ctakes-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From james-mas...@apache.org
Subject svn commit: r1509770 [3/4] - 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
Modified: ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,53 +1,53 @@
-<?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-preprocessor</artifactId>
-	<name>Apache cTAKES document preprocessor</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>xerces</groupId>
-			<artifactId>xercesImpl</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</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-preprocessor</artifactId>
+	<name>Apache cTAKES document preprocessor</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>xerces</groupId>
+			<artifactId>xercesImpl</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+	</dependencies>
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml Fri Aug  2 16:48:14 2013
@@ -3,7 +3,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.1.0</version>
   </parent>
   <artifactId>ctakes-regression-test</artifactId>
   <name>Apache cTAKES Regression-test</name>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java Fri Aug  2 16:48:14 2013
@@ -88,7 +88,7 @@ public class RegressionPipelineTest exte
 						+ file.getName().substring(0,
 								file.getName().indexOf(".")));
 
-				logger.info("Creating Dir" + generated);
+				logger.info("Creating directory: " + generated);
 
 				Assert.assertTrue(
 						"Unable to create " + generated.getAbsolutePath(),

Modified: ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-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-relation-extractor-res</artifactId>
   <name>Apache cTAKES Resources relation-extractor</name>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,168 +1,168 @@
-<?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-relation-extractor</artifactId>
-	<name>Apache cTAKES Relation Extractor</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-relation-extractor-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>org.cleartk</groupId>
-				<artifactId>cleartk-eval</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>com.lexicalscope.jewelcli</groupId>
-			<artifactId>jewelcli</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>com.carrotsearch</groupId>
-				<artifactId>hppc</artifactId>
-			</dependency>
-		
-		
-		<dependency>
-            <groupId>jdom</groupId>
-            <artifactId>jdom</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.apache.ctakes</groupId>
-		<artifactId>ctakes-context-tokenizer</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-constituency-parser</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-ne-contexts</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-chunker</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-dependency-parser</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-dictionary-lookup</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>edu.mit</groupId>
-		<artifactId>jwi</artifactId>
-		<version>2.2.3</version>
-	</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-relation-extractor</artifactId>
+	<name>Apache cTAKES Relation Extractor</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-relation-extractor-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>org.cleartk</groupId>
+				<artifactId>cleartk-eval</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>com.lexicalscope.jewelcli</groupId>
+			<artifactId>jewelcli</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>com.carrotsearch</groupId>
+				<artifactId>hppc</artifactId>
+			</dependency>
+		
+		
+		<dependency>
+            <groupId>jdom</groupId>
+            <artifactId>jdom</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.apache.ctakes</groupId>
+		<artifactId>ctakes-context-tokenizer</artifactId>
+	</dependency>
+	<dependency>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes-constituency-parser</artifactId>
+	</dependency>
+	<dependency>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes-ne-contexts</artifactId>
+	</dependency>
+	<dependency>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes-chunker</artifactId>
+	</dependency>
+	<dependency>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes-dependency-parser</artifactId>
+	</dependency>
+	<dependency>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes-dictionary-lookup</artifactId>
+	</dependency>
+	<dependency>
+		<groupId>edu.mit</groupId>
+		<artifactId>jwi</artifactId>
+		<version>2.2.3</version>
+	</dependency>
+	</dependencies>
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-side-effect-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-side-effect-res</artifactId>
   <name>Apache cTAKES Resources side-effect</name>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,89 +1,89 @@
-<?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-side-effect</artifactId>
-	<name>Apache cTAKES Side Effects</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-side-effect-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-dictionary-lookup</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-drug-ner</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>jdom</groupId>
-			<artifactId>jdom</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-		<dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-        </dependency>
-       	<dependency>
-            <groupId>tw.edu.ntu.csie</groupId>
-            <artifactId>libsvm</artifactId>
-		</dependency>		
-	</dependencies>
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/sideeffect/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-side-effect</artifactId>
+	<name>Apache cTAKES Side Effects</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-side-effect-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-dictionary-lookup</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-drug-ner</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+		<dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-core</artifactId>
+        </dependency>
+       	<dependency>
+            <groupId>tw.edu.ntu.csie</groupId>
+            <artifactId>libsvm</artifactId>
+		</dependency>		
+	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>  	
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-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-smoking-status-res</artifactId>
   <name>Apache cTAKES Resources smoking-status</name>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,89 +1,89 @@
-<?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-smoking-status</artifactId>
-	<name>Apache cTAKES Smoking Status</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-smoking-status-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-dictionary-lookup</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-drug-ner</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>jdom</groupId>
-			<artifactId>jdom</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-		<dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-        </dependency>
-       	<dependency>
-            <groupId>tw.edu.ntu.csie</groupId>
-            <artifactId>libsvm</artifactId>
-		</dependency>
-	</dependencies>	
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/smokingstatus/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-smoking-status</artifactId>
+	<name>Apache cTAKES Smoking Status</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-smoking-status-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-dictionary-lookup</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-drug-ner</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+		<dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-core</artifactId>
+        </dependency>
+       	<dependency>
+            <groupId>tw.edu.ntu.csie</groupId>
+            <artifactId>libsvm</artifactId>
+		</dependency>
+	</dependencies>	
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build> 	
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml Fri Aug  2 16:48:14 2013
@@ -27,7 +27,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>3.1.0-SNAPSHOT</version>
+		<version>3.1.0</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal-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-temporal-res</artifactId>
   <name>Apache cTAKES Resources temporal</name>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml Fri Aug  2 16:48:14 2013
@@ -19,8 +19,7 @@
     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">
+<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-temporal</artifactId>
     <packaging>jar</packaging>
@@ -28,7 +27,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>3.1.0-SNAPSHOT</version>
+		<version>3.1.0</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java Fri Aug  2 16:48:14 2013
@@ -88,12 +88,12 @@ public class EventAnnotator extends Temp
   protected Float featureSelectionThreshold = 1f; //default is not using feature selection, i.e. select 100% of all features.
   
   public static final String PARAM_SMOTE_NUM_NEIGHBORS = "NumOfNeighborForSMOTE";
-  
+
   @ConfigurationParameter(
-	      name = PARAM_SMOTE_NUM_NEIGHBORS,
-	      mandatory = false,
-	      description = "the number of neighbors used for minority instances for SMOTE algorithm")
-	  protected Float smoteNumOfNeighbors = 0f;
+		  name = PARAM_SMOTE_NUM_NEIGHBORS,
+		  mandatory = false,
+		  description = "the number of neighbors used for minority instances for SMOTE algorithm")
+  protected Float smoteNumOfNeighbors = 0f;
 
   public static final String PARAM_FEATURE_SELECTION_URI = "FeatureSelectionURI";
 

Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java Fri Aug  2 16:48:14 2013
@@ -28,6 +28,7 @@ import org.apache.ctakes.temporal.ae.fea
 import org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor;
 import org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection;
 import org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection;
+import org.apache.ctakes.temporal.utils.SMOTEplus;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
@@ -67,7 +68,7 @@ public class TimeAnnotator extends Tempo
 			name = PARAM_FEATURE_SELECTION_THRESHOLD,
 			mandatory = false,
 			description = "the Chi-squared threshold at which features should be removed")
-	protected Float featureSelectionThreshold = 0f;
+	protected Float featureSelectionThreshold = 1f;
 	
 	public static final String PARAM_FEATURE_SELECTION_URI = "FeatureSelectionURI";
 
@@ -76,13 +77,22 @@ public class TimeAnnotator extends Tempo
 			name = PARAM_FEATURE_SELECTION_URI,
 			description = "provides a URI where the feature selection data will be written")
 	protected URI featureSelectionURI;
+	
+	public static final String PARAM_SMOTE_NUM_NEIGHBORS = "NumOfNeighborForSMOTE";
+
+	  @ConfigurationParameter(
+			  name = PARAM_SMOTE_NUM_NEIGHBORS,
+			  mandatory = false,
+			  description = "the number of neighbors used for minority instances for SMOTE algorithm")
+	  protected Float smoteNumOfNeighbors = 0f;
 
 	public static final String TIMEX_VIEW = "TimexView";
 
 	public static AnalysisEngineDescription createDataWriterDescription(
 			Class<?> dataWriterClass,
 					File outputDirectory,
-					float featureSelect) throws ResourceInitializationException {
+					float featureSelect,
+					float smoteNeighborNumber) throws ResourceInitializationException {
 		return AnalysisEngineFactory.createPrimitiveDescription(
 				TimeAnnotator.class,
 				CleartkAnnotator.PARAM_IS_TRAINING,
@@ -92,7 +102,9 @@ public class TimeAnnotator extends Tempo
 				DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
 				outputDirectory,
 				TimeAnnotator.PARAM_FEATURE_SELECTION_THRESHOLD,
-		        featureSelect);
+		        featureSelect,
+		        EventAnnotator.PARAM_SMOTE_NUM_NEIGHBORS,
+		        smoteNeighborNumber);
 	}
 
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
@@ -121,7 +133,7 @@ public class TimeAnnotator extends Tempo
 	private static final String FEATURE_SELECTION_NAME = "SelectNeighborFeatures";
 
 	public static FeatureSelection<String> createFeatureSelection(double threshold) {
-		return new Chi2FeatureSelection<String>(TimeAnnotator.FEATURE_SELECTION_NAME, threshold);
+		return new Chi2FeatureSelection<String>(TimeAnnotator.FEATURE_SELECTION_NAME, threshold, true);
 	}
 	
 	public static URI createFeatureSelectionURI(File outputDirectoryName) {
@@ -159,7 +171,7 @@ public class TimeAnnotator extends Tempo
 		parseExtractor = new ParseSpanFeatureExtractor();
 
 		//initialize feature selection
-		if (featureSelectionThreshold == 0) {
+		if (featureSelectionThreshold == 1) {
 			this.featureSelection = null;
 		} else {
 			this.featureSelection = TimeAnnotator.createFeatureSelection(this.featureSelectionThreshold);
@@ -176,10 +188,13 @@ public class TimeAnnotator extends Tempo
 
 	@Override
 	public void process(JCas jCas, Segment segment) throws AnalysisEngineProcessException {
+		//TRY SMOTE algorithm here to generate more minority class samples
+	    SMOTEplus smote = new SMOTEplus((int)Math.ceil(this.smoteNumOfNeighbors));
+	    
 		// classify tokens within each sentence
 		for (Sentence sentence : JCasUtil.selectCovered(jCas, Sentence.class, segment)) {
 			List<BaseToken> tokens = JCasUtil.selectCovered(jCas, BaseToken.class, sentence);
-
+			
 			// during training, the list of all outcomes for the tokens
 			List<String> outcomes;
 			if (this.isTraining()) {
@@ -234,12 +249,20 @@ public class TimeAnnotator extends Tempo
 		        }
 				
 				// if training, write to data file
-				if (this.isTraining()) {
-					String outcome = outcomes.get(tokenIndex);
-					this.dataWriter.write(new Instance<String>(outcome, features));
-				}else {// if predicting, add prediction to outcomes
-					outcomes.add(this.classifier.classify(features));
-				}
+		        if (this.isTraining()) {
+		        	String outcome = outcomes.get(tokenIndex);
+		        	// if it is an "O" down-sample it
+		        	if (outcome.equals("O")) {
+		        		this.dataWriter.write(new Instance<String>(outcome, features));
+
+		        	}else{//for minority instances:
+		        		Instance<String> minorityInst = new Instance<String>(outcome, features);
+		        		this.dataWriter.write(minorityInst);
+		        		smote.addInstance(minorityInst);//add minority instances to SMOTE algorithm
+		        	}
+		        }else {// if predicting, add prediction to outcomes
+		        	outcomes.add(this.classifier.classify(features));
+		        }
 			}
 
 			// during prediction, convert chunk labels to times and add them to the CAS
@@ -253,5 +276,11 @@ public class TimeAnnotator extends Tempo
 				this.timeChunking.createChunks(timexCas, tokens, outcomes);
 			}
 		}
+		if(this.isTraining() && this.smoteNumOfNeighbors >= 1){ //add synthetic instances to datawriter, if smote is selected
+	    	Iterable<Instance<String>> syntheticInsts = smote.populateMinorityClass();
+	    	for( Instance<String> sytheticInst: syntheticInsts){
+	    		this.dataWriter.write(sytheticInst);
+	    	}
+	    }
 	}
 }

Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java Fri Aug  2 16:48:14 2013
@@ -7,6 +7,7 @@ import java.io.FileReader;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.net.URI;
+import java.util.LinkedHashSet;
 import java.util.Set;
 
 import org.cleartk.classifier.Feature;
@@ -133,6 +134,8 @@ public class Chi2FeatureSelection<OUTCOM
 
 	private boolean yates = false;
 
+	private LinkedHashSet<String> discardedFeatureNames;
+
 	public Chi2FeatureSelection(String name) {
 		this(name, 0.0);
 	}
@@ -199,6 +202,7 @@ public class Chi2FeatureSelection<OUTCOM
 		this.selectedFeatureNames = Sets.newLinkedHashSet(ordering.immutableSortedCopy(featureNames).subList(
 				0,
 				this.numFeatures));
+		this.discardedFeatureNames = Sets.newLinkedHashSet(ordering.immutableSortedCopy(featureNames).subList(this.numFeatures, totalFeatures));
 
 		this.isTrained = true;
 	}
@@ -209,13 +213,24 @@ public class Chi2FeatureSelection<OUTCOM
 			throw new IllegalStateException("Cannot save before training");
 		}
 		File out = new File(uri);
+		final String uriPath = uri.getPath();
+		final int lastIndex = uriPath.lastIndexOf('.');
+		final String discardPath = (lastIndex >= 0 ? uriPath.substring(0, lastIndex) : uriPath ) + "_discarded.dat";
+		final File discardOut = new File( discardPath );
+//		File discardOut = new File(uri.getPath().substring(0,uri.getPath().lastIndexOf(".")) + "_discarded.dat");
 		BufferedWriter writer = new BufferedWriter(new FileWriter(out));
+		BufferedWriter diswriter = new BufferedWriter(new FileWriter(discardOut));
 
 		for (String feature : this.selectedFeatureNames) {
 			writer.append(String.format("%s\t%f\n", feature, this.chi2Function.score(feature)));
 		}
+		
+		for (String feature : this.discardedFeatureNames ){
+			diswriter.append(String.format("%s\t%f\n", feature, this.chi2Function.score(feature)));
+		}
 
 		writer.close();
+		diswriter.close();
 	}
 
 	@Override

Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java Fri Aug  2 16:48:14 2013
@@ -64,8 +64,11 @@ public class EvaluationOfTimeSpans exten
 
 	static interface Options extends Evaluation_ImplBase.Options {
 
-		@Option(longName = "featureSelectionThreshold", defaultValue = "0")
+		@Option(longName = "featureSelectionThreshold", defaultValue = "1")
 		public float getFeatureSelectionThreshold();
+		
+		@Option(longName = "SMOTENeighborNumber", defaultValue = "0")
+	    public float getSMOTENeighborNumber();
 	}
 
 	public static void main(String[] args) throws Exception {
@@ -99,6 +102,7 @@ public class EvaluationOfTimeSpans exten
 					options.getXMIDirectory(),
 					options.getTreebankDirectory(),
 					options.getFeatureSelectionThreshold(),
+					options.getSMOTENeighborNumber(),
 					annotatorClass,
 					options.getPrintOverlappingSpans(),
 					annotatorTrainingArguments.get(annotatorClass));
@@ -131,6 +135,8 @@ public class EvaluationOfTimeSpans exten
 	private String[] trainingArguments;
 	
 	private float featureSelectionThreshold;
+	
+	private float smoteNeighborNumber;
 
 	public EvaluationOfTimeSpans(
 			File baseDirectory,
@@ -140,6 +146,7 @@ public class EvaluationOfTimeSpans exten
 			File xmiDirectory,
 			File treebankDirectory,
 			float featureSelectionThreshold,
+			float numOfSmoteNeighbors,
 			Class<? extends JCasAnnotator_ImplBase> annotatorClass,
 					boolean printOverlapping,
 					String[] trainingArguments) {
@@ -148,6 +155,7 @@ public class EvaluationOfTimeSpans exten
 		this.featureSelectionThreshold = featureSelectionThreshold;
 		this.trainingArguments = trainingArguments;
 		this.printOverlapping = printOverlapping;
+		this.smoteNeighborNumber = numOfSmoteNeighbors;
 	}
 
 	@Override
@@ -164,7 +172,8 @@ public class EvaluationOfTimeSpans exten
 				return TimeAnnotator.createDataWriterDescription(
 						dataWriterClass,
 						this.getModelDirectory(directory),
-						this.featureSelectionThreshold);
+						this.featureSelectionThreshold,
+						this.smoteNeighborNumber);
 			}
 			return AnalysisEngineFactory.createPrimitiveDescription(
 					this.annotatorClass,

Modified: ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,63 +1,63 @@
-<?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-type-system</artifactId>
-	<name>Apache cTAKES common type system</name>
-	<description>Defines the cTAKES type system UIMA annotation classes.</description>
-	<parent>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes</artifactId>
-		<version>3.1.0-SNAPSHOT</version>
-	</parent>
-	<dependencies>
-		<dependency>
-			<groupId>org.apache.uima</groupId>
-			<artifactId>uimaj-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.uimafit</groupId>
-			<artifactId>uimafit</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>tw.edu.ntu.csie</groupId>
-			<artifactId>libsvm</artifactId>
-		</dependency>
-		<dependency>
-        	<groupId>junit</groupId>
-        	<artifactId>junit</artifactId>
-        <scope>test</scope>
-      </dependency>
-	</dependencies>
-
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/typesystem/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-type-system</artifactId>
+	<name>Apache cTAKES common type system</name>
+	<description>Defines the cTAKES type system UIMA annotation classes.</description>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.1.0</version>
+	</parent>
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimaj-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.uimafit</groupId>
+			<artifactId>uimafit</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>tw.edu.ntu.csie</groupId>
+			<artifactId>libsvm</artifactId>
+		</dependency>
+		<dependency>
+        	<groupId>junit</groupId>
+        	<artifactId>junit</artifactId>
+        <scope>test</scope>
+      </dependency>
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+</project>

Modified: ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml Fri Aug  2 16:48:14 2013
@@ -1,62 +1,62 @@
-<?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-utils</artifactId>
-	<name>Apache cTAKES utils</name>
-	<parent>
-		<artifactId>ctakes</artifactId>
-		<groupId>org.apache.ctakes</groupId>
-		<version>3.1.0-SNAPSHOT</version>
-	</parent>
-	<dependencies>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<scope>compile</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-queries</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-queryparser</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-analyzers-common</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-utils</artifactId>
+	<name>Apache cTAKES utils</name>
+	<parent>
+		<artifactId>ctakes</artifactId>
+		<groupId>org.apache.ctakes</groupId>
+		<version>3.1.0</version>
+	</parent>
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-queries</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-queryparser</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-analyzers-common</artifactId>
+		</dependency>
+	</dependencies>
+</project>



Mime
View raw message