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From tm...@apache.org
Subject svn commit: r1625365 [7/10] - 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-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java Tue Sep 16 19:57:19 2014
@@ -44,13 +44,13 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.DataWriter;
-import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.DataWriter;
+import org.cleartk.ml.jar.DefaultDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.collect.Lists;
 
@@ -60,7 +60,7 @@ public class EventEventRelationAnnotator
 		      Class<? extends DataWriter<String>> dataWriterClass,
 		      File outputDirectory,
 		      double probabilityOfKeepingANegativeExample) throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		            EventEventRelationAnnotator.class,
 		            CleartkAnnotator.PARAM_IS_TRAINING,
 		            true,
@@ -75,7 +75,7 @@ public class EventEventRelationAnnotator
 	  
 	  public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
 		      throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		        EventEventRelationAnnotator.class,
 		        CleartkAnnotator.PARAM_IS_TRAINING,
 		        false,
@@ -90,7 +90,7 @@ public class EventEventRelationAnnotator
 	   */	  
 	  public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 		      throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		        EventEventRelationAnnotator.class,
 		        CleartkAnnotator.PARAM_IS_TRAINING,
 		        false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java Tue Sep 16 19:57:19 2014
@@ -48,13 +48,13 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.DataWriter;
-import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.DataWriter;
+import org.cleartk.ml.jar.DefaultDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.collect.Lists;
 
@@ -64,7 +64,7 @@ public class EventTimeRelationAnnotator 
 			Class<? extends DataWriter<String>> dataWriterClass,
 					File outputDirectory,
 					double probabilityOfKeepingANegativeExample) throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				EventTimeRelationAnnotator.class,
 				CleartkAnnotator.PARAM_IS_TRAINING,
 				true,
@@ -79,7 +79,7 @@ public class EventTimeRelationAnnotator 
 
 	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				EventTimeRelationAnnotator.class,
 				CleartkAnnotator.PARAM_IS_TRAINING,
 				false,
@@ -93,7 +93,7 @@ public class EventTimeRelationAnnotator 
 	   */	 
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				EventTimeRelationAnnotator.class,
 				CleartkAnnotator.PARAM_IS_TRAINING,
 				false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java Tue Sep 16 19:57:19 2014
@@ -24,9 +24,9 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.cleartk.timeml.type.Event;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * for every cTAKES EventMention annotation, create a ClearTK Event Annotation
@@ -58,7 +58,7 @@ public class EventToClearTKEventAnnotato
 
 	public static AnalysisEngineDescription getAnnotatorDescription()
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(EventToClearTKEventAnnotator.class);
+		return AnalysisEngineFactory.createEngineDescription(EventToClearTKEventAnnotator.class);
 	}
 
 }

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java Tue Sep 16 19:57:19 2014
@@ -34,17 +34,17 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.util.ViewURIUtil;
+import org.cleartk.util.ViewUriUtil;
 import org.jdom2.Element;
 import org.jdom2.JDOMException;
 import org.jdom2.input.SAXBuilder;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
 
 import com.google.common.collect.Sets;
 
@@ -68,7 +68,7 @@ public class I2B2TemporalXMLReader exten
   
   @Override
   public void process(JCas jcas) throws AnalysisEngineProcessException {
-    File textFile = new File(ViewURIUtil.getURI(jcas));
+    File textFile = new File(ViewUriUtil.getURI(jcas));
     File xmlFile = new File(textFile.getAbsolutePath().substring(0, textFile.getAbsolutePath().length()-4));
     Map<String,Annotation> id2entity = new HashMap<>();
     
@@ -158,7 +158,7 @@ public class I2B2TemporalXMLReader exten
   }
 
   public static AnalysisEngineDescription getDescription(File xmlDirectory) throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(
+    return AnalysisEngineFactory.createEngineDescription(
         I2B2TemporalXMLReader.class,
         I2B2TemporalXMLReader.PARAM_INPUT_DIR,
         xmlDirectory);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java Tue Sep 16 19:57:19 2014
@@ -35,23 +35,23 @@ import org.apache.uima.cas.CASException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.CasCopier;
-import org.cleartk.classifier.CleartkSequenceAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instances;
-import org.cleartk.classifier.SequenceDataWriter;
-import org.cleartk.classifier.chunking.BIOChunking;
-import org.cleartk.classifier.jar.DefaultSequenceDataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.component.ViewCreatorAnnotator;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkSequenceAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instances;
+import org.cleartk.ml.SequenceDataWriter;
+import org.cleartk.ml.chunking.BioChunking;
+import org.cleartk.ml.jar.DefaultSequenceDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+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.util.JCasUtil;
 
 public class MetaTimeAnnotator extends TemporalSequenceAnnotator_ImplBase {
 
-  private BIOChunking<BaseToken, TimeMention> timeChunking;
+  private BioChunking<BaseToken, TimeMention> timeChunking;
 
   @SuppressWarnings("unchecked")
   static Class<? extends JCasAnnotator_ImplBase>[] components = new Class[]{ BackwardsTimeAnnotator.class, TimeAnnotator.class, ConstituencyBasedTimeAnnotator.class, CRFTimeAnnotator.class };
@@ -66,7 +66,7 @@ public class MetaTimeAnnotator extends T
     AggregateBuilder builder = new AggregateBuilder();
     
     for(Class<?> component : components){
-      builder.add(AnalysisEngineFactory.createPrimitiveDescription(ViewCreatorAnnotator.class, ViewCreatorAnnotator.PARAM_VIEW_NAME, component.getSimpleName()));
+      builder.add(AnalysisEngineFactory.createEngineDescription(ViewCreatorAnnotator.class, ViewCreatorAnnotator.PARAM_VIEW_NAME, component.getSimpleName()));
     }
     
     builder.add(TimeAnnotator.createEnsembleDescription(
@@ -82,7 +82,7 @@ public class MetaTimeAnnotator extends T
         new File(directory, CRFTimeAnnotator.class.getSimpleName()), 
         CRFTimeAnnotator.class.getSimpleName()));
     
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(MetaTimeAnnotator.class,
+    builder.add(AnalysisEngineFactory.createEngineDescription(MetaTimeAnnotator.class,
           CleartkSequenceAnnotator.PARAM_IS_TRAINING,
           true,
           DefaultSequenceDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
@@ -96,7 +96,7 @@ public class MetaTimeAnnotator extends T
     AggregateBuilder builder = new AggregateBuilder();
     
     for(Class<?> component : components){
-      builder.add(AnalysisEngineFactory.createPrimitiveDescription(ViewCreatorAnnotator.class, ViewCreatorAnnotator.PARAM_VIEW_NAME, component.getSimpleName()));
+      builder.add(AnalysisEngineFactory.createEngineDescription(ViewCreatorAnnotator.class, ViewCreatorAnnotator.PARAM_VIEW_NAME, component.getSimpleName()));
     }
     builder.add(TimeAnnotator.createEnsembleDescription(
                       new File(directory, TimeAnnotator.class.getSimpleName()),
@@ -110,7 +110,7 @@ public class MetaTimeAnnotator extends T
     builder.add(CRFTimeAnnotator.createEnsembleDescription(
                       new File(directory, CRFTimeAnnotator.class.getSimpleName()), 
                       CRFTimeAnnotator.class.getSimpleName()));
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    builder.add(AnalysisEngineFactory.createEngineDescription(
         MetaTimeAnnotator.class,
         CleartkSequenceAnnotator.PARAM_IS_TRAINING,
         false,
@@ -123,7 +123,7 @@ public class MetaTimeAnnotator extends T
   public void initialize(UimaContext context) throws ResourceInitializationException {
     super.initialize(context);
     // define chunking
-    this.timeChunking = new BIOChunking<>(BaseToken.class, TimeMention.class);
+    this.timeChunking = new BioChunking<>(BaseToken.class, TimeMention.class);
   }
   
   @Override

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java Tue Sep 16 19:57:19 2014
@@ -29,10 +29,10 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class NEPredicateEventAnnotator extends TemporalEntityAnnotator_ImplBase {
 
@@ -89,7 +89,7 @@ public class NEPredicateEventAnnotator e
 
 	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
 		      throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		    	NEPredicateEventAnnotator.class,
 		    	CleartkAnnotator.PARAM_IS_TRAINING,
 		        false,
@@ -104,7 +104,7 @@ public class NEPredicateEventAnnotator e
 	   */	 
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 		      throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		    	NEPredicateEventAnnotator.class,
 		    	CleartkAnnotator.PARAM_IS_TRAINING,
 		        false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java Tue Sep 16 19:57:19 2014
@@ -41,21 +41,21 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.EmptyFSList;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.util.ViewURIUtil;
+import org.cleartk.util.ViewUriUtil;
 import org.cleartk.util.cr.UriCollectionReader;
 import org.jdom2.Element;
 import org.jdom2.JDOMException;
 import org.jdom2.input.SAXBuilder;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.SimplePipeline;
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
@@ -88,12 +88,12 @@ public class THYMEAnaforaXMLReader exten
       ".Temporal-Relation.gold.completed.xml"};
 
   public static AnalysisEngineDescription getDescription() throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(THYMEAnaforaXMLReader.class);
+    return AnalysisEngineFactory.createEngineDescription(THYMEAnaforaXMLReader.class);
   }
 
   public static AnalysisEngineDescription getDescription(File anaforaDirectory)
       throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(
+    return AnalysisEngineFactory.createEngineDescription(
         THYMEAnaforaXMLReader.class,
         THYMEAnaforaXMLReader.PARAM_ANAFORA_DIRECTORY,
         anaforaDirectory);
@@ -102,7 +102,7 @@ public class THYMEAnaforaXMLReader exten
   @Override
   public void process(JCas jCas) throws AnalysisEngineProcessException {
     // determine source text file
-    File textFile = new File(ViewURIUtil.getURI(jCas));
+    File textFile = new File(ViewUriUtil.getURI(jCas));
     LOGGER.info("processing " + textFile);
 
     // determine possible Anafora XML file names
@@ -412,7 +412,7 @@ public class THYMEAnaforaXMLReader exten
       files.add(new File(path));
     }
     CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(files);
-    AnalysisEngine engine = AnalysisEngineFactory.createPrimitive(THYMEAnaforaXMLReader.class);
+    AnalysisEngine engine = AnalysisEngineFactory.createEngine(THYMEAnaforaXMLReader.class);
     SimplePipeline.runPipeline(reader, engine);
   }
 }

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEKnowtatorXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEKnowtatorXMLReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEKnowtatorXMLReader.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEKnowtatorXMLReader.java Tue Sep 16 19:57:19 2014
@@ -33,11 +33,11 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.util.ViewURIUtil;
+import org.cleartk.util.ViewUriUtil;
 import org.cleartk.util.cr.UriCollectionReader;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.SimplePipeline;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -51,7 +51,7 @@ public class THYMEKnowtatorXMLReader ext
 
   public static AnalysisEngineDescription getDescription(File knowtatorXMLDirectory)
       throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(
+    return AnalysisEngineFactory.createEngineDescription(
         THYMEKnowtatorXMLReader.class,
         THYMEKnowtatorXMLReader.PARAM_KNOWTATOR_XML_DIRECTORY,
         knowtatorXMLDirectory);
@@ -59,7 +59,7 @@ public class THYMEKnowtatorXMLReader ext
   
   @Override
   protected URI getTextURI(JCas jCas) throws AnalysisEngineProcessException {
-    return ViewURIUtil.getURI(jCas);
+    return ViewUriUtil.getURI(jCas);
   }
 
   @Override
@@ -106,7 +106,7 @@ public class THYMEKnowtatorXMLReader ext
       }
     }
     CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(files);
-    AnalysisEngine engine = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine engine = AnalysisEngineFactory.createEngine(
         THYMEKnowtatorXMLReader.class,
         THYMEKnowtatorXMLReader.PARAM_KNOWTATOR_XML_DIRECTORY,
         options.getKnowtatorXMLDirectory());

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMETreebankReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMETreebankReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMETreebankReader.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMETreebankReader.java Tue Sep 16 19:57:19 2014
@@ -38,19 +38,19 @@ import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.FeatureStructure;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.FSCollectionFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.StringArray;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.FileUtils;
 import org.apache.uima.util.Level;
-import org.cleartk.corpus.penntreebank.TreebankFormatParser;
-import org.cleartk.util.ViewURIUtil;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.FSCollectionFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.util.ViewUriUtil;
+import org.cleartk.util.treebank.TreebankFormatParser;
 
 public class THYMETreebankReader extends JCasAnnotator_ImplBase {
 
@@ -74,7 +74,7 @@ public class THYMETreebankReader extends
 
 	@Override
 	public void process(JCas jcas) throws AnalysisEngineProcessException {
-		URI uri = ViewURIUtil.getURI(jcas);
+		URI uri = ViewUriUtil.getURI(jcas);
 		logger.info("Document id is: " + uri.toString());
 
 		String fn = uri.getPath().substring(uri.getPath().lastIndexOf('/')+1) + ".xml.tree";
@@ -109,7 +109,7 @@ public class THYMETreebankReader extends
 			fileText.replace(m.start(), m.end(), getWhitespaceString(headerLen));
 		}
 		
-		List<org.cleartk.syntax.constituent.util.TopTreebankNode> utilTrees;
+		List<org.cleartk.util.treebank.TopTreebankNode> utilTrees;
 		try {
 			utilTrees = TreebankFormatParser.parseDocument(tbText, 0, fileText.toString());
 		} catch (Exception e) {
@@ -134,7 +134,7 @@ public class THYMETreebankReader extends
 		
 
 		// add Token, Sentence and TreebankNode annotations for the text
-		for (org.cleartk.syntax.constituent.util.TopTreebankNode utilTree : utilTrees) {
+		for (org.cleartk.util.treebank.TopTreebankNode utilTree : utilTrees) {
 
 			// create a Sentence and set its parse
 			TopTreebankNode tree = convert(utilTree, jcas);
@@ -162,7 +162,7 @@ public class THYMETreebankReader extends
 	// the ctakes syntax typesystem was modeled after cleartk -- as a result, the following methods borrow very liberally from 
 	// org.cleartk.syntax.constituent.util.TreebankNodeUtility, which has a convert method for going from
 	// a "normal" tree to a cleartk/uima tree.  This does the same, except goes to a ctakes/uima tree.
-	private static TopTreebankNode convert(org.cleartk.syntax.constituent.util.TopTreebankNode inTree, JCas jcas){
+	private static TopTreebankNode convert(org.cleartk.util.treebank.TopTreebankNode inTree, JCas jcas){
 		TopTreebankNode outTree = new TopTreebankNode(jcas, inTree.getTextBegin(), inTree.getTextEnd());
 		outTree.setTreebankParse(inTree.getTreebankParse());
 	    convert(inTree, jcas, outTree, null);
@@ -207,7 +207,7 @@ public class THYMETreebankReader extends
 	}
 
 	public static TreebankNode convert(
-			org.cleartk.syntax.constituent.util.TreebankNode pojoNode,
+			org.cleartk.util.treebank.TreebankNode pojoNode,
 			JCas jCas,
 			TreebankNode uimaNode,
 			TreebankNode parentNode) {
@@ -219,7 +219,7 @@ public class THYMETreebankReader extends
 		uimaNode.setParent(parentNode);
 
 		List<TreebankNode> uimaChildren = new ArrayList<TreebankNode>();
-		for (org.cleartk.syntax.constituent.util.TreebankNode child : pojoNode.getChildren()) {
+		for (org.cleartk.util.treebank.TreebankNode child : pojoNode.getChildren()) {
 			TreebankNode childNode;
 			if (child.isLeaf()) {
 				childNode = new TerminalTreebankNode(jCas, child.getTextBegin(), child.getTextEnd());
@@ -244,7 +244,7 @@ public class THYMETreebankReader extends
 
 	public static AnalysisEngineDescription getDescription(File treebankDirectory)
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				THYMETreebankReader.class,
 				THYMETreebankReader.TREEBANK_DIRECTORY,
 				treebankDirectory);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalEntityAnnotator_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalEntityAnnotator_ImplBase.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalEntityAnnotator_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalEntityAnnotator_ImplBase.java Tue Sep 16 19:57:19 2014
@@ -21,9 +21,9 @@ package org.apache.ctakes.temporal.ae;
 import org.apache.ctakes.temporal.eval.THYMEData;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
 
 public abstract class TemporalEntityAnnotator_ImplBase extends CleartkAnnotator<String> {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalSequenceAnnotator_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalSequenceAnnotator_ImplBase.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalSequenceAnnotator_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalSequenceAnnotator_ImplBase.java Tue Sep 16 19:57:19 2014
@@ -21,9 +21,9 @@ package org.apache.ctakes.temporal.ae;
 import org.apache.ctakes.temporal.eval.THYMEData;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.CleartkSequenceAnnotator;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkSequenceAnnotator;
 
 public abstract class TemporalSequenceAnnotator_ImplBase extends
     CleartkSequenceAnnotator<String> {

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java Tue Sep 16 19:57:19 2014
@@ -38,28 +38,27 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
-import org.apache.uima.cas.CASRuntimeException;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+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.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.Following;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor.Preceding;
-import org.cleartk.classifier.feature.extractor.simple.CharacterCategoryPatternExtractor;
-import org.cleartk.classifier.feature.extractor.simple.CharacterCategoryPatternExtractor.PatternType;
-import org.cleartk.classifier.feature.extractor.simple.CombinedExtractor;
-import org.cleartk.classifier.feature.extractor.simple.CoveredTextExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.cleartk.classifier.feature.extractor.simple.TypePathExtractor;
-import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-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.feature.extractor.CleartkExtractor;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Following;
+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.FeatureExtractor1;
+import org.cleartk.ml.feature.extractor.TypePathExtractor;
+import org.cleartk.ml.feature.function.CharacterCategoryPatternFunction;
+import org.cleartk.ml.feature.function.CharacterCategoryPatternFunction.PatternType;
+import org.cleartk.ml.jar.DefaultDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
 
 public class TimeAnnotator extends TemporalEntityAnnotator_ImplBase {
 
@@ -99,7 +98,7 @@ public class TimeAnnotator extends Tempo
 					File outputDirectory,
 					float featureSelect,
 					float smoteNeighborNumber) throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				TimeAnnotator.class,
 				CleartkAnnotator.PARAM_IS_TRAINING,
 				true,
@@ -115,7 +114,7 @@ public class TimeAnnotator extends Tempo
 
 	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				TimeAnnotator.class,
 				CleartkAnnotator.PARAM_IS_TRAINING,
 				false,
@@ -130,7 +129,7 @@ public class TimeAnnotator extends Tempo
 	   */		
 	public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				TimeAnnotator.class,
 				CleartkAnnotator.PARAM_IS_TRAINING,
 				false,
@@ -142,7 +141,7 @@ public class TimeAnnotator extends Tempo
 
 	public static AnalysisEngineDescription createEnsembleDescription(File modelDirectory, String mappedView)
 	    throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(
+    return AnalysisEngineFactory.createEngineDescription(
         TimeAnnotator.class,
         CleartkAnnotator.PARAM_IS_TRAINING,
         false,
@@ -154,14 +153,14 @@ public class TimeAnnotator extends Tempo
         TimeAnnotator.createFeatureSelectionURI(modelDirectory));	  
 	}
 	
-	protected List<SimpleFeatureExtractor> tokenFeatureExtractors;
+	protected List<FeatureExtractor1> tokenFeatureExtractors;
 
 	protected List<CleartkExtractor> contextFeatureExtractors;
 
-	//  protected List<SimpleFeatureExtractor> parseFeatureExtractors;
+	//  protected List<FeatureExtractor1> parseFeatureExtractors;
 	protected ParseSpanFeatureExtractor parseExtractor;
 
-	private BIOChunking<BaseToken, TimeMention> timeChunking;
+	private BioChunking<BaseToken, TimeMention> timeChunking;
 	
 	private FeatureSelection<String> featureSelection;
 
@@ -180,19 +179,19 @@ public class TimeAnnotator extends Tempo
 		super.initialize(context);
 
 		// define chunking
-		this.timeChunking = new BIOChunking<BaseToken, TimeMention>(BaseToken.class, TimeMention.class);
+		this.timeChunking = new BioChunking<BaseToken, TimeMention>(BaseToken.class, TimeMention.class);
 
-		CombinedExtractor allExtractors = new CombinedExtractor(
+		CombinedExtractor1 allExtractors = new CombinedExtractor1(
 				new CoveredTextExtractor(),
-				new CharacterCategoryPatternExtractor(PatternType.REPEATS_MERGED),
-				new CharacterCategoryPatternExtractor(PatternType.ONE_PER_CHAR),
+		        CharacterCategoryPatternFunction.<BaseToken>createExtractor(PatternType.REPEATS_MERGED),
+		        CharacterCategoryPatternFunction.<BaseToken>createExtractor(PatternType.ONE_PER_CHAR),
 				new TypePathExtractor(BaseToken.class, "partOfSpeech"),
 				new TimeWordTypeExtractor());
 
-		//    CombinedExtractor parseExtractors = new CombinedExtractor(
+		//    CombinedExtractor1 parseExtractors = new CombinedExtractor(
 		//        new ParseSpanFeatureExtractor()
 		//        );
-		this.tokenFeatureExtractors = new ArrayList<SimpleFeatureExtractor>();
+		this.tokenFeatureExtractors = new ArrayList<FeatureExtractor1>();
 		this.tokenFeatureExtractors.add(allExtractors);
 
 		this.contextFeatureExtractors = new ArrayList<CleartkExtractor>();
@@ -248,7 +247,7 @@ public class TimeAnnotator extends Tempo
 
 				List<Feature> features = new ArrayList<Feature>();
 				// features from token attributes
-				for (SimpleFeatureExtractor extractor : this.tokenFeatureExtractors) {
+				for (FeatureExtractor1 extractor : this.tokenFeatureExtractors) {
 					features.addAll(extractor.extract(jCas, token));
 				}
 				// features from surrounding tokens
@@ -266,7 +265,7 @@ public class TimeAnnotator extends Tempo
 				features.add(new Feature("SegmentID", segment.getId()));
 
 				// features from dominating parse tree
-				//        for(SimpleFeatureExtractor extractor : this.parseFeatureExtractors){
+				//        for(FeatureExtractor1 extractor : this.parseFeatureExtractors){
 				BaseToken startToken = token;
 				for(int i = tokenIndex-1; i >= 0; --i){
 					String outcome = outcomes.get(i);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java Tue Sep 16 19:57:19 2014
@@ -24,9 +24,9 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.cleartk.timeml.type.Time;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class TimexToClearTKTimexAnnotator extends JCasAnnotator_ImplBase {
 
@@ -42,6 +42,6 @@ public class TimexToClearTKTimexAnnotato
   
   public static AnalysisEngineDescription getAnnotatorDescription()
       throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(TimexToClearTKTimexAnnotator.class);
+    return AnalysisEngineFactory.createEngineDescription(TimexToClearTKTimexAnnotator.class);
   }
 }

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java Tue Sep 16 19:57:19 2014
@@ -35,11 +35,11 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;
@@ -51,7 +51,7 @@ public class F1BaselineEventTimeRelation
 
 	  public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 		      throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		        F1BaselineEventTimeRelationAnnotator.class,
 		        CleartkAnnotator.PARAM_IS_TRAINING,
 		        false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/PrecisionBaselineEventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/PrecisionBaselineEventTimeRelationAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/PrecisionBaselineEventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/PrecisionBaselineEventTimeRelationAnnotator.java Tue Sep 16 19:57:19 2014
@@ -35,11 +35,11 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;
@@ -50,7 +50,7 @@ public class PrecisionBaselineEventTimeR
 
   public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
       throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(
+    return AnalysisEngineFactory.createEngineDescription(
         PrecisionBaselineEventTimeRelationAnnotator.class,
         CleartkAnnotator.PARAM_IS_TRAINING,
         false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventEventRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventEventRelationAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventEventRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventEventRelationAnnotator.java Tue Sep 16 19:57:19 2014
@@ -29,17 +29,17 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class RecallBaselineEventEventRelationAnnotator extends
 		RelationExtractorAnnotator {
 	  public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 		      throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		        RecallBaselineEventEventRelationAnnotator.class,
 		        CleartkAnnotator.PARAM_IS_TRAINING,
 		        false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventTimeRelationAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventTimeRelationAnnotator.java Tue Sep 16 19:57:19 2014
@@ -35,11 +35,11 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;
@@ -51,7 +51,7 @@ public class RecallBaselineEventTimeRela
 
 	  public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 		      throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		        RecallBaselineEventTimeRelationAnnotator.class,
 		        CleartkAnnotator.PARAM_IS_TRAINING,
 		        false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TimidBaselineEventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TimidBaselineEventTimeRelationAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TimidBaselineEventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TimidBaselineEventTimeRelationAnnotator.java Tue Sep 16 19:57:19 2014
@@ -33,11 +33,11 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;
@@ -48,7 +48,7 @@ public class TimidBaselineEventTimeRelat
 
   public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
       throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(
+    return AnalysisEngineFactory.createEngineDescription(
         TimidBaselineEventTimeRelationAnnotator.class,
         CleartkAnnotator.PARAM_IS_TRAINING,
         false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TreeHeightBaseline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TreeHeightBaseline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TreeHeightBaseline.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TreeHeightBaseline.java Tue Sep 16 19:57:19 2014
@@ -32,17 +32,17 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class TreeHeightBaseline extends RelationExtractorAnnotator {
 
 	  public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
 		      throws ResourceInitializationException {
-		    return AnalysisEngineFactory.createPrimitiveDescription(
+		    return AnalysisEngineFactory.createEngineDescription(
 		        TreeHeightBaseline.class,
 		        CleartkAnnotator.PARAM_IS_TRAINING,
 		        false,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CheckSpecialWordRelationExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CheckSpecialWordRelationExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CheckSpecialWordRelationExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CheckSpecialWordRelationExtractor.java Tue Sep 16 19:57:19 2014
@@ -31,8 +31,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 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.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class CheckSpecialWordRelationExtractor implements RelationFeaturesExtractor{
 	

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ChunkingExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ChunkingExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ChunkingExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ChunkingExtractor.java Tue Sep 16 19:57:19 2014
@@ -23,8 +23,8 @@ import java.util.List;
 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.chunking.Chunking;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.chunking.Chunking;
 
 import com.google.common.collect.Lists;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,14 +28,14 @@ import java.util.TreeMap;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 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.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class ClosestVerbExtractor implements SimpleFeatureExtractor {
+public class ClosestVerbExtractor implements FeatureExtractor1 {
 
   private String name;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java Tue Sep 16 19:57:19 2014
@@ -30,14 +30,14 @@ import java.util.logging.Logger;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 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.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 import com.google.common.io.Files;
 import com.google.common.io.LineProcessor;
 
-public class CoveredTextToValuesExtractor implements SimpleFeatureExtractor {
+public class CoveredTextToValuesExtractor implements FeatureExtractor1 {
 
   private String name;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DateAndMeasurementExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DateAndMeasurementExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DateAndMeasurementExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DateAndMeasurementExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,14 +28,14 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation;
 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.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class DateAndMeasurementExtractor implements SimpleFeatureExtractor {
+public class DateAndMeasurementExtractor implements FeatureExtractor1 {
 
   private String name;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyFeatureExtractor.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.TimeMention;
 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.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class DependencyFeatureExtractor implements
 RelationFeaturesExtractor {

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyParseUtils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyParseUtils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyParseUtils.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyParseUtils.java Tue Sep 16 19:57:19 2014
@@ -25,7 +25,7 @@ import java.util.List;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 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;
 
 /**
  * This is a slightly modified version of the same class from relation extraction.

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyPathFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyPathFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyPathFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyPathFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,7 +27,7 @@ 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.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 
 public class DependencyPathFeaturesExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DocTimeRelFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DocTimeRelFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DocTimeRelFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DocTimeRelFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -26,7 +26,7 @@ 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.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 
 public class DocTimeRelFeatureExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,8 +28,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 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.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class EventArgumentPropertyExtractor implements
     RelationFeaturesExtractor {

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java Tue Sep 16 19:57:19 2014
@@ -25,11 +25,11 @@ import java.util.List;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 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.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class EventPropertyExtractor implements SimpleFeatureExtractor {
+public class EventPropertyExtractor implements FeatureExtractor1 {
 
   private String name;
   

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationsFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationsFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationsFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationsFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,8 +27,8 @@ import org.apache.ctakes.typesystem.type
 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.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.collect.Lists;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/FramesetCategoryExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/FramesetCategoryExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/FramesetCategoryExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/FramesetCategoryExtractor.java Tue Sep 16 19:57:19 2014
@@ -24,20 +24,20 @@ import java.util.List;
 import java.util.Map;
 
 import org.apache.ctakes.typesystem.type.textsem.Predicate;
+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.ResourceInitializationException;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
 import com.google.common.io.Resources;
 
-public class FramesetCategoryExtractor implements SimpleFeatureExtractor {
+public class FramesetCategoryExtractor implements FeatureExtractor1 {
   
   private Map<String, String> frameSetCategories;
   

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/IdentifiedAnnotationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/IdentifiedAnnotationFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/IdentifiedAnnotationFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/IdentifiedAnnotationFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -30,12 +30,12 @@ import java.util.logging.Logger;
 
 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.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 import com.google.common.io.Files;
 import com.google.common.io.LineProcessor;
@@ -47,7 +47,7 @@ import com.google.common.io.LineProcesso
  * 2/28/2013
  *
  */
-public class IdentifiedAnnotationFeatureExtractor implements SimpleFeatureExtractor {
+public class IdentifiedAnnotationFeatureExtractor implements FeatureExtractor1 {
 
   private String name;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ListFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ListFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ListFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ListFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -30,8 +30,8 @@ import org.apache.ctakes.typesystem.type
 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.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.collect.Lists;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java Tue Sep 16 19:57:19 2014
@@ -30,8 +30,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 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.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class NearbyVerbTenseRelationExtractor implements RelationFeaturesExtractor{
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,14 +27,14 @@ import java.util.Map;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 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.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class NearbyVerbTenseXExtractor implements SimpleFeatureExtractor {
+public class NearbyVerbTenseXExtractor implements FeatureExtractor1 {
 
   private String name;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearestFlagFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearestFlagFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearestFlagFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearestFlagFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -31,8 +31,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 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.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class NearestFlagFeatureExtractor implements
 RelationFeaturesExtractor {

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java Tue Sep 16 19:57:19 2014
@@ -26,10 +26,9 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 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.cleartk.util.ViewURIUtil;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
 
 public class NumberOfEventTimeBetweenCandidatesExtractor implements
 RelationFeaturesExtractor {
@@ -67,7 +66,7 @@ RelationFeaturesExtractor {
 		
 //		//print long distances
 //		if (eventsInBetween >= 200){
-//			System.out.println("++++++++++Long Distance Relation in "+ ViewURIUtil.getURI(jCas).toString() + "+++++++");
+//			System.out.println("++++++++++Long Distance Relation in "+ ViewUriUtil.getURI(jCas).toString() + "+++++++");
 //			System.out.println("["+arg1.getCoveredText()+"] "+ jCas.getDocumentText().substring(arg1.getEnd(), arg2.getBegin()) +" ["+arg2.getCoveredText()+"]");
 //		}
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,7 +27,7 @@ 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.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 
 public class ParseFeatureExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseSpanFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseSpanFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseSpanFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseSpanFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -24,7 +24,7 @@ import java.util.List;
 import org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils;
 import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 
 public class ParseSpanFeatureExtractor  {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/PredicateArgumentExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/PredicateArgumentExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/PredicateArgumentExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/PredicateArgumentExtractor.java Tue Sep 16 19:57:19 2014
@@ -26,8 +26,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
 import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Lists;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SRLRelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SRLRelationFeaturesExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SRLRelationFeaturesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SRLRelationFeaturesExtractor.java Tue Sep 16 19:57:19 2014
@@ -30,8 +30,8 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSList;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.collect.Lists;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java Tue Sep 16 19:57:19 2014
@@ -26,14 +26,14 @@ import java.util.Map;
 
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
+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.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class SectionHeaderExtractor implements SimpleFeatureExtractor {
+public class SectionHeaderExtractor implements FeatureExtractor1 {
 
   private String name;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java Tue Sep 16 19:57:19 2014
@@ -29,8 +29,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 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.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class SectionHeaderRelationExtractor implements RelationFeaturesExtractor{
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SyntacticParentFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SyntacticParentFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SyntacticParentFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SyntacticParentFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -26,7 +26,7 @@ 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.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 
 import com.google.common.collect.Lists;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,8 +27,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 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.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class TemporalAttributeFeatureExtractor implements
 		RelationFeaturesExtractor {

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeForMixEventTimeExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeForMixEventTimeExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeForMixEventTimeExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeForMixEventTimeExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,8 +27,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 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.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class TemporalAttributeForMixEventTimeExtractor implements
 RelationFeaturesExtractor {

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeWordTypeExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeWordTypeExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeWordTypeExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeWordTypeExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,16 +27,16 @@ import java.util.Map;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 import org.cleartk.timeml.util.TimeWordsExtractor;
 
 import com.google.common.base.Charsets;
 import com.google.common.collect.Maps;
 import com.google.common.io.Resources;
 
-public class TimeWordTypeExtractor implements SimpleFeatureExtractor {
+public class TimeWordTypeExtractor<T extends Annotation> implements FeatureExtractor1<T> {
   
   private static final String FEATURE_NAME = "TimeWordType";
   



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