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From james-mas...@apache.org
Subject svn commit: r1509770 [1/4] - in /ctakes/branches/ctakes-3.1.0: ./ ctakes-assertion-res/ ctakes-assertion-zoner-res/ ctakes-assertion-zoner/ ctakes-assertion/ ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/ ctak...
Date Fri, 02 Aug 2013 16:48:16 GMT
Author: james-masanz
Date: Fri Aug  2 16:48:14 2013
New Revision: 1509770

URL: http://svn.apache.org/r1509770
Log:
Merged latest trunk changes to ctakes-3.1.0 branch to pick up re-trained chunker model and chunker descriptor

Added:
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AnnotationStatisticsCompact.java
      - copied unchanged from r1509769, ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AnnotationStatisticsCompact.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java
      - copied unchanged from r1509769, ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java
    ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunker-model.zip
      - copied unchanged from r1509769, ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunker-model.zip
    ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java
      - copied unchanged from r1509769, ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java
    ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java
      - copied unchanged from r1509769, ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java
Modified:
    ctakes/branches/ctakes-3.1.0/   (props changed)
    ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
    ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java
    ctakes/branches/ctakes-3.1.0/ctakes-chunker/   (props changed)
    ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml
    ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-context-tokenizer/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-core-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-core/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-coreference-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-coreference/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-dependency-parser-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-dependency-parser/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-dictionary-lookup-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-dictionary-lookup/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-distribution/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-drug-ner-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-drug-ner/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-lvg-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-lvg/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-ne-contexts-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-ne-contexts/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-pad-term-spotter-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-pad-term-spotter/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-pos-tagger-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-pos-tagger/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
    ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
    ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
    ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java
    ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
    ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml
    ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml
    ctakes/branches/ctakes-3.1.0/pom.xml

Propchange: ctakes/branches/ctakes-3.1.0/
------------------------------------------------------------------------------
    svn:mergeinfo = /ctakes/trunk:1506998-1509769

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion-res/pom.xml Fri Aug  2 16:48:14 2013
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.1.0</version>
   </parent>
   <artifactId>ctakes-assertion-res</artifactId>
   <name>Apache cTAKES Resources assertion</name>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/pom.xml Fri Aug  2 16:48:14 2013
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.1.0</version>
   </parent>
   <artifactId>ctakes-assertion-zoner-res</artifactId>
   <name>Apache cTAKES Resources assertion-zoner</name>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion-zoner/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,65 +1,65 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Licensed to the Apache Software Foundation (ASF) under one
-    or more contributor license agreements.  See the NOTICE file
-    distributed with this work for additional information
-    regarding copyright ownership.  The ASF licenses this file
-    to you under the Apache License, Version 2.0 (the
-    "License"); you may not use this file except in compliance
-    with the License.  You may obtain a copy of the License at
-
-      http://www.apache.org/licenses/LICENSE-2.0
-
-    Unless required by applicable law or agreed to in writing,
-    software distributed under the License is distributed on an
-    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-    KIND, either express or implied.  See the License for the
-    specific language governing permissions and limitations
-    under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<artifactId>ctakes-assertion-zoner</artifactId>
-	<name>Apache cTAKES Assertion's zoner</name>
-	<parent>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes</artifactId>
-		<version>3.1.0-SNAPSHOT</version>
-	</parent>
-	<dependencies>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-assertion-zoner-res</artifactId>
-		</dependency>	    
-		<dependency>
-			<groupId>net.sf.mastif</groupId>
-			<artifactId>mastif-zoner</artifactId>
-			<version>1.4</version>
-		</dependency>
-		<dependency>
-      <groupId>org.apache.uima</groupId>
-      <artifactId>uimaj-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.uimafit</groupId>
-			<artifactId>uimafit</artifactId>
-		</dependency>
-    <dependency>
-      <groupId>org.apache.ctakes</groupId>
-      <artifactId>ctakes-core</artifactId>
-    </dependency>
-	</dependencies>
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>  
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-assertion-zoner</artifactId>
+	<name>Apache cTAKES Assertion's zoner</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.1.0</version>
+	</parent>
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion-zoner-res</artifactId>
+		</dependency>	    
+		<dependency>
+			<groupId>net.sf.mastif</groupId>
+			<artifactId>mastif-zoner</artifactId>
+			<version>1.4</version>
+		</dependency>
+		<dependency>
+      <groupId>org.apache.uima</groupId>
+      <artifactId>uimaj-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.uimafit</groupId>
+			<artifactId>uimafit</artifactId>
+		</dependency>
+    <dependency>
+      <groupId>org.apache.ctakes</groupId>
+      <artifactId>ctakes-core</artifactId>
+    </dependency>
+	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>  
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,239 +1,239 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Licensed to the Apache Software Foundation (ASF) under one
-    or more contributor license agreements.  See the NOTICE file
-    distributed with this work for additional information
-    regarding copyright ownership.  The ASF licenses this file
-    to you under the Apache License, Version 2.0 (the
-    "License"); you may not use this file except in compliance
-    with the License.  You may obtain a copy of the License at
-
-      http://www.apache.org/licenses/LICENSE-2.0
-
-    Unless required by applicable law or agreed to in writing,
-    software distributed under the License is distributed on an
-    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-    KIND, either express or implied.  See the License for the
-    specific language governing permissions and limitations
-    under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<artifactId>ctakes-assertion</artifactId>
-	<name>Apache cTAKES Assertion</name>
-	<parent>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes</artifactId>
-		<version>3.1.0-SNAPSHOT</version>
-	</parent>
-	<dependencies>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-assertion-res</artifactId>
-		</dependency>	    
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-assertion-zoner</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
-    <dependency>
-      <groupId>org.apache.ctakes</groupId>
-      <artifactId>ctakes-dictionary-lookup</artifactId>
-    </dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-core</artifactId>
-		</dependency>
-    <dependency>
-      <groupId>org.apache.ctakes</groupId>
-      <artifactId>ctakes-constituency-parser</artifactId>
-    </dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-pos-tagger</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dependency-parser</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-ml</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-ml-libsvm</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-ml-opennlp-maxent</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-util</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-eval</artifactId>
-		</dependency>			
-		<dependency>
-			<groupId>args4j</groupId>
-			<artifactId>args4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>commons-io</groupId>
-			<artifactId>commons-io</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>commons-lang</groupId>
-			<artifactId>commons-lang</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>commons-logging</groupId>
-			<artifactId>commons-logging</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>com.google.guava</groupId>
-			<artifactId>guava</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>commons-cli</groupId>
-			<artifactId>commons-cli</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>com.carrotsearch</groupId>
-			<artifactId>hppc</artifactId>
-		</dependency>
-
-
-		<dependency>
-			<groupId>jdom</groupId>
-			<artifactId>jdom</artifactId>
-		</dependency>
-
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-
-				<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-maxent</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-tools</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>tw.edu.ntu.csie</groupId>
-			<artifactId>libsvm</artifactId>
-		</dependency>
-
-		<dependency>
-			<groupId>org.springframework</groupId>
-			<artifactId>spring-core</artifactId>
-		</dependency>
-
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.uimafit</groupId>
-			<artifactId>uimafit</artifactId>
-		</dependency>
-
-		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-core-asl</artifactId>
-			<version>1.5.0</version>
-		</dependency>
-		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-mapper-asl</artifactId>
-			<version>1.5.0</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.scala-lang</groupId>
-			<artifactId>scala-library</artifactId>
-			<version>2.9.0</version>
-		</dependency>
-		<dependency>
-			<groupId>org.scala-tools.sbinary</groupId>
-			<artifactId>sbinary_2.9.0</artifactId>
-			<version>0.4.0</version>
-		</dependency>
-
-		<!-- Dependencies that still need to be uploaded to Maven Central; when 
-			done, the dependency versions should be moved into the parent pom -->
-		<dependency>
-			<groupId>org.mitre.medfacts</groupId>
-			<artifactId>medfacts-i2b2</artifactId>
-			<version>1.2</version>
-			<scope>system</scope>
-			<systemPath>${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
-		</dependency>
-		<dependency>
-			<groupId>org.mitre.medfacts</groupId>
-			<artifactId>medfacts-zoner</artifactId>
-			<version>1.1</version>
-			<scope>system</scope>
-			<systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
-		</dependency>
-		<dependency>
-			<groupId>org.mitre.jcarafe.core</groupId>
-			<artifactId>jcarafe.core</artifactId>
-			<version>2.9.1</version>
-			<scope>system</scope>
-			<systemPath>${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
-		</dependency>
-		<dependency>
-			<groupId>org.mitre.jcarafe.ext</groupId>
-			<artifactId>jcarafe.ext</artifactId>
-			<version>2.9.1</version>
-			<scope>system</scope>
-			<systemPath>${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-lvg</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-context-tokenizer</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-chunker</artifactId>
-		</dependency>
-	</dependencies>	
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml</typeSystem>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>    	
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-assertion</artifactId>
+	<name>Apache cTAKES Assertion</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.1.0</version>
+	</parent>
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion-res</artifactId>
+		</dependency>	    
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion-zoner</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+    <dependency>
+      <groupId>org.apache.ctakes</groupId>
+      <artifactId>ctakes-dictionary-lookup</artifactId>
+    </dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-core</artifactId>
+		</dependency>
+    <dependency>
+      <groupId>org.apache.ctakes</groupId>
+      <artifactId>ctakes-constituency-parser</artifactId>
+    </dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-pos-tagger</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dependency-parser</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml-libsvm</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml-opennlp-maxent</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-util</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-eval</artifactId>
+		</dependency>			
+		<dependency>
+			<groupId>args4j</groupId>
+			<artifactId>args4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-lang</groupId>
+			<artifactId>commons-lang</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-logging</groupId>
+			<artifactId>commons-logging</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.carrotsearch</groupId>
+			<artifactId>hppc</artifactId>
+		</dependency>
+
+
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+
+				<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-maxent</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-tools</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>tw.edu.ntu.csie</groupId>
+			<artifactId>libsvm</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-core</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.uimafit</groupId>
+			<artifactId>uimafit</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.codehaus.jackson</groupId>
+			<artifactId>jackson-core-asl</artifactId>
+			<version>1.5.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.codehaus.jackson</groupId>
+			<artifactId>jackson-mapper-asl</artifactId>
+			<version>1.5.0</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.scala-lang</groupId>
+			<artifactId>scala-library</artifactId>
+			<version>2.9.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.scala-tools.sbinary</groupId>
+			<artifactId>sbinary_2.9.0</artifactId>
+			<version>0.4.0</version>
+		</dependency>
+
+		<!-- Dependencies that still need to be uploaded to Maven Central; when 
+			done, the dependency versions should be moved into the parent pom -->
+		<dependency>
+			<groupId>org.mitre.medfacts</groupId>
+			<artifactId>medfacts-i2b2</artifactId>
+			<version>1.2</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.medfacts</groupId>
+			<artifactId>medfacts-zoner</artifactId>
+			<version>1.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.jcarafe.core</groupId>
+			<artifactId>jcarafe.core</artifactId>
+			<version>2.9.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.jcarafe.ext</groupId>
+			<artifactId>jcarafe.ext</artifactId>
+			<version>2.9.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-lvg</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-context-tokenizer</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker</artifactId>
+		</dependency>
+	</dependencies>	
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>    	
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java Fri Aug  2 16:48:14 2013
@@ -38,9 +38,12 @@ public class Chi2FeatureSelection<OUTCOM
 
     protected Table<String, OUTCOME_T, Integer> featValueClassCount;
 
-    public Chi2Scorer() {
+	private boolean yates = false;
+
+    public Chi2Scorer(boolean yate) {
       this.classCounts = HashMultiset.<OUTCOME_T> create();
       this.featValueClassCount = HashBasedTable.<String, OUTCOME_T, Integer> create();
+      this.yates = yate;
     }
 
     public void update(String featureName, OUTCOME_T outcome, int occurrences) {
@@ -88,13 +91,12 @@ public class Chi2FeatureSelection<OUTCOM
         return chi2val;
       }
 
-      boolean yates = true;
       for (int lbl = 0; lbl < numOfClass; lbl++) {
         // for positive part of feature:
         double expected = (outcomeCounts[lbl] / (double) n) * (posiFeatCount);
         if (expected > 0) {
           double diff = Math.abs(posiOutcomeCounts[lbl] - expected);
-          if (yates) { // apply Yate's correction
+          if (this.yates ) { // apply Yate's correction
             diff -= 0.5;
           }
           if (diff > 0)
@@ -106,7 +108,7 @@ public class Chi2FeatureSelection<OUTCOM
         double observ = outcomeCounts[lbl] - posiOutcomeCounts[lbl];
         if (expected > 0) {
           double diff = Math.abs(observ - expected);
-          if (yates) { // apply Yate's correction
+          if (this.yates) { // apply Yate's correction
             diff -= 0.5;
           }
           if (diff > 0)
@@ -121,6 +123,8 @@ public class Chi2FeatureSelection<OUTCOM
   private double chi2Threshold;
 
   private Chi2Scorer<OUTCOME_T> chi2Function;
+  
+  private boolean yates = false;
 
   public Chi2FeatureSelection(String name) {
     this(name, 0.0);
@@ -131,6 +135,17 @@ public class Chi2FeatureSelection<OUTCOM
     this.chi2Threshold = threshold;
   }
 
+  /**
+   * Constructor that can let use control the yate's correction
+   * @param name
+   * @param threshold
+   * @param yates : true for using yate's correction, false for turn off yate's correction
+   */
+  public Chi2FeatureSelection(String name, double threshold, boolean yates) {
+	    super(name);
+	    this.chi2Threshold = threshold;
+	    this.yates = yates;
+	  }
   @Override
   public boolean apply(Feature feature) {
     return this.selectedFeatureNames.contains(this.getFeatureName(feature));
@@ -139,7 +154,7 @@ public class Chi2FeatureSelection<OUTCOM
   @Override
   public void train(Iterable<Instance<OUTCOME_T>> instances) {
     // aggregate statistics for all features
-    this.chi2Function = new Chi2Scorer<OUTCOME_T>();
+    this.chi2Function = new Chi2Scorer<OUTCOME_T>(this.yates);
     for (Instance<OUTCOME_T> instance : instances) {
       OUTCOME_T outcome = instance.getOutcome();
       for (Feature feature : instance.getFeatures()) {

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java Fri Aug  2 16:48:14 2013
@@ -38,6 +38,7 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.syntax.Chunk;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
@@ -45,7 +46,7 @@ import org.apache.ctakes.typesystem.type
 
 /**
  * @author shalgrim
- *
+ * tmiller says this is the MITRE stuff, ctakes 3.0
  */
 public class HistoryAttributeClassifier {
 
@@ -69,6 +70,18 @@ public class HistoryAttributeClassifier 
 		return classifyWithLogic(vfeat);
 			
 	}
+	
+	/**
+	 * 
+	 * @param jCas - the jcas of the document
+	 * @param arg - the node getting features added to it
+	 * @return whether or not arg is a token preceded by "h/o"
+	 */
+	public static Boolean precededByH_O(JCas jCas, Annotation arg) {
+		Boolean answer = false;
+
+		return answer;
+	}
 
 
 	public static Boolean classifyWithLogic(HashMap<String, Boolean> vfeat) {
@@ -80,9 +93,8 @@ public class HistoryAttributeClassifier 
 		Boolean subsume_summary = (subsumectr>0);
 		if (vfeat.get(DISCUSSION_DEPPATH) || subsume_summary) {
 			return true;
-		} else {
-			return false;
 		}
+		return false;
 	}
 
 
@@ -109,19 +121,32 @@ public class HistoryAttributeClassifier 
 			
 
 			// 2) some other identified annotation subsumes this one?
-			List<IdentifiedAnnotation> lsmentions = JCasUtil.selectPreceding(jCas, IdentifiedAnnotation.class, arg, 5);
-			lsmentions.addAll(JCasUtil.selectFollowing(jCas, IdentifiedAnnotation.class, arg, 5));
+			List<IdentifiedAnnotation> lsmentions = JCasUtil.selectCovering(jCas, IdentifiedAnnotation.class, arg.getBegin(), arg.getEnd());
+			//lsmentions.addAll(JCasUtil.selectFollowing(jCas, IdentifiedAnnotation.class, arg, 5));
 			for (IdentifiedAnnotation annot : lsmentions) {
 				if ( annot.getBegin()>arg.getBegin()) {
+					// it's okay to break here b/c of the ordering?
 					break;
-				} else {
-					if ( annot.getEnd()<arg.getEnd()) {
-						continue;
-					} else if ( !DependencyUtility.equalCoverage(
-							DependencyUtility.getNominalHeadNode(jCas, annot),
-							DependencyUtility.getNominalHeadNode(jCas, arg)) ) {
-						// the case that annot is a superset
-						vfeat.put(SUBSUMED_ANNOT, true);
+				}
+				
+				// INVARIANT: arg starts at or after annot begins
+				if ( annot.getEnd()<arg.getEnd()) {
+					// INVARIANT: arg ends at or after annot ends
+					continue;
+				} else if ( !DependencyUtility.equalCoverage(
+						DependencyUtility.getNominalHeadNode(jCas, annot),
+						DependencyUtility.getNominalHeadNode(jCas, arg)) ) {
+					// INVARIANT: arg start at or before annot starts
+					// INVARIANT: arg ends at or before annot ends
+					// INVARIANT: arg falls within bounds of annot
+					// plus there's that deal that they don't have the same head node
+					// but now we have to verify that annot is an EventMention or EntityMention
+					if ((annot instanceof EntityMention) || (annot instanceof EventMention)) {
+						// Here annot has boundaries at or exceeding those of arg
+						// They also have different head nodes (I guess)
+						// and annot is either an EntityMention of EventMention
+						vfeat.put(SUBSUMED_ANNOT, true);		
+						break; // no reason to keep checking
 					}
 				}
 			}

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java Fri Aug  2 16:48:14 2013
@@ -87,7 +87,6 @@ import org.cleartk.classifier.jar.Direct
 import org.cleartk.classifier.jar.GenericJarClassifierFactory;
 import org.cleartk.classifier.jar.JarClassifierBuilder;
 import org.cleartk.classifier.liblinear.LIBLINEARStringOutcomeDataWriter;
-import org.cleartk.eval.AnnotationStatistics;
 import org.cleartk.eval.Evaluation_ImplBase;
 import org.cleartk.util.Options_ImplBase;
 import org.kohsuke.args4j.Option;
@@ -113,7 +112,7 @@ import com.google.common.collect.Sets;
 //import org.chboston.cnlp.ctakes.relationextractor.eval.RelationExtractorEvaluation;
 //import org.chboston.cnlp.ctakes.relationextractor.ae.ModifierExtractorAnnotator;
 
-public class AssertionEvaluation extends Evaluation_ImplBase<File, Map<String, AnnotationStatistics>> {
+public class AssertionEvaluation extends Evaluation_ImplBase<File, Map<String, AnnotationStatisticsCompact>> {
   
 private static Logger logger = Logger.getLogger(AssertionEvaluation.class); 
 
@@ -352,20 +351,20 @@ private static Logger logger = Logger.ge
     // run cross-validation
     else if(options.crossValidationFolds != null) {
       // run n-fold cross-validation
-      List<Map<String, AnnotationStatistics>> foldStats = evaluation.crossValidation(trainFiles, options.crossValidationFolds);
-      //AnnotationStatistics overallStats = AnnotationStatistics.addAll(foldStats);
-      Map<String, AnnotationStatistics> overallStats = new TreeMap<String, AnnotationStatistics>();
+      List<Map<String, AnnotationStatisticsCompact>> foldStats = evaluation.crossValidation(trainFiles, options.crossValidationFolds);
+      //AnnotationStatisticsCompact overallStats = AnnotationStatisticsCompact.addAll(foldStats);
+      Map<String, AnnotationStatisticsCompact> overallStats = new TreeMap<String, AnnotationStatisticsCompact>();
       
       for (String currentAnnotationType : annotationTypes)
       {
-    	  AnnotationStatistics currentAnnotationStatistics = new AnnotationStatistics();
-    	  overallStats.put(currentAnnotationType, currentAnnotationStatistics);
+    	  AnnotationStatisticsCompact currentAnnotationStatisticsCompact = new AnnotationStatisticsCompact();
+    	  overallStats.put(currentAnnotationType, currentAnnotationStatisticsCompact);
       }
-      for (Map<String, AnnotationStatistics> singleFoldMap : foldStats)
+      for (Map<String, AnnotationStatisticsCompact> singleFoldMap : foldStats)
       {
     	  for (String currentAnnotationType : annotationTypes)
     	  {
-    	    AnnotationStatistics currentFoldStatistics = singleFoldMap.get(currentAnnotationType);
+    	    AnnotationStatisticsCompact currentFoldStatistics = singleFoldMap.get(currentAnnotationType);
     	    overallStats.get(currentAnnotationType).addAll(currentFoldStatistics);
     	  }
       }
@@ -398,7 +397,7 @@ private static Logger logger = Logger.ge
     	  }
     	  logger.debug("testFiles.size() = " + testFiles.size());
     	  CollectionReader testCollectionReader = evaluation.getCollectionReader(testFiles);
-    	  Map<String, AnnotationStatistics> stats = evaluation.test(testCollectionReader, modelsDir);
+    	  Map<String, AnnotationStatisticsCompact> stats = evaluation.test(testCollectionReader, modelsDir);
 
     	  AssertionEvaluation.printScore(stats,  modelsDir.getAbsolutePath());
       }
@@ -476,12 +475,12 @@ private static void printOptionsForDebug
 	logger.info(message);
   }
 
-public static void printScore(Map<String, AnnotationStatistics> map, String directory)
+public static void printScore(Map<String, AnnotationStatisticsCompact> map, String directory)
   {
-      for (Map.Entry<String, AnnotationStatistics> currentEntry : map.entrySet())
+      for (Map.Entry<String, AnnotationStatisticsCompact> currentEntry : map.entrySet())
 	  {
     	  String annotationType = currentEntry.getKey();
-    	  AnnotationStatistics stats = currentEntry.getValue();
+    	  AnnotationStatisticsCompact stats = currentEntry.getValue();
     	  
     	  System.out.format("directory: \"%s\"; assertion type: %s%n%n%s%n%n",
     	    directory,
@@ -491,11 +490,12 @@ public static void printScore(Map<String
     	  try {
     		  if (useEvaluationLogFile) {
     			  evaluationLogFileOut.write(
-    					  String.format("directory: \"%s\"; assertion type: %s%n%n%s%n%n",
-    							  directory,
-    							  annotationType.toUpperCase(),
-    							  stats.toString())
+    					  String.format("%s\t%f\t%s",
+    							  annotationType,
+    							  options.featureSelectionThreshold,
+    							  stats.toTsv())
     					  );
+    			  evaluationLogFileOut.flush();
     		  }
 		} catch (IOException e) {
 			// TODO Auto-generated catch block
@@ -781,7 +781,7 @@ public static void printScore(Map<String
   }
 
   @Override
-  protected Map<String, AnnotationStatistics> test(CollectionReader collectionReader, File directory)
+  protected Map<String, AnnotationStatisticsCompact> test(CollectionReader collectionReader, File directory)
       throws Exception {
 //    AnalysisEngine classifierAnnotator = AnalysisEngineFactory.createPrimitive(AssertionCleartkAnalysisEngine.getDescription(
 //        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
@@ -839,14 +839,14 @@ public static void printScore(Map<String
     
     AnalysisEngine aggregate = builder.createAggregate();
     
-    AnnotationStatistics polarityStats = new AnnotationStatistics();
-    AnnotationStatistics conditionalStats = new AnnotationStatistics();
-    AnnotationStatistics uncertaintyStats = new AnnotationStatistics();
-    AnnotationStatistics subjectStats = new AnnotationStatistics();
-    AnnotationStatistics genericStats = new AnnotationStatistics();
-    AnnotationStatistics historyStats = new AnnotationStatistics();	// srh 3/6/13
+    AnnotationStatisticsCompact polarityStats = new AnnotationStatisticsCompact();
+    AnnotationStatisticsCompact conditionalStats = new AnnotationStatisticsCompact();
+    AnnotationStatisticsCompact uncertaintyStats = new AnnotationStatisticsCompact();
+    AnnotationStatisticsCompact subjectStats = new AnnotationStatisticsCompact();
+    AnnotationStatisticsCompact genericStats = new AnnotationStatisticsCompact();
+    AnnotationStatisticsCompact historyStats = new AnnotationStatisticsCompact();	// srh 3/6/13
     
-    Map<String, AnnotationStatistics> map = new TreeMap<String, AnnotationStatistics>(); 
+    Map<String, AnnotationStatisticsCompact> map = new TreeMap<String, AnnotationStatisticsCompact>(); 
     if (!options.ignorePolarity)
     {
       map.put("polarity",  polarityStats);
@@ -921,8 +921,8 @@ public static void printScore(Map<String
       if (!options.ignorePolarity)
       {
 	      polarityStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("polarity"));
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("polarity"));
 	      if(options.printErrors){
 	    	  printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "polarity", CONST.NE_POLARITY_NEGATION_PRESENT, Integer.class);
 	      }
@@ -931,8 +931,8 @@ public static void printScore(Map<String
       if (!options.ignoreConditional)
       {
 	      conditionalStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("conditional"));
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("conditional"));
 	      if(options.printErrors){
 	    	  printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "conditional", CONST.NE_CONDITIONAL_TRUE, Boolean.class);
 	      }
@@ -941,8 +941,8 @@ public static void printScore(Map<String
       if (!options.ignoreUncertainty)
       {
 	      uncertaintyStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("uncertainty"));
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("uncertainty"));
 	      if(options.printErrors){
 	    	  printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "uncertainty", CONST.NE_UNCERTAINTY_PRESENT, Integer.class);
 	      }
@@ -951,8 +951,8 @@ public static void printScore(Map<String
       if (!options.ignoreSubject)
       {
 	      subjectStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("subject"));
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("subject"));
 	      if(options.printErrors){
 	    	  printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "subject", null, CONST.ATTR_SUBJECT_PATIENT.getClass());
 	      }
@@ -961,8 +961,8 @@ public static void printScore(Map<String
       if (!options.ignoreGeneric)
       {
 	      genericStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
-			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("generic"));
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("generic"));
 	      if(options.printErrors){
 	    	  printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "generic", CONST.NE_GENERIC_TRUE, Boolean.class);
 	      }
@@ -972,8 +972,8 @@ public static void printScore(Map<String
       if (!options.ignoreHistory)
       {
     	  historyStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
-    			  AnnotationStatistics.<IdentifiedAnnotation>annotationToSpan(),
-    			  AnnotationStatistics.<IdentifiedAnnotation>annotationToFeatureValue("historyOf"));
+    			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToSpan(),
+    			  AnnotationStatisticsCompact.<IdentifiedAnnotation>annotationToFeatureValue("historyOf"));
     	  if(options.printErrors){
     		  printErrors(jCas, goldEntitiesAndEvents, systemEntitiesAndEvents, "historyOf", CONST.NE_HISTORY_OF_PRESENT, Integer.class);
     	  }
@@ -993,37 +993,37 @@ public static void printScore(Map<String
 		  FeatureSelection<String> featureSelection; 
 		  if (currentAssertionAttribute.equals("polarity")) {
 			  // TODO: parameterize the thresholds
-			  featureSelection = PolarityCleartkAnalysisEngine.createFeatureSelection(1f);
+			  featureSelection = PolarityCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
 			  featureSelection.train(instances);
 			  featureSelection.save(PolarityCleartkAnalysisEngine.createFeatureSelectionURI(directory));
 		  }
 		  else if (currentAssertionAttribute.equals("uncertainty")) {
 			  // TODO: parameterize the thresholds
-			  featureSelection = UncertaintyCleartkAnalysisEngine.createFeatureSelection(1f);
+			  featureSelection = UncertaintyCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
 			  featureSelection.train(instances);
 			  featureSelection.save(UncertaintyCleartkAnalysisEngine.createFeatureSelectionURI(directory));
 		  }
 		  else if (currentAssertionAttribute.equals("conditional")) {
 			  // TODO: parameterize the thresholds
-			  featureSelection = ConditionalCleartkAnalysisEngine.createFeatureSelection(1f);
+			  featureSelection = ConditionalCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
 			  featureSelection.train(instances);
 			  featureSelection.save(ConditionalCleartkAnalysisEngine.createFeatureSelectionURI(directory));
 		  }
 		  else if (currentAssertionAttribute.equals("subject")) {
 			  // TODO: parameterize the thresholds
-			  featureSelection = SubjectCleartkAnalysisEngine.createFeatureSelection(1f);
+			  featureSelection = SubjectCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
 			  featureSelection.train(instances);
 			  featureSelection.save(SubjectCleartkAnalysisEngine.createFeatureSelectionURI(directory));
 		  }
 		  else if (currentAssertionAttribute.equals("generic")) {
 			  // TODO: parameterize the thresholds
-			  featureSelection = GenericCleartkAnalysisEngine.createFeatureSelection(1f);
+			  featureSelection = GenericCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
 			  featureSelection.train(instances);
 			  featureSelection.save(GenericCleartkAnalysisEngine.createFeatureSelectionURI(directory));
 		  }
 		  else if (currentAssertionAttribute.equals("historyOf")) {
 			  // TODO: parameterize the thresholds
-			  featureSelection = HistoryCleartkAnalysisEngine.createFeatureSelection(1f);
+			  featureSelection = HistoryCleartkAnalysisEngine.createFeatureSelection(options.featureSelectionThreshold);
 			  featureSelection.train(instances);
 			  featureSelection.save(HistoryCleartkAnalysisEngine.createFeatureSelectionURI(directory));
 		  }
@@ -1128,6 +1128,9 @@ private static void output(Object o) {
 private static void printErrors(JCas jCas,
 		  Collection<IdentifiedAnnotation> goldEntitiesAndEvents,
 		  Collection<IdentifiedAnnotation> systemEntitiesAndEvents, String classifierType, Object trueCategory, Class<? extends Object> categoryClass) throws ResourceProcessException {
+
+	String documentId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+	
 	  Map<HashableAnnotation, IdentifiedAnnotation> goldMap = Maps.newHashMap();
 	  for (IdentifiedAnnotation mention : goldEntitiesAndEvents) {
 		  goldMap.put(new HashableAnnotation(mention), mention);
@@ -1176,17 +1179,17 @@ private static void printErrors(JCas jCa
 					  // used for multi-class case:
 					  System.out.println(classifierType+" Incorrectly labeled as " + systemLabel + " when the example was " + goldLabel + ": " + formatError(jCas, goldAnnotation));
 				  }else if(systemLabel.equals(trueCategory)){
-					  System.out.println(classifierType+" FP: " + typeId  + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+					  System.out.println(classifierType+" FP: " + typeId  + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
 				  }else{
-					  System.out.println(classifierType+" FN: " + typeId + " " + formatError(jCas, goldAnnotation)+ "| system:|" + formatError(jCas, systemAnnotation));
+					  System.out.println(classifierType+" FN: " + typeId + " " + formatError(jCas, goldAnnotation)+ "| system:|" + formatError(jCas, systemAnnotation) + " " + documentId);
 				  }
 			  }else{
 			    if(trueCategory == null){
 			      // multi-class case -- probably don't want to print anything?
 			    }else if(systemLabel.equals(trueCategory)){
-					  System.out.println(classifierType+" TP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+					  System.out.println(classifierType+" TP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
 				  }else{
-					  System.out.println(classifierType+" TN: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+					  System.out.println(classifierType+" TN: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
 				  }
 			  }
 		  }

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java Fri Aug  2 16:48:14 2013
@@ -27,6 +27,7 @@ import java.util.Random;
 
 import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
 import org.apache.ctakes.assertion.zoner.types.Zone;
+import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
@@ -358,7 +359,18 @@ public abstract class AssertionCleartkAn
 //      }
 
 
-      instance.add(new Feature("ENTITY_TYPE_" + entityOrEventMention.getTypeID()));
+      // 7/9/13 SRH trying to make it work just for anatomical site
+      int eemTypeId = entityOrEventMention.getTypeID(); 
+      if (eemTypeId == CONST.NE_TYPE_ID_ANATOMICAL_SITE) {
+          // 7/9/13 srh modified per tmiller so it's binary but not numeric feature
+          //instance.add(new Feature("ENTITY_TYPE_" + entityOrEventMention.getTypeID()));
+          instance.add(new Feature("ENTITY_TYPE_ANAT_SITE"));
+      } /* This hurts recall more than it helps precision
+      else if (eemTypeId == CONST.NE_TYPE_ID_DRUG) {
+    	  // 7/10 adding drug
+    	  instance.add(new Feature("ENTITY_TYPE_DRUG"));
+      }
+      */
       
       for (SimpleFeatureExtractor extractor : this.entityFeatureExtractors) {
         instance.addAll(extractor.extract(jCas, entityOrEventMention));

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java Fri Aug  2 16:48:14 2013
@@ -72,7 +72,7 @@ public class ConditionalCleartkAnalysisE
 	      }
 	}
 	public static FeatureSelection<String> createFeatureSelection(double threshold) {
-		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
 		//		  return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
 	}
 

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java Fri Aug  2 16:48:14 2013
@@ -94,7 +94,7 @@ public class GenericCleartkAnalysisEngin
 	      }
 	}
 	public static FeatureSelection<String> createFeatureSelection(double threshold) {
-		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
 		//		  return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
 	}
 

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java Fri Aug  2 16:48:14 2013
@@ -97,7 +97,7 @@ public class HistoryCleartkAnalysisEngin
 	      }
 	}
 	public static FeatureSelection<String> createFeatureSelection(double threshold) {
-		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
 		//		  return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
 	}
 

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java Fri Aug  2 16:48:14 2013
@@ -93,7 +93,7 @@ public class PolarityCleartkAnalysisEngi
 	      }
 	}
 	public static FeatureSelection<String> createFeatureSelection(double threshold) {
-		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
 		//		  return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
 	}
 

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java Fri Aug  2 16:48:14 2013
@@ -97,7 +97,7 @@ public class SubjectCleartkAnalysisEngin
 	      }
 	}
 	public static FeatureSelection<String> createFeatureSelection(double threshold) {
-		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
 		//		  return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
 	}
 

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java Fri Aug  2 16:48:14 2013
@@ -79,7 +79,7 @@ public class UncertaintyCleartkAnalysisE
 	}
 	
 	public static FeatureSelection<String> createFeatureSelection(double threshold) {
-		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold);
+		return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
 		//		  return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
 	}
 

Modified: ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java Fri Aug  2 16:48:14 2013
@@ -14,11 +14,11 @@ public class CrossValidateChi2GridSearch
 		
 		AssertionEvaluation.useEvaluationLogFile = true;
 		
-		float[] threshs = {2f, 5f, 10f, 20f, 50f, 100f};
+		float[] threshs = {1f, 5f, 10f, 50f, 100f};
 		for (Float chi2threshold : threshs ) {
 			System.out.println("BEGIN Chi2 Grid Search with threshold = "+ Float.toString(chi2threshold));
-			AssertionEvaluation.evaluationLogFileOut.write("BEGIN Chi2 Grid Search with threshold = "+ Float.toString(chi2threshold));
-			AssertionEvaluation.evaluationLogFileOut.flush();
+//			AssertionEvaluation.evaluationLogFileOut.write("BEGIN Chi2 Grid Search with threshold = "+ Float.toString(chi2threshold)+"\n");
+//			AssertionEvaluation.evaluationLogFileOut.flush();
 			
 			for (String attribute : AssertionConst.annotationTypes) {
 

Propchange: ctakes/branches/ctakes-3.1.0/ctakes-chunker/
------------------------------------------------------------------------------
  Merged /ctakes/trunk/ctakes-chunker:r1506998-1509769

Modified: ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-chunker-res/pom.xml Fri Aug  2 16:48:14 2013
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.1.0</version>
   </parent>
   <artifactId>ctakes-chunker-res</artifactId>
   <name>Apache cTAKES Resources ctakes-chunker-res</name>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-chunker/desc/Chunker.xml Fri Aug  2 16:48:14 2013
@@ -37,7 +37,7 @@
 			<nameValuePair>
 				<name>ChunkerModelFile</name>
 				<value>
-					<string>org/apache/ctakes/chunker/models/chunk-model.claims-1.5.zip
+					<string>org/apache/ctakes/chunker/models/chunker-model.zip
 					</string>
 				</value>
 			</nameValuePair>
@@ -92,7 +92,7 @@
 				<name>ChunkerModelFile</name>
 				<description></description>
 				<fileResourceSpecifier>
-					<fileUrl>file:org/apache/ctakes/chunker/models/chunk-model.claims-1.5.zip
+					<fileUrl>file:org/apache/ctakes/chunker/models/chunker-model.zip
 					</fileUrl>
 				</fileResourceSpecifier>
 				<implementationName>org.apache.ctakes.core.resource.FileResourceImpl

Modified: ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-chunker/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,69 +1,69 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Licensed to the Apache Software Foundation (ASF) under one
-    or more contributor license agreements.  See the NOTICE file
-    distributed with this work for additional information
-    regarding copyright ownership.  The ASF licenses this file
-    to you under the Apache License, Version 2.0 (the
-    "License"); you may not use this file except in compliance
-    with the License.  You may obtain a copy of the License at
-
-      http://www.apache.org/licenses/LICENSE-2.0
-
-    Unless required by applicable law or agreed to in writing,
-    software distributed under the License is distributed on an
-    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-    KIND, either express or implied.  See the License for the
-    specific language governing permissions and limitations
-    under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<artifactId>ctakes-chunker</artifactId>
-	<name>Apache cTAKES chunker</name>
-	<parent>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes</artifactId>
-		<version>3.1.0-SNAPSHOT</version>
-	</parent>
-	<dependencies>
-      	<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-chunker-res</artifactId>
-		</dependency>		      
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-pos-tagger</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-maxent</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-tools</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-	</dependencies>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-chunker</artifactId>
+	<name>Apache cTAKES chunker</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.1.0</version>
+	</parent>
+	<dependencies>
+      	<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker-res</artifactId>
+		</dependency>		      
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-pos-tagger</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-maxent</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-tools</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+	</dependencies>
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,170 +1,170 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor 
-	license agreements. See the NOTICE file distributed with this work for additional 
-	information regarding copyright ownership. The ASF licenses this file to 
-	you under the Apache License, Version 2.0 (the "License"); you may not use 
-	this file except in compliance with the License. You may obtain a copy of 
-	the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required 
-	by applicable law or agreed to in writing, software distributed under the 
-	License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS 
-	OF ANY KIND, either express or implied. See the License for the specific 
-	language governing permissions and limitations under the License. -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<artifactId>ctakes-clinical-pipeline</artifactId>
-	<name>Apache cTAKES ctakes-clinical-pipeline</name>
-	<parent>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes</artifactId>
-		<version>3.1.0-SNAPSHOT</version>
-	</parent>
-
-
-	<dependencies>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>jdom</groupId>
-			<artifactId>jdom</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-context-tokenizer</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dictionary-lookup</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-preprocessor</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-lvg</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-chunker</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-ne-contexts</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-pos-tagger</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-assertion</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dependency-parser</artifactId>
-		</dependency>
-	</dependencies>
-	<profiles>
-		<profile>
-			<id>runCPE</id>
-			<activation>
-				<property>
-					<name>runCPE</name>
-				</property>
-			</activation>
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>exec-maven-plugin</artifactId>
-						<version>1.2.1</version>
-						<executions>
-							<execution>
-								<!-- depends on other modules being on classpath -->
-								<phase>compile</phase>
-								<goals>
-									<goal>java</goal>
-								</goals>
-							</execution>
-						</executions>
-						<configuration>
-							<includeProjectDependencies>true</includeProjectDependencies>
-							<includePluginDependencies>true</includePluginDependencies>						
-							<mainClass>org.apache.uima.tools.cpm.CpmFrame</mainClass>
-							<arguments>
-								<argument />
-							</arguments>
-						</configuration>
-						<dependencies>
-							<dependency>
-								<groupId>gov.nih.nlm.nls.lvg</groupId>
-								<artifactId>lvg2010dist</artifactId>
-								<version>0.0.1</version>
-							</dependency>
-						</dependencies>						
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-
-		<profile>
-			<id>runCVD</id>
-			<activation>
-				<property>
-					<name>runCVD</name>
-				</property>
-			</activation>
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>exec-maven-plugin</artifactId>
-						<version>1.2.1</version>
-						<executions>
-							<execution>
-								<!-- depends on other modules being on classpath -->
-								<phase>compile</phase>
-								<goals>
-									<goal>java</goal>
-								</goals>
-							</execution>
-						</executions>
-						<configuration>
-							<includeProjectDependencies>true</includeProjectDependencies>
-							<includePluginDependencies>true</includePluginDependencies>
-
-							<mainClass>org.apache.uima.tools.cvd.CVD</mainClass>
-							<!-- Have to specify at least one parameter otherwise, CVD thinks 
-								it's an invalid param because MVN passes null when joining to the mvn thread -->
-							<arguments>
-								<argument>-lookandfeel</argument>
-								<argument>javax.swing.plaf.metal.MetalLookAndFeel</argument>
-							</arguments>
-						</configuration>
-						<dependencies>
-							<dependency>
-								<groupId>gov.nih.nlm.nls.lvg</groupId>
-								<artifactId>lvg2010dist</artifactId>
-								<version>0.0.1</version>
-							</dependency>
-						</dependencies>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-	</profiles>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor 
+	license agreements. See the NOTICE file distributed with this work for additional 
+	information regarding copyright ownership. The ASF licenses this file to 
+	you under the Apache License, Version 2.0 (the "License"); you may not use 
+	this file except in compliance with the License. You may obtain a copy of 
+	the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required 
+	by applicable law or agreed to in writing, software distributed under the 
+	License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS 
+	OF ANY KIND, either express or implied. See the License for the specific 
+	language governing permissions and limitations under the License. -->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-clinical-pipeline</artifactId>
+	<name>Apache cTAKES ctakes-clinical-pipeline</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.1.0</version>
+	</parent>
+
+
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-context-tokenizer</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dictionary-lookup</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-preprocessor</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-lvg</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-ne-contexts</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-pos-tagger</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dependency-parser</artifactId>
+		</dependency>
+	</dependencies>
+	<profiles>
+		<profile>
+			<id>runCPE</id>
+			<activation>
+				<property>
+					<name>runCPE</name>
+				</property>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>exec-maven-plugin</artifactId>
+						<version>1.2.1</version>
+						<executions>
+							<execution>
+								<!-- depends on other modules being on classpath -->
+								<phase>compile</phase>
+								<goals>
+									<goal>java</goal>
+								</goals>
+							</execution>
+						</executions>
+						<configuration>
+							<includeProjectDependencies>true</includeProjectDependencies>
+							<includePluginDependencies>true</includePluginDependencies>						
+							<mainClass>org.apache.uima.tools.cpm.CpmFrame</mainClass>
+							<arguments>
+								<argument />
+							</arguments>
+						</configuration>
+						<dependencies>
+							<dependency>
+								<groupId>gov.nih.nlm.nls.lvg</groupId>
+								<artifactId>lvg2010dist</artifactId>
+								<version>0.0.1</version>
+							</dependency>
+						</dependencies>						
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+
+		<profile>
+			<id>runCVD</id>
+			<activation>
+				<property>
+					<name>runCVD</name>
+				</property>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>exec-maven-plugin</artifactId>
+						<version>1.2.1</version>
+						<executions>
+							<execution>
+								<!-- depends on other modules being on classpath -->
+								<phase>compile</phase>
+								<goals>
+									<goal>java</goal>
+								</goals>
+							</execution>
+						</executions>
+						<configuration>
+							<includeProjectDependencies>true</includeProjectDependencies>
+							<includePluginDependencies>true</includePluginDependencies>
+
+							<mainClass>org.apache.uima.tools.cvd.CVD</mainClass>
+							<!-- Have to specify at least one parameter otherwise, CVD thinks 
+								it's an invalid param because MVN passes null when joining to the mvn thread -->
+							<arguments>
+								<argument>-lookandfeel</argument>
+								<argument>javax.swing.plaf.metal.MetalLookAndFeel</argument>
+							</arguments>
+						</configuration>
+						<dependencies>
+							<dependency>
+								<groupId>gov.nih.nlm.nls.lvg</groupId>
+								<artifactId>lvg2010dist</artifactId>
+								<version>0.0.1</version>
+							</dependency>
+						</dependencies>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-constituency-parser-res/pom.xml Fri Aug  2 16:48:14 2013
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.1.0</version>
   </parent>
   <artifactId>ctakes-constituency-parser-res</artifactId>
   <name>Apache cTAKES Resources constituency-parser</name>



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