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From chen...@apache.org
Subject svn commit: r1388196 [8/12] - in /incubator/ctakes/trunk: ctakes-chunker/desc/ ctakes-chunker/src/main/java/edu/mayo/bmi/uima/adjuster/ ctakes-chunker/src/main/java/edu/mayo/bmi/uima/chunker/ ctakes-chunker/test/data/output/ ctakes-chunker/test/desc/ c...
Date Thu, 20 Sep 2012 20:25:58 GMT
Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc.xml (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc.xml Thu Sep 20 20:25:49 2012
@@ -57,8 +57,8 @@
 				<properties>
 					<property key="textMetaFields" value="text"/>
 					<property key="maxPermutationLevel" value="5"/>
-					<!--	<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.Sentence"/> -->
-					<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation"/>  
+					<!--	<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/> -->
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>  
 					<property key="exclusionTags" value="VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</properties>
 			</lookupInitializer>
@@ -85,8 +85,8 @@
 				<properties>
 					<property key="textMetaFields" value="preferred_designation|other_designation"/>
 					<property key="maxPermutationLevel" value="7"/>
-					<!--	<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.Sentence"/> -->
-					<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation"/>  
+					<!--	<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/> -->
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>  
 					<property key="exclusionTags" value="VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</properties>
 			</lookupInitializer>

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc_Db.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc_Db.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc_Db.xml (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc_Db.xml Thu Sep 20 20:25:49 2012
@@ -58,8 +58,8 @@
 				<properties>
 					<property key="textMetaFields" value="text"/>
 					<property key="maxPermutationLevel" value="7"/>
-					<!--	<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.Sentence"/> -->
-					<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation"/>  
+					<!--	<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/> -->
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>  
 					<property key="exclusionTags" value="VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</properties>
 			</lookupInitializer>
@@ -84,8 +84,8 @@
 				<properties>
 					<property key="textMetaFields" value="preferred_designation|other_designation"/>
 					<property key="maxPermutationLevel" value="7"/>
-					<!--	<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.Sentence"/> -->
-					<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation"/>  
+					<!--	<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/> -->
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>  
 					<property key="exclusionTags" value="VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</properties>
 			</lookupInitializer>

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc_csv_sample.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc_csv_sample.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc_csv_sample.xml (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/resources/lookup/LookupDesc_csv_sample.xml Thu Sep 20 20:25:49 2012
@@ -65,7 +65,7 @@
 				<properties>
 					<property key="textMetaFields" value="preferred_designation|other_designation"/>
 					<property key="maxPermutationLevel" value="7"/>
-					<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>
 					<property key="exclusionTags" value="VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,RP,TO,WDT,WP,WPS,WRB"/>
 				</properties>
 			</lookupInitializer>

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/DirectLookupInitializerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/DirectLookupInitializerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/DirectLookupInitializerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/DirectLookupInitializerImpl.java Thu Sep 20 20:25:49 2012
@@ -36,13 +36,13 @@ import edu.mayo.bmi.lookup.algorithms.Lo
 import edu.mayo.bmi.lookup.phrasebuilder.PhraseBuilder;
 import edu.mayo.bmi.lookup.phrasebuilder.VariantPhraseBuilderImpl;
 import edu.mayo.bmi.lookup.vo.LookupToken;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.ContractionToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
-import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 
 /**
  * @author Mayo Clinic

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java Thu Sep 20 20:25:49 2012
@@ -41,12 +41,12 @@ import edu.mayo.bmi.lookup.algorithms.Lo
 import edu.mayo.bmi.lookup.phrasebuilder.PhraseBuilder;
 import edu.mayo.bmi.lookup.phrasebuilder.VariantPhraseBuilderImpl;
 import edu.mayo.bmi.lookup.vo.LookupToken;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.ContractionToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import edu.mayo.bmi.uima.core.util.JCasUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/NamedEntityLookupConsumerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/NamedEntityLookupConsumerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/NamedEntityLookupConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/NamedEntityLookupConsumerImpl.java Thu Sep 20 20:25:49 2012
@@ -31,12 +31,12 @@ import org.apache.uima.jcas.cas.FSArray;
 
 import edu.mayo.bmi.dictionary.MetaDataHit;
 import edu.mayo.bmi.lookup.vo.LookupHit;
-import edu.mayo.bmi.uima.core.type.refsem.OntologyConcept;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.EventMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention;
-import edu.mayo.bmi.uima.core.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
+import org.apache.ctakes.typesystem.type.constants.CONST;
 
 /**
  * @author Mayo Clinic

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/OrangeBookFilterConsumerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/OrangeBookFilterConsumerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/OrangeBookFilterConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/OrangeBookFilterConsumerImpl.java Thu Sep 20 20:25:49 2012
@@ -39,11 +39,11 @@ import org.apache.uima.jcas.cas.FSArray;
 import edu.mayo.bmi.dictionary.MetaDataHit;
 import edu.mayo.bmi.lookup.vo.LookupHit;
 import edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResource;
-import edu.mayo.bmi.uima.core.type.refsem.OntologyConcept;
-import edu.mayo.bmi.uima.core.type.textsem.EventMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention;
-import edu.mayo.bmi.uima.core.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
+import org.apache.ctakes.typesystem.type.constants.CONST;
 
 /**
  * Implementation that takes Rxnorm dictionary lookup hits and stores only the

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/UmlsToSnomedConsumerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/UmlsToSnomedConsumerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/UmlsToSnomedConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/edu/mayo/bmi/uima/lookup/ae/UmlsToSnomedConsumerImpl.java Thu Sep 20 20:25:49 2012
@@ -37,11 +37,11 @@ import org.apache.uima.jcas.cas.FSArray;
 import edu.mayo.bmi.dictionary.DictionaryException;
 import edu.mayo.bmi.dictionary.MetaDataHit;
 import edu.mayo.bmi.lookup.vo.LookupHit;
-import edu.mayo.bmi.uima.core.type.refsem.UmlsConcept;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.constants.CONST;
 
 /**
  * Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity 

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -36,8 +36,8 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
         </inputs>
         <outputs>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.NamedEntity</type>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -108,8 +108,8 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
         </inputs>
         <outputs>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.NamedEntity</type>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -87,8 +87,8 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.DocumentID</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+          <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>
         </inputs>
         <outputs/>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -87,8 +87,8 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.DocumentID</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+          <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>
         </inputs>
         <outputs/>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -115,13 +115,13 @@
       <description>For subiterator</description>
       <version>1.0</version>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Segment</type>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
       </priorityList>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
       </priorityList>
     </typePriorities>
     <fsIndexCollection/>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -115,13 +115,13 @@
       <description>For subiterator</description>
       <version>1.0</version>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Segment</type>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
       </priorityList>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
       </priorityList>
     </typePriorities>
     <fsIndexCollection/>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -61,7 +61,7 @@
       <nameValuePair>
         <name>srcDrugObjClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.syntax.NP</string>
+          <string>org.apache.ctakes.typesystem.type.syntax.NP</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -114,10 +114,10 @@
       <capability>
         <inputs>
           <type allAnnotatorFeatures="true">uima.tt.CNPAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation</type>
         </outputs>
         <languagesSupported/>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -59,7 +59,7 @@
           <type allAnnotatorFeatures="true">uima.tt.NPListAnnotation</type>
           <type allAnnotatorFeatures="true">uima.tt.NPAnnotation</type>
           <type allAnnotatorFeatures="true">uima.tt.CNPAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.chunker.type.NP</type>
         </inputs>
         <outputs>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -108,13 +108,13 @@
       <nameValuePair>
         <name>DISTANCE_ANN_TYPE</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+          <string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>STATUS_BOUNDARY_ANN_TYPE</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+          <string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
         </value>
       </nameValuePair>
     </configurationParameterSettings>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -122,7 +122,7 @@
 <capability>
 <inputs>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.common.types.NamedEntityAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.ctx.types.ContextAnnotation</type>

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=1388196&r1=1388195&r2=1388196&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 Thu Sep 20 20:25:49 2012
@@ -95,7 +95,7 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
         </inputs>
         <outputs/>
         <inputSofas>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/DrugMention.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/DrugMention.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/DrugMention.java (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/DrugMention.java Thu Sep 20 20:25:49 2012
@@ -28,7 +28,7 @@ import edu.mayo.bmi.fsm.ner.output.eleme
 import edu.mayo.bmi.fsm.ner.output.elements.FrequencyUnitToken;
 import edu.mayo.bmi.fsm.ner.output.elements.RouteToken;
 import edu.mayo.bmi.fsm.output.DateToken;
-import edu.mayo.bmi.uima.core.type.textsem.DateAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
 import edu.mayo.bmi.uima.core.util.FSUtil;
 import edu.mayo.bmi.uima.drugner.type.DosagesAnnotation;
 import edu.mayo.bmi.uima.drugner.type.DrugChangeStatusAnnotation;

Modified: incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/ae/CopyDrugAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/ae/CopyDrugAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/ae/CopyDrugAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/ae/CopyDrugAnnotator.java Thu Sep 20 20:25:49 2012
@@ -127,8 +127,8 @@ public class CopyDrugAnnotator extends J
 	{
 		// iterate over source objects in JCas
 		JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-		Iterator srcObjItr = indexes.getAnnotationIndex(edu.mayo.bmi.uima.core.type.textspan.Segment.type).iterator();
-		edu.mayo.bmi.uima.core.type.textspan.Segment segment = null;
+		Iterator srcObjItr = indexes.getAnnotationIndex(org.apache.ctakes.typesystem.type.textspan.Segment.type).iterator();
+		org.apache.ctakes.typesystem.type.textspan.Segment segment = null;
 		
 		while (srcObjItr.hasNext())
 		{
@@ -145,7 +145,7 @@ public class CopyDrugAnnotator extends J
                 boolean segmentMissing = iv_skipSegmentsSet.isEmpty();
 				if (!segmentMissing){
 					Iterator getSkipSegs = iv_skipSegmentsSet.iterator();
-					segment = (edu.mayo.bmi.uima.core.type.textspan.Segment) srcObj;
+					segment = (org.apache.ctakes.typesystem.type.textspan.Segment) srcObj;
 					while (getSkipSegs.hasNext()  && !okayToSkip){
 						if (getSkipSegs.next().equals(segment.getId())){
 
@@ -172,9 +172,9 @@ public class CopyDrugAnnotator extends J
 				if (okayToSkip) {
 					destObj.addToIndexes();
 				} else {
-					Iterator lookupWindows = FSUtil.getAnnotationsInSpanIterator(jcas, edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation.type, segment.getBegin(), segment.getEnd());
+					Iterator lookupWindows = FSUtil.getAnnotationsInSpanIterator(jcas, org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation.type, segment.getBegin(), segment.getEnd());
 					while (lookupWindows.hasNext()){
-						edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation lookup = (edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation) lookupWindows.next();
+						org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation lookup = (org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation) lookupWindows.next();
 						edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation drugLookup = new edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation(jcas, lookup.getBegin(), lookup.getEnd());
 						drugLookup.addToIndexes();
 					}

Modified: incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/ae/DrugMentionAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/ae/DrugMentionAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/ae/DrugMentionAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/ae/DrugMentionAnnotator.java Thu Sep 20 20:25:49 2012
@@ -82,32 +82,32 @@ import edu.mayo.bmi.uima.core.fsm.adapte
 import edu.mayo.bmi.uima.core.fsm.adapters.PunctuationTokenAdapter;
 import edu.mayo.bmi.uima.core.fsm.adapters.SymbolTokenAdapter;
 import edu.mayo.bmi.uima.core.fsm.adapters.WordTokenAdapter;
-import edu.mayo.bmi.uima.core.type.refsem.Date;
-import edu.mayo.bmi.uima.core.type.refsem.MedicationDosage;
-import edu.mayo.bmi.uima.core.type.refsem.MedicationDuration;
-import edu.mayo.bmi.uima.core.type.refsem.MedicationForm;
-import edu.mayo.bmi.uima.core.type.refsem.MedicationFrequency;
-import edu.mayo.bmi.uima.core.type.refsem.MedicationRoute;
-import edu.mayo.bmi.uima.core.type.refsem.MedicationStatusChange;
-import edu.mayo.bmi.uima.core.type.refsem.MedicationStrength;
-import edu.mayo.bmi.uima.core.type.refsem.OntologyConcept;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.ContractionToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.NumToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.type.textsem.DateAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.refsem.Date;
+import org.apache.ctakes.typesystem.type.refsem.MedicationDosage;
+import org.apache.ctakes.typesystem.type.refsem.MedicationDuration;
+import org.apache.ctakes.typesystem.type.refsem.MedicationForm;
+import org.apache.ctakes.typesystem.type.refsem.MedicationFrequency;
+import org.apache.ctakes.typesystem.type.refsem.MedicationRoute;
+import org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange;
+import org.apache.ctakes.typesystem.type.refsem.MedicationStrength;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.NumToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import edu.mayo.bmi.uima.core.util.DateParser;
 import edu.mayo.bmi.uima.core.util.FSUtil;
 import edu.mayo.bmi.uima.core.util.JCasUtil;
 import edu.mayo.bmi.uima.core.util.ParamUtil;
-import edu.mayo.bmi.uima.core.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.constants.CONST;
 import edu.mayo.bmi.uima.drugner.type.ChunkAnnotation;
 import edu.mayo.bmi.uima.drugner.type.DecimalStrengthAnnotation;
 import edu.mayo.bmi.uima.drugner.type.DosagesAnnotation;
@@ -127,7 +127,7 @@ import edu.mayo.bmi.uima.drugner.type.Su
 import edu.mayo.bmi.uima.ner.DrugMention;
 import edu.mayo.bmi.uima.ner.elements.DrugChangeStatusElement;
 
-import static edu.mayo.bmi.uima.core.type.constants.CONST.*;
+import static org.apache.ctakes.typesystem.type.constants.CONST.*;
 
 
 /**

Modified: incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/cc/ConsumeNamedEntityRecordModel.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/cc/ConsumeNamedEntityRecordModel.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/cc/ConsumeNamedEntityRecordModel.java (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/edu/mayo/bmi/uima/ner/cc/ConsumeNamedEntityRecordModel.java Thu Sep 20 20:25:49 2012
@@ -45,17 +45,17 @@ import org.apache.uima.jcas.cas.TOP;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.ResourceProcessException;
 
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
-import edu.mayo.bmi.uima.core.type.refsem.Date;
-import edu.mayo.bmi.uima.core.type.refsem.MedicationStrength;
-import edu.mayo.bmi.uima.core.type.refsem.OntologyConcept;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.refsem.Date;
+import org.apache.ctakes.typesystem.type.refsem.MedicationStrength;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import edu.mayo.bmi.uima.core.util.FSUtil;
 import edu.mayo.bmi.uima.drugner.type.ChunkAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention;
-import edu.mayo.bmi.uima.core.type.util.Pair;
-import edu.mayo.bmi.uima.core.type.util.Pairs;
+import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
+import org.apache.ctakes.typesystem.type.util.Pair;
+import org.apache.ctakes.typesystem.type.util.Pairs;
 //import edu.mayo.bmi.uima.drugner.type.DrugMentionAnnotation;
 import edu.mayo.bmi.uima.drugner.type.SubSectionAnnotation;
 

Modified: incubator/ctakes/trunk/ctakes-lvg/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-lvg/README?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-lvg/README (original)
+++ incubator/ctakes/trunk/ctakes-lvg/README Thu Sep 20 20:25:49 2012
@@ -75,5 +75,5 @@ The parameters are:
   LemmaCacheFileFrequencyCutoff - 
 
 Note: as distributed, PostLemmas is set to false.  This is done to reduce the size of the CAS.
-Set PostLemmas to true to have edu.mayo.bmi.uima.core.type.Lemma annotations added to the CAS. 
+Set PostLemmas to true to have org.apache.ctakes.typesystem.type.Lemma annotations added to the CAS. 
 

Modified: incubator/ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -216,10 +216,10 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.WordToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.WordToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken</type>
 </outputs>
 <languagesSupported/>
 </capability>

Modified: incubator/ctakes/trunk/ctakes-lvg/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-lvg/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-lvg/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-lvg/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgAnnotator.java Thu Sep 20 20:25:49 2012
@@ -18,9 +18,9 @@
  */
 package edu.mayo.bmi.uima.lvg.ae;
 
-import edu.mayo.bmi.uima.core.type.syntax.Lemma;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.syntax.Lemma;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
 import edu.mayo.bmi.uima.core.util.ListFactory;
 import edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource;
 import gov.nih.nlm.nls.lvg.Api.LvgCmdApi;

Modified: incubator/ctakes/trunk/ctakes-lvg/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgBaseTokenAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-lvg/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgBaseTokenAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-lvg/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgBaseTokenAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-lvg/src/main/java/edu/mayo/bmi/uima/lvg/ae/LvgBaseTokenAnnotator.java Thu Sep 20 20:25:49 2012
@@ -18,9 +18,9 @@
  */
 package edu.mayo.bmi.uima.lvg.ae;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.Lemma;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.Lemma;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
 import edu.mayo.bmi.uima.core.util.ListFactory;
 import edu.mayo.bmi.uima.lvg.resource.LvgCmdApiResource;
 import gov.nih.nlm.nls.lvg.Api.LvgCmdApi;

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/desc/NegationAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/desc/NegationAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/desc/NegationAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/desc/NegationAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -110,19 +110,19 @@
 <nameValuePair>
 <name>WindowAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>FocusAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</string>
+<string>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ContextAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+<string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -141,8 +141,8 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/desc/StatusAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/desc/StatusAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/desc/StatusAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/desc/StatusAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -110,19 +110,19 @@
 <nameValuePair>
 <name>WindowAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>FocusAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</string>
+<string>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ContextAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+<string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -141,9 +141,9 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Sentence</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Sentence</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextHitConsumer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextHitConsumer.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextHitConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextHitConsumer.java Thu Sep 20 20:25:49 2012
@@ -22,7 +22,7 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.textsem.ContextAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.ContextAnnotation;
 
 
 public abstract class NamedEntityContextHitConsumer implements ContextHitConsumer {

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextHitConsumer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextHitConsumer.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextHitConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextHitConsumer.java Thu Sep 20 20:25:49 2012
@@ -22,7 +22,7 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import edu.mayo.bmi.uima.context.ContextHitConsumer;
 import edu.mayo.bmi.uima.context.ContextHit;
 import edu.mayo.bmi.uima.context.NamedEntityContextHitConsumer;

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextHitConsumer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextHitConsumer.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextHitConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextHitConsumer.java Thu Sep 20 20:25:49 2012
@@ -22,7 +22,7 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import edu.mayo.bmi.uima.context.ContextHitConsumer;
 import edu.mayo.bmi.uima.context.ContextHit;
 import edu.mayo.bmi.uima.context.NamedEntityContextHitConsumer;

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/NegationAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/NegationAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/NegationAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/NegationAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -110,19 +110,19 @@
       <nameValuePair>
         <name>WindowAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+          <string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>FocusAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</string>
+          <string>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>ContextAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+          <string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -141,8 +141,8 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SentenceDetectorAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SentenceDetectorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SentenceDetectorAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -37,10 +37,10 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
 </outputs>
 <languagesSupported/>
 </capability>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SimpleSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SimpleSegmentAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SimpleSegmentAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SimpleSegmentAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -48,7 +48,7 @@
       <capability>
         <inputs/>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/StatusAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/StatusAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/StatusAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/StatusAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -110,19 +110,19 @@
       <nameValuePair>
         <name>WindowAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+          <string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>FocusAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</string>
+          <string>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>ContextAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+          <string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -141,9 +141,9 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TestContextAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TestContextAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TestContextAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TestContextAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -111,19 +111,19 @@
       <nameValuePair>
         <name>WindowAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+          <string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>FocusAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+          <string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>ContextAnnotationClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+          <string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -142,8 +142,8 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TokenizerAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TokenizerAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TokenizerAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TokenizerAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -67,10 +67,10 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/ContextAnnotatorTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/ContextAnnotatorTests.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/ContextAnnotatorTests.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/ContextAnnotatorTests.java Thu Sep 20 20:25:49 2012
@@ -33,10 +33,10 @@ import org.apache.uima.resource.Resource
 import org.junit.Test;
 
 import edu.mayo.bmi.uima.core.test.TestUtil;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 public class ContextAnnotatorTests {
 
@@ -63,7 +63,7 @@ public class ContextAnnotatorTests {
 		contextAnnotator.initialize(uimaContext);
 
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.MAX_LEFT_SCOPE_SIZE_PARAM, new Integer(8));
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.syntax.BaseToken");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.syntax.BaseToken");
 
 		AnalysisEngine segmentTokenSentenceAE = TestUtil.getAE(new File("test/desc/SegmentTokenSentenceAggregate.xml"));
 		// this gives us a JCas that has segments, tokens, and sentences
@@ -251,7 +251,7 @@ public class ContextAnnotatorTests {
 		contextAnnotator.initialize(uimaContext);
 
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.MAX_RIGHT_SCOPE_SIZE_PARAM, new Integer(4));
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.syntax.BaseToken");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.syntax.BaseToken");
 
 		AnalysisEngine segmentTokenSentenceAE = TestUtil.getAE(new File("test/desc/SegmentTokenSentenceAggregate.xml"));
 		// this gives us a JCas that has segments, tokens, and sentences
@@ -416,7 +416,7 @@ public class ContextAnnotatorTests {
 		ContextAnnotator contextAnnotator = new ContextAnnotator();
 		contextAnnotator.initialize(uimaContext);
 
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.syntax.BaseToken");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.syntax.BaseToken");
 
 
 		AnalysisEngine segmentTokenSentenceAE = TestUtil.getAE(new File("test/desc/SegmentTokenSentenceAggregate.xml"));

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java Thu Sep 20 20:25:49 2012
@@ -30,7 +30,7 @@ import org.apache.uima.resource.Resource
 import org.junit.Test;
 
 import edu.mayo.bmi.uima.core.test.TestUtil;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class NegationAnnotatorTests {
 
@@ -51,9 +51,9 @@ public class NegationAnnotatorTests {
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.SCOPE_ORDER_PARAM, "RIGHT", 1);
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANALYZER_CLASS_PARAM, "edu.mayo.bmi.uima.context.negation.NegationContextAnalyzer");
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_HIT_CONSUMER_CLASS_PARAM, "edu.mayo.bmi.uima.context.negation.NegationContextHitConsumer");
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.WINDOW_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.textspan.Sentence");
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.FOCUS_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation");
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.syntax.BaseToken");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.WINDOW_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.textspan.Sentence");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.FOCUS_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.syntax.BaseToken");
 
 		AnalysisEngine segmentTokenSentenceAE = TestUtil.getAE(new File("test/desc/SegmentTokenSentenceAggregate.xml"));
 

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java Thu Sep 20 20:25:49 2012
@@ -30,7 +30,7 @@ import org.apache.uima.resource.Resource
 import org.junit.Test;
 
 import edu.mayo.bmi.uima.core.test.TestUtil;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class StatusAnnotatorTests {
 
@@ -49,9 +49,9 @@ public class StatusAnnotatorTests {
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.SCOPE_ORDER_PARAM, "RIGHT", 1);
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANALYZER_CLASS_PARAM, "edu.mayo.bmi.uima.context.status.StatusContextAnalyzer");
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_HIT_CONSUMER_CLASS_PARAM, "edu.mayo.bmi.uima.context.status.StatusContextHitConsumer");
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.WINDOW_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.textspan.Sentence");
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.FOCUS_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.IdentifiedAnnotation");
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "edu.mayo.bmi.uima.core.type.syntax.BaseToken");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.WINDOW_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.textspan.Sentence");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.FOCUS_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.IdentifiedAnnotation");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.syntax.BaseToken");
 
 		AnalysisEngine segmentTokenSentenceAE = TestUtil.getAE(new File("test/desc/SegmentTokenSentenceAggregate.xml"));
 

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -132,19 +132,19 @@
 <nameValuePair>
 <name>WindowAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>FocusAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</string>
+<string>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ContextAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+<string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
 </value>
 </nameValuePair>
 </configurationParameterSettings>
@@ -157,8 +157,8 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -133,19 +133,19 @@
 <nameValuePair>
 <name>WindowAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>FocusAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</string>
+<string>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ContextAnnotationClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+<string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
 </value>
 </nameValuePair>
 </configurationParameterSettings>
@@ -156,8 +156,8 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml Thu Sep 20 20:25:49 2012
@@ -122,7 +122,7 @@
 <nameValuePair>
 <name>DISTANCE_ANN_TYPE</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -134,7 +134,7 @@
 <nameValuePair>
 <name>BACKUP_BOUNDARY_ANN_TYPE</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.Segment</string>
+<string>org.apache.ctakes.typesystem.type.textspan.Segment</string>
 </value>
 </nameValuePair>
 <nameValuePair>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -40,11 +40,11 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
 </outputs>
 <languagesSupported/>
 </capability>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -36,8 +36,8 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.ctx.types.ContextAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/PADSiteAndTerm.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/PADSiteAndTerm.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/PADSiteAndTerm.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/PADSiteAndTerm.xml Thu Sep 20 20:25:49 2012
@@ -32,7 +32,7 @@
     <typeDescription>
       <name>edu.mayo.bmi.uima.pad.type.PADTerm</name>
       <description/>
-      <supertypeName>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</supertypeName>
+      <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
       <features>
         <featureDescription>
           <name>hitDictionaryValue</name>
@@ -56,7 +56,7 @@ Valid values are 0 and 1. Where, 0 is fa
     <typeDescription>
       <name>edu.mayo.bmi.uima.pad.type.PADLocation</name>
       <description/>
-      <supertypeName>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</supertypeName>
+      <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
       <features>
         <featureDescription>
           <name>hitDictionaryValue</name>
@@ -83,7 +83,7 @@ Valid values are 0 and 1. Where, 0 is fa
 Term (in the case of a stand alone term)
 Term + Location
 Location + term</description>
-      <supertypeName>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</supertypeName>
+      <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
       <features>
         <featureDescription>
           <name>uaTerm</name>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/radiology/LookupDesc_PAD.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/radiology/LookupDesc_PAD.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/radiology/LookupDesc_PAD.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/radiology/LookupDesc_PAD.xml Thu Sep 20 20:25:49 2012
@@ -52,7 +52,7 @@
 				<properties>
 					<property key="textMetaFields" value="1"/>
 					<property key="maxPermutationLevel" value="7"/>
-					<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.Sentence"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/>
 				</properties>
 			</lookupInitializer>
 			<lookupConsumer className="edu.mayo.bmi.uima.pad.impl.PADTermConsumerImpl">
@@ -68,7 +68,7 @@
 				<properties>
 					<property key="textMetaFields" value="1"/>
 					<property key="maxPermutationLevel" value="7"/>
-					<property key="windowAnnotations" value="edu.mayo.bmi.uima.core.type.textspan.Sentence"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/>
 				</properties>
 			</lookupInitializer>
 			<lookupConsumer className="edu.mayo.bmi.uima.pad.impl.PADLocationConsumerImpl">

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/DxContextHitConsumerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/DxContextHitConsumerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/DxContextHitConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/DxContextHitConsumerImpl.java Thu Sep 20 20:25:49 2012
@@ -24,8 +24,8 @@ import org.apache.uima.jcas.tcas.Annotat
 import edu.mayo.bmi.uima.context.ContextHit;
 import edu.mayo.bmi.uima.context.ContextHitConsumer;
 import edu.mayo.bmi.uima.context.NamedEntityContextHitConsumer;
-import edu.mayo.bmi.uima.core.type.refsem.Element;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.refsem.Element;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 /**
  * @author Mayo Clinic

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/NegativeContextHitConsumerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/NegativeContextHitConsumerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/NegativeContextHitConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/NegativeContextHitConsumerImpl.java Thu Sep 20 20:25:49 2012
@@ -21,7 +21,7 @@ package edu.mayo.bmi.uima.pad.impl;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import edu.mayo.bmi.uima.context.ContextHitConsumer;
 import edu.mayo.bmi.uima.context.NamedEntityContextHitConsumer;
 import edu.mayo.bmi.uima.context.ContextHit;

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADConsumerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADConsumerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADConsumerImpl.java Thu Sep 20 20:25:49 2012
@@ -27,7 +27,7 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import edu.mayo.bmi.uima.lookup.ae.BaseLookupConsumerImpl;
 import edu.mayo.bmi.uima.lookup.ae.LookupConsumer;
 import edu.mayo.bmi.uima.pad.type.SubSection;

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADLocationConsumerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADLocationConsumerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADLocationConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADLocationConsumerImpl.java Thu Sep 20 20:25:49 2012
@@ -34,7 +34,7 @@ import org.apache.uima.jcas.cas.FSArray;
 
 import edu.mayo.bmi.dictionary.MetaDataHit;
 import edu.mayo.bmi.lookup.vo.LookupHit;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import edu.mayo.bmi.uima.pad.type.PADLocation;
 
 

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADTermConsumerImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADTermConsumerImpl.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADTermConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/pad/impl/PADTermConsumerImpl.java Thu Sep 20 20:25:49 2012
@@ -34,7 +34,7 @@ import org.apache.uima.jcas.cas.FSArray;
 
 import edu.mayo.bmi.dictionary.MetaDataHit;
 import edu.mayo.bmi.lookup.vo.LookupHit;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import edu.mayo.bmi.uima.pad.type.PADTerm;
 
 public class PADTermConsumerImpl 

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/ae/PADHitAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/ae/PADHitAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/ae/PADHitAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/ae/PADHitAnnotator.java Thu Sep 20 20:25:49 2012
@@ -50,7 +50,7 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.apache.uima.resource.ResourceInitializationException;
 
 import edu.mayo.bmi.uima.core.resource.FileResource;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import edu.mayo.bmi.uima.pad.type.PADHit;
 import edu.mayo.bmi.uima.pad.type.PADLocation;
 import edu.mayo.bmi.uima.pad.type.PADTerm;

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/ae/SubSectionAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/ae/SubSectionAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/ae/SubSectionAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/ae/SubSectionAnnotator.java Thu Sep 20 20:25:49 2012
@@ -58,14 +58,14 @@ import edu.mayo.bmi.uima.core.fsm.adapte
 import edu.mayo.bmi.uima.core.fsm.adapters.WordTokenAdapter;
 import edu.mayo.bmi.fsm.token.BaseToken;
 import edu.mayo.bmi.uima.core.resource.FileResource;
-import edu.mayo.bmi.uima.core.type.syntax.ContractionToken;
-import edu.mayo.bmi.uima.core.type.syntax.NumToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
-import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
+import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
+import org.apache.ctakes.typesystem.type.syntax.NumToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
 import edu.mayo.bmi.uima.core.util.FSUtil;
 import edu.mayo.bmi.uima.pad.type.SubSection;
 
@@ -112,10 +112,10 @@ public class SubSectionAnnotator extends
 	private void createSubSections(JCas jcas) throws Exception {
 		JFSIndexRepository indexes = jcas.getJFSIndexRepository();
 		Iterator<?> subSectItr = indexes.getAnnotationIndex(
-				edu.mayo.bmi.uima.core.type.syntax.BaseToken.type).iterator();
+				org.apache.ctakes.typesystem.type.syntax.BaseToken.type).iterator();
 		List<BaseToken> baseTokenList = new ArrayList<BaseToken>();
 		while (subSectItr.hasNext()) {
-			edu.mayo.bmi.uima.core.type.syntax.BaseToken bta = (edu.mayo.bmi.uima.core.type.syntax.BaseToken) subSectItr
+			org.apache.ctakes.typesystem.type.syntax.BaseToken bta = (org.apache.ctakes.typesystem.type.syntax.BaseToken) subSectItr
 					.next();
 			baseTokenList.add(adaptToBaseToken(bta));
 		}
@@ -222,12 +222,12 @@ public class SubSectionAnnotator extends
 									Iterator<?> baseItr = FSUtil
 											.getAnnotationsInSpanIterator(
 													jcas,
-													edu.mayo.bmi.uima.core.type.syntax.BaseToken.type,
+													org.apache.ctakes.typesystem.type.syntax.BaseToken.type,
 													sentenceAnnotation.getEnd(),
 													subsectionNext
 															.getStartOffset() - 1);
 									while (baseItr.hasNext()) {
-										edu.mayo.bmi.uima.core.type.syntax.BaseToken checkToken = (edu.mayo.bmi.uima.core.type.syntax.BaseToken) baseItr
+										org.apache.ctakes.typesystem.type.syntax.BaseToken checkToken = (org.apache.ctakes.typesystem.type.syntax.BaseToken) baseItr
 												.next();
 										if ((checkToken instanceof NewlineToken)
 												|| (checkToken instanceof SymbolToken))
@@ -468,7 +468,7 @@ public class SubSectionAnnotator extends
 
 	}
 
-	private BaseToken adaptToBaseToken(edu.mayo.bmi.uima.core.type.syntax.BaseToken bta)
+	private BaseToken adaptToBaseToken(org.apache.ctakes.typesystem.type.syntax.BaseToken bta)
 			throws Exception {
 		if (bta instanceof WordToken) {
 			WordToken wta = (WordToken) bta;



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