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From chen...@apache.org
Subject svn commit: r1389618 [17/22] - 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-ne-contexts/resources/launch/NegationAnnotatorTests.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/resources/launch/NegationAnnotatorTests.launch?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/resources/launch/NegationAnnotatorTests.launch (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/resources/launch/NegationAnnotatorTests.launch Mon Sep 24 22:04:51 2012
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <launchConfiguration type="org.eclipse.jdt.junit.launchconfig">
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/NE contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java"/>
+<listEntry value="/ctakes-ne-contexts/test/src/main/java/org/apache/ctakes/context/NegationAnnotatorTests.java"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
 <listEntry value="1"/>
@@ -11,6 +11,6 @@
 <booleanAttribute key="org.eclipse.jdt.junit.KEEPRUNNING_ATTR" value="false"/>
 <stringAttribute key="org.eclipse.jdt.junit.TESTNAME" value=""/>
 <stringAttribute key="org.eclipse.jdt.junit.TEST_KIND" value="org.eclipse.jdt.junit.loader.junit4"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="edu.mayo.bmi.uima.context.NegationAnnotatorTests"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.ctakes.necontexts.NegationAnnotatorTests"/>
 <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="NE contexts"/>
 </launchConfiguration>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/resources/launch/StatusAnnotatorTests.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/resources/launch/StatusAnnotatorTests.launch?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/resources/launch/StatusAnnotatorTests.launch (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/resources/launch/StatusAnnotatorTests.launch Mon Sep 24 22:04:51 2012
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <launchConfiguration type="org.eclipse.jdt.junit.launchconfig">
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/NE contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java"/>
+<listEntry value="/ctakes-ne-contexts/test/src/main/java/org/apache/ctakes/context/StatusAnnotatorTests.java"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
 <listEntry value="1"/>
@@ -11,6 +11,6 @@
 <booleanAttribute key="org.eclipse.jdt.junit.KEEPRUNNING_ATTR" value="false"/>
 <stringAttribute key="org.eclipse.jdt.junit.TESTNAME" value=""/>
 <stringAttribute key="org.eclipse.jdt.junit.TEST_KIND" value="org.eclipse.jdt.junit.loader.junit4"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="edu.mayo.bmi.uima.context.StatusAnnotatorTests"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.ctakes.necontexts.StatusAnnotatorTests"/>
 <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="NE contexts"/>
 </launchConfiguration>

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnalyzer.java (from r1388092, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextAnalyzer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnalyzer.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnalyzer.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextAnalyzer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextAnalyzer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnalyzer.java Mon Sep 24 22:04:51 2012
@@ -16,10 +16,11 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context;
+package org.apache.ctakes.necontexts;
 
 import java.util.List;
 
+import org.apache.ctakes.necontexts.negation.NegationContextAnalyzer;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.analysis_engine.annotator.AnnotatorConfigurationException;
@@ -28,7 +29,6 @@ import org.apache.uima.analysis_engine.a
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.context.negation.NegationContextAnalyzer;
 
 /**
  * A context analyzer analyzes a set of annotations that make up a context and

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

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java (from r1388092, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextAnnotator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextAnnotator.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java Mon Sep 24 22:04:51 2012
@@ -16,13 +16,14 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context;
+package org.apache.ctakes.necontexts;
 
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
+import org.apache.ctakes.core.util.JCasUtil;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
@@ -36,7 +37,6 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.apache.uima.jcas.tcas.DocumentAnnotation;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.core.util.JCasUtil;
 
 /**
  * The context annotator iterates through focus annotations and analyzes the

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextHit.java (from r1388092, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextHit.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextHit.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextHit.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextHit.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/ContextHit.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextHit.java Mon Sep 24 22:04:51 2012
@@ -16,12 +16,13 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context;
+package org.apache.ctakes.necontexts;
 
 import java.util.HashMap;
 import java.util.Map;
 
-import edu.mayo.bmi.fsm.output.BaseTokenImpl;
+import org.apache.ctakes.core.fsm.output.BaseTokenImpl;
+
 
 /**
  * Object represents a hit relating to a focus annotation.

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

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

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java (from r1388092, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextAnalyzer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextAnalyzer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextAnalyzer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context;
+package org.apache.ctakes.necontexts;
 
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -24,14 +24,14 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
+import org.apache.ctakes.core.fsm.adapters.TextTokenAdapter;
+import org.apache.ctakes.core.fsm.token.TextToken;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.fsm.token.TextToken;
-import edu.mayo.bmi.uima.core.fsm.adapters.TextTokenAdapter;
 
 /**
  * This context analyzer provides code that is shared by the

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextHitConsumer.java (from r1388196, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextHitConsumer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextHitConsumer.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextHitConsumer.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextHitConsumer.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/NamedEntityContextHitConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextHitConsumer.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context;
+package org.apache.ctakes.necontexts;
 
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextAnalyzer.java (from r1388092, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextAnalyzer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextAnalyzer.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextAnalyzer.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextAnalyzer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextAnalyzer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextAnalyzer.java Mon Sep 24 22:04:51 2012
@@ -16,19 +16,19 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context.negation;
+package org.apache.ctakes.necontexts.negation;
 
 import java.util.List;
 import java.util.Set;
 
+import org.apache.ctakes.core.fsm.machine.NegationFSM;
+import org.apache.ctakes.core.fsm.output.NegationIndicator;
+import org.apache.ctakes.core.fsm.token.TextToken;
+import org.apache.ctakes.necontexts.ContextHit;
+import org.apache.ctakes.necontexts.NamedEntityContextAnalyzer;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.fsm.machine.NegationFSM;
-import edu.mayo.bmi.fsm.output.NegationIndicator;
-import edu.mayo.bmi.fsm.token.TextToken;
-import edu.mayo.bmi.uima.context.ContextHit;
-import edu.mayo.bmi.uima.context.NamedEntityContextAnalyzer;
 
 public class NegationContextAnalyzer extends NamedEntityContextAnalyzer {
 	private NegationFSM _negIndicatorFSM = new NegationFSM();

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextHitConsumer.java (from r1388196, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextHitConsumer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextHitConsumer.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextHitConsumer.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextHitConsumer.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/negation/NegationContextHitConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextHitConsumer.java Mon Sep 24 22:04:51 2012
@@ -16,16 +16,16 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context.negation;
+package org.apache.ctakes.necontexts.negation;
 
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
+import org.apache.ctakes.necontexts.ContextHit;
+import org.apache.ctakes.necontexts.ContextHitConsumer;
+import org.apache.ctakes.necontexts.NamedEntityContextHitConsumer;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.context.ContextHitConsumer;
-import edu.mayo.bmi.uima.context.ContextHit;
-import edu.mayo.bmi.uima.context.NamedEntityContextHitConsumer;
 
 /**
  * @author Mayo Clinic

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextAnalyzer.java (from r1388092, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextAnalyzer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextAnalyzer.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextAnalyzer.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextAnalyzer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextAnalyzer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextAnalyzer.java Mon Sep 24 22:04:51 2012
@@ -16,22 +16,22 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context.status;
+package org.apache.ctakes.necontexts.status;
 
 import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
+import org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM;
+import org.apache.ctakes.core.fsm.output.StatusIndicator;
+import org.apache.ctakes.core.fsm.token.TextToken;
+import org.apache.ctakes.necontexts.ContextAnalyzer;
+import org.apache.ctakes.necontexts.ContextAnnotator;
+import org.apache.ctakes.necontexts.ContextHit;
+import org.apache.ctakes.necontexts.NamedEntityContextAnalyzer;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.fsm.machine.StatusIndicatorFSM;
-import edu.mayo.bmi.fsm.output.StatusIndicator;
-import edu.mayo.bmi.fsm.token.TextToken;
-import edu.mayo.bmi.uima.context.ContextAnnotator;
-import edu.mayo.bmi.uima.context.ContextHit;
-import edu.mayo.bmi.uima.context.ContextAnalyzer;
-import edu.mayo.bmi.uima.context.NamedEntityContextAnalyzer;
 
 public class StatusContextAnalyzer extends NamedEntityContextAnalyzer implements ContextAnalyzer {
 	public static final String CTX_HIT_KEY_STATUS_TYPE = "STATUS_TYPE";

Copied: incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextHitConsumer.java (from r1388196, incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextHitConsumer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextHitConsumer.java?p2=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextHitConsumer.java&p1=incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextHitConsumer.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/edu/mayo/bmi/uima/context/status/StatusContextHitConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextHitConsumer.java Mon Sep 24 22:04:51 2012
@@ -16,16 +16,16 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context.status;
+package org.apache.ctakes.necontexts.status;
 
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
+import org.apache.ctakes.necontexts.ContextHit;
+import org.apache.ctakes.necontexts.ContextHitConsumer;
+import org.apache.ctakes.necontexts.NamedEntityContextHitConsumer;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.context.ContextHitConsumer;
-import edu.mayo.bmi.uima.context.ContextHit;
-import edu.mayo.bmi.uima.context.NamedEntityContextHitConsumer;
 
 /**
  * @author Mayo Clinic

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/NegationAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/NegationAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/NegationAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/NegationAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.context.ContextAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.necontexts.ContextAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>NegationAnnotator</name>
     <configurationParameters>
@@ -104,7 +104,7 @@
       <nameValuePair>
         <name>ContextHitConsumerClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.context.negation.NegationContextHitConsumer</string>
+          <string>org.apache.ctakes.necontexts.negation.NegationContextHitConsumer</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -128,7 +128,7 @@
       <nameValuePair>
         <name>ContextAnalyzerClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.context.negation.NegationContextAnalyzer</string>
+          <string>org.apache.ctakes.necontexts.negation.NegationContextAnalyzer</string>
         </value>
       </nameValuePair>
     </configurationParameterSettings>
@@ -145,7 +145,7 @@
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.necontexts.type.ContextAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SentenceDetectorAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SentenceDetectorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SentenceDetectorAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 <primitive>true</primitive>
-<annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SentenceDetector</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.core.ae.SentenceDetector</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>Sentence Detector annotator</name>
 <description>Discovers sentence boundaries.</description>
@@ -55,7 +55,7 @@
 <externalResourceDependency>
 <key>MaxentModel</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.MaxentModelResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.MaxentModelResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -67,7 +67,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:sentdetect/sample_sd_included.mod</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.SuffixMaxentModelResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.SuffixMaxentModelResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SimpleSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SimpleSegmentAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SimpleSegmentAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/SimpleSegmentAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>SimpleSegmentAnnotator</name>
     <description/>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/StatusAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/StatusAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/StatusAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/StatusAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.context.ContextAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.necontexts.ContextAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>StatusAnnotator</name>
     <configurationParameters>
@@ -104,7 +104,7 @@
       <nameValuePair>
         <name>ContextHitConsumerClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.context.status.StatusContextHitConsumer</string>
+          <string>org.apache.ctakes.necontexts.status.StatusContextHitConsumer</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -128,7 +128,7 @@
       <nameValuePair>
         <name>ContextAnalyzerClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.context.status.StatusContextAnalyzer</string>
+          <string>org.apache.ctakes.necontexts.status.StatusContextAnalyzer</string>
         </value>
       </nameValuePair>
     </configurationParameterSettings>
@@ -146,7 +146,7 @@
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.necontexts.type.ContextAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TestContextAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TestContextAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TestContextAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TestContextAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.context.ContextAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.necontexts.ContextAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>NegationAnnotator</name>
     <configurationParameters>
@@ -105,7 +105,7 @@
       <nameValuePair>
         <name>ContextHitConsumerClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.context.ContextHitConsumerAdapter</string>
+          <string>org.apache.ctakes.necontexts.ContextHitConsumerAdapter</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -129,7 +129,7 @@
       <nameValuePair>
         <name>ContextAnalyzerClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.context.ContextAnalyzerAdapter</string>
+          <string>org.apache.ctakes.necontexts.ContextAnalyzerAdapter</string>
         </value>
       </nameValuePair>
     </configurationParameterSettings>
@@ -146,7 +146,7 @@
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.necontexts.type.ContextAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TokenizerAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TokenizerAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TokenizerAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/desc/TokenizerAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.TokenizerAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.core.ae.TokenizerAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>TokenizerAnnotator</name>
     <description>Discovers tokens in the given text.  These tokens consist of words, punctuation, etc...</description>
@@ -85,7 +85,7 @@
     <externalResourceDependency>
       <key>HyphFreqTable</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.StringIntegerMapResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.StringIntegerMapResource</interfaceName>
       <optional>true</optional>
     </externalResourceDependency>
   </externalResourceDependencies>
@@ -97,7 +97,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:tokenizer/hyphenated.txt</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.StringIntegerMapResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.StringIntegerMapResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/ContextAnnotatorTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/ContextAnnotatorTests.java?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/ContextAnnotatorTests.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/ContextAnnotatorTests.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context;
+package org.apache.ctakes.necontexts;
 
 import static org.junit.Assert.assertEquals;
 

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/NegationAnnotatorTests.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context;
+package org.apache.ctakes.necontexts;
 
 import static org.junit.Assert.assertEquals;
 
@@ -49,8 +49,8 @@ public class NegationAnnotatorTests {
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.MAX_RIGHT_SCOPE_SIZE_PARAM, new Integer(10));
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.SCOPE_ORDER_PARAM, "LEFT", 0);
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.SCOPE_ORDER_PARAM, "RIGHT", 1);
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANALYZER_CLASS_PARAM, "edu.mayo.bmi.uima.context.negation.NegationContextAnalyzer");
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_HIT_CONSUMER_CLASS_PARAM, "edu.mayo.bmi.uima.context.negation.NegationContextHitConsumer");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANALYZER_CLASS_PARAM, "org.apache.ctakes.necontexts.negation.NegationContextAnalyzer");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_HIT_CONSUMER_CLASS_PARAM, "org.apache.ctakes.necontexts.negation.NegationContextHitConsumer");
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.WINDOW_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.textspan.Sentence");
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.FOCUS_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation");
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.syntax.BaseToken");

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/test/src/edu/mayo/bmi/uima/context/StatusAnnotatorTests.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.context;
+package org.apache.ctakes.necontexts;
 
 import static org.junit.Assert.assertEquals;
 
@@ -47,8 +47,8 @@ public class StatusAnnotatorTests {
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.MAX_RIGHT_SCOPE_SIZE_PARAM, new Integer(7));
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.SCOPE_ORDER_PARAM, "LEFT", 0);
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.SCOPE_ORDER_PARAM, "RIGHT", 1);
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANALYZER_CLASS_PARAM, "edu.mayo.bmi.uima.context.status.StatusContextAnalyzer");
-		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_HIT_CONSUMER_CLASS_PARAM, "edu.mayo.bmi.uima.context.status.StatusContextHitConsumer");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANALYZER_CLASS_PARAM, "org.apache.ctakes.necontexts.status.StatusContextAnalyzer");
+		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_HIT_CONSUMER_CLASS_PARAM, "org.apache.ctakes.necontexts.status.StatusContextHitConsumer");
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.WINDOW_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.textspan.Sentence");
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.FOCUS_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.IdentifiedAnnotation");
 		TestUtil.testConfigParam(uimaContext, descriptor, ContextAnnotator.CONTEXT_ANNOTATION_CLASS_PARAM, "org.apache.ctakes.typesystem.type.syntax.BaseToken");

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/README?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/README (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/README Mon Sep 24 22:04:51 2012
@@ -37,7 +37,7 @@ lookup annotator is limited to PAD term 
 Overview of PAD term spotter pipeline
 #####################################
 
-The ‘PAD term spotter’ pipeline processes radiology note textual extractions specifically pertaining to the diagnosis, treatment, etc. of lower
+The �PAD term spotter� pipeline processes radiology note textual extractions specifically pertaining to the diagnosis, treatment, etc. of lower
 limb Peripheral Artery Disease (PAD)(e.g. stenosis/occlusion paired with popliteal/femoral).  The main feature is classifying each document for the presence of PAD. 
 Descriptive text of diagnosis and illness terms are paired with the site designated terms to build a relational tie, indicating a 'hit'. The pipeline 
 assesses presence of phrases indicative of peripheral arterial disease (PAD) in one or more sentences contained in radiology related documents.
@@ -68,7 +68,7 @@ Prerequisite steps
 
 	- Install all the cTAKES components, dependencies (e.g. JVM, UIMA, and Eclipse(optional)).
     
-	- Make sure the clinical documents pipeline of cTAKES and the Apache UIMA are setup correctly by running the CAS Visual Debugger (CVD) as 
+	- Make sure the ctakes-clinical-pipeline of cTAKES and the Apache UIMA are setup correctly by running the CAS Visual Debugger (CVD) as 
 	described in the 'Clinical Text	Analysis and Knowledge Extraction System User Guide' 1.2. Install from PEAR packages.
   
 	- Press the "Run your AE in the CAS Visual Debugger" from the "Local PEAR Installation, Verification and Testing" panel after installing the
@@ -104,7 +104,7 @@ java -cp ^
 %UIMA_HOME%/lib/uima-document-annotations.jar;^
 %UIMA_HOME%/lib/uima-examples.jar;^
 chunker/bin;^
-clinical documents pipeline/bin;^
+ctakes-clinical-pipeline/bin;^
 context dependent tokenizer/bin;^
 core/bin;^
 dictionary lookup/bin;^
@@ -125,7 +125,7 @@ document preprocessor/lib/xercesImpl.jar
 document preprocessor/lib/xml-apis.jar;^
 document preprocessor/lib/xmlParserAPIs.jar;^
 chunker/resources;^
-clinical documents pipeline/resources;^
+ctakes-clinical-pipeline/resources;^
 context dependent tokenizer/resources;^
 core/resources;^
 dictionary lookup/resources;^
@@ -176,14 +176,14 @@ PAD\ term\ spotter/resources:\
 POS\ tagger/resources \
 org.apache.uima.tools.cpm.CpmFrame	 
 
-Step 2: From the pull down menu open the “Radiology_sample.xml” via 'File' => 'Open CPE Descriptor' => 'PAD term spotter/desc/collection_processing _engine/Radiology_sample.xml'.
+Step 2: From the pull down menu open the �Radiology_sample.xml� via 'File' => 'Open CPE Descriptor' => 'PAD term spotter/desc/collection_processing _engine/Radiology_sample.xml'.
 
-This will load the sample Collection Processing Engine (CPE) “Radiology_sample.xml”.  
+This will load the sample Collection Processing Engine (CPE) �Radiology_sample.xml�.  
 A sample CPE has been provided along with de-identified patient information to provide a means to test the pipeline after you have set up the environment. FYI.  '{inst-root-dir}/data/SampleInputRadiologyNotes.txt' contains 
 6 sample radiology notes representing two different patients.
 
-Step 3: In order to run this sample you will need to specify the path where you installed the cTAKES projects or the Eclipse workspace in place of the ‘{inst-root-dir}' (<pipeline-root>) 
-within the existing paths provided in the ‘Input File Name:” and “Filter Exam Types:” fields.  
+Step 3: In order to run this sample you will need to specify the path where you installed the cTAKES projects or the Eclipse workspace in place of the �{inst-root-dir}' (<pipeline-root>) 
+within the existing paths provided in the �Input File Name:� and �Filter Exam Types:� fields.  
  
 Step 4: Additionally, within the 'Output File Name' field specify the path and file name to output the record level radiology on your system ('{inst-root-dir}/PAD term spotter/output/Sample_PAD_record_level.txt' => outfile path and name ).  
 
@@ -218,7 +218,7 @@ Collection reader (input vehicle for pip
 ##############################################
 
 Radiology notes can be input into the system as a simple flat file, containing one or more radiology notes or in a wrapped/encapsulated CDA or similar
-clinical note structure (see the clinical documents pipeline for examples and direction for writing Collection Readers and/or CAS Initializers for 
+clinical note structure (see the ctakes-clinical-pipeline for examples and direction for writing Collection Readers and/or CAS Initializers for 
 this purpose).  This project includes one specialized input collector, located under 'desc/collection_reader' called 
 'RadiologyRecordsCollectionReader.xml'.   
 
@@ -277,13 +277,13 @@ SubSectionBoundaryAnnotator.xml
 is to identify sections within the text that indicate paragraphs, subsections, and groups of text that should be handled as one entity.  The file resource 
 'lookup/radiology/ExamTitleWords.txt' provides the site specific terms used to indicate the start of subsections.  The subsections will span until either another 
 subsection beginning is discover or the end of the document.  
-The file 'desc/analysis_engine/SubSectionBoundaryAnnotator.xml' drives the java class 'edu.mayo.bmi.uima.termspotter.ae.SubSectionAnnotator' which the primary task 
+The file 'desc/analysis_engine/SubSectionBoundaryAnnotator.xml' drives the java class 'org.apache.ctakes.padtermspotter.ae.SubSectionAnnotator' which the primary task 
 
 [NOTE]
 ===============================================================================================================
 The class 'core/src/edu/mayo/bmi/fsm/machine/SubSectionPadIdFSM' will identified section headers and classify as 
 CONFIRMED_STATUS, NEGATED_STATUS, or PROBABLE_STATUS.  However, only 'NEGATED_STATUS' is being implemented within
- the logic ('PAD term spotter/src/edu/mayo/bmi/uima/pad/impl/PADConsumerImpl.java' will not add 'hits' in sections 
+ the logic ('PAD term spotter/src/main/java/org/apache/ctakes/pad/impl/PADConsumerImpl.java' will not add 'hits' in sections 
  tagged with this status). 
 ================================================================================================================
 [NOTE]
@@ -298,7 +298,7 @@ as it pertains to the subsection handlin
 		screened for  relating to PAD, but since they are titles of examinations, revision sections, and generalized
 		screenings they are to be ignored in the Mayo cohort.
 		
-2) 'PAD term spotter/src/edu/mayo/bmi/uima/pad/impl/PADConsumerImpl.java'
+2) 'PAD term spotter/src/main/java/org/apache/ctakes/pad/impl/PADConsumerImpl.java'
 	- terms; "indications:" and "showing" are special terms which often contain the terms being screened for relating 
 		to PAD, but since they are titles of examinations, revision sections, and generalized screenings they are to 
 		be ignored in the Mayo cohort. "maxSubsectionSize" is used to limit the overall scope of where the subsection 
@@ -318,12 +318,12 @@ as it pertains to the subsection handlin
 Radiology_DictionaryLookupCSVAnnotator.xml
 
 The file 'desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml' drives the java class 
-'edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator' which resides in the 'dictionary lookup' project.  It is setup to access the 
+'org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator' which resides in the 'dictionary lookup' project.  It is setup to access the 
 '/resources/lookup/radiology/LookupDesc_PAD.xml' file which specifies what resources will be accessed, 
-which are the PAD Term dictionaries in this case.  Specifically, the files “PAD term spotter\resources\lookup\radiology\pad_anatomical_sites.csv” and 
-“PAD term spotter\resources\lookup\radiology\pad_disorders.csv” are loaded into memory.
+which are the PAD Term dictionaries in this case.  Specifically, the files �PAD term spotter\resources\lookup\radiology\pad_anatomical_sites.csv� and 
+�PAD term spotter\resources\lookup\radiology\pad_disorders.csv� are loaded into memory.
 
-The terms being looked up have been added to dictionary e.g: “PAD term spotter\resources\lookup\radiology\pad_anatomical_sites.csv”
+The terms being looked up have been added to dictionary e.g: �PAD term spotter\resources\lookup\radiology\pad_anatomical_sites.csv�
 Using format as follows: "first-word|first-word plus terms|value"
  
 'value' indicates how the term should be used when paired with the relational term, a context value, or some other special cases which is discussed in more 
@@ -340,7 +340,7 @@ hyphenated, but that term must exist in 
 %%%%%%%%%%%
 PAD_Hit.xml
 
-The file 'desc/analysis_engine/PAD_Hit.xml' drives the java class 'edu.mayo.bmi.uima.termspotter.ae.PADHitAnnotator' which operates on the terms discovered in the dictionary 
+The file 'desc/analysis_engine/PAD_Hit.xml' drives the java class 'org.apache.ctakes.padtermspotter.ae.PADHitAnnotator' which operates on the terms discovered in the dictionary 
 annotator.
 Params: WINDOW_SIZE, ANNOTATION_TYPE, ANNOTATION_PART_ONE_OF_PAIR, ANNOTATION_PART_TWO_OF_PAIR, may be others
 a) If the annotations of type part_one and part_two fall in the window_size of type annotation_type, it is considered a hit.

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/DxStatusAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 <primitive>true</primitive>
-<annotatorImplementationName>edu.mayo.bmi.uima.context.ContextAnnotator</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.necontexts.ContextAnnotator</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>DxStatusAnnotator</name>
 <description></description>
@@ -120,13 +120,13 @@
 <nameValuePair>
 <name>ContextAnalyzerClass</name>
 <value>
-<string>edu.mayo.bmi.uima.pad.impl.DxContextAnalyzerImpl</string>
+<string>org.apache.ctakes.padtermspotter.impl.DxContextAnalyzerImpl</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ContextHitConsumerClass</name>
 <value>
-<string>edu.mayo.bmi.uima.pad.impl.DxContextHitConsumerImpl</string>
+<string>org.apache.ctakes.padtermspotter.impl.DxContextHitConsumerImpl</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -161,7 +161,7 @@
 <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.necontexts.type.ContextAnnotation</type>
 </outputs>
 <languagesSupported/>
 </capability>
@@ -176,7 +176,7 @@
 <externalResourceDependency>
 <key>BoundaryData</key>
 <description>the file resource handle that will be used in the annotator</description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -188,7 +188,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:negation/boundaryData.txt</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/NegationDxAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 <primitive>true</primitive>
-<annotatorImplementationName>edu.mayo.bmi.uima.context.ContextAnnotator</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.necontexts.ContextAnnotator</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>NegationAnnotator</name>
 <description>Changes in 1.1:
@@ -121,13 +121,13 @@
 <nameValuePair>
 <name>ContextAnalyzerClass</name>
 <value>
-<string>edu.mayo.bmi.uima.pad.impl.NegativeContextAnalyzerImpl</string>
+<string>org.apache.ctakes.padtermspotter.impl.NegativeContextAnalyzerImpl</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ContextHitConsumerClass</name>
 <value>
-<string>edu.mayo.bmi.uima.pad.impl.NegativeContextHitConsumerImpl</string>
+<string>org.apache.ctakes.padtermspotter.impl.NegativeContextHitConsumerImpl</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -160,7 +160,7 @@
 <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.context.type.ContextAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.necontexts.type.ContextAnnotation</type>
 </outputs>
 <languagesSupported/>
 </capability>
@@ -175,7 +175,7 @@
 <externalResourceDependency>
 <key>BoundaryData</key>
 <description>the file resource handle that will be used in the annotator</description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -187,7 +187,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:negation/boundaryData.txt</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/PAD_Hit.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 <primitive>true</primitive>
-<annotatorImplementationName>edu.mayo.bmi.uima.termspotter.ae.PADHitAnnotator</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.padtermspotter.ae.PADHitAnnotator</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>PAD_Hit</name>
 <description>Uses PADTerm and PADLocation annotation to create a PADHit.</description>
@@ -104,13 +104,13 @@
 <nameValuePair>
 <name>ANNOTATION_PART_ONE_OF_PAIR</name>
 <value>
-<string>edu.mayo.bmi.uima.pad.type.PADTerm</string>
+<string>org.apache.ctakes.padtermspotter.type.PADTerm</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>ANNOTATION_PART_TWO_OF_PAIR</name>
 <value>
-<string>edu.mayo.bmi.uima.pad.type.PADLocation</string>
+<string>org.apache.ctakes.padtermspotter.type.PADLocation</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -128,7 +128,7 @@
 <nameValuePair>
 <name>BOUNDARY_ANN_TYPE</name>
 <value>
-<string>edu.mayo.bmi.uima.pad.type.SubSection</string>
+<string>org.apache.ctakes.padtermspotter.type.SubSection</string>
 </value>
 </nameValuePair>
 <nameValuePair>
@@ -180,7 +180,7 @@
 <externalResourceDependency>
 <key>StopWordsFile</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -192,7 +192,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:lookup/radiology/StopWords.txt</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 <primitive>true</primitive>
-<annotatorImplementationName>edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>DictionaryLookupAnnotator</name>
 <description>Dictionarylookup for PAD discovery in Radiology reports.</description>
@@ -59,19 +59,19 @@
 <externalResourceDependency>
 <key>LookupDescriptor</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 <externalResourceDependency>
 <key>PAD_Location_File</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 <externalResourceDependency>
 <key>PAD_Terms_File</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -83,7 +83,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:lookup/radiology/LookupDesc_PAD.xml</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 <externalResource>
 <name>PAD_Location_FileResrc</name>
@@ -91,7 +91,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:lookup/radiology/pad_anatomical_sites.csv</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 <externalResource>
 <name>PAD_Terms_FileResrc</name>
@@ -99,7 +99,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:lookup/radiology/pad_disorders.csv</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml Mon Sep 24 22:04:51 2012
@@ -30,31 +30,31 @@
 <import location="DxStatusAnnotator.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="SimpleSegmentAnnotator">
-<import location="../../../core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
+<import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="SubSectionBoundaryAnnotator">
 <import location="SubSectionBoundaryAnnotator.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="Chunker">
-<import location="../../../chunker/desc/Chunker.xml"/>
+<import location="../../../ctakes-chunker/desc/Chunker.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-<import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+<import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="NegationAnnotator">
-<import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+<import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-<import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+<import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="TokenizerAnnotator">
-<import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+<import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="NegationDxAnnotator">
 <import location="NegationDxAnnotator.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="POSTagger">
-<import location="../../../POS tagger/desc/POSTagger.xml"/>
+<import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
 </delegateAnalysisEngine>
 <delegateAnalysisEngine key="Radiology_DictionaryLookupCSVAnnotator">
 <import location="Radiology_DictionaryLookupCSVAnnotator.xml"/>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/SubSectionBoundaryAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 <primitive>true</primitive>
-<annotatorImplementationName>edu.mayo.bmi.uima.termspotter.ae.SubSectionAnnotator</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.padtermspotter.ae.SubSectionAnnotator</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>SubSectionBoundaryAnnotator</name>
 <description></description>
@@ -55,7 +55,7 @@
 <externalResourceDependency>
 <key>ExamTitleWordsFile</key>
 <description></description>
-<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -67,7 +67,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:lookup/radiology/ExamTitleWords.txt</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml Mon Sep 24 22:04:51 2012
@@ -21,7 +21,7 @@
 -->
 <casConsumerDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-<implementationName>edu.mayo.bmi.uima.termspotter.cc.PADOffSetsRecord</implementationName>
+<implementationName>org.apache.ctakes.padtermspotter.cc.PADOffSetsRecord</implementationName>
 <processingResourceMetaData>
 <name>PADOffSetRecord</name>
 <description>Processes a given CAS to identify predetermined list of PAD terms</description>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_reader/RadiologyRecordsCollectionReader.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_reader/RadiologyRecordsCollectionReader.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_reader/RadiologyRecordsCollectionReader.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_reader/RadiologyRecordsCollectionReader.xml Mon Sep 24 22:04:51 2012
@@ -21,7 +21,7 @@
 -->
 <collectionReaderDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-<implementationName>edu.mayo.bmi.uima.termspotter.cr.RadiologyRecordsCollectionReader</implementationName>
+<implementationName>org.apache.ctakes.padtermspotter.cr.RadiologyRecordsCollectionReader</implementationName>
 <processingResourceMetaData>
 <name>lines from file collection reader</name>
 <description>This collection reader facilitates reading "documents" from a single file.  Each line in the document will be considered an entity to be analyzed by the CPE.  That is each line will be treated as a "document" and will have its own CAS.</description>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/PADSiteAndTerm.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/PADSiteAndTerm.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/PADSiteAndTerm.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/PADSiteAndTerm.xml Mon Sep 24 22:04:51 2012
@@ -30,7 +30,7 @@
   </imports>
   <types>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.pad.type.PADTerm</name>
+      <name>org.apache.ctakes.padtermspotter.type.PADTerm</name>
       <description/>
       <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
       <features>
@@ -54,7 +54,7 @@ Valid values are 0 and 1. Where, 0 is fa
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.pad.type.PADLocation</name>
+      <name>org.apache.ctakes.padtermspotter.type.PADLocation</name>
       <description/>
       <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName>
       <features>
@@ -78,7 +78,7 @@ Valid values are 0 and 1. Where, 0 is fa
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.pad.type.PADHit</name>
+      <name>org.apache.ctakes.padtermspotter.type.PADHit</name>
       <description>Would represent one of the following
 Term (in the case of a stand alone term)
 Term + Location
@@ -88,12 +88,12 @@ Location + term</description>
         <featureDescription>
           <name>uaTerm</name>
           <description/>
-          <rangeTypeName>edu.mayo.bmi.uima.pad.type.PADTerm</rangeTypeName>
+          <rangeTypeName>org.apache.ctakes.padtermspotter.type.PADTerm</rangeTypeName>
         </featureDescription>
         <featureDescription>
           <name>uaLocation</name>
           <description/>
-          <rangeTypeName>edu.mayo.bmi.uima.pad.type.PADLocation</rangeTypeName>
+          <rangeTypeName>org.apache.ctakes.padtermspotter.type.PADLocation</rangeTypeName>
         </featureDescription>
       </features>
     </typeDescription>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/SubSection.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/SubSection.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/SubSection.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/type_system/SubSection.xml Mon Sep 24 22:04:51 2012
@@ -26,7 +26,7 @@
 <vendor></vendor>
 <types>
 <typeDescription>
-<name>edu.mayo.bmi.uima.pad.type.SubSection</name>
+<name>org.apache.ctakes.padtermspotter.type.SubSection</name>
 <description></description>
 <supertypeName>uima.tcas.Annotation</supertypeName>
 <features>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/doc/PAD_Overview.html
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/doc/PAD_Overview.html?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/doc/PAD_Overview.html (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/doc/PAD_Overview.html Mon Sep 24 22:04:51 2012
@@ -759,14 +759,14 @@ the full class name of an implementation
 <p>
 <strong>SubSectionBoundaryAnnotator.xml</strong>
 </p>
-<div class="paragraph"><p>The file <tt>desc/analysis_engine/SubSectionBoundaryAnnotator.xml</tt> drives the java class <em>edu.mayo.bmi.uima.termspotter.ae.SubSectionAnnotator</em> which the primary task is to identify sections within the text that indicate paragraphs, subsections, and groups of text that should be handled as one entity.  The file resource <a href="#examtitlewords">lookup/radiology/ExamTitleWords.txt</a> provides the site specific terms used to indicate the start of subsections.  The subsections will span until either another subsection beginning is discover or the end of the document.</p></div>
+<div class="paragraph"><p>The file <tt>desc/analysis_engine/SubSectionBoundaryAnnotator.xml</tt> drives the java class <em>org.apache.ctakes.padtermspotter.ae.SubSectionAnnotator</em> which the primary task is to identify sections within the text that indicate paragraphs, subsections, and groups of text that should be handled as one entity.  The file resource <a href="#examtitlewords">lookup/radiology/ExamTitleWords.txt</a> provides the site specific terms used to indicate the start of subsections.  The subsections will span until either another subsection beginning is discover or the end of the document.</p></div>
 <div class="admonitionblock">
 <table><tr>
 <td class="icon">
 <div class="title">Note</div>
 </td>
 <td class="content">
-<div class="paragraph"><p>The class <tt>core/src/edu/mayo/bmi/fsm/machine/SubSectionPadIdFSM</tt> will identified section headers and classify as CONFIRMED_STATUS, NEGATED_STATUS, or PROBABLE_STATUS.  However, only <em>NEGATED_STATUS</em> is being implemented within the logic (‘/PAD term spotter/src/edu/mayo/bmi/uima/pad/impl/PADConsumerImpl.java’ will not add <em>hits</em> in sections tagged with this status).</p></div>
+<div class="paragraph"><p>The class <tt>core/src/edu/mayo/bmi/fsm/machine/SubSectionPadIdFSM</tt> will identified section headers and classify as CONFIRMED_STATUS, NEGATED_STATUS, or PROBABLE_STATUS.  However, only <em>NEGATED_STATUS</em> is being implemented within the logic (‘/PAD term spotter/src/main/java/org/apache/ctakes/pad/impl/PADConsumerImpl.java’ will not add <em>hits</em> in sections tagged with this status).</p></div>
 </td>
 </tr></table>
 </div>
@@ -783,7 +783,7 @@ subsection handling:</p></div>
 <div class="paragraph"><p>1) ‘/PAD term spotter/src/edu/mayo/bmi/fsm/machine/SubSectionPadIdFSM.java’
 -Terms; "smh","rmh","gonda","romayo" are indicative of names of buildings on the Mayo campus which are used to mark subsection begin/end
 - terms; "indications","bleindications","exam","showing" are special terms which often contain the terms being screened for  relating to PAD, but since they are titles of examinations, revision sections, and generalized screenings they are to be ignored in the Mayo cohort.</p></div>
-<div class="paragraph"><p>2) ‘/PAD term spotter/src/edu/mayo/bmi/uima/pad/impl/PADConsumerImpl.java’
+<div class="paragraph"><p>2) ‘/PAD term spotter/src/main/java/org/apache/ctakes/pad/impl/PADConsumerImpl.java’
 - Terms; "indications:" and "showing" are special terms which often contain the terms being screened for relating to PAD, but since they are titles of examinations, revision sections, and generalized screenings they are to be ignored in the Mayo cohort. "maxSubsectionSize" is used to limit the overall scope of where the subsection tokens will be searched. It has been hardcoded to 300 in the shipped class.</p></div>
 <div class="paragraph"><p>3) <a href="#examtitlewords">‘/PAD term spotter/resources/lookup/radiology/ExamTitleWords.txt’</a>
 - Comma delimited terms which represent key values to distinguish the type of radiology examination being utilized:
@@ -799,14 +799,14 @@ US_EXAM (ultrasound), LOWER_EXT (lower e
 <strong>Radiology_DictionaryLookupCSVAnnotator.xml</strong>
 </p>
 <div class="paragraph"><p>The file <tt>desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml</tt>
-drives the java class  <tt>edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator</tt> which resides in the <tt>dictionary lookup</tt> project.  It is setup to access the <tt>/resources/lookup/radiology/LookupDesc_PAD.xml</tt> file which specifies what resources will be accessed,
+drives the java class  <tt>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator</tt> which resides in the <tt>dictionary lookup</tt> project.  It is setup to access the <tt>/resources/lookup/radiology/LookupDesc_PAD.xml</tt> file which specifies what resources will be accessed,
 which are the PAD Term dictionaries in this case.  Specifically, the files <tt>\PAD term spotter\resources\lookup\radiology\pad_anatomical_sites.csv\</tt> and <tt>\PAD term spotter\resources\lookup\radiology\pad_disorders.csv\</tt> are loaded into memory.</p></div>
 </li>
 <li>
 <p>
 <strong>PAD_Hit.xml</strong>
 </p>
-<div class="paragraph"><p>The file <tt>desc/analysis_engine/PAD_Hit.xml</tt> drives the java class <tt>edu.mayo.bmi.uima.termspotter.ae.PADHitAnnotator</tt> which operates on the terms discovered in the dictionary
+<div class="paragraph"><p>The file <tt>desc/analysis_engine/PAD_Hit.xml</tt> drives the java class <tt>org.apache.ctakes.padtermspotter.ae.PADHitAnnotator</tt> which operates on the terms discovered in the dictionary
 annotator.
 Params: WINDOW_SIZE, ANNOTATION_TYPE, ANNOTATION_PART_ONE_OF_PAIR, ANNOTATION_PART_TWO_OF_PAIR, may be others
 a) If the annotations of type part_one and part_two fall in the window_size of type annotation_type, it is considered a hit.

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (Drug NER).launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA%20CAS%20Visual%20Debugger%20%28Drug%20NER%29.launch?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (Drug NER).launch (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (Drug NER).launch Mon Sep 24 22:04:51 2012
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/DrugNER"/>
+<listEntry value="/ctakes-drug-ner"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
 <listEntry value="4"/>
@@ -12,13 +12,13 @@
 <listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
 <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry containerPath=&quot;org.eclipse.jdt.launching.JRE_CONTAINER&quot; javaProject=&quot;DrugNER&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;?&gt;&#13;&#10;&lt;runtimeClasspathEntry externalArchive=&quot;C:/tools/lucene/lucene-2.4.1/lucene-core-2.4.1.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;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/DrugNER/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;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/ctakes-drug-ner/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;?&gt;&#13;&#10;&lt;runtimeClasspathEntry internalArchive=&quot;/CNI/build/classes&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;?&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;DrugNER&quot;/&gt;&#13;&#10;&lt;/runtimeClasspathEntry&gt;&#13;&#10;"/>
 </listAttribute>
 <booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
 <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="com.ibm.uima.annot_view.Gladis"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="DrugNER"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-drug-ner"/>
 <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="&quot;-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties&quot;  -Xms700M -Xmx700M"/>
 <stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:Abbreviation Annotator}"/>
 </launchConfiguration>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA%20CAS%20Visual%20Debugger%20%28PAD%20Term%20Spotter%29.launch?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch Mon Sep 24 22:04:51 2012
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/PAD term spotter"/>
+<listEntry value="/ctakes-pad-term-spotter"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
 <listEntry value="4"/>
@@ -10,7 +10,7 @@
 <stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
 <stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
 <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="com.ibm.uima.annot_view.Gladis"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="PAD term spotter"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-pad-term-spotter"/>
 <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="&quot;-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties&quot;  -Xms700M -Xmx700M"/>
 <stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:core}"/>
 </launchConfiguration>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/metadata/install.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/metadata/install.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/metadata/install.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/metadata/install.xml Mon Sep 24 22:04:51 2012
@@ -39,7 +39,7 @@
 			<ACTION>set_env_variable</ACTION>
 			<PARAMETERS>
 				<COMMENTS></COMMENTS>
-				<VAR_VALUE>$main_root/bin;$main_root/resources;$main_root/../core/resources;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/trove.jar;$main_root/../POS tagger/resources;$main_root/../POS tagger/bin;$main_root/../chunker/resources;$main_root/../context dependent tokenizer/bin;$main_root/../NE contexts/bin;$main_root/../chunker/bin;$main_root/../core/bin;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/lucene-1.4-final.jar;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;</VAR_VALUE>
+				<VAR_VALUE>$main_root/bin;$main_root/resources;$main_root/../ctakes-core/resources;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/lucene-1.4-final.jar;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-dictionary-lookup/resources;</VAR_VALUE>
 				<VAR_NAME>CLASSPATH</VAR_NAME>
 			</PARAMETERS>
 		</PROCESS>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/radiology/LookupDesc_PAD.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/radiology/LookupDesc_PAD.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/radiology/LookupDesc_PAD.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lookup/radiology/LookupDesc_PAD.xml Mon Sep 24 22:04:51 2012
@@ -48,14 +48,14 @@
 		<lookupBinding>
 			<dictionaryRef idRef="GAZ_CSV_PAD_TERM"/>
 			<!-- NOTE: Only use if windowAnnotations have small # of tokens, sentences are not a good idea! -->
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
 				<properties>
 					<property key="textMetaFields" value="1"/>
 					<property key="maxPermutationLevel" value="7"/>
 					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/>
 				</properties>
 			</lookupInitializer>
-			<lookupConsumer className="edu.mayo.bmi.uima.pad.impl.PADTermConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.padtermspotter.impl.PADTermConsumerImpl">
 				<properties>
 					<!-- property key="stopWordsExtFileResrcKey" value="StopWordsFile"/ -->
 				</properties>
@@ -64,14 +64,14 @@
 		<lookupBinding>
 			<dictionaryRef idRef="GAZ_CSV_PAD_LOC"/>
 			<!-- NOTE: Only use if windowAnnotations have small # of tokens, sentences are not a good idea! -->
-			<lookupInitializer className="edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl">
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
 				<properties>
 					<property key="textMetaFields" value="1"/>
 					<property key="maxPermutationLevel" value="7"/>
 					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/>
 				</properties>
 			</lookupInitializer>
-			<lookupConsumer className="edu.mayo.bmi.uima.pad.impl.PADLocationConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.padtermspotter.impl.PADLocationConsumerImpl">
 				<properties>
 					<!-- property key="stopWordsExtFileResrcKey" value="StopWordsFile"/ -->
 				</properties>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lvg/data/config/lvg.properties.windows
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lvg/data/config/lvg.properties.windows?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lvg/data/config/lvg.properties.windows (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/resources/lvg/data/config/lvg.properties.windows Mon Sep 24 22:04:51 2012
@@ -9,7 +9,7 @@
 # LVG_NONINFO_WORD_FILE: the relative path (to LVG_DIR) of non-info word file.
 # LVG_CONJ_WORD_FILE: the relative path (to LVG_DIR) of conjuction file.
 #-------------------------------------------------------------------
-LVG_DIR=C:/external_workspace/TermSpotter/build/stagingArea/TermSpotter/resources/lvg/
+LVG_DIR=C:/external_workspace/TermSpotter/build/stagingArea/TermSpotter/resources/ctakes-lvg/
 LVG_STOP_WORD_FILE=data/misc/stopWords.data
 LVG_DIACRITICS_FILE=data/misc/diacritics.data
 LVG_LIGATURES_FILE=data/misc/ligatures.data



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