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From chen...@apache.org
Subject svn commit: r1388196 [4/12] - 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-constituency-parser/data/test/output/testfakenote.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/data/test/output/testfakenote.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/data/test/output/testfakenote.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/data/test/output/testfakenote.xml Thu Sep 20 20:25:49 2012
@@ -22,101 +22,101 @@
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+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="312" _ref_sofa="6" begin="110" end="114" tokenNumber="23" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="324" _ref_sofa="6" begin="115" end="118" tokenNumber="24" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="336" _ref_sofa="6" begin="119" end="121" tokenNumber="25" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="348" _ref_sofa="6" begin="122" end="128" tokenNumber="26" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="360" _ref_sofa="6" begin="129" end="133" tokenNumber="27" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="372" _ref_sofa="6" begin="134" end="136" tokenNumber="28" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="384" _ref_sofa="6" begin="137" end="140" tokenNumber="29" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="396" _ref_sofa="6" begin="141" end="146" tokenNumber="30" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="408" _ref_sofa="6" begin="147" end="153" tokenNumber="31" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="420" _ref_sofa="6" begin="154" end="163" tokenNumber="32" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="432" _ref_sofa="6" begin="164" end="166" tokenNumber="33" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="444" _ref_sofa="6" begin="167" end="174" tokenNumber="34" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="456" _ref_sofa="6" begin="175" end="177" tokenNumber="35" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="492" _ref_sofa="6" begin="180" end="183" tokenNumber="39" capitalization="1" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="504" _ref_sofa="6" begin="184" end="191" tokenNumber="40" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="516" _ref_sofa="6" begin="192" end="196" tokenNumber="41" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="528" _ref_sofa="6" begin="197" end="200" tokenNumber="42" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="540" _ref_sofa="6" begin="201" end="210" tokenNumber="43" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="552" _ref_sofa="6" begin="211" end="216" tokenNumber="44" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="564" _ref_sofa="6" begin="217" end="218" tokenNumber="45" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="576" _ref_sofa="6" begin="219" end="224" tokenNumber="46" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="588" _ref_sofa="6" begin="225" end="231" tokenNumber="47" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="600" _ref_sofa="6" begin="232" end="234" tokenNumber="48" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="612" _ref_sofa="6" begin="235" end="238" tokenNumber="49" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="624" _ref_sofa="6" begin="239" end="244" tokenNumber="50" capitalization="1" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="644" _ref_sofa="6" begin="247" end="251" tokenNumber="52" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="656" _ref_sofa="6" begin="252" end="255" tokenNumber="53" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="668" _ref_sofa="6" begin="256" end="260" tokenNumber="54" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="680" _ref_sofa="6" begin="261" end="264" tokenNumber="55" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="692" _ref_sofa="6" begin="265" end="271" tokenNumber="56" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="704" _ref_sofa="6" begin="272" end="275" tokenNumber="57" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="716" _ref_sofa="6" begin="276" end="283" tokenNumber="58" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="728" _ref_sofa="6" begin="284" end="287" tokenNumber="59" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="740" _ref_sofa="6" begin="288" end="290" tokenNumber="60" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="752" _ref_sofa="6" begin="291" end="298" tokenNumber="61" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="764" _ref_sofa="6" begin="299" end="308" tokenNumber="62" capitalization="1" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="776" _ref_sofa="6" begin="309" end="317" tokenNumber="63" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="788" _ref_sofa="6" begin="318" end="328" tokenNumber="64" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="824" _ref_sofa="6" begin="331" end="336" tokenNumber="68" capitalization="1" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="836" _ref_sofa="6" begin="337" end="344" tokenNumber="69" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="848" _ref_sofa="6" begin="345" end="350" tokenNumber="70" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="860" _ref_sofa="6" begin="351" end="354" tokenNumber="71" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="872" _ref_sofa="6" begin="355" end="367" tokenNumber="72" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="892" _ref_sofa="6" begin="369" end="372" tokenNumber="74" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="904" _ref_sofa="6" begin="373" end="380" tokenNumber="75" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="916" _ref_sofa="6" begin="381" end="384" tokenNumber="76" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="928" _ref_sofa="6" begin="385" end="393" tokenNumber="77" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="940" _ref_sofa="6" begin="394" end="396" tokenNumber="78" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="952" _ref_sofa="6" begin="397" end="399" tokenNumber="79" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="964" _ref_sofa="6" begin="400" end="404" tokenNumber="80" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="976" _ref_sofa="6" begin="405" end="408" tokenNumber="81" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="988" _ref_sofa="6" begin="409" end="414" tokenNumber="82" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="1000" _ref_sofa="6" begin="415" end="418" tokenNumber="83" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="1012" _ref_sofa="6" begin="419" end="423" tokenNumber="84" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.WordToken _indexed="1" _id="1024" _ref_sofa="6" begin="424" end="431" tokenNumber="85" capitalization="0" numPosition="0"/>
+    <org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="60" _ref_sofa="6" begin="2" end="3" tokenNumber="1"/>
+    <org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="164" _ref_sofa="6" begin="47" end="48" tokenNumber="10"/>
+    <org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="292" _ref_sofa="6" begin="103" end="104" tokenNumber="21"/>
+    <org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="468" _ref_sofa="6" begin="177" end="178" tokenNumber="36"/>
+    <org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="800" _ref_sofa="6" begin="328" end="329" tokenNumber="65"/>
+    <org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="884" _ref_sofa="6" begin="367" end="368" tokenNumber="73"/>
+    <org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="1036" _ref_sofa="6" begin="431" end="432" tokenNumber="86"/>
+    <org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="476" _ref_sofa="6" begin="178" end="179" tokenNumber="37"/>
+    <org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="484" _ref_sofa="6" begin="179" end="180" tokenNumber="38"/>
+    <org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="808" _ref_sofa="6" begin="329" end="330" tokenNumber="66"/>
+    <org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="816" _ref_sofa="6" begin="330" end="331" tokenNumber="67"/>
+    <org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="1044" _ref_sofa="6" begin="432" end="433" tokenNumber="87"/>
+    <org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="1052" _ref_sofa="6" begin="433" end="434" tokenNumber="88"/>
+    <org.apache.ctakes.typesystem.type.ContractionToken _indexed="1" _id="636" _ref_sofa="6" begin="244" end="246" tokenNumber="51"/>
     <org.chboston.cnlp.ctakes.parser.uima.type.TerminalTreebankNode _indexed="1" _id="1073" _ref_sofa="6" begin="0" end="2" nodeType="Mr" nodeValue="Mr" leaf="true" _ref_parent="1287" headIndex="0" index="0" tokenIndex="0"/>
     <org.chboston.cnlp.ctakes.parser.uima.type.TerminalTreebankNode _indexed="1" _id="1086" _ref_sofa="6" begin="2" end="3" nodeType="." nodeValue="." leaf="true" _ref_parent="1303" headIndex="0" index="1" tokenIndex="1"/>
     <org.chboston.cnlp.ctakes.parser.uima.type.TerminalTreebankNode _indexed="1" _id="1099" _ref_sofa="6" begin="4" end="11" nodeType="Johnson" nodeValue="Johnson" leaf="true" _ref_parent="1319" headIndex="0" index="2" tokenIndex="2"/>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml Thu Sep 20 20:25:49 2012
@@ -67,13 +67,13 @@
       <description>For subiterator</description>
       <version>1.0</version>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Segment</type>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
       </priorityList>
       <priorityList>
-        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
-        <type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
+        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+        <type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
       </priorityList>
     </typePriorities>
     <fsIndexCollection/>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/MaxentParserWrapper.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/MaxentParserWrapper.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/MaxentParserWrapper.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/MaxentParserWrapper.java Thu Sep 20 20:25:49 2012
@@ -36,13 +36,13 @@ import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.StringArray;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.syntax.TerminalTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TopTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 public class MaxentParserWrapper implements ParserWrapper {

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeExtractor.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeExtractor.java Thu Sep 20 20:25:49 2012
@@ -24,9 +24,9 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.chboston.cnlp.util.SimpleTree;
 
-import edu.mayo.bmi.uima.core.type.syntax.TerminalTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TopTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 
 /*
  * This class extracts tree relations between two nodes in a tree (or from 2 separate trees).

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/uima/ae/ParserEvaluationAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/uima/ae/ParserEvaluationAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/uima/ae/ParserEvaluationAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/uima/ae/ParserEvaluationAnnotator.java Thu Sep 20 20:25:49 2012
@@ -15,7 +15,7 @@ import org.apache.uima.analysis_componen
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 
-import edu.mayo.bmi.uima.core.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
 import opennlp.tools.cmdline.parser.ParserTool;
 
 public class ParserEvaluationAnnotator extends JCasAnnotator_ImplBase {

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/uima/co/ParserTreeWriterConsumer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/uima/co/ParserTreeWriterConsumer.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/uima/co/ParserTreeWriterConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/uima/co/ParserTreeWriterConsumer.java Thu Sep 20 20:25:49 2012
@@ -16,7 +16,7 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.ResourceProcessException;
 import org.apache.uima.util.ProcessTrace;
 
-import edu.mayo.bmi.uima.core.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
 
 public class ParserTreeWriterConsumer extends CasConsumer_ImplBase {
 

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

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/util/TreeUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/util/TreeUtils.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/util/TreeUtils.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/util/TreeUtils.java Thu Sep 20 20:25:49 2012
@@ -4,8 +4,8 @@ import opennlp.tools.parser.Parse;
 
 import org.chboston.cnlp.util.SimpleTree;
 
-import edu.mayo.bmi.uima.core.type.syntax.TopTreebankNode;
-import edu.mayo.bmi.uima.core.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 
 import java.util.List;
 import java.util.ArrayList;

Modified: incubator/ctakes/trunk/ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -36,12 +36,12 @@
 <capability>
 <inputs/>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.TimeAnnotation</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.textsem.PersonTitleAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.MeasurementAnnotation</type>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.FractionAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.TimeAnnotation</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.textsem.PersonTitleAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.FractionAnnotation</type>
 </outputs>
 <languagesSupported/>
 </capability>

Modified: incubator/ctakes/trunk/ctakes-context-tokenizer/src/main/java/edu/mayo/bmi/uima/cdt/ae/ContextDependentTokenizerAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-context-tokenizer/src/main/java/edu/mayo/bmi/uima/cdt/ae/ContextDependentTokenizerAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-context-tokenizer/src/main/java/edu/mayo/bmi/uima/cdt/ae/ContextDependentTokenizerAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-context-tokenizer/src/main/java/edu/mayo/bmi/uima/cdt/ae/ContextDependentTokenizerAnnotator.java Thu Sep 20 20:25:49 2012
@@ -56,20 +56,20 @@ import edu.mayo.bmi.uima.core.fsm.adapte
 import edu.mayo.bmi.uima.core.fsm.adapters.PunctuationTokenAdapter;
 import edu.mayo.bmi.uima.core.fsm.adapters.SymbolTokenAdapter;
 import edu.mayo.bmi.uima.core.fsm.adapters.WordTokenAdapter;
-import edu.mayo.bmi.uima.core.type.syntax.ContractionToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.NumToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.type.textsem.DateAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.FractionAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.MeasurementAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.PersonTitleAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.RangeAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.RomanNumeralAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.TimeAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.NumToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.FractionAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.RangeAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.TimeAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 /**
  * Finds tokens based on context.
@@ -110,7 +110,7 @@ public class ContextDependentTokenizerAn
 			JFSIndexRepository indexes = jcas.getJFSIndexRepository();
 			Iterator<?> sentItr = indexes.getAnnotationIndex(Sentence.type).iterator();
 			AnnotationIndex baseTokenIndex = jcas.getJFSIndexRepository().getAnnotationIndex(
-					edu.mayo.bmi.uima.core.type.syntax.BaseToken.type);
+					org.apache.ctakes.typesystem.type.syntax.BaseToken.type);
 			
 			while (sentItr.hasNext()) {
 				Sentence sentAnnot = (Sentence) sentItr.next();
@@ -120,7 +120,7 @@ public class ContextDependentTokenizerAn
 				// machines
 				List<BaseToken> baseTokenList = new ArrayList<BaseToken>();
 				while (btaItr.hasNext()) {
-					edu.mayo.bmi.uima.core.type.syntax.BaseToken bta = (edu.mayo.bmi.uima.core.type.syntax.BaseToken) btaItr
+					org.apache.ctakes.typesystem.type.syntax.BaseToken bta = (org.apache.ctakes.typesystem.type.syntax.BaseToken) btaItr
 							.next();
 					baseTokenList.add(adaptToBaseToken(bta));
 				}
@@ -202,7 +202,7 @@ public class ContextDependentTokenizerAn
 	 * @param obj
 	 * @return
 	 */
-	private BaseToken adaptToBaseToken(edu.mayo.bmi.uima.core.type.syntax.BaseToken obj) throws Exception {
+	private BaseToken adaptToBaseToken(org.apache.ctakes.typesystem.type.syntax.BaseToken obj) throws Exception {
 		if (obj instanceof WordToken) {
 			WordToken wta = (WordToken) obj;
 			return new WordTokenAdapter(wta);

Modified: incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.sentence_annotations.included.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.sentence_annotations.included.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.sentence_annotations.included.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.sentence_annotations.included.xml Thu Sep 20 20:25:49 2012
@@ -22,9 +22,9 @@
 <CAS version="2">
 <uima.cas.Sofa _indexed="0" _id="6" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="S/P right knee arthroscopy.&#10;Knee x-ray.  Patient denies knee pain.&#10;"/>
 <uima.tcas.DocumentAnnotation _indexed="1" _id="13" _ref_sofa="6" begin="0" end="67" language="x-unspecified"/>
-<edu.mayo.bmi.uima.core.type.DocumentID _indexed="1" _id="1" _ref_sofa="6" begin="0" end="0" documentID="sample_note_plaintext"/>
-<edu.mayo.bmi.uima.core.type.textspan.Segment _indexed="1" _id="18" _ref_sofa="6" begin="0" end="67" id="SIMPLE_SEGMENT"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="23" _ref_sofa="6" begin="0" end="27" sentenceNumber="0"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="28" _ref_sofa="6" begin="28" end="39" sentenceNumber="1"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="33" _ref_sofa="6" begin="41" end="66" sentenceNumber="2"/>
+<org.apache.ctakes.typesystem.type.DocumentID _indexed="1" _id="1" _ref_sofa="6" begin="0" end="0" documentID="sample_note_plaintext"/>
+<org.apache.ctakes.typesystem.type.textspan.Segment _indexed="1" _id="18" _ref_sofa="6" begin="0" end="67" id="SIMPLE_SEGMENT"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="23" _ref_sofa="6" begin="0" end="27" sentenceNumber="0"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="28" _ref_sofa="6" begin="28" end="39" sentenceNumber="1"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="33" _ref_sofa="6" begin="41" end="66" sentenceNumber="2"/>
 </CAS>

Modified: incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.token_annotations.included.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.token_annotations.included.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.token_annotations.included.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.token_annotations.included.xml Thu Sep 20 20:25:49 2012
@@ -22,26 +22,26 @@
 <CAS version="2">
 <uima.cas.Sofa _indexed="0" _id="6" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="S/P right knee arthroscopy.&#10;Knee x-ray.  Patient denies knee pain.&#10;"/>
 <uima.tcas.DocumentAnnotation _indexed="1" _id="13" _ref_sofa="6" begin="0" end="67" language="x-unspecified"/>
-<edu.mayo.bmi.uima.core.type.DocumentID _indexed="1" _id="1" _ref_sofa="6" begin="0" end="0" documentID="sample_note_plaintext"/>
-<edu.mayo.bmi.uima.core.type.NewlineToken _indexed="1" _id="107" _ref_sofa="6" begin="27" end="28" tokenNumber="7"/>
-<edu.mayo.bmi.uima.core.type.NewlineToken _indexed="1" _id="194" _ref_sofa="6" begin="66" end="67" tokenNumber="16"/>
-<edu.mayo.bmi.uima.core.type.PunctuationToken _indexed="1" _id="49" _ref_sofa="6" begin="1" end="2" tokenNumber="1"/>
-<edu.mayo.bmi.uima.core.type.PunctuationToken _indexed="1" _id="100" _ref_sofa="6" begin="26" end="27" tokenNumber="6"/>
-<edu.mayo.bmi.uima.core.type.PunctuationToken _indexed="1" _id="136" _ref_sofa="6" begin="38" end="39" tokenNumber="10"/>
-<edu.mayo.bmi.uima.core.type.PunctuationToken _indexed="1" _id="187" _ref_sofa="6" begin="65" end="66" tokenNumber="15"/>
-<edu.mayo.bmi.uima.core.type.textspan.Segment _indexed="1" _id="18" _ref_sofa="6" begin="0" end="67" id="SIMPLE_SEGMENT"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="23" _ref_sofa="6" begin="0" end="27" sentenceNumber="0"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="28" _ref_sofa="6" begin="28" end="39" sentenceNumber="1"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="33" _ref_sofa="6" begin="41" end="66" sentenceNumber="2"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="38" _ref_sofa="6" begin="0" end="1" tokenNumber="0" capitalization="3" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="56" _ref_sofa="6" begin="2" end="3" tokenNumber="2" capitalization="3" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="67" _ref_sofa="6" begin="4" end="9" tokenNumber="3" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="78" _ref_sofa="6" begin="10" end="14" tokenNumber="4" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="89" _ref_sofa="6" begin="15" end="26" tokenNumber="5" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="114" _ref_sofa="6" begin="28" end="32" tokenNumber="8" capitalization="1" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="125" _ref_sofa="6" begin="33" end="38" tokenNumber="9" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="143" _ref_sofa="6" begin="41" end="48" tokenNumber="11" capitalization="1" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="154" _ref_sofa="6" begin="49" end="55" tokenNumber="12" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="165" _ref_sofa="6" begin="56" end="60" tokenNumber="13" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="176" _ref_sofa="6" begin="61" end="65" tokenNumber="14" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.DocumentID _indexed="1" _id="1" _ref_sofa="6" begin="0" end="0" documentID="sample_note_plaintext"/>
+<org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="107" _ref_sofa="6" begin="27" end="28" tokenNumber="7"/>
+<org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="194" _ref_sofa="6" begin="66" end="67" tokenNumber="16"/>
+<org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="49" _ref_sofa="6" begin="1" end="2" tokenNumber="1"/>
+<org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="100" _ref_sofa="6" begin="26" end="27" tokenNumber="6"/>
+<org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="136" _ref_sofa="6" begin="38" end="39" tokenNumber="10"/>
+<org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="187" _ref_sofa="6" begin="65" end="66" tokenNumber="15"/>
+<org.apache.ctakes.typesystem.type.textspan.Segment _indexed="1" _id="18" _ref_sofa="6" begin="0" end="67" id="SIMPLE_SEGMENT"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="23" _ref_sofa="6" begin="0" end="27" sentenceNumber="0"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="28" _ref_sofa="6" begin="28" end="39" sentenceNumber="1"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="33" _ref_sofa="6" begin="41" end="66" sentenceNumber="2"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="38" _ref_sofa="6" begin="0" end="1" tokenNumber="0" capitalization="3" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="56" _ref_sofa="6" begin="2" end="3" tokenNumber="2" capitalization="3" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="67" _ref_sofa="6" begin="4" end="9" tokenNumber="3" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="78" _ref_sofa="6" begin="10" end="14" tokenNumber="4" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="89" _ref_sofa="6" begin="15" end="26" tokenNumber="5" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="114" _ref_sofa="6" begin="28" end="32" tokenNumber="8" capitalization="1" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="125" _ref_sofa="6" begin="33" end="38" tokenNumber="9" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="143" _ref_sofa="6" begin="41" end="48" tokenNumber="11" capitalization="1" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="154" _ref_sofa="6" begin="49" end="55" tokenNumber="12" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="165" _ref_sofa="6" begin="56" end="60" tokenNumber="13" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="176" _ref_sofa="6" begin="61" end="65" tokenNumber="14" capitalization="0" numPosition="0"/>
 </CAS>

Modified: incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/data/test/output/sample_note_plaintext.xml Thu Sep 20 20:25:49 2012
@@ -22,26 +22,26 @@
 <CAS version="2">
 <uima.cas.Sofa _indexed="0" _id="6" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="S/P right knee arthroscopy.&#10;Knee x-ray.  Patient denies knee pain.&#10;"/>
 <uima.tcas.DocumentAnnotation _indexed="1" _id="13" _ref_sofa="6" begin="0" end="67" language="x-unspecified"/>
-<edu.mayo.bmi.uima.core.type.DocumentID _indexed="1" _id="1" _ref_sofa="6" begin="0" end="0" documentID="sample_note_plaintext"/>
-<edu.mayo.bmi.uima.core.type.NewlineToken _indexed="1" _id="114" _ref_sofa="6" begin="27" end="28" tokenNumber="7"/>
-<edu.mayo.bmi.uima.core.type.NewlineToken _indexed="1" _id="210" _ref_sofa="6" begin="66" end="67" tokenNumber="16"/>
-<edu.mayo.bmi.uima.core.type.PunctuationToken _indexed="1" _id="50" _ref_sofa="6" begin="1" end="2" tokenNumber="1"/>
-<edu.mayo.bmi.uima.core.type.PunctuationToken _indexed="1" _id="106" _ref_sofa="6" begin="26" end="27" tokenNumber="6"/>
-<edu.mayo.bmi.uima.core.type.PunctuationToken _indexed="1" _id="146" _ref_sofa="6" begin="38" end="39" tokenNumber="10"/>
-<edu.mayo.bmi.uima.core.type.PunctuationToken _indexed="1" _id="202" _ref_sofa="6" begin="65" end="66" tokenNumber="15"/>
-<edu.mayo.bmi.uima.core.type.textspan.Segment _indexed="1" _id="18" _ref_sofa="6" begin="0" end="67" id="SIMPLE_SEGMENT"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="23" _ref_sofa="6" begin="0" end="27" sentenceNumber="0"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="28" _ref_sofa="6" begin="28" end="39" sentenceNumber="1"/>
-<edu.mayo.bmi.uima.core.type.textspan.Sentence _indexed="1" _id="33" _ref_sofa="6" begin="41" end="66" sentenceNumber="2"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="38" _ref_sofa="6" begin="0" end="1" tokenNumber="0" capitalization="3" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="58" _ref_sofa="6" begin="2" end="3" tokenNumber="2" capitalization="3" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="70" _ref_sofa="6" begin="4" end="9" tokenNumber="3" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="82" _ref_sofa="6" begin="10" end="14" tokenNumber="4" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="94" _ref_sofa="6" begin="15" end="26" tokenNumber="5" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="122" _ref_sofa="6" begin="28" end="32" tokenNumber="8" capitalization="1" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="134" _ref_sofa="6" begin="33" end="38" tokenNumber="9" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="154" _ref_sofa="6" begin="41" end="48" tokenNumber="11" capitalization="1" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="166" _ref_sofa="6" begin="49" end="55" tokenNumber="12" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="178" _ref_sofa="6" begin="56" end="60" tokenNumber="13" capitalization="0" numPosition="0"/>
-<edu.mayo.bmi.uima.core.type.syntax.WordToken _indexed="1" _id="190" _ref_sofa="6" begin="61" end="65" tokenNumber="14" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.DocumentID _indexed="1" _id="1" _ref_sofa="6" begin="0" end="0" documentID="sample_note_plaintext"/>
+<org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="114" _ref_sofa="6" begin="27" end="28" tokenNumber="7"/>
+<org.apache.ctakes.typesystem.type.NewlineToken _indexed="1" _id="210" _ref_sofa="6" begin="66" end="67" tokenNumber="16"/>
+<org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="50" _ref_sofa="6" begin="1" end="2" tokenNumber="1"/>
+<org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="106" _ref_sofa="6" begin="26" end="27" tokenNumber="6"/>
+<org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="146" _ref_sofa="6" begin="38" end="39" tokenNumber="10"/>
+<org.apache.ctakes.typesystem.type.PunctuationToken _indexed="1" _id="202" _ref_sofa="6" begin="65" end="66" tokenNumber="15"/>
+<org.apache.ctakes.typesystem.type.textspan.Segment _indexed="1" _id="18" _ref_sofa="6" begin="0" end="67" id="SIMPLE_SEGMENT"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="23" _ref_sofa="6" begin="0" end="27" sentenceNumber="0"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="28" _ref_sofa="6" begin="28" end="39" sentenceNumber="1"/>
+<org.apache.ctakes.typesystem.type.textspan.Sentence _indexed="1" _id="33" _ref_sofa="6" begin="41" end="66" sentenceNumber="2"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="38" _ref_sofa="6" begin="0" end="1" tokenNumber="0" capitalization="3" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="58" _ref_sofa="6" begin="2" end="3" tokenNumber="2" capitalization="3" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="70" _ref_sofa="6" begin="4" end="9" tokenNumber="3" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="82" _ref_sofa="6" begin="10" end="14" tokenNumber="4" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="94" _ref_sofa="6" begin="15" end="26" tokenNumber="5" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="122" _ref_sofa="6" begin="28" end="32" tokenNumber="8" capitalization="1" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="134" _ref_sofa="6" begin="33" end="38" tokenNumber="9" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="154" _ref_sofa="6" begin="41" end="48" tokenNumber="11" capitalization="1" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="166" _ref_sofa="6" begin="49" end="55" tokenNumber="12" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="178" _ref_sofa="6" begin="56" end="60" tokenNumber="13" capitalization="0" numPosition="0"/>
+<org.apache.ctakes.typesystem.type.syntax.WordToken _indexed="1" _id="190" _ref_sofa="6" begin="61" end="65" tokenNumber="14" capitalization="0" numPosition="0"/>
 </CAS>

Modified: incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/CopyAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/CopyAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/CopyAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/CopyAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -55,13 +55,13 @@
       <nameValuePair>
         <name>srcObjClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.syntax.WordToken</string>
+          <string>org.apache.ctakes.typesystem.type.syntax.WordToken</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>destObjClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.CopyDestAnnotation</string>
+          <string>org.apache.ctakes.typesystem.type.CopyDestAnnotation</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -80,12 +80,12 @@
       </imports>
       <types>
         <typeDescription>
-          <name>edu.mayo.bmi.uima.core.type.CopySrcAnnotation</name>
+          <name>org.apache.ctakes.typesystem.type.CopySrcAnnotation</name>
           <description>Used for testing CopyAnnotator.</description>
           <supertypeName>uima.tcas.Annotation</supertypeName>
         </typeDescription>
         <typeDescription>
-          <name>edu.mayo.bmi.uima.core.type.CopyDestAnnotation</name>
+          <name>org.apache.ctakes.typesystem.type.CopyDestAnnotation</name>
           <description>Used for testing CopyAnnotator.</description>
           <supertypeName>uima.tcas.Annotation</supertypeName>
         </typeDescription>
@@ -94,10 +94,10 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopySrcAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopySrcAnnotation</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopyDestAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopyDestAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/OverlapAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/OverlapAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/OverlapAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/OverlapAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -98,13 +98,13 @@ selector=A or B or BOTH</description>
 <nameValuePair>
 <name>A_ObjectClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+<string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
 </value>
 </nameValuePair>
 <nameValuePair>
 <name>B_ObjectClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
 </value>
 </nameValuePair>
 <nameValuePair>

Modified: incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -50,10 +50,10 @@
 <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-core/desc/analysis_engine/SimpleSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -49,7 +49,7 @@
 <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-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -57,7 +57,7 @@ However, the section ids are specific to
       <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-core/desc/analysis_engine/TokenizerAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -55,10 +55,10 @@
 <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-core/desc/analysis_engine/TokenizerAnnotatorVersion1.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/TokenizerAnnotatorVersion1.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/TokenizerAnnotatorVersion1.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/analysis_engine/TokenizerAnnotatorVersion1.xml Thu Sep 20 20:25:49 2012
@@ -68,10 +68,10 @@
 <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-core/desc/cas_consumer/FileWriterCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml Thu Sep 20 20:25:49 2012
@@ -53,7 +53,7 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.DocumentID</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.DocumentID</type>
 </inputs>
 <outputs/>
 <inputSofas>

Modified: incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/HtmlTableCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/HtmlTableCasConsumer.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/HtmlTableCasConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/HtmlTableCasConsumer.xml Thu Sep 20 20:25:49 2012
@@ -58,14 +58,14 @@ annotation_classname|getter_method</desc
       <nameValuePair>
         <name>TableSpanAnnotation</name>
         <value>
-          <string>edu.mayo.bmi.uima.core.type.textspan.Sentence</string>
+          <string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
         </value>
       </nameValuePair>
       <nameValuePair>
         <name>NestedAnnotations</name>
         <value>
           <array>
-            <string>edu.mayo.bmi.uima.core.type.syntax.BaseToken|getPennTag</string>
+            <string>org.apache.ctakes.typesystem.type.syntax.BaseToken|getPennTag</string>
           </array>
         </value>
       </nameValuePair>

Modified: incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/JdbcCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/JdbcCasConsumer.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/JdbcCasConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/cas_consumer/JdbcCasConsumer.xml Thu Sep 20 20:25:49 2012
@@ -43,7 +43,7 @@
 <nameValuePair>
 <name>NormalizedTokenClass</name>
 <value>
-<string>edu.mayo.bmi.uima.core.type.syntax.BaseToken</string>
+<string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
 </value>
 </nameValuePair>
 <nameValuePair>

Modified: incubator/ctakes/trunk/ctakes-core/desc/test/analysis_engine/SimpleSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/desc/test/analysis_engine/SimpleSegmentAnnotator.xml?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/desc/test/analysis_engine/SimpleSegmentAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/desc/test/analysis_engine/SimpleSegmentAnnotator.xml Thu Sep 20 20:25:49 2012
@@ -55,7 +55,7 @@
       <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-core/src/main/java/edu/mayo/bmi/nlp/tokenizer/TokenizerPTB.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/nlp/tokenizer/TokenizerPTB.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/nlp/tokenizer/TokenizerPTB.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/nlp/tokenizer/TokenizerPTB.java Thu Sep 20 20:25:49 2012
@@ -37,13 +37,13 @@ import java.util.List;
 import org.apache.uima.jcas.JCas;
 
 import edu.mayo.bmi.uima.core.ae.TokenizerAnnotator;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.ContractionToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.NumToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.NumToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 
 /**
  * A class used to break natural text into tokens following PTB rules.

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/FilterAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/FilterAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/FilterAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/FilterAnnotator.java Thu Sep 20 20:25:49 2012
@@ -33,7 +33,7 @@ import org.apache.uima.jcas.JFSIndexRepo
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 
 public class FilterAnnotator extends JCasAnnotator_ImplBase {
 	// TODO parameterize retainAttrTypeId = DISORDER_ANNOTATIONS = 2

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SectionSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SectionSegmentAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SectionSegmentAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SectionSegmentAnnotator.java Thu Sep 20 20:25:49 2012
@@ -37,7 +37,7 @@ import org.jdom.Text;
 import org.jdom.input.SAXBuilder;
 
 import edu.mayo.bmi.uima.core.resource.FileResource;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 import edu.mayo.bmi.uima.core.util.DocumentSection;
 import findstruct.Section;

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SentenceDetector.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SentenceDetector.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SentenceDetector.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SentenceDetector.java Thu Sep 20 20:25:49 2012
@@ -43,8 +43,8 @@ import edu.mayo.bmi.uima.core.resource.M
 import edu.mayo.bmi.uima.core.sentence.EndOfSentenceScannerImpl;
 import edu.mayo.bmi.uima.core.sentence.SentenceDetectorCtakes;
 import edu.mayo.bmi.uima.core.sentence.SentenceSpan;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import edu.mayo.bmi.uima.core.util.ParamUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SimpleSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SimpleSegmentAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SimpleSegmentAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SimpleSegmentAnnotator.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.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SimpleSegmentWithTagsAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SimpleSegmentWithTagsAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SimpleSegmentWithTagsAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/SimpleSegmentWithTagsAnnotator.java Thu Sep 20 20:25:49 2012
@@ -28,7 +28,7 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenConverter.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenConverter.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenConverter.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenConverter.java Thu Sep 20 20:25:49 2012
@@ -21,13 +21,13 @@ package edu.mayo.bmi.uima.core.ae;
 import org.apache.uima.jcas.JCas;
 
 import edu.mayo.bmi.nlp.tokenizer.Token;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.ContractionToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.NumToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.NumToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 
 /**
  * Utilities methods for converting between Java Tokenizer objects and their

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenizerAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenizerAnnotator.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenizerAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenizerAnnotator.java Thu Sep 20 20:25:49 2012
@@ -37,8 +37,8 @@ import org.apache.uima.resource.Resource
 import edu.mayo.bmi.nlp.tokenizer.Token;
 import edu.mayo.bmi.nlp.tokenizer.Tokenizer;
 import edu.mayo.bmi.uima.core.resource.StringIntegerMapResource;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
 import edu.mayo.bmi.uima.core.util.ParamUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenizerAnnotatorPTB.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenizerAnnotatorPTB.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenizerAnnotatorPTB.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/ae/TokenizerAnnotatorPTB.java Thu Sep 20 20:25:49 2012
@@ -42,10 +42,10 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.ResourceInitializationException;
 
 import edu.mayo.bmi.nlp.tokenizer.TokenizerPTB;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.textspan.Segment;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import edu.mayo.bmi.uima.core.util.ParamUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/NormalizedFilesInDirectoryCasConsumer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/NormalizedFilesInDirectoryCasConsumer.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/NormalizedFilesInDirectoryCasConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/NormalizedFilesInDirectoryCasConsumer.java Thu Sep 20 20:25:49 2012
@@ -32,7 +32,7 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.ResourceProcessException;
 
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 /**

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/TokenFreqCasConsumer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/TokenFreqCasConsumer.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/TokenFreqCasConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/TokenFreqCasConsumer.java Thu Sep 20 20:25:49 2012
@@ -37,14 +37,14 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.ResourceProcessException;
 import org.apache.uima.util.ProcessTrace;
 
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 
 /**
  * This class creates a file that contains the frequencies of the word tokens found in a set
  * in a text collection.  This cas consumer could potentially be used to create a frequency
  * file for any kind of annotation but only counts Token annotations at the moment.   
  * 
- *  @see edu.mayo.bmi.uima.core.type.syntax.WordToken.java
+ *  @see org.apache.ctakes.typesystem.type.syntax.WordToken.java
  */
 
 public class TokenFreqCasConsumer extends CasConsumer_ImplBase

Modified: incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/TokenOffsetsCasConsumer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/TokenOffsetsCasConsumer.java?rev=1388196&r1=1388195&r2=1388196&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/TokenOffsetsCasConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/main/java/edu/mayo/bmi/uima/core/cc/TokenOffsetsCasConsumer.java Thu Sep 20 20:25:49 2012
@@ -34,7 +34,7 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.ResourceProcessException;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 /**



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