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From chen...@apache.org
Subject svn commit: r1388196 [9/12] - in /incubator/ctakes/trunk: ctakes-chunker/desc/ ctakes-chunker/src/main/java/edu/mayo/bmi/uima/adjuster/ ctakes-chunker/src/main/java/edu/mayo/bmi/uima/chunker/ ctakes-chunker/test/data/output/ ctakes-chunker/test/desc/ c...
Date Thu, 20 Sep 2012 20:25:58 GMT
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/cc/PADOffSetsRecord.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/cc/PADOffSetsRecord.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/cc/PADOffSetsRecord.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/cc/PADOffSetsRecord.java Thu Sep 20 20:25:49 2012
@@ -43,7 +43,7 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.util.ProcessTrace;
 
 import edu.mayo.bmi.uima.core.cc.NonTerminalConsumer;
-import edu.mayo.bmi.uima.core.type.structured.DocumentID;
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import edu.mayo.bmi.uima.pad.type.PADHit;
 import edu.mayo.bmi.uima.pad.type.PADLocation;
 import edu.mayo.bmi.uima.pad.type.PADTerm;

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/cr/RadiologyRecordsCollectionReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/cr/RadiologyRecordsCollectionReader.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/cr/RadiologyRecordsCollectionReader.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/src/main/java/edu/mayo/bmi/uima/termspotter/cr/RadiologyRecordsCollectionReader.java Thu Sep 20 20:25:49 2012
@@ -39,7 +39,7 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
 
-import edu.mayo.bmi.uima.core.type.structured.DocumentID;
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
 
 /**
  * 

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/utils/src/edu/mayo/bmi/utils/xcas_comparison/ConvertAndCompare.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/utils/src/edu/mayo/bmi/utils/xcas_comparison/ConvertAndCompare.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/utils/src/edu/mayo/bmi/utils/xcas_comparison/ConvertAndCompare.java (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/utils/src/edu/mayo/bmi/utils/xcas_comparison/ConvertAndCompare.java Thu Sep 20 20:25:49 2012
@@ -31,7 +31,7 @@ public class ConvertAndCompare {
 		Hashtable<String, String> map = new Hashtable<String, String>();
 		map.put("edu.mayo.bmi.uima.common.type.DocumentID",
 				"edu.mayo.bmi.uima.common.types.DocumentIDAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation",
+		map.put("org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation",
 				"edu.mayo.bmi.uima.lookup.types.LookupWindowAnnotation");
 //		Specify your mappings here
 /*		map.put("",
@@ -75,25 +75,25 @@ public class ConvertAndCompare {
 				"edu.mayo.bmi.uima.cdt.types.MeasurementAnnotation");
 		map.put("edu.mayo.bmi.uima.cdt.type.PersonTitleAnnotation",
 				"edu.mayo.bmi.uima.cdt.types.PersonTitleAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.textspan.Segment",
+		map.put("org.apache.ctakes.typesystem.type.textspan.Segment",
 				"edu.mayo.bmi.uima.common.types.SegmentAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.textspan.Sentence",
+		map.put("org.apache.ctakes.typesystem.type.textspan.Sentence",
 				"edu.mayo.bmi.uima.common.types.SentenceAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.syntax.WordToken",
+		map.put("org.apache.ctakes.typesystem.type.syntax.WordToken",
 				"edu.mayo.bmi.uima.common.types.WordTokenAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.NumToken",
+		map.put("org.apache.ctakes.typesystem.type.NumToken",
 				"edu.mayo.bmi.uima.common.types.NumTokenAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.PunctuationToken",
+		map.put("org.apache.ctakes.typesystem.type.PunctuationToken",
 				"edu.mayo.bmi.uima.common.types.PunctTokenAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.SymbolToken",
+		map.put("org.apache.ctakes.typesystem.type.SymbolToken",
 				"edu.mayo.bmi.uima.common.types.SymbolTokenAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.NewlineToken",
+		map.put("org.apache.ctakes.typesystem.type.NewlineToken",
 				"edu.mayo.bmi.uima.common.types.NewlineTokenAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation",
+		map.put("org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation",
 				"edu.mayo.bmi.uima.common.types.NamedEntityAnnotation");
-		map.put("edu.mayo.bmi.uima.core.type.UmlsConcept",
+		map.put("org.apache.ctakes.typesystem.type.UmlsConcept",
 				"edu.mayo.bmi.uima.common.types.UmlsConcept");
-		map.put("edu.mayo.bmi.uima.core.type.OntologyConcept",
+		map.put("org.apache.ctakes.typesystem.type.OntologyConcept",
 				"edu.mayo.bmi.uima.common.types.OntologyConcept");
 
 //		Prepare the list of attributes to ignore when comparing elements

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/desc/POSTagger.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/desc/POSTagger.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/desc/POSTagger.xml (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/desc/POSTagger.xml Thu Sep 20 20:25:49 2012
@@ -79,11 +79,11 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </outputs>
 <languagesSupported/>
 </capability>

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/desc/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/desc/SentenceDetectorAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/desc/SentenceDetectorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/desc/SentenceDetectorAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -36,10 +36,10 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
 </outputs>
 <languagesSupported/>
 </capability>

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

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/src/main/java/edu/mayo/bmi/uima/pos_tagger/OpenNLPPOSCollectionReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/src/main/java/edu/mayo/bmi/uima/pos_tagger/OpenNLPPOSCollectionReader.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/src/main/java/edu/mayo/bmi/uima/pos_tagger/OpenNLPPOSCollectionReader.java (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/src/main/java/edu/mayo/bmi/uima/pos_tagger/OpenNLPPOSCollectionReader.java Thu Sep 20 20:25:49 2012
@@ -31,8 +31,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.Progress;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * This collection reader reads in part-of-speech training/test data in the

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/src/main/java/edu/mayo/bmi/uima/pos_tagger/POSTagger.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/src/main/java/edu/mayo/bmi/uima/pos_tagger/POSTagger.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/src/main/java/edu/mayo/bmi/uima/pos_tagger/POSTagger.java (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/src/main/java/edu/mayo/bmi/uima/pos_tagger/POSTagger.java Thu Sep 20 20:25:49 2012
@@ -73,8 +73,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 
 import edu.mayo.bmi.uima.core.resource.FileLocator;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 public class POSTagger extends JCasAnnotator_ImplBase {
 

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/test/desc/POSTagger.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/test/desc/POSTagger.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/test/desc/POSTagger.xml (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/test/desc/POSTagger.xml Thu Sep 20 20:25:49 2012
@@ -79,11 +79,11 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </outputs>
 <languagesSupported/>
 </capability>

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

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

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

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/test/src/edu/mayo/bmi/uima/pos_tagger/test/OpenNLPPOSCollectionReaderTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/test/src/edu/mayo/bmi/uima/pos_tagger/test/OpenNLPPOSCollectionReaderTests.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/test/src/edu/mayo/bmi/uima/pos_tagger/test/OpenNLPPOSCollectionReaderTests.java (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/test/src/edu/mayo/bmi/uima/pos_tagger/test/OpenNLPPOSCollectionReaderTests.java Thu Sep 20 20:25:49 2012
@@ -33,7 +33,7 @@ import org.apache.uima.resource.Resource
 import org.junit.Test;
 
 import edu.mayo.bmi.uima.core.test.TestUtil;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 
 public class OpenNLPPOSCollectionReaderTests {
 

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/test/src/edu/mayo/bmi/uima/pos_tagger/test/POSTaggerTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/test/src/edu/mayo/bmi/uima/pos_tagger/test/POSTaggerTests.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/test/src/edu/mayo/bmi/uima/pos_tagger/test/POSTaggerTests.java (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/test/src/edu/mayo/bmi/uima/pos_tagger/test/POSTaggerTests.java Thu Sep 20 20:25:49 2012
@@ -30,7 +30,7 @@ import org.apache.uima.resource.Resource
 import org.junit.Test;
 
 import edu.mayo.bmi.uima.core.test.TestUtil;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 
 public class POSTaggerTests {
 

Modified: incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml (original)
+++ incubator/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml Thu Sep 20 20:25:49 2012
@@ -41,10 +41,10 @@ The CDA must conform to the DTD resource
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.type.util.Pair</type>
 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.type.util.Pairs</type>
 <type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>

Modified: incubator/ctakes/trunk/ctakes-preprocessor/src/main/java/edu/mayo/bmi/uima/ae/CdaCasInitializer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-preprocessor/src/main/java/edu/mayo/bmi/uima/ae/CdaCasInitializer.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-preprocessor/src/main/java/edu/mayo/bmi/uima/ae/CdaCasInitializer.java (original)
+++ incubator/ctakes/trunk/ctakes-preprocessor/src/main/java/edu/mayo/bmi/uima/ae/CdaCasInitializer.java Thu Sep 20 20:25:49 2012
@@ -42,10 +42,10 @@ import edu.mayo.bmi.uima.core.ci.HyphenT
 import edu.mayo.bmi.uima.core.ci.TextModification;
 import edu.mayo.bmi.uima.core.ci.TextModifier;
 import edu.mayo.bmi.uima.core.resource.FileResource;
-import edu.mayo.bmi.uima.core.type.structured.DocumentID;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
-import edu.mayo.bmi.uima.core.type.util.Pair;
-import edu.mayo.bmi.uima.core.type.util.Pairs;
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.util.Pair;
+import org.apache.ctakes.typesystem.type.util.Pairs;
 
 
 /**

Modified: incubator/ctakes/trunk/ctakes-preprocessor/test/data/output/testpatient_cn_1.xml.included.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-preprocessor/test/data/output/testpatient_cn_1.xml.included.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-preprocessor/test/data/output/testpatient_cn_1.xml.included.xml (original)
+++ incubator/ctakes/trunk/ctakes-preprocessor/test/data/output/testpatient_cn_1.xml.included.xml Thu Sep 20 20:25:49 2012
@@ -23,34 +23,34 @@
 <uima.cas.Sofa _indexed="0" _id="6" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;&lt;!DOCTYPE levelone SYSTEM &quot;NotesIIST_RTF.DTD&quot; [&lt;!ENTITY deg '&amp;#x00B0;'&gt;&lt;!ENTITY sup2 '&amp;#x00B2;'&gt;&lt;!ENTITY micro '&amp;#x00B5;'&gt;]&gt;&lt;levelone&gt;&lt;clinical_document_header&gt;&lt;id EX=&quot;###DOC_ID###&quot; RT=&quot;2.16.840.1.113883.3.2.1.1&quot;/&gt;&lt;set_id EX=&quot;###SET_ID###&quot; RT=&quot;2.16.840.1.113883.3.2.1.2&quot;/&gt;&lt;version_nbr V=&quot;###V_NBR###&quot;/&gt;&lt;document_type_cd V=&quot;687&quot; S=&quot;2.16.840.1.113883.3.2.1.3&quot; DN=&quot;Nutrition Consult&quot;/&gt;&lt;origination_dttm V=&quot;20030822T131513&quot;/&gt;&lt;confidentiality_cd V=&quot;0&quot; S=&quot;2.16.840.1.113883.3.2.1.4&quot;/&gt;&lt;patient_encounter&gt;&lt;practice_setting_cd V=&quot;4284&quot; S=&quot;2.16.840.1.113883.3.2.1.7&quot; DN=&quot;Nutr Clinic&quot;/&gt;&lt;en
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+<org.apache.ctakes.typesystem.type.Property _id="164" _ref_sofa="18" begin="0" end="0" key="SIGNATURE_ID" value="99999999"/>
+<org.apache.ctakes.typesystem.type.Property _id="158" _ref_sofa="18" begin="0" end="0" key="PT_GENDER" value="F"/>
+<org.apache.ctakes.typesystem.type.Property _id="152" _ref_sofa="18" begin="0" end="0" key="PATIENT_STATE" value="MN"/>
+<org.apache.ctakes.typesystem.type.Property _id="146" _ref_sofa="18" begin="0" end="0" key="PATIENT_ADDR" value="100 Quality Control Avenue"/>
+<org.apache.ctakes.typesystem.type.Property _id="140" _ref_sofa="18" begin="0" end="0" key="DOC_CONFIDENTIAL_IND" value="0"/>
+<org.apache.ctakes.typesystem.type.Property _id="134" _ref_sofa="18" begin="0" end="0" key="SERVICE_CODE" value="MNT"/>
+<org.apache.ctakes.typesystem.type.Property _id="128" _ref_sofa="18" begin="0" end="0" key="PATIENT_CNT" value="US"/>
+<org.apache.ctakes.typesystem.type.Property _id="122" _ref_sofa="18" begin="0" end="0" key="SITE_CODE" value="RCH"/>
+<org.apache.ctakes.typesystem.type.Property _id="116" _ref_sofa="18" begin="0" end="0" key="TRANSCRIPTION_DATE" value="1061576113000"/>
+<org.apache.ctakes.typesystem.type.Property _id="110" _ref_sofa="18" begin="0" end="0" key="PROVIDER_ID" value="99999999"/>
+<org.apache.ctakes.typesystem.type.Property _id="104" _ref_sofa="18" begin="0" end="0" key="TRANSCRIBER_ID" value="99999999"/>
+<org.apache.ctakes.typesystem.type.Property _id="98" _ref_sofa="18" begin="0" end="0" key="NOTE_DATE" value="1061528400000"/>
+<org.apache.ctakes.typesystem.type.Property _id="92" _ref_sofa="18" begin="0" end="0" key="DOC_STATUS_CODE" value="Fnl"/>
+<org.apache.ctakes.typesystem.type.Property _id="86" _ref_sofa="18" begin="0" end="0" key="DOC_LINK_ID" value="000000000"/>
+<org.apache.ctakes.typesystem.type.Property _id="80" _ref_sofa="18" begin="0" end="0" key="REV_DATE" value="1061576113000"/>
+<org.apache.ctakes.typesystem.type.Property _id="74" _ref_sofa="18" begin="0" end="0" key="PATIENT_ZIP" value="55905"/>
 <uima.cas.FSArray _id="50" size="22">
 <i>74</i>
 <i>80</i>

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml Thu Sep 20 20:25:49 2012
@@ -317,13 +317,13 @@
                         <description>For subiterator</description>
                         <version>1.0</version>
                         <priorityList>
-                            <type>edu.mayo.bmi.uima.core.type.textspan.Segment</type>
-                            <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-                            <type>edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+                            <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+                            <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+                            <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
                         </priorityList>
                         <priorityList>
-                            <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-                            <type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
+                            <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+                            <type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
                         </priorityList>
                     </typePriorities>
                     <fsIndexCollection/>
@@ -331,48 +331,48 @@
                         <capability>
                             <inputs/>
                             <outputs>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NewlineToken</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.WordToken</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.VP</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.refsem.UmlsConcept</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.UCP</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.TimeAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.SymbolToken</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspanSegment</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.SBAR</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.RomanNumeralAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.RangeAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PunctuationToken</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.Property</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.Properties</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.PersonTitleAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PRT</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PP</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.OntologyConcept</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NumToken</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.MeasurementAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NewlineToken</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.VP</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.UCP</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.TimeAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SymbolToken</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspanSegment</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SBAR</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RangeAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PunctuationToken</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Property</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Properties</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PRT</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PP</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.OntologyConcept</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NumToken</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation</type>
                                 <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Lemma</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.LST</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.INTJ</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.FractionAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.structured.DocumentID</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Lemma</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.LST</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.INTJ</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.FractionAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.structured.DocumentID</type>
                                 <type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.DateAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopySrcAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopyDestAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.ContractionToken</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.ContextAnnotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Chunk</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.CONJP</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.DateAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopySrcAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopyDestAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.ContractionToken</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.ContextAnnotation</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Chunk</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.CONJP</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
                                 <type allAnnotatorFeatures="true">uima.cas.AnnotationBase</type>
                                 <type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.ADVP</type>
-                                <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.ADJP</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADVP</type>
+                                <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADJP</type>
                             </outputs>
                             <languagesSupported/>
                         </capability>

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorPreprocessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorPreprocessor.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorPreprocessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorPreprocessor.xml Thu Sep 20 20:25:49 2012
@@ -137,13 +137,13 @@
       <description>For subiterator</description>
       <version>1.0</version>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Segment</type>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
       </priorityList>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
       </priorityList>
     </typePriorities>
     <fsIndexCollection/>
@@ -151,48 +151,48 @@
       <capability>
         <inputs/>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NewlineToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.WordToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.VP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.refsem.UmlsConcept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.UCP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.TimeAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.SymbolToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspanSegment</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.SBAR</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.RomanNumeralAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.RangeAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PunctuationToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.Property</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.Properties</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.PersonTitleAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PRT</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.OntologyConcept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NumToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.MeasurementAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NewlineToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.VP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.UCP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.TimeAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SymbolToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspanSegment</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SBAR</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RangeAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PunctuationToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Property</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Properties</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PRT</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.OntologyConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NumToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation</type>
           <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Lemma</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.LST</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.INTJ</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.FractionAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.structured.DocumentID</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Lemma</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.LST</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.INTJ</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.FractionAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.structured.DocumentID</type>
           <type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.DateAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopySrcAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopyDestAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.ContractionToken</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.ContextAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Chunk</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.CONJP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.DateAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopySrcAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopyDestAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.ContractionToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.ContextAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Chunk</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.CONJP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
           <type allAnnotatorFeatures="true">uima.cas.AnnotationBase</type>
           <type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.ADVP</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.ADJP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADVP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADJP</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java Thu Sep 20 20:25:49 2012
@@ -27,11 +27,11 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.relation.BinaryTextRelation;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.Modifier;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.Modifier;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * Identifies Degree_Of relation between entities and modifiers

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java Thu Sep 20 20:25:49 2012
@@ -28,10 +28,10 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.uimafit.descriptor.ConfigurationParameter;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.relation.BinaryTextRelation;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * Identifies and classifies relations between pairs of named entities

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java Thu Sep 20 20:25:49 2012
@@ -35,9 +35,9 @@ import org.uimafit.factory.AnalysisEngin
 import org.uimafit.factory.ConfigurationParameterFactory;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textsem.Modifier;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.Modifier;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 public class ModifierExtractorAnnotator extends CleartkAnnotator<String> {
 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java Thu Sep 20 20:25:49 2012
@@ -50,10 +50,10 @@ import org.uimafit.util.JCasUtil;
 import com.google.common.base.Objects;
 import com.google.common.io.Files;
 
-import edu.mayo.bmi.uima.core.type.relation.BinaryTextRelation;
-import edu.mayo.bmi.uima.core.type.relation.RelationArgument;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public abstract class RelationExtractorAnnotator extends CleartkAnnotator<String> {
 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java Thu Sep 20 20:25:49 2012
@@ -24,7 +24,7 @@ import java.util.List;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.cleartk.classifier.Feature;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 /**
  * Features that indicate the order of the arguments (e.g. before or after).

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java Thu Sep 20 20:25:49 2012
@@ -26,7 +26,7 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 
 public class DependencyParseUtils {
 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java Thu Sep 20 20:25:49 2012
@@ -26,8 +26,8 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.cleartk.classifier.Feature;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class DependencyPathFeaturesExtractor implements RelationFeaturesExtractor {
 	

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java Thu Sep 20 20:25:49 2012
@@ -25,8 +25,8 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.cleartk.classifier.Feature;
 
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class DependencyTreeFeaturesExtractor implements RelationFeaturesExtractor{
 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java Thu Sep 20 20:25:49 2012
@@ -26,8 +26,8 @@ import org.apache.uima.jcas.JCas;
 import org.cleartk.classifier.Feature;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.syntax.NP;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.NP;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 /**
  * Features that indicate whether both arguments are contained within an NP. 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java Thu Sep 20 20:25:49 2012
@@ -31,8 +31,8 @@ import org.cleartk.classifier.feature.ex
 import org.cleartk.classifier.feature.extractor.simple.NamingExtractor;
 import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
 
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class NamedEntityFeaturesExtractor implements RelationFeaturesExtractor {
 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java Thu Sep 20 20:25:49 2012
@@ -31,8 +31,8 @@ import org.cleartk.classifier.feature.ex
 import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
 import org.cleartk.classifier.feature.extractor.simple.TypePathExtractor;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class PartOfSpeechFeaturesExtractor implements RelationFeaturesExtractor {
 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java Thu Sep 20 20:25:49 2012
@@ -25,9 +25,9 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.cleartk.classifier.Feature;
 import org.uimafit.util.JCasUtil;
-import edu.mayo.bmi.uima.core.type.syntax.TerminalTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class PhraseChunkingExtractor implements RelationFeaturesExtractor {
 	  

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java Thu Sep 20 20:25:49 2012
@@ -28,8 +28,8 @@ import org.apache.uima.jcas.JCas;
 import org.cleartk.classifier.Feature;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 /**
  * Features that indicate whether there is a preposition between the two arguments. 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java Thu Sep 20 20:25:49 2012
@@ -26,8 +26,8 @@ import org.apache.uima.jcas.JCas;
 import org.cleartk.classifier.Feature;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 /**
  * Features that capture punctuation marks between the two arguments.

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java Thu Sep 20 20:25:49 2012
@@ -24,7 +24,7 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.cleartk.classifier.Feature;
 
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 /**
  * Define an interface for people to implement feature extractors.

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java Thu Sep 20 20:25:49 2012
@@ -36,8 +36,8 @@ import org.cleartk.classifier.feature.ex
 import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
 import org.cleartk.classifier.feature.extractor.simple.SpannedTextExtractor;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class TokenFeaturesExtractor implements RelationFeaturesExtractor {
 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java Thu Sep 20 20:25:49 2012
@@ -38,11 +38,11 @@ import org.jdom.JDOMException;
 import org.jdom.input.SAXBuilder;
 import org.uimafit.component.JCasAnnotator_ImplBase;
 
-import edu.mayo.bmi.uima.core.type.constants.CONST;
-import edu.mayo.bmi.uima.core.type.relation.BinaryTextRelation;
-import edu.mayo.bmi.uima.core.type.relation.RelationArgument;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.Modifier;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.Modifier;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java Thu Sep 20 20:25:49 2012
@@ -37,8 +37,8 @@ import org.jdom.JDOMException;
 import org.jdom.input.SAXBuilder;
 import org.uimafit.component.JCasAnnotator_ImplBase;
 
-import edu.mayo.bmi.uima.core.type.constants.CONST;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java Thu Sep 20 20:25:49 2012
@@ -18,7 +18,7 @@
  */
 package org.chboston.cnlp.ctakes.relationextractor.cr;
 
-import edu.mayo.bmi.uima.core.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.constants.CONST;
 
 /**
  * Map various category names to their ctakes integer id. 

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/data/Stats.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/data/Stats.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/data/Stats.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/data/Stats.java Thu Sep 20 20:25:49 2012
@@ -31,7 +31,7 @@ import org.jdom.Document;
 import org.jdom.JDOMException;
 import org.jdom.input.SAXBuilder;
 
-import edu.mayo.bmi.uima.core.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.constants.CONST;
 
 /**
  * Calculate relation frequencies in a data set that consists of XML files exported from Knowtator.

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java Thu Sep 20 20:25:49 2012
@@ -45,7 +45,7 @@ import org.uimafit.pipeline.JCasIterable
 import org.uimafit.pipeline.SimplePipeline;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.textsem.Modifier;
+import org.apache.ctakes.typesystem.type.textsem.Modifier;
 
 public class ModifierExtractorEvaluation extends Evaluation_ImplBase<File, AnnotationStatistics> {
 



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