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From tm...@apache.org
Subject svn commit: r1625365 [5/10] - in /ctakes/trunk: ./ ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/ ctakes-assertion-zoner-res/src/main/resources/META-INF/org.uimafit/ ctakes-assertion-zoner/ ctakes-assertion-zoner/src/main/j...
Date Tue, 16 Sep 2014 19:57:25 GMT
Modified: ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml (original)
+++ ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml Tue Sep 16 19:57:19 2014
@@ -42,28 +42,28 @@
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                            <name>classifierFactoryClassName</name>
                             <description>provides the full name of the ClassifierFactory class to be used.</description>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                            <name>dataWriterFactoryClassName</name>
                             <description>provides the full name of the DataWriterFactory class to be used.</description>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.isTraining</name>
+                            <name>isTraining</name>
                             <description>determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.</description>
                             <type>Boolean</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                            <name>classifierJarPath</name>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
@@ -71,25 +71,25 @@
                     </configurationParameters>
                     <configurationParameterSettings>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                            <name>classifierFactoryClassName</name>
                             <value>
-                                <string>org.cleartk.classifier.jar.JarClassifierFactory</string>
+                                <string>org.cleartk.ml.jar.JarClassifierFactory</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                            <name>dataWriterFactoryClassName</name>
                             <value>
-                                <string>org.cleartk.classifier.jar.DefaultDataWriterFactory</string>
+                                <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
                             <name>ProbabilityOfKeepingANegativeExample</name>
                             <value>
-                                <float>1.0</float>
+                                <float>0.5</float>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                            <name>classifierJarPath</name>
                             <value>
                                 <string>/org/apache/ctakes/relationextractor/models/location_of/model.jar</string>
                             </value>
@@ -100,6 +100,7 @@
                             <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
                         </imports>
                     </typeSystemDescription>
+                    <typePriorities/>
                     <fsIndexCollection/>
                     <capabilities/>
                     <operationalProperties>
@@ -300,28 +301,28 @@
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                            <name>classifierFactoryClassName</name>
                             <description>provides the full name of the ClassifierFactory class to be used.</description>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                            <name>dataWriterFactoryClassName</name>
                             <description>provides the full name of the DataWriterFactory class to be used.</description>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.isTraining</name>
+                            <name>isTraining</name>
                             <description>determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.</description>
                             <type>Boolean</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                            <name>classifierJarPath</name>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
@@ -329,25 +330,25 @@
                     </configurationParameters>
                     <configurationParameterSettings>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                            <name>classifierFactoryClassName</name>
                             <value>
-                                <string>org.cleartk.classifier.jar.JarClassifierFactory</string>
+                                <string>org.cleartk.ml.jar.JarClassifierFactory</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                            <name>dataWriterFactoryClassName</name>
                             <value>
-                                <string>org.cleartk.classifier.jar.DefaultDataWriterFactory</string>
+                                <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
                             <name>ProbabilityOfKeepingANegativeExample</name>
                             <value>
-                                <float>1.0</float>
+                                <float>0.5</float>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                            <name>classifierJarPath</name>
                             <value>
                                 <string>/org/apache/ctakes/relationextractor/models/degree_of/model.jar</string>
                             </value>
@@ -358,6 +359,7 @@
                             <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
                         </imports>
                     </typeSystemDescription>
+                    <typePriorities/>
                     <fsIndexCollection/>
                     <capabilities/>
                     <operationalProperties>
@@ -380,28 +382,28 @@
                     <vendor>org.apache.ctakes.relationextractor.ae</vendor>
                     <configurationParameters>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                            <name>classifierFactoryClassName</name>
                             <description>provides the full name of the ClassifierFactory class to be used.</description>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                            <name>dataWriterFactoryClassName</name>
                             <description>provides the full name of the DataWriterFactory class to be used.</description>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.CleartkAnnotator.isTraining</name>
+                            <name>isTraining</name>
                             <description>determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.</description>
                             <type>Boolean</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
                         </configurationParameter>
                         <configurationParameter>
-                            <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                            <name>classifierJarPath</name>
                             <type>String</type>
                             <multiValued>false</multiValued>
                             <mandatory>false</mandatory>
@@ -409,19 +411,19 @@
                     </configurationParameters>
                     <configurationParameterSettings>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                            <name>classifierFactoryClassName</name>
                             <value>
-                                <string>org.cleartk.classifier.jar.JarClassifierFactory</string>
+                                <string>org.cleartk.ml.jar.JarClassifierFactory</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                            <name>dataWriterFactoryClassName</name>
                             <value>
-                                <string>org.cleartk.classifier.jar.DefaultDataWriterFactory</string>
+                                <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
                             </value>
                         </nameValuePair>
                         <nameValuePair>
-                            <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                            <name>classifierJarPath</name>
                             <value>
                                 <string>/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar</string>
                             </value>
@@ -432,6 +434,7 @@
                             <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
                         </imports>
                     </typeSystemDescription>
+                    <typePriorities/>
                     <fsIndexCollection/>
                     <capabilities/>
                     <operationalProperties>

Modified: ctakes/trunk/ctakes-relation-extractor/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/pom.xml (original)
+++ ctakes/trunk/ctakes-relation-extractor/pom.xml Tue Sep 16 19:57:19 2014
@@ -132,10 +132,6 @@
 			<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>
@@ -164,5 +160,13 @@
 		<artifactId>jwi</artifactId>
 		<version>2.2.3</version>
 	</dependency>
+	<dependency>
+		<groupId>org.apache.uima</groupId>
+		<artifactId>uimafit-core</artifactId>
+	</dependency>
+	<dependency>
+		<groupId>org.cleartk</groupId>
+		<artifactId>cleartk-ml-liblinear</artifactId>
+	</dependency>
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -28,9 +28,9 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.Modifier;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
 
 /**
  * Identifies Degree_Of relations between {@link EventMention}s and

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java Tue Sep 16 19:57:19 2014
@@ -30,8 +30,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -30,7 +30,7 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * Identifies Location_Of relations between {@link EventMention}s and

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -27,22 +27,22 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.ConfigurationParameterFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.chunking.BIOChunking;
-import org.cleartk.classifier.chunking.Chunking;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.chunking.BioChunking;
+import org.cleartk.ml.chunking.Chunking;
 
 public class ModifierExtractorAnnotator extends CleartkAnnotator<String> {
 
   public static AnalysisEngineDescription getDescription(Object... additionalConfiguration)
       throws ResourceInitializationException {
-    AnalysisEngineDescription desc = AnalysisEngineFactory.createPrimitiveDescription(ModifierExtractorAnnotator.class);
+    AnalysisEngineDescription desc = AnalysisEngineFactory.createEngineDescription(ModifierExtractorAnnotator.class);
     if (additionalConfiguration.length > 0) {
       ConfigurationParameterFactory.addConfigurationParameters(desc, additionalConfiguration);
     }
@@ -57,7 +57,7 @@ public class ModifierExtractorAnnotator 
   public void initialize(UimaContext context) throws ResourceInitializationException {
     RelationExtractorAnnotator.allowClassifierModelOnClasspath(context);
     super.initialize(context);
-    this.chunking = new BIOChunking<BaseToken, Modifier>(BaseToken.class, Modifier.class, "typeID");
+    this.chunking = new BioChunking<BaseToken, Modifier>(BaseToken.class, Modifier.class, "typeID");
   }
 
   @Override

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -39,17 +39,17 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.UimaContext;
 import org.apache.uima.UimaContextAdmin;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ConfigurationManager;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.CleartkProcessingException;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.CleartkProcessingException;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
 
 import com.google.common.collect.Lists;
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -24,8 +24,8 @@ import java.util.List;
 import org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.CleartkProcessingException;
-import org.cleartk.classifier.Feature;
+import org.cleartk.ml.CleartkProcessingException;
+import org.cleartk.ml.Feature;
 
 /**
  * Annotated degree_of relation in sentences containing a single entity mention

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -24,10 +24,10 @@ import java.util.List;
 import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
 
 import com.google.common.collect.Lists;
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -29,11 +29,11 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.CleartkProcessingException;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkProcessingException;
+import org.cleartk.ml.Feature;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -30,10 +30,10 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -32,10 +32,10 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.Modifier;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -31,10 +31,10 @@ import org.apache.ctakes.relationextract
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline4EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline4EntityMentionPairRelationExtractorAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline4EntityMentionPairRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline4EntityMentionPairRelationExtractorAnnotator.java Tue Sep 16 19:57:19 2014
@@ -26,10 +26,10 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
 
 /**
  * Annotate location_of relation between two entities whenever 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java Tue Sep 16 19:57:19 2014
@@ -32,7 +32,7 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
 import org.apache.uima.jcas.JCas;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class Utils {
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -21,10 +21,10 @@ package org.apache.ctakes.relationextrac
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.cleartk.ml.Feature;
 
 /**
  * Features that indicate the order of the arguments (e.g. before or after).

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyParseUtils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyParseUtils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyParseUtils.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyParseUtils.java Tue Sep 16 19:57:19 2014
@@ -24,7 +24,7 @@ import java.util.List;
 
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -18,16 +18,15 @@
  */
 package org.apache.ctakes.relationextractor.ae.features;
 
-import java.util.ArrayList;
-import java.util.LinkedList;
-import java.util.List;
-
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-
-import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
 
 public class DependencyPathFeaturesExtractor implements RelationFeaturesExtractor {
 	

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -18,15 +18,14 @@
  */
 package org.apache.ctakes.relationextractor.ae.features;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-
-import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
 
 public class DependencyTreeFeaturesExtractor implements RelationFeaturesExtractor{
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -21,13 +21,12 @@ package org.apache.ctakes.relationextrac
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
-
 import org.apache.ctakes.typesystem.type.syntax.NP;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
 
 /**
  * Features that indicate whether both arguments are contained within an NP. 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,9 +28,9 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.utils.tree.SimpleTree;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
 
 public class FlatTreeFeatureExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -22,21 +22,20 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.annotationpair.DistanceExtractor;
-import org.cleartk.classifier.feature.extractor.simple.NamingExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.DistanceExtractor;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+import org.cleartk.ml.feature.extractor.NamingExtractor1;
 
 public class NamedEntityFeaturesExtractor implements RelationFeaturesExtractor {
 
-  private SimpleFeatureExtractor namedEntityType = new SimpleFeatureExtractor() {
+  private FeatureExtractor1 namedEntityType = new FeatureExtractor1() {
     @Override
     public List<Feature> extract(JCas jCas, Annotation ann) throws CleartkExtractorException {
       IdentifiedAnnotation idAnn = (IdentifiedAnnotation)ann;
@@ -47,14 +46,14 @@ public class NamedEntityFeaturesExtracto
   /**
    * All extractors for mention 1, with features named to distinguish them from mention 2
    */
-  private SimpleFeatureExtractor mention1FeaturesExtractor = new NamingExtractor(
+  private FeatureExtractor1 mention1FeaturesExtractor = new NamingExtractor1(
       "mention1",
       namedEntityType);
 
   /**
    * All extractors for mention 2, with features named to distinguish them from mention 1
    */
-  private SimpleFeatureExtractor mention2FeaturesExtractor = new NamingExtractor(
+  private FeatureExtractor1 mention2FeaturesExtractor = new NamingExtractor1(
       "mention2",
       namedEntityType);
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PETFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PETFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PETFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PETFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -29,7 +29,7 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.utils.tree.SimpleTree;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 
 public class PETFeatureExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -21,27 +21,26 @@ package org.apache.ctakes.relationextrac
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.Bag;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.Covered;
-import org.cleartk.classifier.feature.extractor.simple.NamingExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.cleartk.classifier.feature.extractor.simple.TypePathExtractor;
-
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractor;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Bag;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Covered;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+import org.cleartk.ml.feature.extractor.NamingExtractor1;
+import org.cleartk.ml.feature.extractor.TypePathExtractor;
 
 public class PartOfSpeechFeaturesExtractor implements RelationFeaturesExtractor {
 
-  private SimpleFeatureExtractor pos = new TypePathExtractor(BaseToken.class, "partOfSpeech");
+  private FeatureExtractor1 pos = new TypePathExtractor(BaseToken.class, "partOfSpeech");
 
   /**
    * All part-of-speech tags of the mention as a bag
    */
-  private SimpleFeatureExtractor tokenPOS = new CleartkExtractor(
+  private FeatureExtractor1 tokenPOS = new CleartkExtractor(
       BaseToken.class,
       pos,
       new Bag(new Covered()));
@@ -49,14 +48,14 @@ public class PartOfSpeechFeaturesExtract
   /**
    * All extractors for mention 1, with features named to distinguish them from mention 2
    */
-  private SimpleFeatureExtractor mention1FeaturesExtractor = new NamingExtractor(
+  private FeatureExtractor1 mention1FeaturesExtractor = new NamingExtractor1(
       "mention1",
       tokenPOS);
 
   /**
    * All extractors for mention 2, with features named to distinguish them from mention 1
    */
-  private SimpleFeatureExtractor mention2FeaturesExtractor = new NamingExtractor(
+  private FeatureExtractor1 mention2FeaturesExtractor = new NamingExtractor1(
       "mention2",
       tokenPOS);
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java Tue Sep 16 19:57:19 2014
@@ -21,13 +21,13 @@ package org.apache.ctakes.relationextrac
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
 import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
 import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
 
 public class PhraseChunkingExtractor implements RelationFeaturesExtractor {
 	  

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -23,13 +23,12 @@ import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
 
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
-
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
 
 /**
  * Features that indicate whether there is a preposition between the two arguments. 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -21,13 +21,12 @@ package org.apache.ctakes.relationextrac
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
-
 import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
 
 /**
  * Features that capture punctuation marks between the two arguments.

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -20,11 +20,10 @@ package org.apache.ctakes.relationextrac
 
 import java.util.List;
 
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.cleartk.ml.Feature;
 
 /**
  * Define an interface for people to implement feature extractors.

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,31 +28,32 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.Bag;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.Covered;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.FirstCovered;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.Following;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.LastCovered;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.Preceding;
-import org.cleartk.classifier.feature.extractor.annotationpair.DistanceExtractor;
-import org.cleartk.classifier.feature.extractor.simple.CoveredTextExtractor;
-import org.cleartk.classifier.feature.extractor.simple.NamingExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractor;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Bag;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Covered;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.FirstCovered;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Following;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.LastCovered;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding;
+import org.cleartk.ml.feature.extractor.CombinedExtractor1;
+import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
+import org.cleartk.ml.feature.extractor.DistanceExtractor;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+import org.cleartk.ml.feature.extractor.NamingExtractor1;
 
 public class TokenFeaturesExtractor implements RelationFeaturesExtractor {
 
-  private SimpleFeatureExtractor coveredText = new CoveredTextExtractor();
+  private FeatureExtractor1 coveredText = new CoveredTextExtractor();
 
   /**
    * First word of the mention, last word of the mention, all words of the mention as a bag, the
    * preceding 3 words, the following 3 words
    */
-  private SimpleFeatureExtractor tokenContext = new CleartkExtractor(
+  private FeatureExtractor1 tokenContext = new CleartkExtractor(
       BaseToken.class,
       coveredText,
       new FirstCovered(1),
@@ -64,25 +65,23 @@ public class TokenFeaturesExtractor impl
   /**
    * All extractors for mention 1, with features named to distinguish them from mention 2
    */
-  private SimpleFeatureExtractor mention1FeaturesExtractor = new NamingExtractor(
+  private FeatureExtractor1 mention1FeaturesExtractor = new NamingExtractor1(
       "mention1",
-      coveredText,
-      tokenContext);
+      new CombinedExtractor1(coveredText, tokenContext));
 
   /**
    * All extractors for mention 2, with features named to distinguish them from mention 1
    */
-  private SimpleFeatureExtractor mention2FeaturesExtractor = new NamingExtractor(
+  private FeatureExtractor1 mention2FeaturesExtractor = new NamingExtractor1(
       "mention2",
-      coveredText,
-      tokenContext);
+      new CombinedExtractor1(coveredText, tokenContext));
 
   /**
    * First word, last word, and all words between the mentions
    */
   private CleartkExtractor tokensBetween = new CleartkExtractor(
       BaseToken.class,
-      new NamingExtractor("BetweenMentions", coveredText),
+      new NamingExtractor1("BetweenMentions", coveredText),
       new FirstCovered(1),
       new LastCovered(1),
       new Bag(new Covered()));

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TreeFragmentFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TreeFragmentFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TreeFragmentFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TreeFragmentFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -36,7 +36,7 @@ import org.apache.ctakes.utils.tree.Frag
 import org.apache.ctakes.utils.tree.SimpleTree;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 
 /* 
  * This class implements a ClearTK feature extractor for tree kernel fragment features

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/WordNetFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/WordNetFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/WordNetFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/WordNetFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -24,9 +24,9 @@ import java.util.List;
 
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
 
 import edu.mit.jwi.IDictionary;
 

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysisPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysisPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysisPipeline.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysisPipeline.java Tue Sep 16 19:57:19 2014
@@ -25,11 +25,11 @@ import java.util.List;
 import org.apache.ctakes.relationextractor.eval.XMIReader;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
-import org.cleartk.util.Options_ImplBase;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
 
 /**
  * 
@@ -40,7 +40,7 @@ import org.uimafit.pipeline.SimplePipeli
  */
 public class GoldAnnotationAnalysisPipeline {
 
-  public static class Options extends Options_ImplBase {
+  public static class Options {
 
     @Option(
         name = "--input-dir",
@@ -50,14 +50,14 @@ public class GoldAnnotationAnalysisPipel
   }
   
 	public static void main(String[] args) throws Exception {
-		
-		Options options = new Options();
-		options.parseOptions(args);
+      Options options = new Options();
+      CmdLineParser parser = new CmdLineParser(options);
+      parser.parseArgument(args);
 
-		List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
-    CollectionReader collectionReader = getCollectionReader(trainFiles);
+      List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
+      CollectionReader collectionReader = getCollectionReader(trainFiles);
 		
-    AnalysisEngine goldAnnotationStatsCalculator = AnalysisEngineFactory.createPrimitive(
+      AnalysisEngine goldAnnotationStatsCalculator = AnalysisEngineFactory.createEngine(
     		GoldAnnotationStatsCalculator.class);
     		
 		SimplePipeline.runPipeline(collectionReader, goldAnnotationStatsCalculator);
@@ -72,7 +72,7 @@ public class GoldAnnotationAnalysisPipel
     }
     
     // return a reader that will load each of the XMI files
-    return CollectionReaderFactory.createCollectionReader(
+    return CollectionReaderFactory.createReader(
         XMIReader.class,
         XMIReader.PARAM_FILES,
         paths);

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java Tue Sep 16 19:57:19 2014
@@ -35,8 +35,8 @@ import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.collect.HashMultiset;
 import com.google.common.collect.Multiset;

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java Tue Sep 16 19:57:19 2014
@@ -20,6 +20,7 @@ package org.apache.ctakes.relationextrac
 
 import java.io.File;
 import java.util.Collection;
+import java.util.Iterator;
 import java.util.List;
 
 import javax.annotation.Nullable;
@@ -31,18 +32,18 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-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.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.jar.DefaultDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.jar.JarClassifierBuilder;
+import org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter;
 
 import com.google.common.base.Function;
 import com.google.common.collect.Lists;
@@ -51,8 +52,8 @@ import com.lexicalscope.jewel.cli.CliFac
 public class ModifierExtractorEvaluation extends SHARPXMI.Evaluation_ImplBase {
 
   public static final ParameterSettings BEST_PARAMETERS = new ParameterSettings(
-      LIBLINEARStringOutcomeDataWriter.class,
-      new String[] { "-s", "1", "-c", "0.5" });
+      LibLinearStringOutcomeDataWriter.class,
+      new String[] { "-s", "0", "-c", "100.0" });
 
   public static void main(String[] args) throws Exception {
     // parse the options, validate them, and generate XMI if necessary
@@ -61,13 +62,13 @@ public class ModifierExtractorEvaluation
     SHARPXMI.generateXMI(options);
 
     // determine the grid of parameters to search through
-    // for the full set of LIBLINEAR parameters, see:
+    // for the full set of LibLinear parameters, see:
     // https://github.com/bwaldvogel/liblinear-java/blob/master/src/main/java/de/bwaldvogel/liblinear/Train.java
     List<ParameterSettings> gridOfSettings = Lists.newArrayList();
     for (int solver : new int[] { 0 /* logistic regression */, 1 /* SVM */}) {
       for (double svmCost : new double[] { 0.01, 0.05, 0.1, 0.5, 1, 5, 10, 50, 100 }) {
         gridOfSettings.add(new ParameterSettings(
-            LIBLINEARStringOutcomeDataWriter.class,
+            LibLinearStringOutcomeDataWriter.class,
             new String[] { "-s", String.valueOf(solver), "-c", String.valueOf(svmCost) }));
       }
     }
@@ -99,7 +100,7 @@ public class ModifierExtractorEvaluation
 
     SimplePipeline.runPipeline(
         collectionReader,
-        AnalysisEngineFactory.createPrimitiveDescription(OnlyGoldModifiers.class),
+        AnalysisEngineFactory.createEngineDescription(OnlyGoldModifiers.class),
         ModifierExtractorAnnotator.getDescription(
             DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
             this.parameterSettings.dataWriterClass,
@@ -112,12 +113,13 @@ public class ModifierExtractorEvaluation
   protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
       throws Exception {
     AnalysisEngine classifierAnnotator =
-        AnalysisEngineFactory.createPrimitive(ModifierExtractorAnnotator.getDescription(
+        AnalysisEngineFactory.createEngine(ModifierExtractorAnnotator.getDescription(
             GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
             JarClassifierBuilder.getModelJarFile(directory)));
 
     AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
-    for (JCas jCas : new JCasIterable(collectionReader, classifierAnnotator)) {
+    for (Iterator<JCas> casIter = new JCasIterator(collectionReader, classifierAnnotator); casIter.hasNext();) {
+      JCas jCas = casIter.next();
       JCas goldView;
       try {
         goldView = jCas.getView(SHARPXMI.GOLD_VIEW_NAME);

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ParameterSettings.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ParameterSettings.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ParameterSettings.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ParameterSettings.java Tue Sep 16 19:57:19 2014
@@ -20,8 +20,8 @@ package org.apache.ctakes.relationextrac
 
 import java.util.Arrays;
 
-import org.cleartk.classifier.DataWriter;
 import org.cleartk.eval.AnnotationStatistics;
+import org.cleartk.ml.DataWriter;
 
 import com.google.common.base.Objects;
 import com.google.common.base.Objects.ToStringHelper;

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java Tue Sep 16 19:57:19 2014
@@ -23,26 +23,25 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.util.Options_ImplBase;
 import org.cleartk.util.cr.FilesCollectionReader;
 import org.cleartk.util.cr.XReader;
+import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.JCasFactory;
-import org.uimafit.util.JCasUtil;
 
 import com.google.common.collect.HashMultiset;
 import com.google.common.collect.Multiset;
 
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
-
 public class PrintRelationStatistics {
 
-  public static class Options extends Options_ImplBase {
+  public static class Options {
 
     @Option(
         name = "--train-dir",
@@ -55,9 +54,10 @@ public class PrintRelationStatistics {
 
   public static void main(String[] args) throws Exception {
     Options options = new Options();
-    options.parseOptions(args);
+    CmdLineParser parser = new CmdLineParser(options);
+    parser.parseArgument(args);
 
-    CollectionReader reader = CollectionReaderFactory.createCollectionReader(
+    CollectionReader reader = CollectionReaderFactory.createReader(
         XReader.class,
         FilesCollectionReader.PARAM_ROOT_FILE,
         options.trainDirectory.getPath());

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java Tue Sep 16 19:57:19 2014
@@ -22,6 +22,7 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -47,24 +48,24 @@ import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
 import org.apache.uima.cas.Feature;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.ConfigurationParameterFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.util.CasCopier;
 import org.apache.uima.util.Level;
 import org.apache.uima.util.XMLInputSource;
-import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-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.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.jar.DefaultDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.jar.JarClassifierBuilder;
+import org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter;
 
 import com.google.common.base.Function;
 import com.google.common.base.Objects;
@@ -120,18 +121,18 @@ public class RelationExtractorEvaluation
     RELATION_CLASSES.put("degree_of", DegreeOfTextRelation.class);
     ANNOTATOR_CLASSES.put(DegreeOfTextRelation.class, DegreeOfRelationExtractorAnnotator.class);
     BEST_PARAMETERS.put(DegreeOfTextRelation.class, new ParameterSettings(
-        LIBLINEARStringOutcomeDataWriter.class,
+        LibLinearStringOutcomeDataWriter.class,
         new Object[] { RelationExtractorAnnotator.PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE,
-            1.0f },
-        new String[] { "-s", "1", "-c", "10.0" }));
+            0.5f },
+        new String[] { "-s", "1", "-c", "0.5" }));
 
     RELATION_CLASSES.put("location_of", LocationOfTextRelation.class);
     ANNOTATOR_CLASSES.put(LocationOfTextRelation.class, LocationOfRelationExtractorAnnotator.class);
     BEST_PARAMETERS.put(LocationOfTextRelation.class, new ParameterSettings(
-        LIBLINEARStringOutcomeDataWriter.class,
+        LibLinearStringOutcomeDataWriter.class,
         new Object[] { RelationExtractorAnnotator.PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE,
-            1.0f },
-        new String[] { "-s", "1", "-c", "0.05" }));
+            0.5f },
+        new String[] { "-s", "0", "-c", "1.0" }));
   }
 
   public static void main(String[] args) throws Exception {
@@ -141,14 +142,14 @@ public class RelationExtractorEvaluation
     SHARPXMI.generateXMI(options);
 
     // determine the grid of parameters to search through
-    // for the full set of LIBLINEAR parameters, see:
+    // for the full set of LibLinear parameters, see:
     // https://github.com/bwaldvogel/liblinear-java/blob/master/src/main/java/de/bwaldvogel/liblinear/Train.java
     List<ParameterSettings> gridOfSettings = Lists.newArrayList();
     for (float probabilityOfKeepingANegativeExample : new float[] { 0.5f, 1.0f }) {
       for (int solver : new int[] { 0 /* logistic regression */, 1 /* SVM */}) {
         for (double svmCost : new double[] { 0.01, 0.05, 0.1, 0.5, 1, 5, 10, 50, 100 }) {
           gridOfSettings.add(new ParameterSettings(
-              LIBLINEARStringOutcomeDataWriter.class,
+              LibLinearStringOutcomeDataWriter.class,
               new Object[] {
                   RelationExtractorAnnotator.PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE,
                   probabilityOfKeepingANegativeExample },
@@ -269,10 +270,10 @@ public class RelationExtractorEvaluation
     AggregateBuilder builder = new AggregateBuilder();
     // remove cTAKES entity mentions and modifiers in the system view and copy
     // in the gold relations
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveCTakesMentionsAndCopyGoldRelations.class));
+    builder.add(AnalysisEngineFactory.createEngineDescription(RemoveCTakesMentionsAndCopyGoldRelations.class));
     // add the relation extractor, configured for training mode
     AnalysisEngineDescription classifierAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(
+        AnalysisEngineFactory.createEngineDescription(
             this.classifierAnnotatorClass,
             this.parameterSettings.configurationParameters);
     ConfigurationParameterFactory.addConfigurationParameters(
@@ -300,15 +301,15 @@ public class RelationExtractorEvaluation
       XMLInputSource source = new XMLInputSource(file);
       builder.add(UIMAFramework.getXMLParser().parseAnalysisEngineDescription(source));
       // remove extraneous entity mentions
-      builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveSmallerEventMentions.class));
+      builder.add(AnalysisEngineFactory.createEngineDescription(RemoveSmallerEventMentions.class));
     } else {
       // replace cTAKES entity mentions and modifiers in the system view with
       // the gold annotations
-      builder.add(AnalysisEngineFactory.createPrimitiveDescription(ReplaceCTakesMentionsWithGoldMentions.class));
+      builder.add(AnalysisEngineFactory.createEngineDescription(ReplaceCTakesMentionsWithGoldMentions.class));
     }
     // add the relation extractor, configured for classification mode
     AnalysisEngineDescription classifierAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(
+        AnalysisEngineFactory.createEngineDescription(
             this.classifierAnnotatorClass,
             this.parameterSettings.configurationParameters);
     ConfigurationParameterFactory.addConfigurationParameters(
@@ -332,8 +333,8 @@ public class RelationExtractorEvaluation
 
     // calculate statistics, iterating over the results of the classifier
     AnalysisEngine engine = builder.createAggregate();
-    for (JCas jCas : new JCasIterable(collectionReader, engine)) {
-
+    for (Iterator<JCas> casIter = new JCasIterator(collectionReader, engine); casIter.hasNext();) {
+      JCas jCas = casIter.next();
       // get the gold view
       JCas goldView;
       try {

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java Tue Sep 16 19:57:19 2014
@@ -23,6 +23,7 @@ import java.io.FileOutputStream;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
@@ -36,21 +37,21 @@ import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
 import org.apache.uima.cas.impl.XmiCasSerializer;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.component.ViewCreatorAnnotator;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.util.XMLInputSource;
 import org.apache.uima.util.XMLParser;
 import org.apache.uima.util.XMLSerializer;
 import org.cleartk.eval.AnnotationStatistics;
-import org.cleartk.util.ViewURIUtil;
+import org.cleartk.util.ViewUriUtil;
 import org.cleartk.util.ae.UriToDocumentTextAnnotator;
 import org.cleartk.util.cr.UriCollectionReader;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.component.ViewCreatorAnnotator;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.JCasIterable;
 import org.xml.sax.ContentHandler;
 
 import com.google.common.base.Function;
@@ -167,22 +168,25 @@ public class SHARPXMI {
       XMLParser parser = UIMAFramework.getXMLParser();
       XMLInputSource source = new XMLInputSource(preprocessDescFile);
       builder.add(parser.parseAnalysisEngineDescription(source));
-      builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+      builder.add(AnalysisEngineFactory.createEngineDescription(
           ViewCreatorAnnotator.class,
           ViewCreatorAnnotator.PARAM_VIEW_NAME,
           GOLD_VIEW_NAME));
-      builder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyDocumentTextToGoldView.class));
+      builder.add(AnalysisEngineFactory.createEngineDescription(CopyDocumentTextToGoldView.class));
       builder.add(
-          AnalysisEngineFactory.createPrimitiveDescription(DocumentIDAnnotator.class),
+          AnalysisEngineFactory.createEngineDescription(DocumentIDAnnotator.class),
           CAS.NAME_DEFAULT_SOFA,
           GOLD_VIEW_NAME);
       builder.add(
-          AnalysisEngineFactory.createPrimitiveDescription(SHARPKnowtatorXMLReader.class),
+          AnalysisEngineFactory.createEngineDescription(SHARPKnowtatorXMLReader.class,
+        		  SHARPKnowtatorXMLReader.PARAM_SET_DEFAULTS,
+        		  true),
           CAS.NAME_DEFAULT_SOFA,
           GOLD_VIEW_NAME);
 
       // write out an XMI for each file
-      for (JCas jCas : new JCasIterable(reader, builder.createAggregate())) {
+      for (Iterator<JCas> casIter = new JCasIterator(reader, builder.createAggregate()); casIter.hasNext();) {
+    	JCas jCas = casIter.next();
         JCas goldView = jCas.getView(GOLD_VIEW_NAME);
         String documentID = DocumentIDAnnotationUtil.getDocumentID(goldView);
         if (documentID == null) {
@@ -203,7 +207,7 @@ public class SHARPXMI {
 
   public static interface EvaluationOptions extends Options {
     @Option(
-        longName = "evalute-on",
+        longName = "evaluate-on",
         defaultValue = "DEV",
         description = "perform evaluation using the training (TRAIN), development (DEV) or test "
             + "(TEST) data.")
@@ -223,7 +227,7 @@ public class SHARPXMI {
 
     @Override
     public CollectionReader getCollectionReader(List<File> items) throws Exception {
-      return CollectionReaderFactory.createCollectionReader(
+      return CollectionReaderFactory.createReader(
           XMIReader.class,
           TypeSystemDescriptionFactory.createTypeSystemDescription(),
           XMIReader.PARAM_FILES,
@@ -324,7 +328,7 @@ public class SHARPXMI {
 
     @Override
     public void process(JCas jCas) throws AnalysisEngineProcessException {
-      String documentID = new File(ViewURIUtil.getURI(jCas)).getPath();
+      String documentID = new File(ViewUriUtil.getURI(jCas)).getPath();
       DocumentID documentIDAnnotation = new DocumentID(jCas);
       documentIDAnnotation.setDocumentID(documentID);
       documentIDAnnotation.addToIndexes();

Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java Tue Sep 16 19:57:19 2014
@@ -32,8 +32,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
-import org.uimafit.component.JCasCollectionReader_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.component.JCasCollectionReader_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
 import org.xml.sax.SAXException;
 
 /**



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