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From james-mas...@apache.org
Subject svn commit: r1403989 [25/28] - 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/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/DocumentMetaData.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/DocumentMetaData.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/DocumentMetaData.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/DocumentMetaData.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
@@ -21,120 +14,120 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.nlp.preprocessor;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-/**
- *
- * @author Mayo Clinic
- */
-public class DocumentMetaData
-{	
-	private String iv_text;
-	
-	private List iv_scAnnotationList = new ArrayList();
-	
-	// key = unique key, value = document meta data
-	private Map iv_docMetaDataMap = new HashMap();
-	
-	// key = segment ID, value = SegmentMetaData object
-	private Map<String, SegmentMetaData> iv_segMetaDataHash = new HashMap<String, SegmentMetaData>();
-
-	/**
-	 * Adds a meta data entry for the document.
-	 * @param key
-	 * @param value
-	 */
-	public void addMetaData(Object key, Object value)
-	{
-		iv_docMetaDataMap.put(key, value);
-	}
-
-	/**
-	 * Gets a map of meta data about the document.
-	 * @return
-	 */
-	public Map getMetaData()
-	{
-		return iv_docMetaDataMap;
-	}
-
-	/**
-	 * Adds a segment.
-	 * @param smd
-	 */
-	public void addSegment(SegmentMetaData smd)
-	{
-		iv_segMetaDataHash.put(smd.id, smd);
-	}
-
-	/**
-	 * Gets a set of segment identifiers.  Each identifier is a String object.
-	 * @return Set of String objects, each String is a segment identifier.
-	 */
-	public Set<String> getSegmentIdentifiers()
-	{
-		return (Set<String>)iv_segMetaDataHash.keySet();
-	}
-
-	/**
-	 * Gets meta data about the specified segment.
-	 * @param segmentID Identifier of segment.
-	 * @return SegmentMetaData object that contains meta data about the
-	 * 	       specified segment.
-	 */
-	public SegmentMetaData getSegment(String segmentID)
-	{
-		return (SegmentMetaData) iv_segMetaDataHash.get(segmentID);
-	}
-	
-	/**
-	 * Adds a single annotation to the syntactic cue annotation list.
-	 * @param a
-	 */
-	public void addAnnotation(Annotation a)
-	{
-		iv_scAnnotationList.add(a);
-	}
-	
-	/**
-	 * Adds a list of annotations to the syntactic cue annotation list.
-	 * @param aList
-	 */
-	public void addAnnotations(List aList)
-	{
-		iv_scAnnotationList.addAll(aList);
-	}
-
-	/**
-	 * Gets a list of Annotation objects that represent annotations based 
-	 * off of document syntactic cues.
-	 * @return List of Annotation objects.
-	 */
-	public List getAnnotations()
-	{
-		return iv_scAnnotationList;
-	}
-
-    /**
-     * @return
-     */
-    public String getText()
-    {
-        return iv_text;
-    }
-
-    /**
-     * @param string
-     */
-    public void setText(String string)
-    {
-        iv_text = string;
-    }
-
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ *
+ * @author Mayo Clinic
+ */
+public class DocumentMetaData
+{	
+	private String iv_text;
+	
+	private List iv_scAnnotationList = new ArrayList();
+	
+	// key = unique key, value = document meta data
+	private Map iv_docMetaDataMap = new HashMap();
+	
+	// key = segment ID, value = SegmentMetaData object
+	private Map<String, SegmentMetaData> iv_segMetaDataHash = new HashMap<String, SegmentMetaData>();
+
+	/**
+	 * Adds a meta data entry for the document.
+	 * @param key
+	 * @param value
+	 */
+	public void addMetaData(Object key, Object value)
+	{
+		iv_docMetaDataMap.put(key, value);
+	}
+
+	/**
+	 * Gets a map of meta data about the document.
+	 * @return
+	 */
+	public Map getMetaData()
+	{
+		return iv_docMetaDataMap;
+	}
+
+	/**
+	 * Adds a segment.
+	 * @param smd
+	 */
+	public void addSegment(SegmentMetaData smd)
+	{
+		iv_segMetaDataHash.put(smd.id, smd);
+	}
+
+	/**
+	 * Gets a set of segment identifiers.  Each identifier is a String object.
+	 * @return Set of String objects, each String is a segment identifier.
+	 */
+	public Set<String> getSegmentIdentifiers()
+	{
+		return (Set<String>)iv_segMetaDataHash.keySet();
+	}
+
+	/**
+	 * Gets meta data about the specified segment.
+	 * @param segmentID Identifier of segment.
+	 * @return SegmentMetaData object that contains meta data about the
+	 * 	       specified segment.
+	 */
+	public SegmentMetaData getSegment(String segmentID)
+	{
+		return (SegmentMetaData) iv_segMetaDataHash.get(segmentID);
+	}
+	
+	/**
+	 * Adds a single annotation to the syntactic cue annotation list.
+	 * @param a
+	 */
+	public void addAnnotation(Annotation a)
+	{
+		iv_scAnnotationList.add(a);
+	}
+	
+	/**
+	 * Adds a list of annotations to the syntactic cue annotation list.
+	 * @param aList
+	 */
+	public void addAnnotations(List aList)
+	{
+		iv_scAnnotationList.addAll(aList);
+	}
+
+	/**
+	 * Gets a list of Annotation objects that represent annotations based 
+	 * off of document syntactic cues.
+	 * @return List of Annotation objects.
+	 */
+	public List getAnnotations()
+	{
+		return iv_scAnnotationList;
+	}
+
+    /**
+     * @return
+     */
+    public String getText()
+    {
+        return iv_text;
+    }
+
+    /**
+     * @param string
+     */
+    public void setText(String string)
+    {
+        iv_text = string;
+    }
+
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/IntegerRange.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/IntegerRange.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/IntegerRange.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/IntegerRange.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
@@ -21,14 +14,14 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.nlp.preprocessor;
-
-/**
- * Defines a range of integers.
- * @author Mayo Clinic
- */
-public class IntegerRange
-{
-	public int start;
-	public int end;
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+/**
+ * Defines a range of integers.
+ * @author Mayo Clinic
+ */
+public class IntegerRange
+{
+	public int start;
+	public int end;
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/PreProcessor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/PreProcessor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/PreProcessor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/PreProcessor.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
@@ -21,20 +14,20 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.nlp.preprocessor;
-
-
-/**
- *
- * @author Mayo Clinic
- */
-public interface PreProcessor
-{
-	/**
-	 * Process a document to retrieve meta data about the document.
-	 * @param document
-	 * @return
-	 * @throws Exception
-	 */
-	public DocumentMetaData process(String document) throws Exception;
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+
+/**
+ *
+ * @author Mayo Clinic
+ */
+public interface PreProcessor
+{
+	/**
+	 * Process a document to retrieve meta data about the document.
+	 * @param document
+	 * @return
+	 * @throws Exception
+	 */
+	public DocumentMetaData process(String document) throws Exception;
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/SegmentMetaData.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/SegmentMetaData.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/SegmentMetaData.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/SegmentMetaData.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
@@ -21,17 +14,17 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.nlp.preprocessor;
-
-import java.util.List;
-
-/**
- * MetaData about a segment.
- * @author Mayo Clinic
- */
-public class SegmentMetaData
-{
-	public IntegerRange span;
-	public String id;
-	public List textSpans;
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+import java.util.List;
+
+/**
+ * MetaData about a segment.
+ * @author Mayo Clinic
+ */
+public class SegmentMetaData
+{
+	public IntegerRange span;
+	public String id;
+	public List textSpans;
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/Utility.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/Utility.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/Utility.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/Utility.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
@@ -21,76 +14,76 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.nlp.preprocessor;
-
-/**
- *
- * @author Mayo Clinic
- */
-public class Utility
-{
-	/**
-	 * Replaces any non-ascii characters with the specified char.
-	 * @param sb
-	 */
-	public static void replaceNonAsciiChars(StringBuffer sb, char replacementChar)
-	{
-		for (int i = 0; i < sb.length(); i++)
-		{
-			char c = sb.charAt(i);
-			// Unicode range 0000-007f Basic Latin
-			// equivalent to ASCII charset
-			if (c > 0x007f)
-			{
-				// character is outside ASCII range of unicode char set
-				sb.setCharAt(i, replacementChar);
-			}
-		}
-	}
-
-	/**
-	 * remove leading and trailing whitespace from each line
-	 * @param sb
-	 * @return
-	 */
-	public static String compress(StringBuffer sb)
-	{
-		StringBuffer compressedSB = new StringBuffer();
-		if (sb == null)
-		{
-			return compressedSB.toString();
-		}
-
-		int indexOfLastNewline = 0;
-		// use for loop to handle through the last newline character
-		for (int i = 0; i < sb.length(); i++)
-		{
-			char currentChar = sb.charAt(i);
-			if (currentChar == '\n')
-			{
-				if ((i - indexOfLastNewline) > 1)
-				{
-					String lineText = sb.substring(indexOfLastNewline, i);
-					String compressedText = lineText.trim();
-					if (compressedText.length() > 0)
-					{
-						compressedSB.append(compressedText);
-						compressedSB.append('\n');
-					}
-				}
-				indexOfLastNewline = i;
-			}
-		}
-		
-		// handles text after last newline character, or text if 
-		// there were no newline characters
-		if (indexOfLastNewline < sb.length())
-		{
-			String lineText = sb.substring(indexOfLastNewline, sb.length());
-			String compressedText = lineText.trim();
-			compressedSB.append(compressedText);
-		}
-
-		return compressedSB.toString();
-	}
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+/**
+ *
+ * @author Mayo Clinic
+ */
+public class Utility
+{
+	/**
+	 * Replaces any non-ascii characters with the specified char.
+	 * @param sb
+	 */
+	public static void replaceNonAsciiChars(StringBuffer sb, char replacementChar)
+	{
+		for (int i = 0; i < sb.length(); i++)
+		{
+			char c = sb.charAt(i);
+			// Unicode range 0000-007f Basic Latin
+			// equivalent to ASCII charset
+			if (c > 0x007f)
+			{
+				// character is outside ASCII range of unicode char set
+				sb.setCharAt(i, replacementChar);
+			}
+		}
+	}
+
+	/**
+	 * remove leading and trailing whitespace from each line
+	 * @param sb
+	 * @return
+	 */
+	public static String compress(StringBuffer sb)
+	{
+		StringBuffer compressedSB = new StringBuffer();
+		if (sb == null)
+		{
+			return compressedSB.toString();
+		}
+
+		int indexOfLastNewline = 0;
+		// use for loop to handle through the last newline character
+		for (int i = 0; i < sb.length(); i++)
+		{
+			char currentChar = sb.charAt(i);
+			if (currentChar == '\n')
+			{
+				if ((i - indexOfLastNewline) > 1)
+				{
+					String lineText = sb.substring(indexOfLastNewline, i);
+					String compressedText = lineText.trim();
+					if (compressedText.length() > 0)
+					{
+						compressedSB.append(compressedText);
+						compressedSB.append('\n');
+					}
+				}
+				indexOfLastNewline = i;
+			}
+		}
+		
+		// handles text after last newline character, or text if 
+		// there were no newline characters
+		if (indexOfLastNewline < sb.length())
+		{
+			String lineText = sb.substring(indexOfLastNewline, sb.length());
+			String compressedText = lineText.trim();
+			compressedSB.append(compressedText);
+		}
+
+		return compressedSB.toString();
+	}
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/test/TestDriver.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/test/TestDriver.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/test/TestDriver.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/test/TestDriver.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
@@ -21,134 +14,134 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.nlp.test;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Set;
-
-import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
-import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
-import edu.mayo.bmi.nlp.preprocessor.PreProcessor;
-import edu.mayo.bmi.nlp.preprocessor.SegmentMetaData;
-
-/**
- * 
- * @author Mayo Clinic
- */
-public class TestDriver
-{
-
-    public static void main(String[] args)
-    {
-        if (args.length < 1 || args.length > 2)
-        {
-            System.out.println("Usage: TestDriver <input file> [<dtd file>]");
-            // example parameters: "test/data/testpatient_cn_1.xml"
-            // example parameters: "test/data/testpatient_cn_1.xml" "resources/cda/NotesIIST_RTF.DTD"
-            System.exit(1);
-        }
-        try
-        {
-            String hl7Text = load(args[0]);
-            String dtdFilename = "resources/cda/NotesIIST_RTF.DTD";
-            if (args.length > 1) {
-            	dtdFilename = args[1];
-            }
-
-            
-            long timestamp, elapsedTime;
-            Set sectionNames;
-            Iterator snItr;
-
-            File dtdFile = new File(dtdFilename);
-            if (!exists(dtdFile)) {
-            	System.exit(-1);
-            }
-            
-            PreProcessor pp = new ClinicalNotePreProcessor(dtdFile, false);
-
-            timestamp = System.currentTimeMillis();
-            DocumentMetaData dmd = pp.process(hl7Text);
-            elapsedTime = System.currentTimeMillis() - timestamp;
-            System.out.println("PreProcessor Took " + elapsedTime + "ms");
-
-            System.out.println("Plain Text Start");
-            System.out.println(dmd.getText());
-            System.out.println("Plain Text End");
-
-            sectionNames = dmd.getSegmentIdentifiers();
-            snItr = sectionNames.iterator();
-            while (snItr.hasNext())
-            {
-                String sectionId = (String) snItr.next();
-                SegmentMetaData smd = dmd.getSegment(sectionId);
-                System.out.println("SECTION="
-                        + sectionId
-                        + "\tSTART_OFFSET="
-                        + smd.span.start
-                        + "\tEND_OFFSET="
-                        + smd.span.end);
-                //System.out.println(dmd.getText().substring(smd.span.start, smd.span.end));
-            }
-
-            Map metaDataMap = dmd.getMetaData();
-            Iterator keyItr = metaDataMap.keySet().iterator();
-            while (keyItr.hasNext())
-            {
-                Object key = keyItr.next();
-                Object value = metaDataMap.get(key);
-                System.out.println("MetaData KEY="
-                        + key.toString()
-                        + " VALUE="
-                        + value.toString());
-            }
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
-    }
-
-    /**
-     * Loads text from a file.
-     * 
-     * @param filename
-     * @return
-     * @throws FileNotFoundException
-     * @throws IOException
-     */
-    public static String load(String filename)
-            throws FileNotFoundException, IOException
-    {
-        String msg = "";
-        File f = new File(filename);
-        exists(f); // output error message if file does not exist
-        BufferedReader br = new BufferedReader(new FileReader(f));
-        String line = br.readLine();
-        while (line != null)
-        {
-            msg += line + "\n";
-            line = br.readLine();
-        }
-        br.close();
-
-        return msg;
-    }
-
-    public static boolean exists(File f) {
-    	
-    	if (f.exists()) {
-    		return true;
-    	}
-    	
-    	System.out.println("cwd = " + new File(".").getAbsolutePath());
-    	System.out.println("File " + f + " does not exist.");
-    	return false;
-    }
-}
+package edu.mayo.bmi.nlp.test;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+
+import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
+import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
+import edu.mayo.bmi.nlp.preprocessor.PreProcessor;
+import edu.mayo.bmi.nlp.preprocessor.SegmentMetaData;
+
+/**
+ * 
+ * @author Mayo Clinic
+ */
+public class TestDriver
+{
+
+    public static void main(String[] args)
+    {
+        if (args.length < 1 || args.length > 2)
+        {
+            System.out.println("Usage: TestDriver <input file> [<dtd file>]");
+            // example parameters: "test/data/testpatient_cn_1.xml"
+            // example parameters: "test/data/testpatient_cn_1.xml" "resources/cda/NotesIIST_RTF.DTD"
+            System.exit(1);
+        }
+        try
+        {
+            String hl7Text = load(args[0]);
+            String dtdFilename = "resources/cda/NotesIIST_RTF.DTD";
+            if (args.length > 1) {
+            	dtdFilename = args[1];
+            }
+
+            
+            long timestamp, elapsedTime;
+            Set sectionNames;
+            Iterator snItr;
+
+            File dtdFile = new File(dtdFilename);
+            if (!exists(dtdFile)) {
+            	System.exit(-1);
+            }
+            
+            PreProcessor pp = new ClinicalNotePreProcessor(dtdFile, false);
+
+            timestamp = System.currentTimeMillis();
+            DocumentMetaData dmd = pp.process(hl7Text);
+            elapsedTime = System.currentTimeMillis() - timestamp;
+            System.out.println("PreProcessor Took " + elapsedTime + "ms");
+
+            System.out.println("Plain Text Start");
+            System.out.println(dmd.getText());
+            System.out.println("Plain Text End");
+
+            sectionNames = dmd.getSegmentIdentifiers();
+            snItr = sectionNames.iterator();
+            while (snItr.hasNext())
+            {
+                String sectionId = (String) snItr.next();
+                SegmentMetaData smd = dmd.getSegment(sectionId);
+                System.out.println("SECTION="
+                        + sectionId
+                        + "\tSTART_OFFSET="
+                        + smd.span.start
+                        + "\tEND_OFFSET="
+                        + smd.span.end);
+                //System.out.println(dmd.getText().substring(smd.span.start, smd.span.end));
+            }
+
+            Map metaDataMap = dmd.getMetaData();
+            Iterator keyItr = metaDataMap.keySet().iterator();
+            while (keyItr.hasNext())
+            {
+                Object key = keyItr.next();
+                Object value = metaDataMap.get(key);
+                System.out.println("MetaData KEY="
+                        + key.toString()
+                        + " VALUE="
+                        + value.toString());
+            }
+        }
+        catch (Exception e)
+        {
+            e.printStackTrace();
+        }
+    }
+
+    /**
+     * Loads text from a file.
+     * 
+     * @param filename
+     * @return
+     * @throws FileNotFoundException
+     * @throws IOException
+     */
+    public static String load(String filename)
+            throws FileNotFoundException, IOException
+    {
+        String msg = "";
+        File f = new File(filename);
+        exists(f); // output error message if file does not exist
+        BufferedReader br = new BufferedReader(new FileReader(f));
+        String line = br.readLine();
+        while (line != null)
+        {
+            msg += line + "\n";
+            line = br.readLine();
+        }
+        br.close();
+
+        return msg;
+    }
+
+    public static boolean exists(File f) {
+    	
+    	if (f.exists()) {
+    		return true;
+    	}
+    	
+    	System.out.println("cwd = " + new File(".").getAbsolutePath());
+    	System.out.println("File " + f + " does not exist.");
+    	return false;
+    }
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/uima/ae/CdaCasInitializer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/uima/ae/CdaCasInitializer.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/uima/ae/CdaCasInitializer.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/uima/ae/CdaCasInitializer.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.ae;
-
+package edu.mayo.bmi.uima.ae;
+
 import java.io.File;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -51,143 +44,143 @@ import edu.mayo.bmi.uima.core.type.struc
 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;
-
-
-/**
- * Bootstraps the CAS by:
- * <ol>
- * <li>Transforms document's original CDA text into plain text,
- * inserting section (segment) markers into text .</li>
- * <li>Transformation also inserts hyphens into words that should be hyphenated</li>
- * <li>Stores the resulting text in a new View (which has its own Sofa)</li>
- * <li>Detects sections and adds Segment (aka section) annotations </li>
- * <li>Extracts document level data and stores in CAS as Property annotations.</li>
- * </ol>
- * 
- */
-public class CdaCasInitializer extends JCasAnnotator_ImplBase
-{
-    // LOG4J logger based on class name
-    private Logger logger = Logger.getLogger(getClass().getName());
-
-    private File dtdFile;
-    private Boolean includeSectionMarkers;
-
-    private TextModifier tm;
-    
-    
-    private UimaContext uimaContext; 
-    
-	public void initialize(UimaContext aCtx) throws ResourceInitializationException {
-		
-		super.initialize(aCtx);
-		
-		uimaContext = aCtx;
-		initialize();
-
-	}
-    
-    
-    public void initialize() throws ResourceInitializationException
-    {
-    	// TODO Consider using a parameter for includeSectionMarkers
-        //includeSectionMarkers = (Boolean) getConfigParameterValue("IncludeSectionMarkers");
-    	includeSectionMarkers = new Boolean(false);
-
-    	// TODO Consider using a parameter for hyphWindow/HyphenDetectionWindow
-        //int hyphWindow = ((Integer) getConfigParameterValue("HyphenDetectionWindow")).intValue();
-        int hyphWindow = 3;
-
-        try {
-            FileResource hyphResrc = (FileResource) uimaContext.getResourceObject("HyphenDictionary");
-            File hyphFile = hyphResrc.getFile();
-        	logger.info("Hyphen dictionary: " + hyphFile.getAbsolutePath());
-
-            tm = new HyphenTextModifierImpl(
-                    hyphFile.getAbsolutePath(),
-                    hyphWindow);
-
-            FileResource dtdResrc = (FileResource) uimaContext.getResourceObject("DTD");
-            dtdFile = dtdResrc.getFile();
-        	logger.info("DTD: " + dtdFile.getAbsolutePath());
-        }
-        catch (Exception e) {
-            throw new ResourceInitializationException(e);
-        }
-    }
-
-    
-
-    /**
-     * Apply text modifier to the text 
-     * TODO - move this to <code>TextModifier</code> and take a <code>Logger</code>
-     * 		See <code>HyphenTextModifierImpl</code>
-     * @param sb
-     * @return
-     */
-    private void applyTextModifier(String text, StringBuffer sb) throws Exception {
-        TextModification[] textModArr = tm.modify(text);
-        for (int i = 0; i < textModArr.length; i++) {
-
-        	TextModification textMod = textModArr[i];
-            
-            if ((textMod.getOrigStartOffset() != textMod.getNewStartOffset())
-                    || (textMod.getOrigEndOffset() != textMod.getNewEndOffset())) {
-                logger.warn("UNSUPPORTED: TextModification with offset changes.");
-            }
-            else {
-            	sb.replace(textMod.getOrigStartOffset(), 
-        				textMod.getOrigEndOffset(), 
-        				textMod.getNewText());
-            }
-        }  
-    }
-    
-    
-	public void process(JCas jcas) throws AnalysisEngineProcessException {
-
-    	logger.info(" process(JCas)");
-		
-		String originalText = null;
-	    DocumentMetaData dmd;
-
+
+
+/**
+ * Bootstraps the CAS by:
+ * <ol>
+ * <li>Transforms document's original CDA text into plain text,
+ * inserting section (segment) markers into text .</li>
+ * <li>Transformation also inserts hyphens into words that should be hyphenated</li>
+ * <li>Stores the resulting text in a new View (which has its own Sofa)</li>
+ * <li>Detects sections and adds Segment (aka section) annotations </li>
+ * <li>Extracts document level data and stores in CAS as Property annotations.</li>
+ * </ol>
+ * 
+ */
+public class CdaCasInitializer extends JCasAnnotator_ImplBase
+{
+    // LOG4J logger based on class name
+    private Logger logger = Logger.getLogger(getClass().getName());
+
+    private File dtdFile;
+    private Boolean includeSectionMarkers;
+
+    private TextModifier tm;
+    
+    
+    private UimaContext uimaContext; 
+    
+	public void initialize(UimaContext aCtx) throws ResourceInitializationException {
+		
+		super.initialize(aCtx);
+		
+		uimaContext = aCtx;
+		initialize();
+
+	}
+    
+    
+    public void initialize() throws ResourceInitializationException
+    {
+    	// TODO Consider using a parameter for includeSectionMarkers
+        //includeSectionMarkers = (Boolean) getConfigParameterValue("IncludeSectionMarkers");
+    	includeSectionMarkers = new Boolean(false);
+
+    	// TODO Consider using a parameter for hyphWindow/HyphenDetectionWindow
+        //int hyphWindow = ((Integer) getConfigParameterValue("HyphenDetectionWindow")).intValue();
+        int hyphWindow = 3;
+
         try {
-            
-        	JCas originalView = jcas.getView("_InitialView");
-        	originalText = originalView.getSofaDataString();
-
-            PreProcessor pp = new ClinicalNotePreProcessor(
-                    dtdFile,
-                    includeSectionMarkers.booleanValue());
-            dmd = pp.process(originalText);
-
-            String text = dmd.getText();
-            StringBuffer sb = new StringBuffer(text);
-
-            applyTextModifier(text, sb); 
-            
-            // Create a view (and its Sofa) to hold the plain text version of
-            // the CDA document
-            JCas plaintextView = jcas.createView("plaintext");           
-            plaintextView.setDocumentText(sb.toString());
-            
-            // Add section (segment) annotations
-            Iterator<String> segmentItr = (Iterator<String>)dmd.getSegmentIdentifiers().iterator();
+            FileResource hyphResrc = (FileResource) uimaContext.getResourceObject("HyphenDictionary");
+            File hyphFile = hyphResrc.getFile();
+        	logger.info("Hyphen dictionary: " + hyphFile.getAbsolutePath());
+
+            tm = new HyphenTextModifierImpl(
+                    hyphFile.getAbsolutePath(),
+                    hyphWindow);
+
+            FileResource dtdResrc = (FileResource) uimaContext.getResourceObject("DTD");
+            dtdFile = dtdResrc.getFile();
+        	logger.info("DTD: " + dtdFile.getAbsolutePath());
+        }
+        catch (Exception e) {
+            throw new ResourceInitializationException(e);
+        }
+    }
+
+    
+
+    /**
+     * Apply text modifier to the text 
+     * TODO - move this to <code>TextModifier</code> and take a <code>Logger</code>
+     * 		See <code>HyphenTextModifierImpl</code>
+     * @param sb
+     * @return
+     */
+    private void applyTextModifier(String text, StringBuffer sb) throws Exception {
+        TextModification[] textModArr = tm.modify(text);
+        for (int i = 0; i < textModArr.length; i++) {
+
+        	TextModification textMod = textModArr[i];
+            
+            if ((textMod.getOrigStartOffset() != textMod.getNewStartOffset())
+                    || (textMod.getOrigEndOffset() != textMod.getNewEndOffset())) {
+                logger.warn("UNSUPPORTED: TextModification with offset changes.");
+            }
+            else {
+            	sb.replace(textMod.getOrigStartOffset(), 
+        				textMod.getOrigEndOffset(), 
+        				textMod.getNewText());
+            }
+        }  
+    }
+    
+    
+	public void process(JCas jcas) throws AnalysisEngineProcessException {
+
+    	logger.info(" process(JCas)");
+		
+		String originalText = null;
+	    DocumentMetaData dmd;
+
+        try {
+            
+        	JCas originalView = jcas.getView("_InitialView");
+        	originalText = originalView.getSofaDataString();
+
+            PreProcessor pp = new ClinicalNotePreProcessor(
+                    dtdFile,
+                    includeSectionMarkers.booleanValue());
+            dmd = pp.process(originalText);
+
+            String text = dmd.getText();
+            StringBuffer sb = new StringBuffer(text);
+
+            applyTextModifier(text, sb); 
+            
+            // Create a view (and its Sofa) to hold the plain text version of
+            // the CDA document
+            JCas plaintextView = jcas.createView("plaintext");           
+            plaintextView.setDocumentText(sb.toString());
+            
+            // Add section (segment) annotations
+            Iterator<String> segmentItr = (Iterator<String>)dmd.getSegmentIdentifiers().iterator();
             while (segmentItr.hasNext()) 
-            {
-                String segmentID = (String) segmentItr.next();
-                SegmentMetaData smd = dmd.getSegment(segmentID);
-
-                Segment sa = new Segment(plaintextView);
-                sa.setBegin(smd.span.start);
-                sa.setEnd(smd.span.end);
-                sa.setId(smd.id);
-
-                sa.addToIndexes();
+            {
+                String segmentID = (String) segmentItr.next();
+                SegmentMetaData smd = dmd.getSegment(segmentID);
+
+                Segment sa = new Segment(plaintextView);
+                sa.setBegin(smd.span.start);
+                sa.setEnd(smd.span.end);
+                sa.setId(smd.id);
+
+                sa.addToIndexes();
             }
             
-            // Store meta data about the document
-            Pairs propAnnot = new Pairs(plaintextView); 
+            // Store meta data about the document
+            Pairs propAnnot = new Pairs(plaintextView); 
             Map metaDataMap = dmd.getMetaData();
             
             String docID = (String)metaDataMap.get(ClinicalNotePreProcessor.MD_KEY_DOC_ID);
@@ -197,33 +190,33 @@ public class CdaCasInitializer extends J
             	newDocId.addToIndexes();
         	
         	}
-            
-            FSArray fsArr = new FSArray(plaintextView, metaDataMap.size());
-            Iterator keyItr = metaDataMap.keySet().iterator();
-            int pos = 0;
-            while (keyItr.hasNext()) {
-
-                String key = (String) keyItr.next();
-                Object value = metaDataMap.get(key);
-
-                if (value instanceof String) {
-                    Pair prop = new Pair(plaintextView);               
-                    prop.setAttribute(key);
-                    prop.setValue((String) value);
-                    fsArr.set(pos++, prop);
-                }
-                else if (value instanceof HashSet) {
-                }
-
-            }
-
-            propAnnot.setPairs(fsArr);
-            propAnnot.addToIndexes();
-        }
-        catch (Exception e) {
-            throw new AnalysisEngineProcessException(e);
-        }
-
-    }
-
-}
+            
+            FSArray fsArr = new FSArray(plaintextView, metaDataMap.size());
+            Iterator keyItr = metaDataMap.keySet().iterator();
+            int pos = 0;
+            while (keyItr.hasNext()) {
+
+                String key = (String) keyItr.next();
+                Object value = metaDataMap.get(key);
+
+                if (value instanceof String) {
+                    Pair prop = new Pair(plaintextView);               
+                    prop.setAttribute(key);
+                    prop.setValue((String) value);
+                    fsArr.set(pos++, prop);
+                }
+                else if (value instanceof HashSet) {
+                }
+
+            }
+
+            propAnnot.setPairs(fsArr);
+            propAnnot.addToIndexes();
+        }
+        catch (Exception e) {
+            throw new AnalysisEngineProcessException(e);
+        }
+
+    }
+
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.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
@@ -21,125 +14,125 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.test.preprocessor;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.net.URLDecoder;
-import java.util.Map;
-
-import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
-import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
-
-import junit.framework.TestCase;
-
-/**
- * Unit tests for the ClinicalNotePreProcessor class.  These test the class
- * against clinical note XML data and determine whether the preprocessor
- * successfully parsed out the correct info.
- * 
- * @author Mayo Clinic
- */
-public class ClinicalNotePreProcessorTest extends TestCase
-{
-    private ClinicalNotePreProcessor iv_cnotePreProcessor;
-    private String iv_cnoteXML;
-
-    /**
-     * Constructor for ClinicalNotePreProcessorTest.
-     * @param arg0
-     */
-    public ClinicalNotePreProcessorTest(String arg0)
-    {
-        super(arg0);
-    }
-
-    /*
-     * @see TestCase#setUp()
-     */
-    protected void setUp() throws Exception
-    {
-        super.setUp();
-
-        String dtdLocation = "resources/cda/NotesIIST_RTF.DTD";
-        File dtd = new File(dtdLocation);
-        iv_cnotePreProcessor = new ClinicalNotePreProcessor(dtd, false);
-
-		//String cnoteLocationOnCp = "/test/data/testpatient_cn_1.xml";
-		String cnoteLocationOnCp = "../../../../../data/testpatient_cn_1.xml";
-        String cnoteLocation =
-            URLDecoder.decode(getClass().getResource(cnoteLocationOnCp).getPath());
-        
-        if (cnoteLocation == null) {
-        	throw new FileNotFoundException("Unable to find: " + cnoteLocationOnCp);
-        }
-        iv_cnoteXML = load(cnoteLocation);
-    }
-
-    /*
-     * @see TestCase#tearDown()
-     */
-    protected void tearDown() throws Exception
-    {
-        super.tearDown();
-    }
-
-    /**
-     * Tests the process method.
-     */
-    public void testProcess()
-    {
-        try
-        {
-            DocumentMetaData dmd = iv_cnotePreProcessor.process(iv_cnoteXML);
-
-            // validate document properties
-            String docID = "000000000";
-            String serviceCode = "MNT";
-            Map docProperties = dmd.getMetaData();
-            String cnote_docID =
-                (String) docProperties.get(
-                    ClinicalNotePreProcessor.MD_KEY_DOC_ID);
-            String cnote_serviceCode =
-                (String) docProperties.get(
-                    ClinicalNotePreProcessor.MD_KEY_SERVICE_CODE);
-            assertEquals(docID, cnote_docID);
-            assertEquals(serviceCode, cnote_serviceCode);
-
-            // validate each section
-            // TODO Consider validating each section           
-        }
-        catch (Exception e)
-        {
-        	e.printStackTrace(System.err);
-            fail(e.getMessage());
-        }
-    }
-
-    /**
-     * Loads text from a file.
-     * @param filename
-     * @return
-     * @throws FileNotFoundException
-     * @throws IOException
-     */
-    private String load(String filename)
-        throws FileNotFoundException, IOException
-    {
-        String msg = "";
-        File f = new File(filename);
-        BufferedReader br = new BufferedReader(new FileReader(f));
-        String line = br.readLine();
-        while (line != null)
-        {
-            msg += line + "\n";
-            line = br.readLine();
-        }
-        br.close();
-
-        return msg;
-    }
-}
+package edu.mayo.bmi.test.preprocessor;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.net.URLDecoder;
+import java.util.Map;
+
+import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
+import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
+
+import junit.framework.TestCase;
+
+/**
+ * Unit tests for the ClinicalNotePreProcessor class.  These test the class
+ * against clinical note XML data and determine whether the preprocessor
+ * successfully parsed out the correct info.
+ * 
+ * @author Mayo Clinic
+ */
+public class ClinicalNotePreProcessorTest extends TestCase
+{
+    private ClinicalNotePreProcessor iv_cnotePreProcessor;
+    private String iv_cnoteXML;
+
+    /**
+     * Constructor for ClinicalNotePreProcessorTest.
+     * @param arg0
+     */
+    public ClinicalNotePreProcessorTest(String arg0)
+    {
+        super(arg0);
+    }
+
+    /*
+     * @see TestCase#setUp()
+     */
+    protected void setUp() throws Exception
+    {
+        super.setUp();
+
+        String dtdLocation = "resources/cda/NotesIIST_RTF.DTD";
+        File dtd = new File(dtdLocation);
+        iv_cnotePreProcessor = new ClinicalNotePreProcessor(dtd, false);
+
+		//String cnoteLocationOnCp = "/test/data/testpatient_cn_1.xml";
+		String cnoteLocationOnCp = "../../../../../data/testpatient_cn_1.xml";
+        String cnoteLocation =
+            URLDecoder.decode(getClass().getResource(cnoteLocationOnCp).getPath());
+        
+        if (cnoteLocation == null) {
+        	throw new FileNotFoundException("Unable to find: " + cnoteLocationOnCp);
+        }
+        iv_cnoteXML = load(cnoteLocation);
+    }
+
+    /*
+     * @see TestCase#tearDown()
+     */
+    protected void tearDown() throws Exception
+    {
+        super.tearDown();
+    }
+
+    /**
+     * Tests the process method.
+     */
+    public void testProcess()
+    {
+        try
+        {
+            DocumentMetaData dmd = iv_cnotePreProcessor.process(iv_cnoteXML);
+
+            // validate document properties
+            String docID = "000000000";
+            String serviceCode = "MNT";
+            Map docProperties = dmd.getMetaData();
+            String cnote_docID =
+                (String) docProperties.get(
+                    ClinicalNotePreProcessor.MD_KEY_DOC_ID);
+            String cnote_serviceCode =
+                (String) docProperties.get(
+                    ClinicalNotePreProcessor.MD_KEY_SERVICE_CODE);
+            assertEquals(docID, cnote_docID);
+            assertEquals(serviceCode, cnote_serviceCode);
+
+            // validate each section
+            // TODO Consider validating each section           
+        }
+        catch (Exception e)
+        {
+        	e.printStackTrace(System.err);
+            fail(e.getMessage());
+        }
+    }
+
+    /**
+     * Loads text from a file.
+     * @param filename
+     * @return
+     * @throws FileNotFoundException
+     * @throws IOException
+     */
+    private String load(String filename)
+        throws FileNotFoundException, IOException
+    {
+        String msg = "";
+        File f = new File(filename);
+        BufferedReader br = new BufferedReader(new FileReader(f));
+        String line = br.readLine();
+        while (line != null)
+        {
+            msg += line + "\n";
+            line = br.readLine();
+        }
+        br.close();
+
+        return msg;
+    }
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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
@@ -76,9 +70,9 @@ public class DependencyParseUtils {
 	 * @return
 	 */
 	public static ConllDependencyNode findAnnotationHead(JCas jcas, Annotation annotation) {
-	
+	
 	    for (ConllDependencyNode depNode : JCasUtil.selectCovered(jcas, ConllDependencyNode.class, annotation)) {
-	    	
+	    	
 	    	ConllDependencyNode head = depNode.getHead();
 	    	if (head == null || head.getEnd() <= annotation.getBegin() || head.getBegin() > annotation.getEnd()) {
 	    		// The head is outside the bounds of the annotation, so this node must be the annotation's head
@@ -115,9 +109,9 @@ public class DependencyParseUtils {
 			return path;
 		}
 		
-		// Join the two paths
+		// Join the two paths
 		if (!srcToAncestorPath.isEmpty()) {
-			srcToAncestorPath.removeLast();
+			srcToAncestorPath.removeLast();
 		}
 		path = srcToAncestorPath;
 		while (!tgtToAncestorPath.isEmpty()) {

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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
@@ -45,8 +39,8 @@ public class DependencyPathFeaturesExtra
 		List<Feature> features = new ArrayList<Feature>();
 		
 	    ConllDependencyNode node1 = DependencyParseUtils.findAnnotationHead(jCas, arg1);
-	    ConllDependencyNode node2 = DependencyParseUtils.findAnnotationHead(jCas, arg2);
-	    if (node1 == null || node2 == null) { return features; }
+	    ConllDependencyNode node2 = DependencyParseUtils.findAnnotationHead(jCas, arg2);
+	    if (node1 == null || node2 == null) { return features; }
 	    
 	    List<LinkedList<ConllDependencyNode>> paths = DependencyParseUtils.getPathsToCommonAncestor(node1, node2);
 	    LinkedList<ConllDependencyNode> path1 = paths.get(0);

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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
@@ -49,7 +43,7 @@ public class DependencyTreeFeaturesExtra
 	public List<Feature> extractForNode(JCas jCas, IdentifiedAnnotation mention, String ftrPrefix) {
 	    List<Feature> features = new ArrayList<Feature>();
 	    ConllDependencyNode mentionHeadNode = DependencyParseUtils.findAnnotationHead(jCas, mention);
-		
+		
 	    if (mentionHeadNode != null) {
 	    	ConllDependencyNode dependsOn = mentionHeadNode.getHead();
 	    	if (dependsOn != null) {
@@ -62,7 +56,7 @@ public class DependencyTreeFeaturesExtra
 	    		features.add(new Feature(ftrPrefix + "_HEAD_WORD-GOVERNING_WORD", String.format("%s-%s", mentionHeadNode.getCoveredText(), dependsOn.getCoveredText())));
 	    		features.add(new Feature(ftrPrefix + "_TYPE-GOVERNING_POS", String.format("%d-%s", mention.getTypeID(), dependsOn.getPostag())));
 	    		features.add(new Feature(ftrPrefix + "_HEAD_POS-GOVERNING_POS", String.format("%s-%s", mentionHeadNode.getPostag(), dependsOn.getPostag())));
-	    	}
+	    	}
 	    }
 	    return features;
 	}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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
@@ -50,4 +44,4 @@ public interface RelationFeaturesExtract
    */
   public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1, IdentifiedAnnotation arg2)
       throws AnalysisEngineProcessException;
-}
\ No newline at end of file
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Constants.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Constants.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Constants.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Constants.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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
@@ -109,4 +103,4 @@ public class GoldEntityReader extends JC
 				entityMention.addToIndexes();
 			}
 	}
-}
\ No newline at end of file
+}

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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

Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/data/CategoricalDistribution.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/data/CategoricalDistribution.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/data/CategoricalDistribution.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/data/CategoricalDistribution.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
 /*
  * Copyright: (c) 2012  Children's Hospital Boston, Regents of the University of Colorado 
  *
- * 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



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