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From chen...@apache.org
Subject svn commit: r1389618 [14/22] - in /incubator/ctakes/trunk: ./ ctakes-chunker/ ctakes-chunker/desc/ ctakes-chunker/resources/launch/ ctakes-chunker/src/main/java/edu/ ctakes-chunker/src/main/java/org/ ctakes-chunker/src/main/java/org/apache/ ctakes-chun...
Date Mon, 24 Sep 2012 22:05:23 GMT
Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/PermutationUtil.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/algorithms/PermutationUtil.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/PermutationUtil.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/PermutationUtil.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/algorithms/PermutationUtil.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/algorithms/PermutationUtil.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/PermutationUtil.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.lookup.algorithms;
+package org.apache.ctakes.dictionary.lookup.algorithms;
 
 import java.util.ArrayList;
 import java.util.Collection;

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/CollectionFilter.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/CollectionFilter.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/CollectionFilter.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/CollectionFilter.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/CollectionFilter.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/CollectionFilter.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/CollectionFilter.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
 import java.util.Collection;
 

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/FilterException.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/FilterException.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/FilterException.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/FilterException.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/FilterException.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/FilterException.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/FilterException.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
 /**
  *

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/MetaDataPostLookupFilterImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/MetaDataPostLookupFilterImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/MetaDataPostLookupFilterImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/MetaDataPostLookupFilterImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/MetaDataPostLookupFilterImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/MetaDataPostLookupFilterImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/MetaDataPostLookupFilterImpl.java Mon Sep 24 22:04:51 2012
@@ -16,11 +16,11 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
-import edu.mayo.bmi.dictionary.DictionaryEngine;
-import edu.mayo.bmi.dictionary.DictionaryException;
-import edu.mayo.bmi.dictionary.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.DictionaryEngine;
+import org.apache.ctakes.dictionary.lookup.DictionaryException;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
 
 /**
  *

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilter.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PostLookupFilter.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilter.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilter.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PostLookupFilter.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PostLookupFilter.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilter.java Mon Sep 24 22:04:51 2012
@@ -16,9 +16,9 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
-import edu.mayo.bmi.dictionary.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
 
 /**
  *

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilterGroupImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PostLookupFilterGroupImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilterGroupImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilterGroupImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PostLookupFilterGroupImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PostLookupFilterGroupImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilterGroupImpl.java Mon Sep 24 22:04:51 2012
@@ -16,9 +16,9 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
-import edu.mayo.bmi.dictionary.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
 
 /**
  * Groups multiple PostLookupFilter objects together and applies boolean logic

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PreLookupFilter.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PreLookupFilter.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PreLookupFilter.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PreLookupFilter.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PreLookupFilter.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/PreLookupFilter.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PreLookupFilter.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
 /**
  *

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/SetValuePostLookupFilterImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/SetValuePostLookupFilterImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/SetValuePostLookupFilterImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/SetValuePostLookupFilterImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/SetValuePostLookupFilterImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/SetValuePostLookupFilterImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/SetValuePostLookupFilterImpl.java Mon Sep 24 22:04:51 2012
@@ -16,10 +16,10 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
-import edu.mayo.bmi.dictionary.MetaDataHit;
-import edu.mayo.bmi.dictionary.MetaDataHitConst;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.MetaDataHitConst;
 
 /**
  * A filter that uses a value to filter against a MetaDataHit.

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/StringPreLookupFilterImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/StringPreLookupFilterImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/StringPreLookupFilterImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/StringPreLookupFilterImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/StringPreLookupFilterImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/StringPreLookupFilterImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/StringPreLookupFilterImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
 import java.util.Set;
 

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/TruncateCollectionFilterImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/TruncateCollectionFilterImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/TruncateCollectionFilterImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/TruncateCollectionFilterImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/TruncateCollectionFilterImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/filter/TruncateCollectionFilterImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/TruncateCollectionFilterImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.filter;
+package org.apache.ctakes.dictionary.lookup.filter;
 
 import java.util.ArrayList;
 import java.util.Collection;

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/jdbc/JdbcDictionaryImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/jdbc/JdbcDictionaryImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/jdbc/JdbcDictionaryImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/jdbc/JdbcDictionaryImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/jdbc/JdbcDictionaryImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/jdbc/JdbcDictionaryImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/jdbc/JdbcDictionaryImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.jdbc;
+package org.apache.ctakes.dictionary.lookup.jdbc;
 
 import java.sql.Connection;
 import java.sql.PreparedStatement;
@@ -29,11 +29,12 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Set;
 
-import edu.mayo.bmi.dictionary.BaseDictionaryImpl;
-import edu.mayo.bmi.dictionary.Dictionary;
-import edu.mayo.bmi.dictionary.DictionaryException;
-import edu.mayo.bmi.dictionary.GenericMetaDataHitImpl;
-import edu.mayo.bmi.dictionary.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl;
+import org.apache.ctakes.dictionary.lookup.Dictionary;
+import org.apache.ctakes.dictionary.lookup.DictionaryException;
+import org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
+
 
 /**
  *

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/lucene/LuceneDictionaryImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/lucene/LuceneDictionaryImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/lucene/LuceneDictionaryImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.lucene;
+package org.apache.ctakes.dictionary.lookup.lucene;
 
 import java.io.IOException;
 import java.util.BitSet;
@@ -24,6 +24,10 @@ import java.util.Collection;
 import java.util.HashSet;
 import java.util.Set;
 
+import org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl;
+import org.apache.ctakes.dictionary.lookup.Dictionary;
+import org.apache.ctakes.dictionary.lookup.DictionaryException;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
 import org.apache.log4j.Logger;
 import org.apache.lucene.analysis.KeywordAnalyzer;
 import org.apache.lucene.analysis.standard.StandardAnalyzer;
@@ -39,10 +43,6 @@ import org.apache.lucene.search.TopDocs;
 import org.apache.lucene.search.WildcardQuery;
 import org.apache.lucene.util.Version;
 
-import edu.mayo.bmi.dictionary.BaseDictionaryImpl;
-import edu.mayo.bmi.dictionary.Dictionary;
-import edu.mayo.bmi.dictionary.DictionaryException;
-import edu.mayo.bmi.dictionary.MetaDataHit;
 
 /**
  *

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDocumentMetaDataHitImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/lucene/LuceneDocumentMetaDataHitImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDocumentMetaDataHitImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDocumentMetaDataHitImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/lucene/LuceneDocumentMetaDataHitImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/lucene/LuceneDocumentMetaDataHitImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDocumentMetaDataHitImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.lucene;
+package org.apache.ctakes.dictionary.lookup.lucene;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -26,12 +26,12 @@ import java.util.List;
 import java.util.ListIterator;
 import java.util.Set;
 
+import org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.document.Field;
 import org.apache.lucene.document.Fieldable;
 
-import edu.mayo.bmi.dictionary.BaseMetaDataHitImpl;
-import edu.mayo.bmi.dictionary.MetaDataHit;
 
 /**
  * 

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/PhraseBuilder.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/phrasebuilder/PhraseBuilder.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/PhraseBuilder.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/PhraseBuilder.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/phrasebuilder/PhraseBuilder.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/phrasebuilder/PhraseBuilder.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/PhraseBuilder.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.lookup.phrasebuilder;
+package org.apache.ctakes.dictionary.lookup.phrasebuilder;
 
 import java.util.List;
 

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/VariantPhraseBuilderImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/phrasebuilder/VariantPhraseBuilderImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/VariantPhraseBuilderImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/VariantPhraseBuilderImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/phrasebuilder/VariantPhraseBuilderImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/phrasebuilder/VariantPhraseBuilderImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/VariantPhraseBuilderImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.lookup.phrasebuilder;
+package org.apache.ctakes.dictionary.lookup.phrasebuilder;
 
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -24,7 +24,8 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
-import edu.mayo.bmi.lookup.vo.LookupToken;
+import org.apache.ctakes.dictionary.lookup.vo.LookupToken;
+
 
 /**
  * Builds phrases based on various variants of a LookupToken. For instance, a

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraint.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/FieldConstraint.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraint.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraint.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/FieldConstraint.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/FieldConstraint.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraint.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.strtable;
+package org.apache.ctakes.dictionary.lookup.strtable;
 
 /**
  * Defines when a row should NOT be added to a StringTable object. If a field

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/FieldConstraintImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/FieldConstraintImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/FieldConstraintImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java Mon Sep 24 22:04:51 2012
@@ -20,7 +20,7 @@
  * Created on May 20, 2005
  *
  */
-package edu.mayo.bmi.dictionary.strtable;
+package org.apache.ctakes.dictionary.lookup.strtable;
 
 /**
  * @author Mayo Clinic

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTable.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTable.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTable.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTable.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTable.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTable.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTable.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.strtable;
+package org.apache.ctakes.dictionary.lookup.strtable;
 
 import java.util.Collection;
 import java.util.HashMap;

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableDictionaryImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableDictionaryImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableDictionaryImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableDictionaryImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableDictionaryImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableDictionaryImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableDictionaryImpl.java Mon Sep 24 22:04:51 2012
@@ -16,16 +16,17 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.strtable;
+package org.apache.ctakes.dictionary.lookup.strtable;
 
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.Set;
 
-import edu.mayo.bmi.dictionary.BaseDictionaryImpl;
-import edu.mayo.bmi.dictionary.Dictionary;
-import edu.mayo.bmi.dictionary.DictionaryException;
-import edu.mayo.bmi.dictionary.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl;
+import org.apache.ctakes.dictionary.lookup.Dictionary;
+import org.apache.ctakes.dictionary.lookup.DictionaryException;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
+
 
 /**
  *

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableFactory.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableFactory.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableFactory.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableFactory.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableFactory.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableFactory.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableFactory.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.strtable;
+package org.apache.ctakes.dictionary.lookup.strtable;
 
 import java.io.BufferedReader;
 import java.io.IOException;

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRow.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableRow.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRow.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRow.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableRow.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableRow.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRow.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.strtable;
+package org.apache.ctakes.dictionary.lookup.strtable;
 
 import java.util.Collection;
 import java.util.HashMap;

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRowMetaDataHitImpl.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableRowMetaDataHitImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRowMetaDataHitImpl.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRowMetaDataHitImpl.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableRowMetaDataHitImpl.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/dictionary/strtable/StringTableRowMetaDataHitImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRowMetaDataHitImpl.java Mon Sep 24 22:04:51 2012
@@ -16,13 +16,14 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.dictionary.strtable;
+package org.apache.ctakes.dictionary.lookup.strtable;
 
 import java.util.Collection;
 import java.util.Set;
 
-import edu.mayo.bmi.dictionary.BaseMetaDataHitImpl;
-import edu.mayo.bmi.dictionary.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
+
 
 /**
  * 

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotation.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupAnnotation.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotation.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotation.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupAnnotation.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupAnnotation.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotation.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.lookup.vo;
+package org.apache.ctakes.dictionary.lookup.vo;
 
 /**
  * Value object that models a text annotation.

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotationToTokAdapter.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupAnnotationToTokAdapter.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotationToTokAdapter.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotationToTokAdapter.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupAnnotationToTokAdapter.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupAnnotationToTokAdapter.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotationToTokAdapter.java Mon Sep 24 22:04:51 2012
@@ -20,12 +20,13 @@
  * Created on Aug 24, 2005
  *
  */
-package edu.mayo.bmi.lookup.vo;
+package org.apache.ctakes.dictionary.lookup.vo;
 
 import java.util.HashMap;
 import java.util.Map;
 
-import edu.mayo.bmi.nlp.tokenizer.Token;
+import org.apache.ctakes.core.nlp.tokenizer.Token;
+
 
 /**
  * @author Mayo Clinic

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupHit.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupHit.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupHit.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupHit.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupHit.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupHit.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupHit.java Mon Sep 24 22:04:51 2012
@@ -16,14 +16,15 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.lookup.vo;
+package org.apache.ctakes.dictionary.lookup.vo;
 
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
-import edu.mayo.bmi.dictionary.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
+
 
 /**
  * Represents a single hit found by a lookup algorithm. Meta data returned by

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupToken.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupToken.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupToken.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupToken.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupToken.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupToken.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupToken.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.lookup.vo;
+package org.apache.ctakes.dictionary.lookup.vo;
 
 
 /**

Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupTokenComparator.java (from r1388092, incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupTokenComparator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupTokenComparator.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupTokenComparator.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupTokenComparator.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/lookup/vo/LookupTokenComparator.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupTokenComparator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.lookup.vo;
+package org.apache.ctakes.dictionary.lookup.vo;
 
 import java.util.Comparator;
 

Modified: incubator/ctakes/trunk/ctakes-drug-ner/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/README?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/README (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/README Mon Sep 24 22:04:51 2012
@@ -18,11 +18,11 @@ This project utilizes various cTAKES com
 
 
 ############################################################################
-Running the clinical documents pipeline
+Running the ctakes-clinical-pipeline
 ############################################################################
 
 This project (or PEAR file), the "Drug NER", relies on other projects/PEAR files such as 
-'clinical documents pipeline', 'context dependent tokenizer', 'core', 'dictionary lookup',
+'ctakes-clinical-pipeline', 'context dependent tokenizer', 'core', 'dictionary lookup',
 'LVG' and 'NE contexts'.
 
 

Modified: incubator/ctakes/trunk/ctakes-drug-ner/data/output/doc0.sample_output
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/data/output/doc0.sample_output?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/data/output/doc0.sample_output (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/data/output/doc0.sample_output Mon Sep 24 22:04:51 2012
@@ -1 +1 @@

[... 5 lines stripped ...]
Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>DictionaryLookupAnnotator</name>
     <description/>
@@ -55,13 +55,13 @@
     <externalResourceDependency>
       <key>LookupDescriptor</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>RxnormIndexReader</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
   </externalResourceDependencies>
@@ -73,7 +73,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:lookup/LookupDesc_DrugNER.xml</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>RxnormIndex</name>
@@ -112,7 +112,7 @@
             </configurationParameterSettings>
           </resourceMetaData>
         </configurableDataResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.lookup.ae.UmlsDictionaryLookupAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>UmlsDictionaryLookupAnnotator</name>
     <description/>
@@ -127,13 +127,13 @@
     <externalResourceDependency>
       <key>LookupDescriptor</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>RxnormIndexReader</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
   </externalResourceDependencies>
@@ -145,7 +145,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:lookup/LookupDesc_DrugNER.xml</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>RxnormIndex</name>
@@ -184,7 +184,7 @@
             </configurationParameterSettings>
           </resourceMetaData>
         </configurableDataResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregateCDAProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregateCDAProcessor.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregateCDAProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregateCDAProcessor.xml Mon Sep 24 22:04:51 2012
@@ -27,25 +27,25 @@
       <import location="DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="CdaCasInitializer">
-      <import location="../../../document preprocessor/desc/CdaCasInitializer.xml"/>
+      <import location="../../../ctakes-preprocessor/desc/CdaCasInitializer.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugLookupWindowAnnotator">
       <import location="DrugLookupWindowAnnotator.xml"/>
@@ -54,10 +54,10 @@
       <import location="DictionaryLookupAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>
@@ -89,7 +89,7 @@
         <inputs>
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.DocumentID</type>
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.drugner.type.DrugMentionAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.drugner.type.DrugMentionAnnotation</type>
         </inputs>
         <outputs/>
         <outputSofas>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregateCDAUMLSProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregateCDAUMLSProcessor.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregateCDAUMLSProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregateCDAUMLSProcessor.xml Mon Sep 24 22:04:51 2012
@@ -27,25 +27,25 @@
       <import location="DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="CdaCasInitializer">
-      <import location="../../../document preprocessor/desc/CdaCasInitializer.xml"/>
+      <import location="../../../ctakes-preprocessor/desc/CdaCasInitializer.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugLookupWindowAnnotator">
       <import location="DrugLookupWindowAnnotator.xml"/>
@@ -54,10 +54,10 @@
       <import location="DictionaryLookupAnnotatorUMLS.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>
@@ -89,7 +89,7 @@
         <inputs>
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.DocumentID</type>
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.drugner.type.DrugMentionAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.drugner.type.DrugMentionAnnotation</type>
         </inputs>
         <outputs/>
         <outputSofas>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml Mon Sep 24 22:04:51 2012
@@ -27,22 +27,22 @@
       <import location="DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DictionaryLookupAnnotator">
       <import location="DictionaryLookupAnnotator.xml"/>
@@ -51,13 +51,13 @@
       <import location="DrugLookupWindowAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SimpleSegmentAnnotator">
-      <import location="../../../core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml Mon Sep 24 22:04:51 2012
@@ -27,22 +27,22 @@
       <import location="DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DictionaryLookupAnnotator">
       <import location="DictionaryLookupAnnotatorUMLS.xml"/>
@@ -51,13 +51,13 @@
       <import location="DrugLookupWindowAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SimpleSegmentAnnotator">
-      <import location="../../../core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.ner.ae.CopyDrugAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.drugner.ae.CopyDrugAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>CNP to DrugLookupWindow</name>
     <description>Copies Shallow Parse CNP annotations to be used as lookup windows for dictionary lookup.</description>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -24,13 +24,13 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="NP2LookupWindow">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/NP2LookupWindow.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugCNP2LookupWindow">
       <import location="DrugCNP2LookupWindow.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="MaxLookupWindows">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/MaxLookupWindows.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.ner.ae.DrugMentionAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.drugner.ae.DrugMentionAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>DrugMentionAnnotator</name>
     <description>Generates DrugMentions and related attributes such as strength, dosage, frequency, etc.</description>
@@ -127,10 +127,10 @@
           <type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.drugner.type.RangeAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.drugner.type.MeasurementAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.drugner.type.FractionAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.drugner.type.DrugMentionAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.drugner.type.RangeAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.drugner.type.MeasurementAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.drugner.type.FractionAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.drugner.type.DrugMentionAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -104,13 +104,13 @@
 <nameValuePair>
 <name>ContextInitializerClass</name>
 <value>
-<string>edu.mayo.bmi.uima.ner.ae.impl.NegContextInitializerImpl</string>
+<string>org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ContextConsumerClass</name>
 <value>
-<string>edu.mayo.bmi.uima.ner.ae.impl.NegContextConsumerImpl</string>
+<string>org.apache.ctakes.drugner.ae.impl.NegContextConsumerImpl</string>
 </value>
 </nameValuePair>
 </configurationParameterSettings>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml Mon Sep 24 22:04:51 2012
@@ -21,7 +21,7 @@
 -->
 <casConsumerDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-  <implementationName>edu.mayo.bmi.uima.ner.cc.ConsumeNamedEntityRecordModel</implementationName>
+  <implementationName>org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel</implementationName>
   <processingResourceMetaData>
     <name>ConsumeNamedEntityRecord</name>
     <description>Processes a given CAS to identify predetermined list of NER items</description>
@@ -87,7 +87,7 @@
     <typeSystemDescription>
       <imports>
         <import location="../type_system/NERTypeSystem.xml"/>
-        <import location="../../../clinical documents pipeline/desc/CDAToTextTypeSystem.xml"/>
+        <import location="../../../ctakes-clinical-pipeline/desc/CDAToTextTypeSystem.xml"/>
       </imports>
     </typeSystemDescription>
     <typePriorities/>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml Mon Sep 24 22:04:51 2012
@@ -23,13 +23,13 @@
 <collectionReader>
 <collectionIterator>
 <descriptor>
-<import location="../../../core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
+<import location="../../../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
 </descriptor>
 <configurationParameterSettings>
 <nameValuePair>
 <name>InputDirectory</name>
 <value>
-<string>/path_to_your_workspace/Drug NER/data</string>
+<string>/path_to_your_workspace/ctakes-drug-ner/data</string>
 </value>
 </nameValuePair>
 </configurationParameterSettings>
@@ -50,7 +50,7 @@
 </casProcessor>
 <casProcessor deployment="integrated" name="XCAS Writer CAS Consumer">
 <descriptor>
-<import location="../../../core/desc/cas_consumer/XCasWriterCasConsumer.xml"/>
+<import location="../../../ctakes-core/desc/cas_consumer/XCasWriterCasConsumer.xml"/>
 </descriptor>
 <deploymentParameters/>
 <errorHandling>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml Mon Sep 24 22:04:51 2012
@@ -23,7 +23,7 @@
     <collectionReader>
         <collectionIterator>
             <descriptor>
-                <import location="../../../core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
+                <import location="../../../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
             </descriptor>
             <configurationParameterSettings>
                 <nameValuePair>
@@ -50,7 +50,7 @@
         </casProcessor>
         <casProcessor deployment="integrated" name="XCAS Writer CAS Consumer">
             <descriptor>
-                <import location="../../../core/desc/cas_consumer/XCasWriterCasConsumer.xml"/>
+                <import location="../../../ctakes-core/desc/cas_consumer/XCasWriterCasConsumer.xml"/>
             </descriptor>
             <deploymentParameters/>
             <errorHandling>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/type_system/NERTypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/type_system/NERTypeSystem.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/type_system/NERTypeSystem.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/type_system/NERTypeSystem.xml Mon Sep 24 22:04:51 2012
@@ -28,17 +28,17 @@
   </imports>
   <types>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.FrequencyAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.FrequencyAnnotation</name>
       <description>The frequency determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.DurationAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.DurationAnnotation</name>
       <description>The duration determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.RouteAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.RouteAnnotation</name>
       <description>The route determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -50,27 +50,27 @@
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.SuffixStrengthAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.SuffixStrengthAnnotation</name>
       <description>The suffix portion of dosage strength determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.FractionStrengthAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.FractionStrengthAnnotation</name>
       <description>The fraction portion of dosages strength determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.RangeStrengthAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.RangeStrengthAnnotation</name>
       <description>The range portion of dosages stength determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.DecimalStrengthAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.DecimalStrengthAnnotation</name>
       <description>The decimal portion of dosages stength determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.DrugChangeStatusAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation</name>
       <description>The change status of dosages determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -82,22 +82,22 @@
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.DosagesAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.DosagesAnnotation</name>
       <description>The dosage determination for the Drug NER profile.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.StrengthAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.StrengthAnnotation</name>
       <description>Holds the value representing the unit of the drug dosage.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.StrengthUnitAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.StrengthUnitAnnotation</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.FrequencyUnitAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.FrequencyUnitAnnotation</name>
       <description>The value represents the unit portion of the drug frequency.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -109,12 +109,12 @@
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.FormAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.FormAnnotation</name>
       <description>The value represents the form portion of the drug mention.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.SubSectionAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.SubSectionAnnotation</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -151,7 +151,7 @@
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.DrugMentionAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.DrugMentionAnnotation</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -315,7 +315,7 @@ Strongly encouraged to use bold text</de
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.drugner.type.ChunkAnnotation</name>
+      <name>org.apache.ctakes.drugner.type.ChunkAnnotation</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/metadata/install.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/metadata/install.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/metadata/install.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/metadata/install.xml Mon Sep 24 22:04:51 2012
@@ -39,7 +39,7 @@
 			<ACTION>set_env_variable</ACTION>
 			<PARAMETERS>
 				<COMMENTS></COMMENTS>
-				<VAR_VALUE>$main_root/bin;$main_root/resources;$main_root/../core/resources;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/trove.jar;$main_root/../POS tagger/resources;$main_root/../POS tagger/bin;$main_root/../LVG/bin;$main_root/../LVG/resources;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../chunker/resources;$main_root/../context dependent tokenizer/bin;$main_root/../NE contexts/bin;$main_root/../chunker/bin;$main_root/../core/bin;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;</VAR_VALUE>
+				<VAR_VALUE>$main_root/bin;$main_root/resources;$main_root/../ctakes-core/resources;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-dictionary-lookup/resources;</VAR_VALUE>
 				<VAR_NAME>CLASSPATH</VAR_NAME>
 			</PARAMETERS>
 		</PROCESS>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch Mon Sep 24 22:04:51 2012
@@ -2,13 +2,13 @@
 <launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
 <stringAttribute key="bad_container_name" value="//resources/launch"/>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/Drug NER"/>
+<listEntry value="/ctakes-drug-ner"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
 <listEntry value="4"/>
 </listAttribute>
 <booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
 <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="Drug NER"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-drug-ner"/>
 <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx1024M"/>
 </launchConfiguration>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CVD--Drug NER.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CVD--Drug%20NER.launch?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CVD--Drug NER.launch (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CVD--Drug NER.launch Mon Sep 24 22:04:51 2012
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/Drug NER"/>
+<listEntry value="/ctakes-drug-ner"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
 <listEntry value="4"/>
@@ -10,6 +10,6 @@
 <stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
 <stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
 <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="Drug NER"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-drug-ner"/>
 <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="&quot;-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties&quot;  -Xms500M -Xmx900M"/>
 </launchConfiguration>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/resources/lookup/LookupDesc_DrugNER.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/resources/lookup/LookupDesc_DrugNER.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/resources/lookup/LookupDesc_DrugNER.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/resources/lookup/LookupDesc_DrugNER.xml Mon Sep 24 22:04:51 2012
@@ -128,7 +128,7 @@
 	<lookupBindings>
 		<lookupBinding>
 			<dictionaryRef idRef="GAZ_RXNORM"/>
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
 				<properties>
 					<property key="textMetaFields" value="preferred_designation|other_designation"/>
 					<property key="maxPermutationLevel" value="3"/>
@@ -136,7 +136,7 @@
 					<property key="exclusionTags" value="CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"/> <!-- ohnlp ID# 3378705 -->
 				</properties>
 			</lookupInitializer>
-			<lookupConsumer className="edu.mayo.bmi.uima.lookup.ae.NamedEntityLookupConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl">
 				<properties>
 					<property key="codingScheme" value="RXNORM"/>
 					<property key="codeMetaField" value="codeRxNorm"/> <!--  change this to value="code" for UMLS CUIs -->



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