraint = constraintFactory.embedConstraint(endFeaturePath, windowConstraint);
+	    
+	    FSMatchConstraint spanConstraint = constraintFactory.and(beginSpanConstraint, endSpanConstraint);
+	    
+	    JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+	    FSIndex annotIndex = indexes.getAnnotationIndex(type);
+	    FSIterator annotsInSpanItr = jcas.createFilteredIterator(annotIndex.iterator(), spanConstraint);
+	    return annotsInSpanItr;
 	}
 	
 	/**
@@ -88,7 +81,7 @@ public class FSUtil {
 	    FSIterator itr = annIdx.subiterator(ann);
 	    ann.removeFromIndexes();
 	    return itr;
-	}
+	}
 
 	/**
 	 * Does not use {@link #getAnnotationsInSpan(JCas, int, int, int, int[])} so we don't create a collection
@@ -165,5 +158,5 @@ public class FSUtil {
 	public static boolean isAnnotationPresentInSpan(JCas jcas, int type, int beginSpan, int endSpan)
 	{
 	    return (countAnnotationsInSpan(jcas, type, beginSpan, endSpan)>0);
-	}	
-}
+	}	
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/JCasUtil.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/JCasUtil.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/JCasUtil.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/JCasUtil.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
@@ -21,33 +14,33 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.uima.core.util;
-
-import java.lang.reflect.Field;
-
-import org.apache.uima.jcas.cas.TOP;
-import org.apache.uima.jcas.tcas.Annotation;
-
-public class JCasUtil {
-
-	public static int getType(String className) {
-		try {
-			Class<?> cls = Class.forName(className);
-			Class<? extends TOP> annotationCls = cls.asSubclass(Annotation.class);
-			return JCasUtil.getType(annotationCls);
-		} catch (Exception e) {
-			throw new IllegalArgumentException(e);
-		}
-	}
-	
-	public static int getType(Class<? extends TOP> cls) {
-		try {
-			Field typeField = cls.getDeclaredField("type");
-			// return value of static field
-			return typeField.getInt(null);
-		} catch (Exception e) {
-			throw new IllegalArgumentException(e);
-		}
-
-	}
-}
+package edu.mayo.bmi.uima.core.util;
+
+import java.lang.reflect.Field;
+
+import org.apache.uima.jcas.cas.TOP;
+import org.apache.uima.jcas.tcas.Annotation;
+
+public class JCasUtil {
+
+	public static int getType(String className) {
+		try {
+			Class<?> cls = Class.forName(className);
+			Class<? extends TOP> annotationCls = cls.asSubclass(Annotation.class);
+			return JCasUtil.getType(annotationCls);
+		} catch (Exception e) {
+			throw new IllegalArgumentException(e);
+		}
+	}
+	
+	public static int getType(Class<? extends TOP> cls) {
+		try {
+			Field typeField = cls.getDeclaredField("type");
+			// return value of static field
+			return typeField.getInt(null);
+		} catch (Exception e) {
+			throw new IllegalArgumentException(e);
+		}
+
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/ListFactory.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/ListFactory.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/ListFactory.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/ListFactory.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
@@ -21,53 +14,53 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.uima.core.util;
-
-import org.apache.uima.jcas.cas.EmptyFSList;
-import org.apache.uima.jcas.cas.FSList;
-import org.apache.uima.jcas.cas.NonEmptyFSList;
-import org.apache.uima.jcas.cas.TOP;
-import org.apache.uima.jcas.JCas;
-
-/**
- * Factory to build List of built-in CAS types such as FloatList, IntegerList,
- * StringList, and FSList.
- * 
- * @author Mayo Clinic
- */
-public class ListFactory {
-
-	/**
-	 * Builds a FSList from an array of JCas objects.
-	 * @param jcas The current JCas.
-	 * @param objArr Array of JCas objects (objects must extend from TOP).
-	 * @return FSList populated with the JCas objects.
-	 */
-	public static FSList buildList(JCas jcas, TOP[] objArr)
-	{
-		if (objArr.length == 0)
-		{
-			return new EmptyFSList(jcas);
-		}
-		
-		NonEmptyFSList firstList = new NonEmptyFSList(jcas);
-		NonEmptyFSList list = firstList;		
-		for (int i=0; i < objArr.length; i++)
-		{			
-			list.setHead(objArr[i]);
-			list.addToIndexes();
-			
-			if ((i+1) < objArr.length)
-			{
-				NonEmptyFSList nextList = new NonEmptyFSList(jcas);
-				list.setTail(nextList);
-				list = nextList;
-			}
-		}
-		
-		// set tail to empty list
-		list.setTail(new EmptyFSList(jcas));		
-		
-		return firstList;
-	}
-}
+package edu.mayo.bmi.uima.core.util;
+
+import org.apache.uima.jcas.cas.EmptyFSList;
+import org.apache.uima.jcas.cas.FSList;
+import org.apache.uima.jcas.cas.NonEmptyFSList;
+import org.apache.uima.jcas.cas.TOP;
+import org.apache.uima.jcas.JCas;
+
+/**
+ * Factory to build List of built-in CAS types such as FloatList, IntegerList,
+ * StringList, and FSList.
+ * 
+ * @author Mayo Clinic
+ */
+public class ListFactory {
+
+	/**
+	 * Builds a FSList from an array of JCas objects.
+	 * @param jcas The current JCas.
+	 * @param objArr Array of JCas objects (objects must extend from TOP).
+	 * @return FSList populated with the JCas objects.
+	 */
+	public static FSList buildList(JCas jcas, TOP[] objArr)
+	{
+		if (objArr.length == 0)
+		{
+			return new EmptyFSList(jcas);
+		}
+		
+		NonEmptyFSList firstList = new NonEmptyFSList(jcas);
+		NonEmptyFSList list = firstList;		
+		for (int i=0; i < objArr.length; i++)
+		{			
+			list.setHead(objArr[i]);
+			list.addToIndexes();
+			
+			if ((i+1) < objArr.length)
+			{
+				NonEmptyFSList nextList = new NonEmptyFSList(jcas);
+				list.setTail(nextList);
+				list = nextList;
+			}
+		}
+		
+		// set tail to empty list
+		list.setTail(new EmptyFSList(jcas));		
+		
+		return firstList;
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/ParamUtil.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/ParamUtil.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/ParamUtil.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/src/edu/mayo/bmi/uima/core/util/ParamUtil.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
@@ -21,54 +14,54 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.uima.core.util;
-
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-
+package edu.mayo.bmi.uima.core.util;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+
 import org.apache.uima.UimaContext;
-import org.apache.uima.analysis_engine.annotator.AnnotatorContextException;
+import org.apache.uima.analysis_engine.annotator.AnnotatorContextException;
 import org.apache.uima.resource.ResourceAccessException;
-
-public class ParamUtil {
-
-	/**
-	 * 
-	 * @param parameterName
-	 * @param annotatorContext
-	 * @return does not return null - but will return empty set if parameter is
-	 *         optional or not set.
-	 * @throws AnnotatorContextException
-	 */
-	public static Set<String> getStringParameterValuesSet(String parameterName, UimaContext annotatorContext)
-			throws ResourceAccessException {
-		Set<String> returnValues = new HashSet<String>();
-		String[] strings = (String[]) annotatorContext.getConfigParameterValue(parameterName);
-		if (strings == null)
-			return returnValues;
-
-		for (int i = 0; i < strings.length; i++) {
-			returnValues.add(strings[i]);
-		}
-		return returnValues;
-	}
-
-	public static Map<String, String> getStringParameterValuesMap(String parameterName,
-			UimaContext annotatorContext, String keyValueDelimiter) throws ResourceAccessException {
-		String[] paramValues = (String[]) annotatorContext.getConfigParameterValue(parameterName);
-		Map<String, String> map = new HashMap<String, String>();
-		for (int i = 0; i < paramValues.length; i++) {
-			int delimiterIndex = paramValues[i].lastIndexOf(keyValueDelimiter);
-			if (delimiterIndex == -1)
-				continue;
-			String key = paramValues[i].substring(0, delimiterIndex);
-			String value = paramValues[i].substring(delimiterIndex + 1);
-			map.put(key, value);
-		}
-		return map;
-	}
-
-}
+
+public class ParamUtil {
+
+	/**
+	 * 
+	 * @param parameterName
+	 * @param annotatorContext
+	 * @return does not return null - but will return empty set if parameter is
+	 *         optional or not set.
+	 * @throws AnnotatorContextException
+	 */
+	public static Set<String> getStringParameterValuesSet(String parameterName, UimaContext annotatorContext)
+			throws ResourceAccessException {
+		Set<String> returnValues = new HashSet<String>();
+		String[] strings = (String[]) annotatorContext.getConfigParameterValue(parameterName);
+		if (strings == null)
+			return returnValues;
+
+		for (int i = 0; i < strings.length; i++) {
+			returnValues.add(strings[i]);
+		}
+		return returnValues;
+	}
+
+	public static Map<String, String> getStringParameterValuesMap(String parameterName,
+			UimaContext annotatorContext, String keyValueDelimiter) throws ResourceAccessException {
+		String[] paramValues = (String[]) annotatorContext.getConfigParameterValue(parameterName);
+		Map<String, String> map = new HashMap<String, String>();
+		for (int i = 0; i < paramValues.length; i++) {
+			int delimiterIndex = paramValues[i].lastIndexOf(keyValueDelimiter);
+			if (delimiterIndex == -1)
+				continue;
+			String key = paramValues[i].substring(0, delimiterIndex);
+			String value = paramValues[i].substring(delimiterIndex + 1);
+			map.put(key, value);
+		}
+		return map;
+	}
+
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ae/test/SimpleSegmentAnnotatorTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ae/test/SimpleSegmentAnnotatorTests.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ae/test/SimpleSegmentAnnotatorTests.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ae/test/SimpleSegmentAnnotatorTests.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
@@ -21,29 +14,29 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.uima.core.ae.test;
-
-import static org.junit.Assert.assertEquals;
-
-import java.io.File;
-
-import org.apache.uima.analysis_engine.AnalysisEngine;
-import org.apache.uima.jcas.JCas;
-import org.apache.uima.resource.ResourceInitializationException;
-import org.junit.Test;
-
-import edu.mayo.bmi.uima.core.test.TestUtil;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
-
-public class SimpleSegmentAnnotatorTests {
-
-	@Test
-    public void testSimpleSegment() throws ResourceInitializationException {
-		AnalysisEngine ae = TestUtil.getAE(new File("desc/test/analysis_engine/SimpleSegmentAnnotator.xml"));
-		JCas jCas = TestUtil.processAE(ae, "data/test/mother_goose/OneMistyMorning.txt");
-		Segment segment = TestUtil.getFeatureStructureAtIndex(jCas, Segment.class, 0);
-		assertEquals(0, segment.getBegin());
-		assertEquals(42, segment.getEnd());
-		assertEquals("seg1234", segment.getId());
-	}
-}
+package edu.mayo.bmi.uima.core.ae.test;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.File;
+
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.junit.Test;
+
+import edu.mayo.bmi.uima.core.test.TestUtil;
+import edu.mayo.bmi.uima.core.type.textspan.Segment;
+
+public class SimpleSegmentAnnotatorTests {
+
+	@Test
+    public void testSimpleSegment() throws ResourceInitializationException {
+		AnalysisEngine ae = TestUtil.getAE(new File("desc/test/analysis_engine/SimpleSegmentAnnotator.xml"));
+		JCas jCas = TestUtil.processAE(ae, "data/test/mother_goose/OneMistyMorning.txt");
+		Segment segment = TestUtil.getFeatureStructureAtIndex(jCas, Segment.class, 0);
+		assertEquals(0, segment.getBegin());
+		assertEquals(42, segment.getEnd());
+		assertEquals("seg1234", segment.getId());
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ae/test/TokenizerAnnotatorPTBTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ae/test/TokenizerAnnotatorPTBTests.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ae/test/TokenizerAnnotatorPTBTests.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ae/test/TokenizerAnnotatorPTBTests.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
 /*
- * Copyright: (c) 2011   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.core.ae.test;
-
+package edu.mayo.bmi.uima.core.ae.test;
+
 import static org.junit.Assert.assertEquals;
 
 import java.io.File;
@@ -41,8 +34,8 @@ import edu.mayo.bmi.uima.core.type.synta
 import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
 import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
 import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-
-public class TokenizerAnnotatorPTBTests {
+
+public class TokenizerAnnotatorPTBTests {
 
     TestData<SimpleToken []>[] tests;
     private static final Logger logger = Logger.getLogger(TokenizerAnnotatorPTBTests.class.getName());

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ci/test/HyphenTextModifierImplTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ci/test/HyphenTextModifierImplTests.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ci/test/HyphenTextModifierImplTests.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/ci/test/HyphenTextModifierImplTests.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
@@ -21,98 +14,98 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-/**
- * 
- */
-package edu.mayo.bmi.uima.core.ci.test;
-
-import java.util.ArrayList;
-
-import org.junit.Test;
-
-import edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl;
-
-/**
- * @author Mayo Clinic
- *
- */
-public class HyphenTextModifierImplTests {
-
-	/**
-	 * Test method for {@link edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl#HyphenTextModifierImpl(java.lang.String, int)}.
-	 */
-	//	@Test
-	//	public void testHyphenTextModifierImpl() {
-	//		fail("Not yet implemented"); // TODO
-	//	}
-
-	/**
-	 * Test method for {@link edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl#modify(java.lang.String)}.
-	 */
-	//	@Test
-	//	public void testModify() {
-	//		fail("Not yet implemented"); // TODO
-	//	}
-
-	/**
-	 * Test method for {@link edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl#test(edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl, java.lang.String)}.
-	 * Performs two tests - one that has two blanks between some words that could be hyphenated. Since there are two blanks,
-	 * the text is not modified (the blanks are not replaced by hyphens).
-	 * For the second test, the appropriate blanks are replaced by hyphens. 
-	 */
-	@Test
-	public void testTest() {
-
-		// The messages about "UNSUPPORTED" go to stderr, and are not returned by test() 
-		// Same for "New:  (new text not generated, see previous messages)"
-		String [] expectedMessages = {
-				// "UNSUPPORTED: TextModification with offset changes.",
-				// "UNSUPPORTED: TextModification with offset changes.",
-				// "UNSUPPORTED: TextModification with offset changes.",
-				"Orig: Non  Hodgkin's the x  ray without any non small  cell complications.",
-				// "New:  (new text not generated, see previous messages)",
-				"Non-Hodgkin Orig: 0-12 New: 0-11",
-				"x-ray Orig: 19-25 New: 18-23",
-				"non-small-cell Orig: 38-53 New: 36-50",
-				
-				"Orig: Non Hodgkin's the x ray without any non small cell complications.",
-				"New:  Non-Hodgkin's the x-ray without any non-small-cell complications.",
-				"Non-Hodgkin Orig: 0-11 New: 0-11",
-				"x-ray Orig: 18-23 New: 18-23",
-				"non-small-cell Orig: 36-50 New: 36-50",
-		};
-		String [] expectedStderr = {
-				"UNSUPPORTED: TextModification with offset changes.",
-				"UNSUPPORTED: TextModification with offset changes.",
-				"UNSUPPORTED: TextModification with offset changes.",
-				"New:  (new text not generated, see previous messages)",
-		};
-		String [] receivedMessages = new String[expectedMessages.length];
-
-		int errCount = expectedStderr.length;
-		System.out.println("OK to see the following " + errCount + " had been written to stderr:");
-		for (String s: expectedStderr) {
-			System.out.println(s);
-		}
-		
-		String filename = "resources/tokenizer/hyphenated.txt";
-		HyphenTextModifierImpl tm = new HyphenTextModifierImpl(filename, 7);
-		ArrayList<String> messages;
-		String t = "Non  Hodgkin's the x  ray without any non small  cell complications.";
-		messages = HyphenTextModifierImpl.test(tm, t); // extra blanks
-		assert(messages.toArray(receivedMessages).equals(expectedMessages));
-		t = t.replace("  ", " "); // change text to only have single blanks between words
-		// t = "Non Hodgkin's the x ray without any non small cell complications.";
-		messages = HyphenTextModifierImpl.test(tm, t); // single blanks
-
-	}
-
-	/**
-	 * Test method for {@link edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl#main(java.lang.String[])}.
-	 */
-	//	@Test
-	//	public void testMain() {
-	//		fail("Not yet implemented"); // TODO
-	//	}
-
-}
+/**
+ * 
+ */
+package edu.mayo.bmi.uima.core.ci.test;
+
+import java.util.ArrayList;
+
+import org.junit.Test;
+
+import edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl;
+
+/**
+ * @author Mayo Clinic
+ *
+ */
+public class HyphenTextModifierImplTests {
+
+	/**
+	 * Test method for {@link edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl#HyphenTextModifierImpl(java.lang.String, int)}.
+	 */
+	//	@Test
+	//	public void testHyphenTextModifierImpl() {
+	//		fail("Not yet implemented"); // TODO
+	//	}
+
+	/**
+	 * Test method for {@link edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl#modify(java.lang.String)}.
+	 */
+	//	@Test
+	//	public void testModify() {
+	//		fail("Not yet implemented"); // TODO
+	//	}
+
+	/**
+	 * Test method for {@link edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl#test(edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl, java.lang.String)}.
+	 * Performs two tests - one that has two blanks between some words that could be hyphenated. Since there are two blanks,
+	 * the text is not modified (the blanks are not replaced by hyphens).
+	 * For the second test, the appropriate blanks are replaced by hyphens. 
+	 */
+	@Test
+	public void testTest() {
+
+		// The messages about "UNSUPPORTED" go to stderr, and are not returned by test() 
+		// Same for "New:  (new text not generated, see previous messages)"
+		String [] expectedMessages = {
+				// "UNSUPPORTED: TextModification with offset changes.",
+				// "UNSUPPORTED: TextModification with offset changes.",
+				// "UNSUPPORTED: TextModification with offset changes.",
+				"Orig: Non  Hodgkin's the x  ray without any non small  cell complications.",
+				// "New:  (new text not generated, see previous messages)",
+				"Non-Hodgkin Orig: 0-12 New: 0-11",
+				"x-ray Orig: 19-25 New: 18-23",
+				"non-small-cell Orig: 38-53 New: 36-50",
+				
+				"Orig: Non Hodgkin's the x ray without any non small cell complications.",
+				"New:  Non-Hodgkin's the x-ray without any non-small-cell complications.",
+				"Non-Hodgkin Orig: 0-11 New: 0-11",
+				"x-ray Orig: 18-23 New: 18-23",
+				"non-small-cell Orig: 36-50 New: 36-50",
+		};
+		String [] expectedStderr = {
+				"UNSUPPORTED: TextModification with offset changes.",
+				"UNSUPPORTED: TextModification with offset changes.",
+				"UNSUPPORTED: TextModification with offset changes.",
+				"New:  (new text not generated, see previous messages)",
+		};
+		String [] receivedMessages = new String[expectedMessages.length];
+
+		int errCount = expectedStderr.length;
+		System.out.println("OK to see the following " + errCount + " had been written to stderr:");
+		for (String s: expectedStderr) {
+			System.out.println(s);
+		}
+		
+		String filename = "resources/tokenizer/hyphenated.txt";
+		HyphenTextModifierImpl tm = new HyphenTextModifierImpl(filename, 7);
+		ArrayList<String> messages;
+		String t = "Non  Hodgkin's the x  ray without any non small  cell complications.";
+		messages = HyphenTextModifierImpl.test(tm, t); // extra blanks
+		assert(messages.toArray(receivedMessages).equals(expectedMessages));
+		t = t.replace("  ", " "); // change text to only have single blanks between words
+		// t = "Non Hodgkin's the x ray without any non small cell complications.";
+		messages = HyphenTextModifierImpl.test(tm, t); // single blanks
+
+	}
+
+	/**
+	 * Test method for {@link edu.mayo.bmi.uima.core.ci.HyphenTextModifierImpl#main(java.lang.String[])}.
+	 */
+	//	@Test
+	//	public void testMain() {
+	//		fail("Not yet implemented"); // TODO
+	//	}
+
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/test/TestUtil.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/test/TestUtil.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/test/TestUtil.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/core/test/edu/mayo/bmi/uima/core/test/TestUtil.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
@@ -21,208 +14,208 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.uima.core.test;
-
-import static org.junit.Assert.assertEquals;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.charset.Charset;
-
-import org.apache.uima.UIMAFramework;
-import org.apache.uima.UimaContext;
-import org.apache.uima.analysis_engine.AnalysisEngine;
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.cas.FSIndex;
-import org.apache.uima.cas.FSIterator;
-import org.apache.uima.collection.CollectionReader;
-import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.cas.TOP;
-import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.uima.resource.ResourceSpecifier;
-import org.apache.uima.util.FileUtils;
-import org.apache.uima.util.InvalidXMLException;
-import org.apache.uima.util.XMLInputSource;
-import org.apache.uima.util.XMLParser;
-
-
-public class TestUtil {
-
-	/**
-	 * This method simply calls
-	 * {@link #createAnalysisEngineJCas(File, File, String)} with the
-	 * charSetName equal to "UTF-8".
-	 * 
-	 * @param analysisEngineDescriptorFile
-	 *            a descriptor file for a UIMA Analysis Engine.
-	 * @param textFile
-	 *            a file that contains text that the analysis engine will
-	 *            process.
-	 * @return a JCas that represents the analysis engine's processing of the
-	 *         text file.
-	 * @throws ResourceInitializationException
-	 * @see {@link #createAnalysisEngineJCas(File, File, String)}
-	 */
-	public static JCas processAE(AnalysisEngine ae, File textFile) throws ResourceInitializationException {
-		return processAE(ae, textFile, "UTF-8");
-	}
-
-	/**
-	 * This method reads in the text from the text file using the provided
-	 * character set and then calls {@link #getJCas(File, String)}
-	 * 
-	 * @param analysisEngineDescriptorFile
-	 *            a descriptor file for a UIMA Analysis Engine.
-	 * @param textFile
-	 *            a file that contains text that the analysis engine will
-	 *            process.
-	 * @param charSetName
-	 *            the name of the character encoding of the file
-	 * @return a JCas that represents the analysis engine's processing of the
-	 *         text file.
-	 * @throws ResourceInitializationException
-	 * @see {@link #getJCas(File, String)}
-	 * @see Charset
-	 */
-	public static JCas processAE(AnalysisEngine ae, File textFile, String charSetName)
-			throws ResourceInitializationException {
-
-		try {
-			String text = FileUtils.file2String(textFile, charSetName);
-			return processAE(ae, text);
-		} catch (IOException ioe) {
-			throw new ResourceInitializationException(ioe);
-		}
-	}
-
-	/**
-	 * This method creates a JCas for the provided analysis engine descriptor
-	 * file and then processes the provided text and returns the JCas. This
-	 * method is convenient for unit testing because the first line of a unit
-	 * test can be. <br>
-	 * 
-	 * <pre>
-	 * JCas jCas = createAnalysisEngineJCas(someAEDescriptorFile, someText);
-	 * </pre>
-	 * 
-	 * <br>
-	 * The subsequent lines can then be assertions that query the expected
-	 * contents of the JCas.
-	 * 
-	 * @param analysisEngineDescriptorFile
-	 *            a descriptor file for a UIMA Analysis Engine.
-	 * @param text
-	 *            text that the analysis engine will process.
-	 * 
-	 * @return a JCas that represents the analysis engine's processing of the
-	 *         text file.
-	 * @throws ResourceInitializationException
-	 * 
-	 * The code for this method was found here:
-	 * http://article.gmane.org/gmane.comp.apache.uima.general/880/match=push+documents+into+cpe+collectionreader
-	 * 
-	 */
-
-	public static JCas processAE(AnalysisEngine ae, String text) throws ResourceInitializationException {
-		try {
-			JCas jCas = ae.newJCas();
-			jCas.setDocumentText(text);
-			ae.process(jCas);
-			return jCas;
-		} catch (AnalysisEngineProcessException aepe) {
-			throw new ResourceInitializationException(aepe);
-		}
-	}
-
-	public static AnalysisEngine getAE(File analysisEngineDescriptorFile) throws ResourceInitializationException {
-		try {
-			XMLInputSource xmlInputSource = new XMLInputSource(analysisEngineDescriptorFile);
-			XMLParser xmlParser = UIMAFramework.getXMLParser();
-			ResourceSpecifier resourceSpecifier = xmlParser.parseResourceSpecifier(xmlInputSource);
-			AnalysisEngine analysisEngine = UIMAFramework.produceAnalysisEngine(resourceSpecifier);
-			return analysisEngine;
-		} catch (IOException ioe) {
-			throw new ResourceInitializationException(ioe);
-		} catch (InvalidXMLException ixe) {
-			throw new ResourceInitializationException(ixe);
-		}
-
-	}
-
-	public static CollectionReader getCR(File collectionReaderDescriptorFile) throws ResourceInitializationException {
-		try {
-			XMLInputSource xmlInputSource = new XMLInputSource(collectionReaderDescriptorFile);
-			XMLParser xmlParser = UIMAFramework.getXMLParser();
-			ResourceSpecifier resourceSpecifier = xmlParser.parseResourceSpecifier(xmlInputSource);
-			CollectionReader collectionReader = UIMAFramework.produceCollectionReader(resourceSpecifier);
-			return collectionReader;
-		} catch (IOException ioe) {
-			throw new ResourceInitializationException(ioe);
-		} catch (InvalidXMLException ixe) {
-			throw new ResourceInitializationException(ixe);
-		}
-
-	}
-
-	public static <T extends TOP> int getFeatureStructureSize(JCas jCas, Class<T> cls) {
-
-		try {
-		
-			int type = (Integer) cls.getField("type").get(null);
-			FSIndex fsIndex = jCas.getAnnotationIndex(type);
-
-			FSIterator iterator = fsIndex.iterator();
-			int size = 0;
-			while (iterator.hasNext()) {
-				iterator.next();
-				size++;
-			}
-			return size; 
-			
-		} catch (IllegalAccessException iae) {
-			throw new IllegalArgumentException("class passed in caused an exception: class=" + cls.getCanonicalName(), iae);
-		} catch (NoSuchFieldException nsfe) {
-			throw new IllegalArgumentException("class passed in caused an exception: class=" + cls.getCanonicalName(), nsfe);
-		}
-		
-	}
-
-	public static <T extends TOP> T getFeatureStructureAtIndex(JCas jCas, Class<T> cls, int index) {
-
-		try {
-			int type = (Integer) cls.getField("type").get(null);
-			FSIndex fsIndex = jCas.getAnnotationIndex(type);
-			if (index < 0)
-				throw new IllegalArgumentException("index less than zero: index=" + index);
-			if (index >= fsIndex.size())
-				throw new IllegalArgumentException("index greater than or equal to fsIndex.size(): index=" + index);
-
-			FSIterator iterator = fsIndex.iterator();
-			Object obj = null;
-			for (int i = 0; i <= index; i++) {
-				obj = iterator.next();
-			}
-			return cls.cast(obj);
-		} catch (IllegalAccessException iae) {
-			throw new IllegalArgumentException("class passed in caused an exception: class=" + cls.getCanonicalName(),
-					iae);
-		} catch (NoSuchFieldException nsfe) {
-			throw new IllegalArgumentException("class passed in caused an exception: class=" + cls.getCanonicalName(),
-					nsfe);
-		}
-	}
-
-	static String unexpectedParamValueMsg = "unexpected parameter value for descriptor file %1$s for param: %2$s";
-
-	public static void testConfigParam(UimaContext uimaContext, String descriptorFile, String paramName, Object paramValue) {
-		testConfigParam(uimaContext, descriptorFile, paramName, paramValue, null);
-	}
-	public static void testConfigParam(UimaContext uimaContext, String descriptorFile, String paramName, Object paramValue, Integer arrayIndex) {
-		if(arrayIndex == null) {
-			assertEquals(String.format(unexpectedParamValueMsg, descriptorFile, paramName), paramValue, uimaContext
-				.getConfigParameterValue(paramName));
-		} else
-			assertEquals(String.format(unexpectedParamValueMsg, descriptorFile, paramName), paramValue, ((Object[])uimaContext
-					.getConfigParameterValue(paramName))[arrayIndex]);
-	}
-}
+package edu.mayo.bmi.uima.core.test;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.Charset;
+
+import org.apache.uima.UIMAFramework;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.FSIndex;
+import org.apache.uima.cas.FSIterator;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.cas.TOP;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.ResourceSpecifier;
+import org.apache.uima.util.FileUtils;
+import org.apache.uima.util.InvalidXMLException;
+import org.apache.uima.util.XMLInputSource;
+import org.apache.uima.util.XMLParser;
+
+
+public class TestUtil {
+
+	/**
+	 * This method simply calls
+	 * {@link #createAnalysisEngineJCas(File, File, String)} with the
+	 * charSetName equal to "UTF-8".
+	 * 
+	 * @param analysisEngineDescriptorFile
+	 *            a descriptor file for a UIMA Analysis Engine.
+	 * @param textFile
+	 *            a file that contains text that the analysis engine will
+	 *            process.
+	 * @return a JCas that represents the analysis engine's processing of the
+	 *         text file.
+	 * @throws ResourceInitializationException
+	 * @see {@link #createAnalysisEngineJCas(File, File, String)}
+	 */
+	public static JCas processAE(AnalysisEngine ae, File textFile) throws ResourceInitializationException {
+		return processAE(ae, textFile, "UTF-8");
+	}
+
+	/**
+	 * This method reads in the text from the text file using the provided
+	 * character set and then calls {@link #getJCas(File, String)}
+	 * 
+	 * @param analysisEngineDescriptorFile
+	 *            a descriptor file for a UIMA Analysis Engine.
+	 * @param textFile
+	 *            a file that contains text that the analysis engine will
+	 *            process.
+	 * @param charSetName
+	 *            the name of the character encoding of the file
+	 * @return a JCas that represents the analysis engine's processing of the
+	 *         text file.
+	 * @throws ResourceInitializationException
+	 * @see {@link #getJCas(File, String)}
+	 * @see Charset
+	 */
+	public static JCas processAE(AnalysisEngine ae, File textFile, String charSetName)
+			throws ResourceInitializationException {
+
+		try {
+			String text = FileUtils.file2String(textFile, charSetName);
+			return processAE(ae, text);
+		} catch (IOException ioe) {
+			throw new ResourceInitializationException(ioe);
+		}
+	}
+
+	/**
+	 * This method creates a JCas for the provided analysis engine descriptor
+	 * file and then processes the provided text and returns the JCas. This
+	 * method is convenient for unit testing because the first line of a unit
+	 * test can be. <br>
+	 * 
+	 * <pre>
+	 * JCas jCas = createAnalysisEngineJCas(someAEDescriptorFile, someText);
+	 * </pre>
+	 * 
+	 * <br>
+	 * The subsequent lines can then be assertions that query the expected
+	 * contents of the JCas.
+	 * 
+	 * @param analysisEngineDescriptorFile
+	 *            a descriptor file for a UIMA Analysis Engine.
+	 * @param text
+	 *            text that the analysis engine will process.
+	 * 
+	 * @return a JCas that represents the analysis engine's processing of the
+	 *         text file.
+	 * @throws ResourceInitializationException
+	 * 
+	 * The code for this method was found here:
+	 * http://article.gmane.org/gmane.comp.apache.uima.general/880/match=push+documents+into+cpe+collectionreader
+	 * 
+	 */
+
+	public static JCas processAE(AnalysisEngine ae, String text) throws ResourceInitializationException {
+		try {
+			JCas jCas = ae.newJCas();
+			jCas.setDocumentText(text);
+			ae.process(jCas);
+			return jCas;
+		} catch (AnalysisEngineProcessException aepe) {
+			throw new ResourceInitializationException(aepe);
+		}
+	}
+
+	public static AnalysisEngine getAE(File analysisEngineDescriptorFile) throws ResourceInitializationException {
+		try {
+			XMLInputSource xmlInputSource = new XMLInputSource(analysisEngineDescriptorFile);
+			XMLParser xmlParser = UIMAFramework.getXMLParser();
+			ResourceSpecifier resourceSpecifier = xmlParser.parseResourceSpecifier(xmlInputSource);
+			AnalysisEngine analysisEngine = UIMAFramework.produceAnalysisEngine(resourceSpecifier);
+			return analysisEngine;
+		} catch (IOException ioe) {
+			throw new ResourceInitializationException(ioe);
+		} catch (InvalidXMLException ixe) {
+			throw new ResourceInitializationException(ixe);
+		}
+
+	}
+
+	public static CollectionReader getCR(File collectionReaderDescriptorFile) throws ResourceInitializationException {
+		try {
+			XMLInputSource xmlInputSource = new XMLInputSource(collectionReaderDescriptorFile);
+			XMLParser xmlParser = UIMAFramework.getXMLParser();
+			ResourceSpecifier resourceSpecifier = xmlParser.parseResourceSpecifier(xmlInputSource);
+			CollectionReader collectionReader = UIMAFramework.produceCollectionReader(resourceSpecifier);
+			return collectionReader;
+		} catch (IOException ioe) {
+			throw new ResourceInitializationException(ioe);
+		} catch (InvalidXMLException ixe) {
+			throw new ResourceInitializationException(ixe);
+		}
+
+	}
+
+	public static <T extends TOP> int getFeatureStructureSize(JCas jCas, Class<T> cls) {
+
+		try {
+		
+			int type = (Integer) cls.getField("type").get(null);
+			FSIndex fsIndex = jCas.getAnnotationIndex(type);
+
+			FSIterator iterator = fsIndex.iterator();
+			int size = 0;
+			while (iterator.hasNext()) {
+				iterator.next();
+				size++;
+			}
+			return size; 
+			
+		} catch (IllegalAccessException iae) {
+			throw new IllegalArgumentException("class passed in caused an exception: class=" + cls.getCanonicalName(), iae);
+		} catch (NoSuchFieldException nsfe) {
+			throw new IllegalArgumentException("class passed in caused an exception: class=" + cls.getCanonicalName(), nsfe);
+		}
+		
+	}
+
+	public static <T extends TOP> T getFeatureStructureAtIndex(JCas jCas, Class<T> cls, int index) {
+
+		try {
+			int type = (Integer) cls.getField("type").get(null);
+			FSIndex fsIndex = jCas.getAnnotationIndex(type);
+			if (index < 0)
+				throw new IllegalArgumentException("index less than zero: index=" + index);
+			if (index >= fsIndex.size())
+				throw new IllegalArgumentException("index greater than or equal to fsIndex.size(): index=" + index);
+
+			FSIterator iterator = fsIndex.iterator();
+			Object obj = null;
+			for (int i = 0; i <= index; i++) {
+				obj = iterator.next();
+			}
+			return cls.cast(obj);
+		} catch (IllegalAccessException iae) {
+			throw new IllegalArgumentException("class passed in caused an exception: class=" + cls.getCanonicalName(),
+					iae);
+		} catch (NoSuchFieldException nsfe) {
+			throw new IllegalArgumentException("class passed in caused an exception: class=" + cls.getCanonicalName(),
+					nsfe);
+		}
+	}
+
+	static String unexpectedParamValueMsg = "unexpected parameter value for descriptor file %1$s for param: %2$s";
+
+	public static void testConfigParam(UimaContext uimaContext, String descriptorFile, String paramName, Object paramValue) {
+		testConfigParam(uimaContext, descriptorFile, paramName, paramValue, null);
+	}
+	public static void testConfigParam(UimaContext uimaContext, String descriptorFile, String paramName, Object paramValue, Integer arrayIndex) {
+		if(arrayIndex == null) {
+			assertEquals(String.format(unexpectedParamValueMsg, descriptorFile, paramName), paramValue, uimaContext
+				.getConfigParameterValue(paramName));
+		} else
+			assertEquals(String.format(unexpectedParamValueMsg, descriptorFile, paramName), paramValue, ((Object[])uimaContext
+					.getConfigParameterValue(paramName))[arrayIndex]);
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AbstractClassifier.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AbstractClassifier.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AbstractClassifier.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AbstractClassifier.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotOffsetComparator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotOffsetComparator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotOffsetComparator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotOffsetComparator.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotationCounter.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotationCounter.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotationCounter.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotationCounter.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotationSelector.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotationSelector.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotationSelector.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AnnotationSelector.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/AttributeCalculator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AttributeCalculator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AttributeCalculator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/AttributeCalculator.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/CorefConsts.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/CorefConsts.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/CorefConsts.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/CorefConsts.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/EditDistance.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/EditDistance.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/EditDistance.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/EditDistance.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/FSIteratorToList.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/FSIteratorToList.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/FSIteratorToList.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/FSIteratorToList.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/FeatureVector.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/FeatureVector.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/FeatureVector.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/FeatureVector.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/GoldStandardLabeler.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/GoldStandardLabeler.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/GoldStandardLabeler.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/GoldStandardLabeler.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/MarkableDepUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/MarkableDepUtils.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/MarkableDepUtils.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/MarkableDepUtils.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/MarkableTreeUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/MarkableTreeUtils.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/MarkableTreeUtils.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/MarkableTreeUtils.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/PairAttributeCalculator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/PairAttributeCalculator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/PairAttributeCalculator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/PairAttributeCalculator.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/ParentPtrTree.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/ParentPtrTree.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/ParentPtrTree.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/ParentPtrTree.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/SvmUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SvmUtils.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SvmUtils.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SvmUtils.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/SvmVectorCreator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SvmVectorCreator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SvmVectorCreator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SvmVectorCreator.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/edu/mayo/bmi/coref/util/TextMatch.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/TextMatch.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/TextMatch.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/edu/mayo/bmi/coref/util/TextMatch.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/org/chboston/cnlp/ctakes/coref/eval/helpers/B3Type.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/org/chboston/cnlp/ctakes/coref/eval/helpers/B3Type.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/org/chboston/cnlp/ctakes/coref/eval/helpers/B3Type.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/org/chboston/cnlp/ctakes/coref/eval/helpers/B3Type.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*   Copyright 2011 Children's Hospital Boston
-   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/coref-resolver/src/org/chboston/cnlp/ctakes/coref/eval/helpers/CEAFType.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/org/chboston/cnlp/ctakes/coref/eval/helpers/CEAFType.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/org/chboston/cnlp/ctakes/coref/eval/helpers/CEAFType.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/coref-resolver/src/org/chboston/cnlp/ctakes/coref/eval/helpers/CEAFType.java Wed Oct 31 05:26:43 2012
@@ -1,8 +1,10 @@
-/*    Copyright 2011 Children's Hospital Boston
-   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



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