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From chen...@apache.org
Subject svn commit: r1389618 [21/22] - 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
Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/cas_consumer/SideEffectSentenceCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/cas_consumer/SideEffectSentenceCasConsumer.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/cas_consumer/SideEffectSentenceCasConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/cas_consumer/SideEffectSentenceCasConsumer.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.sideeffect.cc.SideEffectSentenceCasConsumer</implementationName>
+<implementationName>org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer</implementationName>
 <processingResourceMetaData>
 <name>SideEffectSentenceCasConsumer</name>
 <description>Can write sentences containing side effects found by both SideEffectAnnotator (rule based) and SESentenceClassifierAnnotator (ML - C4.5). 

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectCPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectCPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectCPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectCPE.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>
@@ -70,7 +70,7 @@
         </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-side-effect/desc/cpe/SideEffectSentenceCPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectSentenceCPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectSentenceCPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectSentenceCPE.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>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectSentence_CDA_CPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectSentence_CDA_CPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectSentence_CDA_CPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffectSentence_CDA_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>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffect_CDA_CPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffect_CDA_CPE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffect_CDA_CPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/cpe/SideEffect_CDA_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>
@@ -70,7 +70,7 @@
         </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-side-effect/desc/type_system/SideEffectTypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/type_system/SideEffectTypeSystem.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/type_system/SideEffectTypeSystem.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/type_system/SideEffectTypeSystem.xml Mon Sep 24 22:04:51 2012
@@ -28,7 +28,7 @@
   </imports>
   <types>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.sideeffect.type.SideEffectAnnotation</name>
+      <name>org.apache.ctakes.sideeffect.type.SideEffectAnnotation</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -45,24 +45,24 @@
         <featureDescription>
           <name>sentence</name>
           <description>sentence containing side effect</description>
-          <rangeTypeName>edu.mayo.bmi.uima.sideeffect.type.SESentence</rangeTypeName>
+          <rangeTypeName>org.apache.ctakes.sideeffect.type.SESentence</rangeTypeName>
         </featureDescription>
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.sideeffect.type.PSESentence</name>
+      <name>org.apache.ctakes.sideeffect.type.PSESentence</name>
       <description>sentence(s) that contains potential side effect and causing drug</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.sideeffect.type.PSESentenceFeature</name>
+      <name>org.apache.ctakes.sideeffect.type.PSESentenceFeature</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
         <featureDescription>
           <name>pseSen</name>
           <description/>
-          <rangeTypeName>edu.mayo.bmi.uima.sideeffect.type.PSESentence</rangeTypeName>
+          <rangeTypeName>org.apache.ctakes.sideeffect.type.PSESentence</rangeTypeName>
         </featureDescription>
         <featureDescription>
           <name>features</name>
@@ -72,7 +72,7 @@
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.sideeffect.type.SESentence</name>
+      <name>org.apache.ctakes.sideeffect.type.SESentence</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>

Modified: incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/lookup/LookupDesc_sideEffect.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/lookup/LookupDesc_sideEffect.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/lookup/LookupDesc_sideEffect.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/lookup/LookupDesc_sideEffect.xml Mon Sep 24 22:04:51 2012
@@ -195,7 +195,7 @@
 	<lookupBindings>
 		<lookupBinding>
 			<dictionaryRef idRef="GAZ_UMLS_MS_2009"/>
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
 				<properties>
 					<property key="textMetaFields" value="text"/>
 					<property key="maxPermutationLevel" value="5"/>
@@ -203,7 +203,7 @@
 					<property key="exclusionTags" value="AUX,AUXD,AUXG,AUXN,AUXP,AUXZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</properties>
 			</lookupInitializer>
-			<lookupConsumer className="edu.mayo.bmi.uima.lookup.ae.UmlsToSnomedLuceneConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl">
 				<properties>
 					<property key="codingScheme" value="SNOMED"/>
 					<property key="cuiMetaField" value="cui"/>
@@ -221,7 +221,7 @@
 		</lookupBinding>
 		<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="5"/>
@@ -229,7 +229,7 @@
 					<property key="exclusionTags" value="AUX,AUXD,AUXG,AUXN,AUXP,AUXZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</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="code"/>
@@ -244,14 +244,14 @@
 		<!-- Supplement Terms for the side effect project -->
 		<lookupBinding>
 			<dictionaryRef idRef="GAZ_CSV_SE"/>												
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
 				<properties>
 					<property key="textMetaFields" value="1"/>
 					<property key="maxPermutationLevel" value="5"/>
 					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>		
 				</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="CT"/>
 					<property key="typeIdField" value="2"/>

Modified: incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/resources/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml Mon Sep 24 22:04:51 2012
@@ -195,7 +195,7 @@
 	<lookupBindings>
 		<lookupBinding>
 			<dictionaryRef idRef="DICT_UMLS_MS"/>
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
 				<properties>
 					<property key="textMetaFields" value="text"/>
 					<property key="maxPermutationLevel" value="5"/>
@@ -203,7 +203,7 @@
 					<property key="exclusionTags" value="AUX,AUXD,AUXG,AUXN,AUXP,AUXZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</properties>
 			</lookupInitializer>
-			<lookupConsumer className="edu.mayo.bmi.uima.lookup.ae.UmlsToSnomedDbConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl">
 				<properties>
 					<property key="codingScheme" value="SNOMED"/>
 					<property key="cuiMetaField" value="cui"/>
@@ -222,7 +222,7 @@
 		</lookupBinding>
 		<lookupBinding>
 			<dictionaryRef idRef="DICT_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="5"/>
@@ -230,7 +230,7 @@
 					<property key="exclusionTags" value="AUX,AUXD,AUXG,AUXN,AUXP,AUXZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</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="code"/>
@@ -245,14 +245,14 @@
 		<!-- Supplement Terms for the side effect project -->
 		<lookupBinding>
 			<dictionaryRef idRef="GAZ_CSV_SE"/>												
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
 				<properties>
 					<property key="textMetaFields" value="1"/>
 					<property key="maxPermutationLevel" value="5"/>
 					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>		
 				</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="CT"/>
 					<property key="typeIdField" value="2"/>

Copied: incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/PSESentenceAnnotator.java (from r1388196, incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/PSESentenceAnnotator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/PSESentenceAnnotator.java?p2=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/PSESentenceAnnotator.java&p1=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/PSESentenceAnnotator.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/PSESentenceAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/PSESentenceAnnotator.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.uima.sideeffect.ae;
+package org.apache.ctakes.sideeffect.ae;
 
 import java.util.HashSet;
 import java.util.Iterator;
@@ -29,11 +29,11 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.resource.ResourceInitializationException;
 
+import org.apache.ctakes.core.util.FSUtil;
+import org.apache.ctakes.sideeffect.util.SEUtil;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import edu.mayo.bmi.uima.core.util.FSUtil;
-import edu.mayo.bmi.uima.sideeffect.type.PSESentence;
-import edu.mayo.bmi.uima.sideeffect.util.SEUtil;
+import org.apache.ctakes.sideeffect.type.PSESentence;
 
 /**
  * Identify the sentence(s) that contains PSE (signs/symptoms or

Copied: incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceClassifierAnnotator.java (from r1388092, incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SESentenceClassifierAnnotator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceClassifierAnnotator.java?p2=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceClassifierAnnotator.java&p1=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SESentenceClassifierAnnotator.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SESentenceClassifierAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceClassifierAnnotator.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.uima.sideeffect.ae;
+package org.apache.ctakes.sideeffect.ae;
 
 import java.util.HashMap;
 import java.util.HashSet;
@@ -37,9 +37,9 @@ import org.apache.uima.analysis_engine.a
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.jcas.JCas;
 
-import edu.mayo.bmi.uima.sideeffect.type.PSESentenceFeature;
-import edu.mayo.bmi.uima.sideeffect.type.SESentence;
-import edu.mayo.bmi.uima.sideeffect.type.SideEffectAnnotation;
+import org.apache.ctakes.sideeffect.type.PSESentenceFeature;
+import org.apache.ctakes.sideeffect.type.SESentence;
+import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
 
 /**
  * Classify side effect sentences and add them to SESentence

Copied: incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java (from r1388196, incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SESentenceFeatureAnnotator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java?p2=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java&p1=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SESentenceFeatureAnnotator.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SESentenceFeatureAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.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.uima.sideeffect.ae;
+package org.apache.ctakes.sideeffect.ae;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -38,11 +38,11 @@ import org.apache.uima.jcas.JFSIndexRepo
 import org.apache.uima.jcas.cas.StringArray;
 import org.apache.uima.resource.ResourceInitializationException;
 
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.FSUtil;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
-import edu.mayo.bmi.uima.core.util.FSUtil;
-import edu.mayo.bmi.uima.sideeffect.type.PSESentence;
-import edu.mayo.bmi.uima.sideeffect.type.PSESentenceFeature;
+import org.apache.ctakes.sideeffect.type.PSESentence;
+import org.apache.ctakes.sideeffect.type.PSESentenceFeature;
 
 /**
  * Extract SE sentence (from PSESentence) features and add them to

Copied: incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java (from r1388196, incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SideEffectAnnotator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java?p2=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java&p1=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SideEffectAnnotator.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/ae/SideEffectAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.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.uima.sideeffect.ae;
+package org.apache.ctakes.sideeffect.ae;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -43,16 +43,17 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.core.resource.FileResource;
+
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.core.util.FSUtil;
+import org.apache.ctakes.sideeffect.util.PatternMatch;
+import org.apache.ctakes.sideeffect.util.SEUtil;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
-import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
-import edu.mayo.bmi.uima.core.util.FSUtil;
-import edu.mayo.bmi.uima.drugner.type.SubSectionAnnotation;
-import edu.mayo.bmi.uima.sideeffect.type.SESentence;
-import edu.mayo.bmi.uima.sideeffect.type.SideEffectAnnotation;
-import edu.mayo.bmi.uima.sideeffect.util.PatternMatch;
-import edu.mayo.bmi.uima.sideeffect.util.SEUtil;
+import org.apache.ctakes.drugner.type.SubSectionAnnotation;
+import org.apache.ctakes.sideeffect.type.SESentence;
+import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
 
 /**
  * Rule-based side effect extraction. 

Copied: incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java (from r1388092, incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/cc/SideEffectCasConsumer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java?p2=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java&p1=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/cc/SideEffectCasConsumer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/cc/SideEffectCasConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.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.uima.sideeffect.cc;
+package org.apache.ctakes.sideeffect.cc;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -24,6 +24,8 @@ import java.io.FileWriter;
 import java.io.IOException;
 import java.util.Iterator;
 
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.sideeffect.util.SEUtil;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CasConsumer_ImplBase;
 import org.apache.uima.jcas.JCas;
@@ -32,9 +34,7 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.ResourceProcessException;
 import org.apache.uima.util.ProcessTrace;
 
-import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
-import edu.mayo.bmi.uima.sideeffect.type.SideEffectAnnotation;
-import edu.mayo.bmi.uima.sideeffect.util.SEUtil;
+import org.apache.ctakes.sideeffect.type.SideEffectAnnotation;
 
 public class SideEffectCasConsumer extends CasConsumer_ImplBase {
 	public static final String PARAM_OUTPUT_FILE = "OutputFile";

Copied: incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java (from r1388092, incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/cc/SideEffectSentenceCasConsumer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java?p2=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java&p1=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/cc/SideEffectSentenceCasConsumer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/cc/SideEffectSentenceCasConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.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.uima.sideeffect.cc;
+package org.apache.ctakes.sideeffect.cc;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -24,6 +24,8 @@ import java.io.FileWriter;
 import java.io.IOException;
 import java.util.Iterator;
 
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.sideeffect.util.SEUtil;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CasConsumer_ImplBase;
 import org.apache.uima.jcas.JCas;
@@ -32,9 +34,7 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.ResourceProcessException;
 import org.apache.uima.util.ProcessTrace;
 
-import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
-import edu.mayo.bmi.uima.sideeffect.type.SESentence;
-import edu.mayo.bmi.uima.sideeffect.util.SEUtil;
+import org.apache.ctakes.sideeffect.type.SESentence;
 
 public class SideEffectSentenceCasConsumer extends CasConsumer_ImplBase {
 	public static final String PARAM_OUTPUT_FILE = "OutputFile";

Copied: incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/PatternMatch.java (from r1388092, incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/util/PatternMatch.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/PatternMatch.java?p2=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/PatternMatch.java&p1=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/util/PatternMatch.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/util/PatternMatch.java (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/PatternMatch.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.uima.sideeffect.util;
+package org.apache.ctakes.sideeffect.util;
 
 import java.util.List;
 import java.util.regex.Matcher;

Copied: incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.java (from r1388196, incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/util/SEUtil.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.java?p2=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.java&p1=incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/util/SEUtil.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/bmi/uima/sideeffect/util/SEUtil.java (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.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.uima.sideeffect.util;
+package org.apache.ctakes.sideeffect.util;
 
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -30,12 +30,12 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.jcas.tcas.Annotation;
 
+import org.apache.ctakes.core.util.FSUtil;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.util.FSUtil;
 
 /**
  * Utility methods used in the project

Modified: incubator/ctakes/trunk/ctakes-smoking-status/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/README?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/README (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/README Mon Sep 24 22:04:51 2012
@@ -78,7 +78,7 @@ Prerequisite steps
 
 	- Install all the cTAKES components, dependencies (e.g. JVM, UIMA, and Eclipse(optional)).
     
-	- Make sure the clinical documents pipeline of cTAKES and the Apache UIMA are setup correctly by running the CAS Visual Debugger (CVD) as 
+	- Make sure the ctakes-clinical-pipeline of cTAKES and the Apache UIMA are setup correctly by running the CAS Visual Debugger (CVD) as 
 	described in the 'Clinical Text	Analysis and Knowledge Extraction System User Guide' 1.2. Install from PEAR packages.
   
 	- Install the 'smoking status.pear' after completing the installation of the core and related pears, as per above.
@@ -113,7 +113,7 @@ java -cp ^
 %UIMA_HOME%/lib/uima-examples.jar;^
 smoking status/bin;^
 chunker/bin;^
-clinical documents pipeline/bin;^
+ctakes-clinical-pipeline/bin;^
 context dependent tokenizer/bin;^
 core/bin;^
 dictionary lookup/bin;^
@@ -135,7 +135,7 @@ document preprocessor/lib/xercesImpl.jar
 document preprocessor/lib/xml-apis.jar;^
 document preprocessor/lib/xmlParserAPIs.jar;^
 chunker/resources;^
-clinical documents pipeline/resources;^
+ctakes-clinical-pipeline/resources;^
 context dependent tokenizer/resources;^
 core/resources;^
 dictionary lookup/resources;^
@@ -188,7 +188,7 @@ smoking\ status/resources:\
 POS\ tagger/resources \
 org.apache.uima.tools.cpm.CpmFrame	 
 
-Step 2: From the pull down menu open the “Sample_SmokingStatus_output_flatfile.xml” via 'File' => 'Open CPE Descriptor' => 'smoking status/desc/collection_processing _engine/Sample_SmokingStatus_output_flatfile.xml'.
+Step 2: From the pull down menu open the �Sample_SmokingStatus_output_flatfile.xml� via 'File' => 'Open CPE Descriptor' => 'smoking status/desc/collection_processing _engine/Sample_SmokingStatus_output_flatfile.xml'.
 
 This will load the sample Collection Processing Engine (CPE) 'Sample_SmokingStatus_output_flatfile.xml'.  
 A sample CPE has been provided along with de-identified patient information to provide a means to test the pipeline after you have set up the environment. FYI.  '{inst-root-dir}/data/test' contains 5 sample notes representing one patients
@@ -268,13 +268,13 @@ Debugging issues
  #############
  
 One of the next releases will look into addressing the following:
-  - class 'edu.mayo.bmi.fsm.smoking.machine.NegationFSM.java' must inherit from 'core/edu.mayo.bmi.fsm.machine.NegationFSM.java'
-  - edu.mayo.bmi.smoking.context.negation.NegationContextAnalyzer - needs to use 'NE Contexts/edu.mayo.bmi.uima.context.negation.NegationContextAnalyzer'
+  - class 'edu.mayo.bmi.fsm.smoking.machine.NegationFSM.java' must inherit from 'core/org.apache.ctakes.core.fsm.machine.NegationFSM.java'
+  - org.apache.ctakes.smokingstatus.context.negation.NegationContextAnalyzer - needs to use 'NE Contexts/org.apache.ctakes.necontexts.negation.NegationContextAnalyzer'
   - ResolutionAnnotator.java references 'TypeSystemConst.NE_CERTAINTY_NEGATED' which has been commented out, uncomment in both places for next major release
   - FIXED -Parameters probably need to be changed? /smoking status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
   - FIXED - CdaCasInitializer.xml must be used from 'document preprocessor'
   - FIXED - SimulatedProdSmokingTAE.xml -> ExternalBaseAggregateTAE.xml -> ./SimpleSegmentAnnotator.xml -- need to reference the one in core 
-    edu.mayo.bmi.smoking.ae.SimpleSegmentAnnotator - must use core/edu.mayo.bmi.uima.core.ae.SimpleSegmentAnnotator.java
+    org.apache.ctakes.smokingstatus.ae.SimpleSegmentAnnotator - must use core/org.apache.ctakes.core.ae.SimpleSegmentAnnotator.java
     
    Version 1.2 Addendum
    - FIXED - The LibSVM features in the previous cTAKES version are not fed into the system in correct order and cause incorrect "past smoker", "current smoker", and "smoker" classification. The new version fixed this problem. 

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ArtificialSentenceAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ArtificialSentenceAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ArtificialSentenceAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ArtificialSentenceAnnotator.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.core.ae.CopyAnnotator</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.core.ae.CopyAnnotator</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>ArtificialSentenceAnnotator</name>
 <description>Artificially creates a new SentenceAnnotation object by treating the entire document as a sentence.  The offset values from the DocumentAnnotation object are transferred over to the new SentenceAnnotation object.</description>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.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.smoking.ae.ClassifiableEntries</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.ClassifiableEntries</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>ClassigiableEntriesAnnotator</name>
     <description>Converts Sentences to ClassifiableEntries (required by SmokingStatus pipeline) and ultimately to RecordSentence.
@@ -42,7 +42,7 @@ This param is optional.  If not specifie
       </configurationParameter>
       <configurationParameter>
         <name>AllowedClassifications</name>
-        <description>See edu.mayo.bmi.smoking.Const.java for permitted string values.</description>
+        <description>See org.apache.ctakes.smokingstatus.Const.java for permitted string values.</description>
         <type>String</type>
         <multiValued>true</multiValued>
         <mandatory>false</mandatory>
@@ -106,19 +106,19 @@ This param is optional.  If not specifie
     <externalResourceDependency>
       <key>UimaDescriptorStep1Key</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>UimaDescriptorStep2Key</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>negationContradictionWordsKey</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
   </externalResourceDependencies>
@@ -130,7 +130,7 @@ This param is optional.  If not specifie
         <fileResourceSpecifier>
           <fileUrl>file:analysis_engine/ProductionPostSentenceAggregate_step1.xml</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>UimaDescriptorStep2</name>
@@ -138,7 +138,7 @@ This param is optional.  If not specifie
         <fileResourceSpecifier>
           <fileUrl>file:analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>negationContradictionWords</name>
@@ -146,7 +146,7 @@ This param is optional.  If not specifie
         <fileResourceSpecifier>
           <fileUrl>file:ss/data/context/negationContradictionWords.txt</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE.xml Mon Sep 24 22:04:51 2012
@@ -24,16 +24,16 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentDetectAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.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>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE_CDA.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE_CDA.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE_CDA.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE_CDA.xml Mon Sep 24 22:04:51 2012
@@ -24,16 +24,16 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.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="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.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.smoking.ae.KuRuleBasedClassifierAnnotator</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>KuRuleBasedClassifierAnnotator</name>
 <description>Known vs Unknow classifier using smoking related keywords</description>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.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>NonsmokerDictionaryLookupAnnotator</name>
 <description>Performs nonsmoker dictionary lookup and stores the hits as NonsmokerNamedEntityAnnotation objects.</description>
@@ -59,13 +59,13 @@
 <externalResourceDependency>
 <key>LookupDescriptor</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 <externalResourceDependency>
 <key>NonSmokerDictionary</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -77,7 +77,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:ss/data/SmokingStatusLookupConfig.xml</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 <externalResource>
 <name>DictionaryFileNonSmoker</name>
@@ -85,7 +85,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:ss/data/nonsmoker.dictionary</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.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.smoking.ae.PcsClassifierAnnotator_libsvm</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>PcsClassifierAnnotator_libsvm</name>
 <description>PCS classifier using libsvm. This annotator plays the same role as PcsBOWFeatureAnnotator.xml, PcsClassifierAnnotator.xml, and BOWFeatureRemovalAnnotator.xml, which use Weka.</description>
@@ -75,19 +75,19 @@
 <externalResourceDependency>
 <key>PathOfModel</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 <externalResourceDependency>
 <key>StopWordsFile</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 <externalResourceDependency>
 <key>PCSKeyWordFile</key>
 <description/>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -99,7 +99,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:ss/data/PCS/pcs_libsvm-2.91.model</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 <externalResource>
 <name>PCSKeyWordFileResc</name>
@@ -107,7 +107,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:ss/data/PCS/keywords_PCS.txt</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 <externalResource>
 <name>StopWordsFileResc</name>
@@ -115,7 +115,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:ss/data/PCS/stopwords_PCS.txt</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml Mon Sep 24 22:04:51 2012
@@ -24,13 +24,13 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="KuRuleBasedClassifierAnnotator">
       <import location="KuRuleBasedClassifierAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ResolutionAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ResolutionAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ResolutionAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ResolutionAnnotator.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.smoking.ae.ResolutionAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>ResolutionAnnotator</name>
     <description>Resolves the data produced by the KU classifier, negation detection, and PCS

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SentenceAdjuster.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SentenceAdjuster.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SentenceAdjuster.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SentenceAdjuster.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.watson.ibm.com/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.smoking.ae.SentenceAdjuster</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.SentenceAdjuster</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>Sentence Adjuster</name>
     <description>This annotator expands sentence annotations of type "Tobacco: none" to allow the correct negation  recognition of the relevant NEs.</description>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SentenceDetectorAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SentenceDetectorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SentenceDetectorAnnotator.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.core.ae.SentenceDetector</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.core.ae.SentenceDetector</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>Sentence Detector annotator</name>
     <description>Discovers sentence boundaries.</description>
@@ -80,7 +80,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:sentdetect/sdmed.mod</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.SuffixMaxentModelResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.SuffixMaxentModelResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.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>Performs dictionary lookup and stores the hits as NamedEntityAnnotation objects. </description>
@@ -57,19 +57,19 @@
 <externalResourceDependency>
 <key>LookupDescriptor</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 <externalResourceDependency>
 <key>SmokerDictionary</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 <externalResourceDependency>
 <key>NonSmokerDictionary</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -81,7 +81,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:ss/data/SmokingStatusLookupConfig.xml</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 <externalResource>
 <name>DictionaryFileSmoker</name>
@@ -89,7 +89,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:ss/data/smoker.dictionary</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 <externalResource>
 <name>DictionaryFileNonSmoker</name>
@@ -97,7 +97,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:ss/data/nonsmoker.dictionary</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/cas_consumer/RecordResolutionCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/cas_consumer/RecordResolutionCasConsumer.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/cas_consumer/RecordResolutionCasConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/cas_consumer/RecordResolutionCasConsumer.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.smoking.cc.RecordResolutionCasConsumer</implementationName>
+<implementationName>org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer</implementationName>
 <processingResourceMetaData>
 <name>RecordResolutionCasConsumer</name>
 <description>Iterates over all sentences (each CAS equals one sentence) for a record and

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/I2b2TypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/I2b2TypeSystem.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/I2b2TypeSystem.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/I2b2TypeSystem.xml Mon Sep 24 22:04:51 2012
@@ -25,7 +25,7 @@
 <version>1.0</version>
 <types>
 <typeDescription>
-<name>edu.mayo.bmi.smoking.i2b2.type.RecordSentence</name>
+<name>org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence</name>
 <description>Represents a single sentence from an I2B2 record.</description>
 <supertypeName>uima.tcas.Annotation</supertypeName>
 <features>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml Mon Sep 24 22:04:51 2012
@@ -31,7 +31,7 @@
   </imports>
   <types>
     <typeDescription>
-      <name>edu.mayo.bmi.smoking.i2b2.type.RecordSentence</name>
+      <name>org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence</name>
       <description>Represents a single sentence from an I2B2 record.</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -58,17 +58,17 @@
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.SmokingStatus.type.SmokerNamedEntityAnnotation</name>
+      <name>org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation</name>
       <description/>
       <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.SmokingStatus.type.NonSmokerNamedEntityAnnotation</name>
+      <name>org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation</name>
       <description/>
       <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.smoking.type.SmokingDocumentClassification</name>
+      <name>org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification</name>
       <description>Represents classification related to the document</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -85,7 +85,7 @@
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.SmokingStatus.type.UnknownSmokerNamedEntityAnnotation</name>
+      <name>org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation</name>
       <description/>
       <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
     </typeDescription>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/metadata/install.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/metadata/install.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/metadata/install.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/metadata/install.xml Mon Sep 24 22:04:51 2012
@@ -39,7 +39,7 @@
 			<ACTION>set_env_variable</ACTION>
 			<PARAMETERS>
 				<COMMENTS></COMMENTS>
-				<VAR_VALUE>$main_root/bin;/Applications/eclipse/plugins/org.junit_4.8.1.v4_8_1_v20100427-1100/junit.jar;/Applications/eclipse/plugins/org.hamcrest.core_1.1.0.v20090501071000.jar;$main_root/bin;$main_root/../core/bin;$main_root/../core/resources;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/trove.jar;$main_root/../core/lib/OpenAI_FSM.jar;/Applications/apache-uima/lib/uimaj-bootstrap.jar;/Applications/apache-uima/lib/uima-tools.jar;/Applications/apache-uima/lib/uima-examples.jar;/Applications/apache-uima/lib/uima-document-annotation.jar;/Applications/apache-uima/lib/uima-cpe.jar;/Applications/apache-uima/lib/uima-core.jar;/Applications/apache-uima/lib/uima-adapter-vinci.jar;/Applications/apache-uima/lib/uima-adapter-soap.jar;/Applications/apache-uima/lib/jVinci.jar;/Applications/eclipse/plugins/o
 rg.junit_4.8.1.v4_8_1_v20100427-1100/junit.jar;/Applications/eclipse/plugins/org.hamcrest.core_1.1.0.v20090501071000.jar;$main_root/../core/lib/MIRUtility.jar;$main_root/../NE contexts/bin;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../context dependent tokenizer/bin;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../LVG/bin;$main_root/../LVG/resources;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/resources;$main_root/desc;$main_root/../clinical documents pipeline/bin;$main_root/../clinical documents pipeline/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/lib/log4j-1.2.8.jar;$main_root/../document preprocessor/resources;$main_root/../document preprocessor/lib/xercesImpl.jar;$main_root/../document preprocessor/lib/xml-apis.jar;$main_root/../document preprocessor/lib/xmlParserAPIs.jar;$main_root/lib/libsvm-2
 .91.jar;$main_root/lib/lucene-core-3.0.2.jar;$main_root/resources;$main_root/desc;$main_root/lib/libsvm-2.91.jar;$main_root/lib/lucene-core-3.0.2.jar;</VAR_VALUE>
+				<VAR_VALUE>$main_root/bin;/Applications/eclipse/plugins/org.junit_4.8.1.v4_8_1_v20100427-1100/junit.jar;/Applications/eclipse/plugins/org.hamcrest.core_1.1.0.v20090501071000.jar;$main_root/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/resources;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;/Applications/apache-uima/lib/uimaj-bootstrap.jar;/Applications/apache-uima/lib/uima-tools.jar;/Applications/apache-uima/lib/uima-examples.jar;/Applications/apache-uima/lib/uima-document-annotation.jar;/Applications/apache-uima/lib/uima-cpe.jar;/Applications/apache-uima/lib/uima-core.jar;/Applications/apache-uima/lib/uima-adapter-vinci.jar;/Applications/apache-uima/lib/uima-adapter-soap.jar;/Applicat
 ions/apache-uima/lib/jVinci.jar;/Applications/eclipse/plugins/org.junit_4.8.1.v4_8_1_v20100427-1100/junit.jar;/Applications/eclipse/plugins/org.hamcrest.core_1.1.0.v20090501071000.jar;$main_root/../ctakes-core/lib/MIRUtility.jar;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/resources;$main_root/desc;$main_root/../ctakes-clinical-pipeline/bin;$main_root/../ctakes-clinical-pipeline/resources;$main_root/../ctakes-preprocessor/bin;$main_root/../ctakes-preprocessor/lib/log4j-1.2.8.jar;$main_root/../ctakes-preprocessor/resources;$main_root/../ctakes-preprocessor/lib/xercesImpl.jar;$main_root/
 ../ctakes-preprocessor/lib/xml-apis.jar;$main_root/../ctakes-preprocessor/lib/xmlParserAPIs.jar;$main_root/lib/libsvm-2.91.jar;$main_root/lib/lucene-core-3.0.2.jar;$main_root/resources;$main_root/desc;$main_root/lib/libsvm-2.91.jar;$main_root/lib/lucene-core-3.0.2.jar;</VAR_VALUE>
 				<VAR_NAME>CLASSPATH</VAR_NAME>
 			</PARAMETERS>
 		</PROCESS>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/metadata/setenv.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/metadata/setenv.txt?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/metadata/setenv.txt (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/metadata/setenv.txt Mon Sep 24 22:04:51 2012
@@ -2,6 +2,6 @@
 ### to appropriate existing environment variables
 ### to run the smoking status component
 
-CLASSPATH=$main_root/bin;/Applications/eclipse/plugins/org.junit_4.8.1.v4_8_1_v20100427-1100/junit.jar;/Applications/eclipse/plugins/org.hamcrest.core_1.1.0.v20090501071000.jar;$main_root/bin;$main_root/../core/bin;$main_root/../core/resources;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/trove.jar;$main_root/../core/lib/OpenAI_FSM.jar;/Applications/apache-uima/lib/uimaj-bootstrap.jar;/Applications/apache-uima/lib/uima-tools.jar;/Applications/apache-uima/lib/uima-examples.jar;/Applications/apache-uima/lib/uima-document-annotation.jar;/Applications/apache-uima/lib/uima-cpe.jar;/Applications/apache-uima/lib/uima-core.jar;/Applications/apache-uima/lib/uima-adapter-vinci.jar;/Applications/apache-uima/lib/uima-adapter-soap.jar;/Applications/apache-uima/lib/jVinci.jar;/Applications/eclipse/plugins/org.ju
 nit_4.8.1.v4_8_1_v20100427-1100/junit.jar;/Applications/eclipse/plugins/org.hamcrest.core_1.1.0.v20090501071000.jar;$main_root/../core/lib/MIRUtility.jar;$main_root/../NE contexts/bin;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../context dependent tokenizer/bin;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../LVG/bin;$main_root/../LVG/resources;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/resources;$main_root/desc;$main_root/../clinical documents pipeline/bin;$main_root/../clinical documents pipeline/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/lib/log4j-1.2.8.jar;$main_root/../document preprocessor/resources;$main_root/../document preprocessor/lib/xercesImpl.jar;$main_root/../document preprocessor/lib/xml-apis.jar;$main_root/../document preprocessor/lib/xmlParserAPIs.jar;$main_root/lib/libsvm-2.91.j
 ar;$main_root/lib/lucene-core-3.0.2.jar;$main_root/resources;$main_root/desc;$main_root/lib/libsvm-2.91.jar;$main_root/lib/lucene-core-3.0.2.jar;
+CLASSPATH=$main_root/bin;/Applications/eclipse/plugins/org.junit_4.8.1.v4_8_1_v20100427-1100/junit.jar;/Applications/eclipse/plugins/org.hamcrest.core_1.1.0.v20090501071000.jar;$main_root/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/resources;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;/Applications/apache-uima/lib/uimaj-bootstrap.jar;/Applications/apache-uima/lib/uima-tools.jar;/Applications/apache-uima/lib/uima-examples.jar;/Applications/apache-uima/lib/uima-document-annotation.jar;/Applications/apache-uima/lib/uima-cpe.jar;/Applications/apache-uima/lib/uima-core.jar;/Applications/apache-uima/lib/uima-adapter-vinci.jar;/Applications/apache-uima/lib/uima-adapter-soap.jar;/Applications/
 apache-uima/lib/jVinci.jar;/Applications/eclipse/plugins/org.junit_4.8.1.v4_8_1_v20100427-1100/junit.jar;/Applications/eclipse/plugins/org.hamcrest.core_1.1.0.v20090501071000.jar;$main_root/../ctakes-core/lib/MIRUtility.jar;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/resources;$main_root/desc;$main_root/../ctakes-clinical-pipeline/bin;$main_root/../ctakes-clinical-pipeline/resources;$main_root/../ctakes-preprocessor/bin;$main_root/../ctakes-preprocessor/lib/log4j-1.2.8.jar;$main_root/../ctakes-preprocessor/resources;$main_root/../ctakes-preprocessor/lib/xercesImpl.jar;$main_root/../ct
 akes-preprocessor/lib/xml-apis.jar;$main_root/../ctakes-preprocessor/lib/xmlParserAPIs.jar;$main_root/lib/libsvm-2.91.jar;$main_root/lib/lucene-core-3.0.2.jar;$main_root/resources;$main_root/desc;$main_root/lib/libsvm-2.91.jar;$main_root/lib/lucene-core-3.0.2.jar;
 #PATH=/Users/m039575/Documents/ctakes_workspace/smoking status/bin
 #uima.datapath=

Modified: incubator/ctakes/trunk/ctakes-smoking-status/resources/ss/data/SmokingStatusLookupConfig.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/resources/ss/data/SmokingStatusLookupConfig.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/resources/ss/data/SmokingStatusLookupConfig.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/resources/ss/data/SmokingStatusLookupConfig.xml Mon Sep 24 22:04:51 2012
@@ -41,10 +41,10 @@
 	<lookupBindings>
 		<lookupBinding>
 			<dictionaryRef idRef="GAZ_SMOKING_STATUS"/>
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.DirectLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl">
 				<properties/>
 			</lookupInitializer>
-			<lookupConsumer className="edu.mayo.bmi.uima.lookup.ae.SmokerNamedEntityLookupConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.SmokerNamedEntityLookupConsumerImpl">
 				<properties>
 					<property key="codingScheme" value="NONE"/>
 					<property key="codeMetaField" value="0"/>
@@ -53,10 +53,10 @@
 		</lookupBinding>
 		<lookupBinding>
 			<dictionaryRef idRef="GAZ_NONSMOKING_STATUS"/>
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.DirectLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl">
 				<properties/>
 			</lookupInitializer>
-			<lookupConsumer className="edu.mayo.bmi.uima.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl">
 				<properties>
 					<property key="codingScheme" value="NONE"/>
 					<property key="codeMetaField" value="0"/>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/fsm/smoking/machine/NegationFSM.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/fsm/smoking/machine/NegationFSM.java?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/fsm/smoking/machine/NegationFSM.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/fsm/smoking/machine/NegationFSM.java Mon Sep 24 22:04:51 2012
@@ -25,17 +25,18 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import org.apache.ctakes.core.fsm.condition.DisjoinCondition;
+import org.apache.ctakes.core.fsm.condition.NegateCondition;
+import org.apache.ctakes.core.fsm.condition.TextSetCondition;
+import org.apache.ctakes.core.fsm.output.NegationIndicator;
+import org.apache.ctakes.core.fsm.state.NamedState;
+import org.apache.ctakes.core.fsm.state.NonTerminalEndState;
+import org.apache.ctakes.core.fsm.token.BaseToken;
+
 import net.openai.util.fsm.AnyCondition;
 import net.openai.util.fsm.Condition;
 import net.openai.util.fsm.Machine;
 import net.openai.util.fsm.State;
-import edu.mayo.bmi.fsm.condition.DisjoinCondition;
-import edu.mayo.bmi.fsm.condition.NegateCondition;
-import edu.mayo.bmi.fsm.condition.TextSetCondition;
-import edu.mayo.bmi.fsm.output.NegationIndicator;
-import edu.mayo.bmi.fsm.state.NamedState;
-import edu.mayo.bmi.fsm.state.NonTerminalEndState;
-import edu.mayo.bmi.fsm.token.BaseToken;
 
 /**
  * Uses one or more finite state machines to detect dates in the given input of

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.java (from r1388092, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/Const.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/Const.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/Const.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.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.smoking;
+package org.apache.ctakes.smokingstatus;
 
 /**
  * Constants used by the SmokingStatus project.

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java (from r1388092, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/MLutil/GenerateTrainingData.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/MLutil/GenerateTrainingData.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/MLutil/GenerateTrainingData.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.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.smoking.MLutil;
+package org.apache.ctakes.smokingstatus.MLutil;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -32,7 +32,8 @@ import java.util.List;
 import java.util.Set;
 import java.util.StringTokenizer;
 
-import edu.mayo.bmi.smoking.Const;
+import org.apache.ctakes.smokingstatus.Const;
+
 
 public class GenerateTrainingData {
 	Set<String> keywords;

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/ClassifiableEntries.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/ClassifiableEntries.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/ClassifiableEntries.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java Mon Sep 24 22:04:51 2012
@@ -19,7 +19,7 @@
 /**
  * 
  */
-package edu.mayo.bmi.smoking.ae;
+package org.apache.ctakes.smokingstatus.ae;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -53,13 +53,14 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.util.CasCreationUtils;
 import org.apache.uima.util.XMLInputSource;
 
-import edu.mayo.bmi.smoking.Const;
-import edu.mayo.bmi.smoking.i2b2.type.RecordSentence;
+import org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence;
 
-import edu.mayo.bmi.smoking.type.SmokingDocumentClassification;
-import edu.mayo.bmi.smoking.util.ClassifiableEntry;
-import edu.mayo.bmi.smoking.util.TruthValue;
-import edu.mayo.bmi.uima.core.resource.FileResource;
+import org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification;
+
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.smokingstatus.Const;
+import org.apache.ctakes.smokingstatus.util.ClassifiableEntry;
+import org.apache.ctakes.smokingstatus.util.TruthValue;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
@@ -629,7 +630,7 @@ public class ClassifiableEntries extends
 	private Map<Integer, TruthValue> iv_truthMap;
 
 	// set of classification values of type java.lang.String
-	// see edu.mayo.bmi.smoking.Const for proper String values
+	// see org.apache.ctakes.smokingstatus.Const for proper String values
 	private Set<String> iv_allowedClassifications;
 
 	private AnalysisEngine taeStep1;

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/KuRuleBasedClassifierAnnotator.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/KuRuleBasedClassifierAnnotator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/KuRuleBasedClassifierAnnotator.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/KuRuleBasedClassifierAnnotator.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/KuRuleBasedClassifierAnnotator.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/KuRuleBasedClassifierAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/KuRuleBasedClassifierAnnotator.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.smoking.ae;
+package org.apache.ctakes.smokingstatus.ae;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -31,9 +31,10 @@ import org.apache.uima.analysis_componen
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.resource.ResourceInitializationException;
-import edu.mayo.bmi.smoking.Const;
-import edu.mayo.bmi.uima.SmokingStatus.type.UnknownSmokerNamedEntityAnnotation;
-import edu.mayo.bmi.uima.core.resource.FileLocator;
+import org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation;
+
+import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.smokingstatus.Const;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import edu.mayo.bmi.uima.libsvm.type.NominalAttributeValue;
 

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifierAnnotator_libsvm.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/PcsClassifierAnnotator_libsvm.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifierAnnotator_libsvm.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifierAnnotator_libsvm.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/PcsClassifierAnnotator_libsvm.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/PcsClassifierAnnotator_libsvm.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifierAnnotator_libsvm.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.smoking.ae;
+package org.apache.ctakes.smokingstatus.ae;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -39,8 +39,9 @@ import org.apache.uima.jcas.JFSIndexRepo
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.smoking.Const;
-import edu.mayo.bmi.uima.core.resource.FileResource;
+
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.smokingstatus.Const;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import edu.mayo.bmi.uima.libsvm.type.NominalAttributeValue;
 



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