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From chen...@apache.org
Subject svn commit: r1389618 [11/22] - in /incubator/ctakes/trunk: ./ ctakes-chunker/ ctakes-chunker/desc/ ctakes-chunker/resources/launch/ ctakes-chunker/src/main/java/edu/ ctakes-chunker/src/main/java/org/ ctakes-chunker/src/main/java/org/apache/ ctakes-chun...
Date Mon, 24 Sep 2012 22:05:23 GMT
Modified: incubator/ctakes/trunk/ctakes-coreference/resources/launch/UIMA_CVD--coref-resolver.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/resources/launch/UIMA_CVD--coref-resolver.launch?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/resources/launch/UIMA_CVD--coref-resolver.launch (original)
+++ incubator/ctakes/trunk/ctakes-coreference/resources/launch/UIMA_CVD--coref-resolver.launch Mon Sep 24 22:04:51 2012
@@ -9,31 +9,31 @@
 <listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
 <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry containerPath=&quot;org.eclipse.jdt.launching.JRE_CONTAINER&quot; javaProject=&quot;coref-resolver&quot; path=&quot;1&quot; type=&quot;4&quot;/&gt;&#13;&#10;"/>
 <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry id=&quot;org.eclipse.jdt.launching.classpathentry.defaultClasspath&quot;&gt;&#13;&#10;&lt;memento exportedEntriesOnly=&quot;false&quot; project=&quot;coref-resolver&quot;/&gt;&#13;&#10;&lt;/runtimeClasspathEntry&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry path=&quot;3&quot; projectName=&quot;clinical documents pipeline&quot; type=&quot;1&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry path=&quot;3&quot; projectName=&quot;ctakes-clinical-pipeline&quot; type=&quot;1&quot;/&gt;&#13;&#10;"/>
 <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry path=&quot;3&quot; projectName=&quot;core&quot; type=&quot;1&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/core/lib/opennlp-tools-1.4.3.jar&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/core/lib/maxent-2.5.0.jar&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/core/lib/log4j-1.2.8.jar&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/core/lib/trove.jar&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-core/lib/opennlp-tools-1.4.3.jar&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-core/lib/maxent-2.5.0.jar&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-core/lib/log4j-1.2.8.jar&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-core/lib/trove.jar&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
 <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry path=&quot;3&quot; projectName=&quot;dictionary lookup&quot; type=&quot;1&quot;/&gt;&#13;&#10;"/>
 <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry path=&quot;3&quot; projectName=&quot;Constituency Parser&quot; type=&quot;1&quot;/&gt;&#13;&#10;"/>
 <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry containerPath=&quot;org.eclipse.jdt.USER_LIBRARY/cTakes&quot; path=&quot;3&quot; type=&quot;4&quot;/&gt;&#13;&#10;"/>
 <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry containerPath=&quot;org.eclipse.jdt.USER_LIBRARY/UIMA&quot; path=&quot;3&quot; type=&quot;4&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/chunker/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/chunker/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/clinical documents pipeline/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/clinical documents pipeline/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/core/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/core/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/dependency parser/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/dependency parser/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/dictionary lookup/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/dictionary lookup/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/LVG/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/LVG/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/NE contexts/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/POS tagger/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
-<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/POS tagger/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-chunker/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-chunker/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-clinical-pipeline/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-clinical-pipeline/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-core/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-core/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-dependency-parser/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-dependency-parser/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-dictionary-lookup/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-dictionary-lookup/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-lvg/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-lvg/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-ne-contexts/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-pos-tagger/desc&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-pos-tagger/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
 </listAttribute>
 <booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
 <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/>

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableCreator.java (from r1388196, 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/apache/ctakes/coreference/ae/MipacqMarkableCreator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableCreator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableCreator.java&r1=1388196&r2=1389618&rev=1389618&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/apache/ctakes/coreference/ae/MipacqMarkableCreator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.uima.ae;
+package org.apache.ctakes.coreference.ae;
 
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -29,12 +29,12 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.coref.util.AnnotationSelector;
+import org.apache.ctakes.coreference.util.AnnotationSelector;
 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;
+import org.apache.ctakes.coreference.type.DemMarkable;
+import org.apache.ctakes.coreference.type.NEMarkable;
+import org.apache.ctakes.coreference.type.PronounMarkable;
 
 public class MipacqMarkableCreator extends JCasAnnotator_ImplBase {
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableExpander.java (from r1388196, 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/apache/ctakes/coreference/ae/MipacqMarkableExpander.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableExpander.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkableExpander.java&r1=1388196&r2=1389618&rev=1389618&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/apache/ctakes/coreference/ae/MipacqMarkableExpander.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.uima.ae;
+package org.apache.ctakes.coreference.ae;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -29,15 +29,15 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.Span;
 
-import edu.mayo.bmi.coref.util.FSIteratorToList;
-import edu.mayo.bmi.coref.util.MarkableTreeUtils;
+import org.apache.ctakes.coreference.eval.helpers.Span;
+import org.apache.ctakes.coreference.util.FSIteratorToList;
+import org.apache.ctakes.coreference.util.MarkableTreeUtils;
 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;
+import org.apache.ctakes.coreference.type.DemMarkable;
+import org.apache.ctakes.coreference.type.Markable;
+import org.apache.ctakes.coreference.type.NEMarkable;
 
 public class MipacqMarkableExpander extends JCasAnnotator_ImplBase {
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java (from r1388196, 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/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqMarkablePairGenerator.java&r1=1388196&r2=1389618&rev=1389618&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/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.uima.ae;
+package org.apache.ctakes.coreference.ae;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -36,27 +36,28 @@ import org.apache.uima.jcas.cas.FSList;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
 import org.apache.uima.jcas.cas.NonEmptyFloatList;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.chboston.cnlp.ctakes.common.type.BooleanLabeledFS;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.Span;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.SpanAlignment;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.SpanOffsetComparator;
-
-import edu.mayo.bmi.coref.util.CorefConsts;
-import edu.mayo.bmi.coref.util.FSIteratorToList;
-import edu.mayo.bmi.coref.util.MarkableTreeUtils;
-import edu.mayo.bmi.coref.util.PairAttributeCalculator;
-import edu.mayo.bmi.coref.util.ParentPtrTree;
-import edu.mayo.bmi.uima.core.resource.FileResource;
+import org.apache.ctakes.coreference.type.BooleanLabeledFS;
+
+
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.coreference.eval.helpers.Span;
+import org.apache.ctakes.coreference.eval.helpers.SpanAlignment;
+import org.apache.ctakes.coreference.eval.helpers.SpanOffsetComparator;
+import org.apache.ctakes.coreference.util.CorefConsts;
+import org.apache.ctakes.coreference.util.FSIteratorToList;
+import org.apache.ctakes.coreference.util.MarkableTreeUtils;
+import org.apache.ctakes.coreference.util.PairAttributeCalculator;
+import org.apache.ctakes.coreference.util.ParentPtrTree;
 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;
-import edu.mayo.bmi.uima.coref.type.MarkablePair;
-import edu.mayo.bmi.uima.coref.type.MarkablePairSet;
-import edu.mayo.bmi.uima.coref.type.NEMarkable;
-import edu.mayo.bmi.uima.coref.type.PronounMarkable;
+import org.apache.ctakes.coreference.type.DemMarkable;
+import org.apache.ctakes.coreference.type.Markable;
+import org.apache.ctakes.coreference.type.MarkablePair;
+import org.apache.ctakes.coreference.type.MarkablePairSet;
+import org.apache.ctakes.coreference.type.NEMarkable;
+import org.apache.ctakes.coreference.type.PronounMarkable;
 
 public class MipacqMarkablePairGenerator extends JCasAnnotator_ImplBase {
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java (from r1388196, 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/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/ae/MipacqSvmChainCreator.java&r1=1388196&r2=1389618&rev=1389618&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/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.uima.ae;
+package org.apache.ctakes.coreference.ae;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
@@ -43,26 +43,27 @@ import org.apache.uima.jcas.cas.FSList;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.chboston.cnlp.ctakes.common.type.BooleanLabeledFS;
+import org.apache.ctakes.coreference.type.BooleanLabeledFS;
 
-import edu.mayo.bmi.coref.util.AbstractClassifier;
-import edu.mayo.bmi.coref.util.CorefConsts;
-import edu.mayo.bmi.coref.util.FSIteratorToList;
-import edu.mayo.bmi.coref.util.FeatureVector;
-import edu.mayo.bmi.coref.util.MarkableTreeUtils;
-import edu.mayo.bmi.coref.util.ParentPtrTree;
-import edu.mayo.bmi.coref.util.SyntaxAttributeCalculator;
-import edu.mayo.bmi.uima.core.resource.FileResource;
+
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.coreference.util.AbstractClassifier;
+import org.apache.ctakes.coreference.util.CorefConsts;
+import org.apache.ctakes.coreference.util.FSIteratorToList;
+import org.apache.ctakes.coreference.util.FeatureVector;
+import org.apache.ctakes.coreference.util.MarkableTreeUtils;
+import org.apache.ctakes.coreference.util.ParentPtrTree;
+import org.apache.ctakes.coreference.util.SyntaxAttributeCalculator;
 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;
-import edu.mayo.bmi.uima.coref.type.NEMarkable;
-import edu.mayo.bmi.uima.coref.type.PronounMarkable;
+import org.apache.ctakes.coreference.type.DemMarkable;
+import org.apache.ctakes.coreference.type.Markable;
+import org.apache.ctakes.coreference.type.MarkablePairSet;
+import org.apache.ctakes.coreference.type.NEMarkable;
+import org.apache.ctakes.coreference.type.PronounMarkable;
 
 public class MipacqSvmChainCreator extends JCasAnnotator_ImplBase {
 
@@ -77,7 +78,7 @@ public class MipacqSvmChainCreator exten
 	private svm_model mod_anaphoricity;
 	// positive class label index in libsvm's prob_est array
 	private int anaphoricity_idx, coref_idx;
-	private edu.mayo.bmi.coref.util.SvmVectorCreator vecCreator = null;
+	private org.apache.ctakes.coreference.util.SvmVectorCreator vecCreator = null;
 	
 	ParentPtrTree ppt;
 
@@ -129,7 +130,7 @@ public class MipacqSvmChainCreator exten
 				else if (i < 0)
 					stopwords.add(l.trim());
 			}
-			vecCreator = new edu.mayo.bmi.coref.util.SvmVectorCreator(stopwords, mod_anaphoricity);
+			vecCreator = new org.apache.ctakes.coreference.util.SvmVectorCreator(stopwords, mod_anaphoricity);
 
 			treeFrags = new ArrayList<String>();
 			r = (FileResource) uc.getResourceObject("frags");

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java (from r1388196, 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/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/uima/cc/ODIEVectorFileWriter.java&r1=1388196&r2=1389618&rev=1389618&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/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.uima.cc;
+package org.apache.ctakes.coreference.cc;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -45,31 +45,32 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.ResourceProcessException;
 import org.apache.uima.util.ProcessTrace;
-import org.chboston.cnlp.ctakes.common.type.BooleanLabeledFS;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.Span;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.SpanAlignment;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.SpanOffsetComparator;
-import org.chboston.cnlp.ctakes.parser.treekernel.TreeExtractor;
-import org.chboston.cnlp.ctakes.parser.util.TreeUtils;
-import org.chboston.cnlp.util.SimpleTree;
-
-import edu.mayo.bmi.coref.util.CorefConsts;
-import edu.mayo.bmi.coref.util.FSIteratorToList;
-import edu.mayo.bmi.coref.util.GoldStandardLabeler;
-import edu.mayo.bmi.coref.util.MarkableTreeUtils;
-import edu.mayo.bmi.coref.util.PairAttributeCalculator;
-import edu.mayo.bmi.coref.util.ParentPtrTree;
-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 org.apache.ctakes.coreference.type.BooleanLabeledFS;
+
+
+import org.apache.ctakes.constituency.parser.treekernel.TreeExtractor;
+import org.apache.ctakes.constituency.parser.util.TreeUtils;
+import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.coreference.eval.helpers.Span;
+import org.apache.ctakes.coreference.eval.helpers.SpanAlignment;
+import org.apache.ctakes.coreference.eval.helpers.SpanOffsetComparator;
+import org.apache.ctakes.coreference.util.CorefConsts;
+import org.apache.ctakes.coreference.util.FSIteratorToList;
+import org.apache.ctakes.coreference.util.GoldStandardLabeler;
+import org.apache.ctakes.coreference.util.MarkableTreeUtils;
+import org.apache.ctakes.coreference.util.PairAttributeCalculator;
+import org.apache.ctakes.coreference.util.ParentPtrTree;
+import org.apache.ctakes.coreference.util.SvmUtils;
+import org.apache.ctakes.coreference.util.SvmVectorCreator;
 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;
-import edu.mayo.bmi.uima.coref.type.DemMarkable;
-import edu.mayo.bmi.uima.coref.type.NEMarkable;
-import edu.mayo.bmi.uima.coref.type.PronounMarkable;
+import org.apache.ctakes.typesystem.util.SimpleTree;
+import org.apache.ctakes.coreference.type.MarkablePairSet;
+import org.apache.ctakes.coreference.type.Markable;
+import org.apache.ctakes.coreference.type.DemMarkable;
+import org.apache.ctakes.coreference.type.NEMarkable;
+import org.apache.ctakes.coreference.type.PronounMarkable;
 
 import libsvm.svm;
 import libsvm.svm_model;

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/B3Type.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/B3Type.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/B3Type.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/B3Type.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/B3Type.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/B3Type.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/B3Type.java Mon Sep 24 22:04:51 2012
@@ -16,6 +16,6 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.eval.helpers;
+package org.apache.ctakes.coreference.eval.helpers;
 
 public enum B3Type { CLASS, ENTITY }

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/CEAFType.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/CEAFType.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/CEAFType.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/CEAFType.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/CEAFType.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/CEAFType.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/CEAFType.java Mon Sep 24 22:04:51 2012
@@ -16,6 +16,6 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.eval.helpers;
+package org.apache.ctakes.coreference.eval.helpers;
 
 public enum CEAFType { ENTITY, MENTION }

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/KAlphaType.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/KAlphaType.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/KAlphaType.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/KAlphaType.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/KAlphaType.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/KAlphaType.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/KAlphaType.java Mon Sep 24 22:04:51 2012
@@ -16,6 +16,6 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.eval.helpers;
+package org.apache.ctakes.coreference.eval.helpers;
 
 public enum KAlphaType { RAW, MASI };

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/MatType.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/MatType.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/MatType.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/MatType.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/MatType.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/MatType.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/MatType.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.eval.helpers;
+package org.apache.ctakes.coreference.eval.helpers;
 
 
 public enum MatType {

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/PairType.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/PairType.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/PairType.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/PairType.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/PairType.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/PairType.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/PairType.java Mon Sep 24 22:04:51 2012
@@ -16,6 +16,6 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.eval.helpers;
+package org.apache.ctakes.coreference.eval.helpers;
 
 public enum PairType { IDENT, PWHOLE, SSUBSET, NONIDENT }

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Span.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/Span.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Span.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Span.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/Span.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/Span.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Span.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.eval.helpers;
+package org.apache.ctakes.coreference.eval.helpers;
 
 public class Span {
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/SpanAlignment.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/SpanAlignment.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/SpanAlignment.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/SpanAlignment.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/SpanAlignment.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/SpanAlignment.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/SpanAlignment.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.eval.helpers;
+package org.apache.ctakes.coreference.eval.helpers;
 
 public class SpanAlignment {
 

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

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Test.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/Test.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Test.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Test.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/Test.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/eval/helpers/Test.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Test.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.eval.helpers;
+package org.apache.ctakes.coreference.eval.helpers;
 
 public class Test {
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/KernelMatrixCompositor.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/KernelMatrixCompositor.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/KernelMatrixCompositor.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/KernelMatrixCompositor.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/KernelMatrixCompositor.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/KernelMatrixCompositor.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/KernelMatrixCompositor.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.treekernel.training;
+package org.apache.ctakes.coreference.treekernel.training;
 
 import java.io.File;
 import java.io.FileNotFoundException;

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/LinearKernelMatrixWriter.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/LinearKernelMatrixWriter.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/LinearKernelMatrixWriter.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/LinearKernelMatrixWriter.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/LinearKernelMatrixWriter.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/LinearKernelMatrixWriter.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/LinearKernelMatrixWriter.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.treekernel.training;
+package org.apache.ctakes.coreference.treekernel.training;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -24,12 +24,12 @@ import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.Scanner;
 
-import org.chboston.cnlp.ctakes.kernel.Kernel;
-import org.chboston.cnlp.ctakes.kernel.LinearKernel;
-import org.chboston.cnlp.ctakes.kernel.PolyKernel;
-import org.chboston.cnlp.ctakes.kernel.RBFKernel;
+import org.apache.ctakes.coreference.util.ThreadDelegator;
+import org.apache.ctakes.typesystem.kernel.Kernel;
+import org.apache.ctakes.typesystem.kernel.LinearKernel;
+import org.apache.ctakes.typesystem.kernel.PolyKernel;
+import org.apache.ctakes.typesystem.kernel.RBFKernel;
 
-import edu.mayo.bmi.coref.util.ThreadDelegator;
 
 import libsvm.svm_node;
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/RowFillerThread.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/RowFillerThread.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/RowFillerThread.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/RowFillerThread.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/RowFillerThread.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/RowFillerThread.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/RowFillerThread.java Mon Sep 24 22:04:51 2012
@@ -16,14 +16,14 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.treekernel.training;
+package org.apache.ctakes.coreference.treekernel.training;
 
 import java.util.ArrayList;
 
-import org.chboston.cnlp.ctakes.kernel.Kernel;
-import org.chboston.cnlp.ctakes.parser.treekernel.TreeKernel;
+import org.apache.ctakes.constituency.parser.treekernel.TreeKernel;
+import org.apache.ctakes.coreference.util.ThreadDelegator;
+import org.apache.ctakes.typesystem.kernel.Kernel;
 
-import edu.mayo.bmi.coref.util.ThreadDelegator;
 
 import opennlp.tools.parser.Parse;
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/TreeKernelTrainer.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/TreeKernelTrainer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/TreeKernelTrainer.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/TreeKernelTrainer.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/TreeKernelTrainer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/chboston/cnlp/ctakes/coref/treekernel/training/TreeKernelTrainer.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/TreeKernelTrainer.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.coref.treekernel.training;
+package org.apache.ctakes.coreference.treekernel.training;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -24,9 +24,9 @@ import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.Scanner;
 
-import org.chboston.cnlp.ctakes.parser.treekernel.TreeKernel;
+import org.apache.ctakes.constituency.parser.treekernel.TreeKernel;
+import org.apache.ctakes.coreference.util.ThreadDelegator;
 
-import edu.mayo.bmi.coref.util.ThreadDelegator;
 
 import opennlp.tools.parser.Parse;
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AbstractClassifier.java (from r1388196, 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/org/apache/ctakes/coreference/util/AbstractClassifier.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AbstractClassifier.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AbstractClassifier.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/AbstractClassifier.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.io.File;
 import java.io.IOException;
@@ -28,7 +28,7 @@ import libsvm.svm_node;
 import org.apache.uima.UimaContext;
 import org.apache.uima.resource.ResourceAccessException;
 
-import edu.mayo.bmi.uima.core.resource.FileResource;
+import org.apache.ctakes.core.resource.FileResource;
 import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 
 public class AbstractClassifier {

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnaphoricityAttributeCalculator.java (from r1388196, 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/org/apache/ctakes/coreference/util/AnaphoricityAttributeCalculator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnaphoricityAttributeCalculator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnaphoricityAttributeCalculator.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/AnaphoricityAttributeCalculator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -32,7 +32,7 @@ import org.apache.ctakes.typesystem.type
 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;
+import org.apache.ctakes.coreference.type.Markable;
 
 public class AnaphoricityAttributeCalculator extends AttributeCalculator {
 

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

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

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java (from r1388196, 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/org/apache/ctakes/coreference/util/AnnotationSelector.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AnnotationSelector.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/AnnotationSelector.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.util.ArrayList;
 import java.util.HashSet;

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AttributeCalculator.java (from r1388196, 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/org/apache/ctakes/coreference/util/AttributeCalculator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AttributeCalculator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/AttributeCalculator.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/AttributeCalculator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -30,7 +30,7 @@ import org.apache.uima.jcas.tcas.Annotat
 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;
+import org.apache.ctakes.coreference.type.Markable;
 
 public class AttributeCalculator {
 

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

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

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

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

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/GoldStandardLabeler.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/GoldStandardLabeler.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/GoldStandardLabeler.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/GoldStandardLabeler.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/GoldStandardLabeler.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/GoldStandardLabeler.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/GoldStandardLabeler.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -26,12 +26,12 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
+import org.apache.ctakes.coreference.eval.helpers.Span;
+import org.apache.ctakes.coreference.eval.helpers.SpanAlignment;
+import org.apache.ctakes.coreference.eval.helpers.SpanOffsetComparator;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.Span;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.SpanAlignment;
-import org.chboston.cnlp.ctakes.coref.eval.helpers.SpanOffsetComparator;
 
-import edu.mayo.bmi.uima.coref.type.Markable;
+import org.apache.ctakes.coreference.type.Markable;
 
 public class GoldStandardLabeler {
 	private String dir = null;

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/HobbsTreeNavigator.java (from r1388196, 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/org/apache/ctakes/coreference/util/HobbsTreeNavigator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/HobbsTreeNavigator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/HobbsTreeNavigator.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/HobbsTreeNavigator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.util.HashMap;
 import java.util.HashSet;
@@ -30,7 +30,7 @@ import org.apache.uima.jcas.tcas.Annotat
 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;
+import org.apache.ctakes.coreference.type.Markable;
 
 public class HobbsTreeNavigator {
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableDepUtils.java (from r1388196, 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/org/apache/ctakes/coreference/util/MarkableDepUtils.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableDepUtils.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableDepUtils.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/MarkableDepUtils.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableTreeUtils.java (from r1388196, 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/org/apache/ctakes/coreference/util/MarkableTreeUtils.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableTreeUtils.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/MarkableTreeUtils.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/MarkableTreeUtils.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.util.Iterator;
 
@@ -27,7 +27,7 @@ import org.apache.uima.jcas.tcas.Annotat
 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;
+import org.apache.ctakes.coreference.type.Markable;
 
 public class MarkableTreeUtils {
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java (from r1388196, 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/org/apache/ctakes/coreference/util/PairAttributeCalculator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/PairAttributeCalculator.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/PairAttributeCalculator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -36,7 +36,8 @@ import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.StringArray;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.resource.FileLocator;
+import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.coreference.util.AnnotationSelector;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
@@ -44,11 +45,10 @@ import org.apache.ctakes.typesystem.type
 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;
-import edu.mayo.bmi.uima.coref.type.NEMarkable;
-import edu.mayo.bmi.uima.coref.type.PronounMarkable;
+import org.apache.ctakes.coreference.type.DemMarkable;
+import org.apache.ctakes.coreference.type.Markable;
+import org.apache.ctakes.coreference.type.NEMarkable;
+import org.apache.ctakes.coreference.type.PronounMarkable;
 
 public class PairAttributeCalculator extends AttributeCalculator {
 

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ParentPtrTree.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/ParentPtrTree.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ParentPtrTree.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ParentPtrTree.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/ParentPtrTree.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/ParentPtrTree.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ParentPtrTree.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 public class ParentPtrTree {
 	private int[] parents;

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

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/SvmVectorCreator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/SvmVectorCreator.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/SvmVectorCreator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.lang.reflect.Method;
 import java.util.ArrayList;
@@ -30,14 +30,14 @@ import libsvm.svm_node;
 
 import opennlp.tools.parser.Parse;
 
+import org.apache.ctakes.constituency.parser.treekernel.TreeExtractor;
+import org.apache.ctakes.constituency.parser.util.TreeUtils;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.chboston.cnlp.ctakes.parser.treekernel.TreeExtractor;
-import org.chboston.cnlp.ctakes.parser.util.TreeUtils;
-import org.chboston.cnlp.util.FragmentUtils;
-import org.chboston.cnlp.util.SimpleTree;
 
-import edu.mayo.bmi.uima.coref.type.Markable;
+import org.apache.ctakes.coreference.type.Markable;
+import org.apache.ctakes.typesystem.util.FragmentUtils;
+import org.apache.ctakes.typesystem.util.SimpleTree;
 
 public class SvmVectorCreator {
 	HashSet<String> stopwords = null;

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SyntaxAttributeCalculator.java (from r1388196, 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/org/apache/ctakes/coreference/util/SyntaxAttributeCalculator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SyntaxAttributeCalculator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/SyntaxAttributeCalculator.java&r1=1388196&r2=1389618&rev=1389618&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/org/apache/ctakes/coreference/util/SyntaxAttributeCalculator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
 import java.io.FileNotFoundException;
 import java.rmi.UnexpectedException;
@@ -29,14 +29,14 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.StringArray;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.resource.FileLocator;
+import org.apache.ctakes.core.resource.FileLocator;
 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;
-import edu.mayo.bmi.uima.coref.type.PronounMarkable;
+import org.apache.ctakes.coreference.type.Markable;
+import org.apache.ctakes.coreference.type.DemMarkable;
+import org.apache.ctakes.coreference.type.NEMarkable;
+import org.apache.ctakes.coreference.type.PronounMarkable;
 
 public class SyntaxAttributeCalculator extends PairAttributeCalculator {
 

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

Copied: incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ThreadDelegator.java (from r1388092, incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/ThreadDelegator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ThreadDelegator.java?p2=incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ThreadDelegator.java&p1=incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/ThreadDelegator.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/src/main/java/edu/mayo/bmi/coref/util/ThreadDelegator.java (original)
+++ incubator/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ThreadDelegator.java Mon Sep 24 22:04:51 2012
@@ -16,9 +16,9 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.coref.util;
+package org.apache.ctakes.coreference.util;
 
-import org.chboston.cnlp.ctakes.coref.treekernel.training.RowFillerThread;
+import org.apache.ctakes.coreference.treekernel.training.RowFillerThread;
 
 public interface ThreadDelegator {
 	public void threadDone(RowFillerThread t);

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=1389618&r1=1389617&r2=1389618&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 Mon Sep 24 22:04:51 2012
@@ -22,12 +22,12 @@
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>true</primitive>
-    <annotatorImplementationName>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
+    <annotatorImplementationName>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</annotatorImplementationName>
     <analysisEngineMetaData>
-        <name>edu.mayo.bmi.nlp.parser.ae.ClearParserDependencyParserAE</name>
+        <name>org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE</name>
         <description>Descriptor automatically generated by uimaFIT</description>
         <version>unknown</version>
-        <vendor>edu.mayo.bmi.nlp.parser.ae</vendor>
+        <vendor>org.apache.ctakes.dependency.parser.ae</vendor>
         <configurationParameters>
             <configurationParameter>
                 <name>ParserModelFileName</name>
@@ -67,7 +67,7 @@
         </configurationParameterSettings>
         <typeSystemDescription>
             <imports>
-                <import location="../../../common-type-system/desc/common_type_system.xml"/>
+                <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
             </imports>
         </typeSystemDescription>
         <fsIndexCollection/>



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