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From chen...@apache.org
Subject svn commit: r1388196 [7/12] - 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-coreference/desc/analysis_engine/CorefProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/CorefProcessor.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/CorefProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/CorefProcessor.xml Thu Sep 20 20:25:49 2012
@@ -123,13 +123,13 @@
       <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-coreference/desc/analysis_engine/CorefUMLSProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/CorefUMLSProcessor.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/CorefUMLSProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/CorefUMLSProcessor.xml Thu Sep 20 20:25:49 2012
@@ -131,13 +131,13 @@
       <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-coreference/desc/analysis_engine/MarkablePairPlaintextDBProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/MarkablePairPlaintextDBProcessor.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/MarkablePairPlaintextDBProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/MarkablePairPlaintextDBProcessor.xml Thu Sep 20 20:25:49 2012
@@ -131,13 +131,13 @@
       <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-coreference/desc/analysis_engine/ODIESvmVectorCreator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/ODIESvmVectorCreator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/ODIESvmVectorCreator.xml (original)
+++ incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/ODIESvmVectorCreator.xml Thu Sep 20 20:25:49 2012
@@ -193,13 +193,13 @@
       <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-coreference/desc/analysis_engine/ODIESvmVectorCreator_wSection.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/ODIESvmVectorCreator_wSection.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/ODIESvmVectorCreator_wSection.xml (original)
+++ incubator/ctakes/trunk/ctakes-coreference/desc/analysis_engine/ODIESvmVectorCreator_wSection.xml Thu Sep 20 20:25:49 2012
@@ -197,13 +197,13 @@
       <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-coreference/desc/cas_consumer/ODIEVectorFileWriterCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/desc/cas_consumer/ODIEVectorFileWriterCasConsumer.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/desc/cas_consumer/ODIEVectorFileWriterCasConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-coreference/desc/cas_consumer/ODIEVectorFileWriterCasConsumer.xml Thu Sep 20 20:25:49 2012
@@ -104,7 +104,7 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.DocumentID</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.DocumentID</type>
         </inputs>
         <outputs/>
         <inputSofas>

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AbstractClassifier.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AbstractClassifier.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AbstractClassifier.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AbstractClassifier.java Thu Sep 20 20:25:49 2012
@@ -29,7 +29,7 @@ import org.apache.uima.UimaContext;
 import org.apache.uima.resource.ResourceAccessException;
 
 import edu.mayo.bmi.uima.core.resource.FileResource;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 
 public class AbstractClassifier {
 

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java Thu Sep 20 20:25:49 2012
@@ -25,13 +25,13 @@ import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.constants.CONST;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.TerminalTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import edu.mayo.bmi.uima.coref.type.Markable;
 
 public class AnaphoricityAttributeCalculator extends AttributeCalculator {

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnnotationSelector.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnnotationSelector.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnnotationSelector.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnnotationSelector.java Thu Sep 20 20:25:49 2012
@@ -29,14 +29,14 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.Chunk;
-import edu.mayo.bmi.uima.core.type.syntax.TerminalTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 // TODO: This class hardcoded all the criteria,
 // which should be replaced by a parser of

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AttributeCalculator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AttributeCalculator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AttributeCalculator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AttributeCalculator.java Thu Sep 20 20:25:49 2012
@@ -27,9 +27,9 @@ import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
-//import edu.mayo.bmi.uima.core.type.NamedEntity;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+//import org.apache.ctakes.typesystem.type.NamedEntity;
 import edu.mayo.bmi.uima.coref.type.Markable;
 
 public class AttributeCalculator {

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java Thu Sep 20 20:25:49 2012
@@ -27,9 +27,9 @@ import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.syntax.TopTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
 import edu.mayo.bmi.uima.coref.type.Markable;
 
 public class HobbsTreeNavigator {

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableDepUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableDepUtils.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableDepUtils.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableDepUtils.java Thu Sep 20 20:25:49 2012
@@ -22,9 +22,9 @@ import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.syntax.TerminalTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 
 public class MarkableDepUtils {
 

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableTreeUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableTreeUtils.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableTreeUtils.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableTreeUtils.java Thu Sep 20 20:25:49 2012
@@ -24,9 +24,9 @@ import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.syntax.TerminalTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TopTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 import edu.mayo.bmi.uima.coref.type.Markable;
 
 public class MarkableTreeUtils {

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/PairAttributeCalculator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/PairAttributeCalculator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/PairAttributeCalculator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/PairAttributeCalculator.java Thu Sep 20 20:25:49 2012
@@ -37,13 +37,13 @@ import org.apache.uima.jcas.cas.StringAr
 import org.apache.uima.jcas.tcas.Annotation;
 
 import edu.mayo.bmi.uima.core.resource.FileLocator;
-import edu.mayo.bmi.uima.core.type.constants.CONST;
-import edu.mayo.bmi.uima.core.type.refsem.UmlsConcept;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
 import edu.mayo.bmi.coref.util.AnnotationSelector;
 import edu.mayo.bmi.uima.coref.type.DemMarkable;
 import edu.mayo.bmi.uima.coref.type.Markable;

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java Thu Sep 20 20:25:49 2012
@@ -30,9 +30,9 @@ import org.apache.uima.jcas.cas.StringAr
 import org.apache.uima.jcas.tcas.Annotation;
 
 import edu.mayo.bmi.uima.core.resource.FileLocator;
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
 import edu.mayo.bmi.uima.coref.type.Markable;
 import edu.mayo.bmi.uima.coref.type.DemMarkable;
 import edu.mayo.bmi.uima.coref.type.NEMarkable;

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableCreator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableCreator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableCreator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableCreator.java Thu Sep 20 20:25:49 2012
@@ -30,8 +30,8 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.apache.uima.resource.ResourceInitializationException;
 
 import edu.mayo.bmi.coref.util.AnnotationSelector;
-import edu.mayo.bmi.uima.core.type.syntax.Chunk;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import edu.mayo.bmi.uima.coref.type.DemMarkable;
 import edu.mayo.bmi.uima.coref.type.NEMarkable;
 import edu.mayo.bmi.uima.coref.type.PronounMarkable;

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableExpander.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableExpander.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableExpander.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableExpander.java Thu Sep 20 20:25:49 2012
@@ -33,8 +33,8 @@ import org.chboston.cnlp.ctakes.coref.ev
 
 import edu.mayo.bmi.coref.util.FSIteratorToList;
 import edu.mayo.bmi.coref.util.MarkableTreeUtils;
-import edu.mayo.bmi.uima.core.type.syntax.Chunk;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 import edu.mayo.bmi.uima.coref.type.DemMarkable;
 import edu.mayo.bmi.uima.coref.type.Markable;
 import edu.mayo.bmi.uima.coref.type.NEMarkable;

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkablePairGenerator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkablePairGenerator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkablePairGenerator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkablePairGenerator.java Thu Sep 20 20:25:49 2012
@@ -47,9 +47,9 @@ import edu.mayo.bmi.coref.util.MarkableT
 import edu.mayo.bmi.coref.util.PairAttributeCalculator;
 import edu.mayo.bmi.coref.util.ParentPtrTree;
 import edu.mayo.bmi.uima.core.resource.FileResource;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.Chunk;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 import edu.mayo.bmi.uima.coref.type.DemMarkable;
 import edu.mayo.bmi.uima.coref.type.Markable;

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqSvmChainCreator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqSvmChainCreator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqSvmChainCreator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqSvmChainCreator.java Thu Sep 20 20:25:49 2012
@@ -53,11 +53,11 @@ import edu.mayo.bmi.coref.util.MarkableT
 import edu.mayo.bmi.coref.util.ParentPtrTree;
 import edu.mayo.bmi.coref.util.SyntaxAttributeCalculator;
 import edu.mayo.bmi.uima.core.resource.FileResource;
-import edu.mayo.bmi.uima.core.type.relation.CollectionTextRelation;
-import edu.mayo.bmi.uima.core.type.relation.CoreferenceRelation;
-import edu.mayo.bmi.uima.core.type.relation.RelationArgument;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
+import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import edu.mayo.bmi.uima.coref.type.DemMarkable;
 import edu.mayo.bmi.uima.coref.type.Markable;
 import edu.mayo.bmi.uima.coref.type.MarkablePairSet;

Modified: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/cc/ODIEVectorFileWriter.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/cc/ODIEVectorFileWriter.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/cc/ODIEVectorFileWriter.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/cc/ODIEVectorFileWriter.java Thu Sep 20 20:25:49 2012
@@ -63,7 +63,7 @@ import edu.mayo.bmi.coref.util.SvmUtils;
 import edu.mayo.bmi.coref.util.SvmVectorCreator;
 import edu.mayo.bmi.uima.core.resource.FileLocator;
 import edu.mayo.bmi.uima.core.resource.FileResource;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 import edu.mayo.bmi.uima.coref.type.MarkablePairSet;
 import edu.mayo.bmi.uima.coref.type.Markable;

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml Thu Sep 20 20:25:49 2012
@@ -74,11 +74,11 @@
         <capabilities>
             <capability>
                 <inputs>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:normalizedForm</feature>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:normalizedForm</feature>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
                 </inputs>
                 <outputs/>
                 <languagesSupported/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserPlaintextAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserPlaintextAggregate.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserPlaintextAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserPlaintextAggregate.xml Thu Sep 20 20:25:49 2012
@@ -79,11 +79,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:normalizedForm</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:normalizedForm</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -292,10 +292,10 @@
                     <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>
@@ -371,10 +371,10 @@
                     <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>
@@ -420,10 +420,10 @@
                     <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>
@@ -489,7 +489,7 @@
                         <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>
@@ -561,11 +561,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</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.syntax.BaseToken</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-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedAggregate.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedAggregate.xml Thu Sep 20 20:25:49 2012
@@ -79,11 +79,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:normalizedForm</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:normalizedForm</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -292,10 +292,10 @@
                     <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>
@@ -361,7 +361,7 @@
                         <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-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedInfPosAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedInfPosAggregate.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedInfPosAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserTokenizedInfPosAggregate.xml Thu Sep 20 20:25:49 2012
@@ -79,11 +79,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:normalizedForm</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:normalizedForm</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -292,10 +292,10 @@
                     <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>
@@ -361,7 +361,7 @@
                         <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>
@@ -433,11 +433,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</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.syntax.BaseToken</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-dependency-parser/desc/analysis_engine/ClearParserSRLPlaintextAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLPlaintextAggregate.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLPlaintextAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLPlaintextAggregate.xml Thu Sep 20 20:25:49 2012
@@ -79,11 +79,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:normalizedForm</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:normalizedForm</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -292,10 +292,10 @@
                     <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>
@@ -371,10 +371,10 @@
                     <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>
@@ -431,11 +431,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
-                                <type>edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode</type>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
+                                <type>org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode</type>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -481,10 +481,10 @@
                     <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>
@@ -550,7 +550,7 @@
                         <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>
@@ -622,11 +622,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</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.syntax.BaseToken</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-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedAggregate.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedAggregate.xml Thu Sep 20 20:25:49 2012
@@ -79,11 +79,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:normalizedForm</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:normalizedForm</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -292,10 +292,10 @@
                     <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>
@@ -377,11 +377,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
-                                <type>edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode</type>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
+                                <type>org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode</type>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -422,7 +422,7 @@
                         <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-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml Thu Sep 20 20:25:49 2012
@@ -79,11 +79,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:normalizedForm</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:normalizedForm</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -292,10 +292,10 @@
                     <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>
@@ -377,11 +377,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                                <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
-                                <type>edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode</type>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                                <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
+                                <type>org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode</type>
                             </inputs>
                             <outputs/>
                             <languagesSupported/>
@@ -422,7 +422,7 @@
                         <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>
@@ -494,11 +494,11 @@
                     <capabilities>
                         <capability>
                             <inputs>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</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.syntax.BaseToken</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-dependency-parser/desc/analysis_engine/ClearParserSemanticRoleLabelerAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSemanticRoleLabelerAE.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSemanticRoleLabelerAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/ClearParserSemanticRoleLabelerAE.xml Thu Sep 20 20:25:49 2012
@@ -61,11 +61,11 @@
         <capabilities>
             <capability>
                 <inputs>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech</feature>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber</feature>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:end</feature>
-                    <feature>edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin</feature>
-                    <type>edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode</type>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech</feature>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber</feature>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:end</feature>
+                    <feature>org.apache.ctakes.typesystem.type.syntax.BaseToken:begin</feature>
+                    <type>org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode</type>
                 </inputs>
                 <outputs/>
                 <languagesSupported/>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.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-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml Thu Sep 20 20:25:49 2012
@@ -73,7 +73,7 @@ The default is CONLL-x tab-delimited for
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.DocumentID</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.DocumentID</type>
         </inputs>
         <outputs/>
         <inputSofas>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/DependencyNodeWriter.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/DependencyNodeWriter.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/DependencyNodeWriter.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/DependencyNodeWriter.java Thu Sep 20 20:25:49 2012
@@ -55,8 +55,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.ResourceProcessException;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserDependencyParserAE.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserDependencyParserAE.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserDependencyParserAE.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserDependencyParserAE.java Thu Sep 20 20:25:49 2012
@@ -40,9 +40,9 @@ import clear.dep.DepTree;
 import clear.morph.MorphEnAnalyzer;
 import clear.parse.AbstractDepParser;
 import edu.mayo.bmi.nlp.parser.util.ClearDependencyUtility;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * <br>
@@ -61,11 +61,11 @@ import edu.mayo.bmi.uima.core.type.texts
  */
 @TypeCapability(
 		inputs = { 
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech",
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:normalizedForm",
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber",
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:end",
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin"
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech",
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:normalizedForm",
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber",
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:end",
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:begin"
 		})
 public class ClearParserDependencyParserAE extends JCasAnnotator_ImplBase {
 

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserSemanticRoleLabelerAE.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserSemanticRoleLabelerAE.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserSemanticRoleLabelerAE.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/ClearParserSemanticRoleLabelerAE.java Thu Sep 20 20:25:49 2012
@@ -46,12 +46,12 @@ import clear.dep.srl.SRLHead;
 import clear.morph.MorphEnAnalyzer;
 import clear.parse.AbstractSRLParser;
 import clear.reader.AbstractReader;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.textsem.Predicate;
-import edu.mayo.bmi.uima.core.type.textsem.SemanticArgument;
-import edu.mayo.bmi.uima.core.type.textsem.SemanticRoleRelation;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.Predicate;
+import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
+import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import edu.mayo.bmi.uima.core.util.ListFactory;
 
 /**
@@ -72,11 +72,11 @@ import edu.mayo.bmi.uima.core.util.ListF
  */
 @TypeCapability(
 		inputs = { 
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:partOfSpeech",
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:tokenNumber",
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:end",
-				"edu.mayo.bmi.uima.core.type.syntax.BaseToken:begin",
-				"edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode"
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:partOfSpeech",
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:tokenNumber",
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:end",
+				"org.apache.ctakes.typesystem.type.syntax.BaseToken:begin",
+				"org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode"
 		})
 public class ClearParserSemanticRoleLabelerAE extends JCasAnnotator_ImplBase {
 

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/LemAssigner.java Thu Sep 20 20:25:49 2012
@@ -55,9 +55,9 @@ import org.apache.uima.cas.text.Annotati
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 public class LemAssigner extends JCasAnnotator_ImplBase{
 

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/PosAssigner.java Thu Sep 20 20:25:49 2012
@@ -55,9 +55,9 @@ import org.apache.uima.cas.text.Annotati
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 public class PosAssigner extends JCasAnnotator_ImplBase{
 

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/TestClearParserAnalysisEngines.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/TestClearParserAnalysisEngines.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/TestClearParserAnalysisEngines.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/ae/util/TestClearParserAnalysisEngines.java Thu Sep 20 20:25:49 2012
@@ -42,7 +42,7 @@ import edu.mayo.bmi.nlp.parser.ae.ClearP
 import edu.mayo.bmi.nlp.parser.ae.ClearParserSemanticRoleLabelerAE;
 import edu.mayo.bmi.nlp.parser.util.DependencyUtility;
 import edu.mayo.bmi.nlp.parser.util.SRLUtility;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * This class illustrates the pipeline needed to run the ClearParser dependency parser and SRL systems

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/cr/DependencyFileCollectionReader.java Thu Sep 20 20:25:49 2012
@@ -56,9 +56,9 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.Progress;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * This collection reader reads in dependency tree training/test data in a tab-

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/ClearDependencyUtility.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/ClearDependencyUtility.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/ClearDependencyUtility.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/ClearDependencyUtility.java Thu Sep 20 20:25:49 2012
@@ -27,11 +27,11 @@ import org.apache.uima.jcas.tcas.Annotat
 
 import clear.dep.DepNode;
 import clear.dep.DepTree;
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textsem.Predicate;
-import edu.mayo.bmi.uima.core.type.textsem.SemanticRoleRelation;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.Predicate;
+import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * @author m081914

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyPath.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyPath.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyPath.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyPath.java Thu Sep 20 20:25:49 2012
@@ -20,7 +20,7 @@ package edu.mayo.bmi.nlp.parser.util;
 
 import java.util.LinkedList;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 
 public class DependencyPath extends LinkedList<ConllDependencyNode>{
 	

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyRegex.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyRegex.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyRegex.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyRegex.java Thu Sep 20 20:25:49 2012
@@ -26,7 +26,7 @@ import java.util.regex.Pattern;
 import clear.dep.DepLib;
 import clear.dep.DepNode;
 import clear.ftr.FtrLib;
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 
 /**
  * @author m081914

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyUtility.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyUtility.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyUtility.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/DependencyUtility.java Thu Sep 20 20:25:49 2012
@@ -29,8 +29,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * @author m081914

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/SRLUtility.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/SRLUtility.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/SRLUtility.java (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/edu/mayo/bmi/nlp/parser/util/SRLUtility.java Thu Sep 20 20:25:49 2012
@@ -21,8 +21,8 @@ package edu.mayo.bmi.nlp.parser.util;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.textsem.Predicate;
-import edu.mayo.bmi.uima.core.type.textsem.SemanticRoleRelation;
+import org.apache.ctakes.typesystem.type.textsem.Predicate;
+import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;
 
 public class SRLUtility {
 	public static String dumpSRLOutput(Annotation annotation) {

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -54,11 +54,11 @@
     <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.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.core.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml Thu Sep 20 20:25:49 2012
@@ -54,11 +54,11 @@
     <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.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.core.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorDB.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorDB.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorDB.xml (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorDB.xml Thu Sep 20 20:25:49 2012
@@ -54,11 +54,11 @@
     <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.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.core.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml Thu Sep 20 20:25:49 2012
@@ -111,11 +111,11 @@
     <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.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.core.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>



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