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From tm...@apache.org
Subject svn commit: r1625365 [8/10] - 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/feature/TimeXExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java Tue Sep 16 19:57:19 2014
@@ -35,15 +35,15 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 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.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;
 
-public class TimeXExtractor implements SimpleFeatureExtractor {
+public class TimeXExtractor implements FeatureExtractor1 {
 
   private String name;
 //  private TemporalPETExtractor path;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -30,8 +30,8 @@ import org.apache.ctakes.utils.struct.Co
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CASException;
 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.Lists;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsSingleFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsSingleFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsSingleFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsSingleFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -24,16 +24,16 @@ import java.util.List;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.utils.struct.CounterMap;
+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.collect.Lists;
 
-public class UmlsSingleFeatureExtractor implements SimpleFeatureExtractor {
+public class UmlsSingleFeatureExtractor implements FeatureExtractor1 {
 
   @Override
   public List<Feature> extract(JCas jCas, Annotation focusAnnotation)

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistSemFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistSemFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistSemFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistSemFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -18,8 +18,8 @@ import org.apache.ctakes.utils.distsem.W
 import org.apache.ctakes.utils.distsem.WordVectorReader;
 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 DistSemFeatureExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistanceFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistanceFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistanceFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/DistanceFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -10,8 +10,8 @@ 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 DistanceFeatureExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/StringMatchingFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/StringMatchingFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/StringMatchingFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/StringMatchingFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -11,8 +11,8 @@ 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;
 
 public class StringMatchingFeatureExtractor implements
 		RelationFeaturesExtractor {

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

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/UMLSFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/UMLSFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/UMLSFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/coreference/UMLSFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -13,8 +13,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class UMLSFeatureExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationDistributionFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationDistributionFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationDistributionFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationDistributionFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,14 +27,14 @@ import java.util.Map;
 import org.apache.ctakes.temporal.duration.Utils;
 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.base.Charsets;
 import com.google.common.io.Files;
 
-public class DurationDistributionFeatureExtractor implements SimpleFeatureExtractor {
+public class DurationDistributionFeatureExtractor implements FeatureExtractor1 {
 
   @Override
   public List<Feature> extract(JCas view, Annotation annotation) throws CleartkExtractorException { 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventEventFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventEventFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventEventFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventEventFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -29,7 +29,7 @@ import org.apache.ctakes.temporal.durati
 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.base.Charsets;
 import com.google.common.io.Files;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventTimeFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventTimeFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventTimeFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventTimeFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -30,7 +30,7 @@ import org.apache.ctakes.temporal.durati
 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.base.Charsets;
 import com.google.common.io.Files;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationExpectationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationExpectationFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationExpectationFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationExpectationFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,14 +28,14 @@ import org.apache.ctakes.temporal.durati
 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.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.base.Charsets;
 import com.google.common.io.Files;
 
-public class DurationExpectationFeatureExtractor implements SimpleFeatureExtractor {
+public class DurationExpectationFeatureExtractor implements FeatureExtractor1 {
 
   @Override
   public List<Feature> extract(JCas view, Annotation annotation) throws CleartkExtractorException { 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationTimeUnitFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationTimeUnitFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationTimeUnitFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationTimeUnitFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,7 +27,7 @@ import org.apache.ctakes.temporal.durati
 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 org.threeten.bp.temporal.TemporalUnit;
 
 import scala.collection.immutable.Set;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -28,9 +28,9 @@ import java.net.URI;
 import java.util.LinkedHashSet;
 import java.util.Set;
 
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.transform.TransformableFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.TransformableFeature;
 
 import com.google.common.base.Function;
 import com.google.common.collect.HashBasedTable;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -28,9 +28,9 @@ import java.net.URI;
 import java.util.LinkedHashSet;
 import java.util.Set;
 
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.transform.TransformableFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.TransformableFeature;
 
 import com.google.common.base.Function;
 import com.google.common.collect.HashBasedTable;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/FeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/FeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/FeatureSelection.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/FeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -22,10 +22,10 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
-import org.cleartk.classifier.feature.transform.TrainableExtractor_ImplBase;
-import org.cleartk.classifier.feature.transform.TransformableFeature;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
+import org.cleartk.ml.feature.transform.TrainableExtractor_ImplBase;
+import org.cleartk.ml.feature.transform.TransformableFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
 
 import com.google.common.base.Predicate;
 import com.google.common.collect.Collections2;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/MutualInformationFeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/MutualInformationFeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/MutualInformationFeatureSelection.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/MutualInformationFeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -29,9 +29,9 @@ import java.util.Collection;
 import java.util.Map;
 import java.util.Set;
 
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.transform.TransformableFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.TransformableFeature;
 
 import com.google.common.base.Function;
 import com.google.common.base.Joiner;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -27,9 +27,9 @@ import java.io.IOException;
 import java.net.URI;
 import java.util.Set;
 
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.transform.TransformableFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.TransformableFeature;
 
 import com.google.common.base.Function;
 import com.google.common.collect.HashBasedTable;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/DependencySingleTreeExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/DependencySingleTreeExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/DependencySingleTreeExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/DependencySingleTreeExtractor.java Tue Sep 16 19:57:19 2014
@@ -19,28 +19,23 @@
 package org.apache.ctakes.temporal.ae.feature.treekernel;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
-import java.util.Map;
 
-import org.apache.ctakes.dependency.parser.util.AnnotationDepUtils;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
-import org.apache.ctakes.typesystem.type.textsem.EventMention;
-import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.ctakes.utils.tree.SimpleTree;
+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.TreeFeature;
-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.TreeFeature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 /**
  * Given a focused annotation, get the whole sentence-level dependency tree that cover this annotation.
  * @author CH151862
  *
  */
-public class DependencySingleTreeExtractor implements SimpleFeatureExtractor {
+public class DependencySingleTreeExtractor implements FeatureExtractor1 {
 
 	public static final String FEAT_NAME = "TK_DepSingleT";
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/EventTimeFlatTreeFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/EventTimeFlatTreeFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/EventTimeFlatTreeFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/EventTimeFlatTreeFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -29,9 +29,9 @@ 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.classifier.TreeFeature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.TreeFeature;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Function;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/SyntaticSingleTreeExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/SyntaticSingleTreeExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/SyntaticSingleTreeExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/SyntaticSingleTreeExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,16 +28,16 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.utils.tree.SimpleTree;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.TreeFeature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.TreeFeature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 /**
  * Given a focused annotation, get the whole sentence-level parse tree that cover this annotation.
  * @author CH151862
  *
  */
-public class SyntaticSingleTreeExtractor implements SimpleFeatureExtractor {
+public class SyntaticSingleTreeExtractor implements FeatureExtractor1 {
 
 	public static final String FEAT_NAME = "TK_SingleT";
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalFTExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalFTExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalFTExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalFTExtractor.java Tue Sep 16 19:57:19 2014
@@ -32,8 +32,8 @@ 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.classifier.TreeFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.TreeFeature;
 
 public class TemporalFTExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPETExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPETExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPETExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPETExtractor.java Tue Sep 16 19:57:19 2014
@@ -32,9 +32,9 @@ 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.classifier.TreeFeature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.TreeFeature;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class TemporalPETExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPathExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPathExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPathExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPathExtractor.java Tue Sep 16 19:57:19 2014
@@ -32,8 +32,8 @@ 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.classifier.TreeFeature;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.TreeFeature;
 
 public class TemporalPathExtractor implements RelationFeaturesExtractor {
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java Tue Sep 16 19:57:19 2014
@@ -35,8 +35,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.factory.JCasFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.base.Objects;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CoreferenceLinkDistanceAnalyzer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CoreferenceLinkDistanceAnalyzer.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CoreferenceLinkDistanceAnalyzer.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CoreferenceLinkDistanceAnalyzer.java Tue Sep 16 19:57:19 2014
@@ -9,6 +9,7 @@ import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -18,7 +19,6 @@ import org.apache.ctakes.temporal.eval.E
 import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader;
 import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
-import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import org.apache.ctakes.typesystem.type.textsem.Markable;
 import org.apache.ctakes.typesystem.type.textspan.Paragraph;
@@ -28,17 +28,16 @@ import org.apache.ctakes.utils.distsem.W
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSList;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
-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.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -64,11 +63,11 @@ public class CoreferenceLinkDistanceAnal
     CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(getFiles(options.getInputDirectory(), options.getXMIDirectory()));
     AggregateBuilder aggregateBuilder = new AggregateBuilder();
     aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
         XMIReader.class,
         XMIReader.PARAM_XMI_DIRECTORY,
         options.getXMIDirectory()));
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ParagraphAnnotator.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ParagraphAnnotator.class));
     
     WordEmbeddings words = WordVectorReader.getEmbeddings(FileLocator.getAsStream("org/apache/ctakes/coreference/distsem/mimic_vectors.txt"));
 
@@ -83,10 +82,11 @@ public class CoreferenceLinkDistanceAnal
     // compute paragraph vectors for every paragraph
     AnalysisEngine ae = aggregateBuilder.createAggregate();
     
-    for(JCas jcas : new JCasIterable(reader, ae)){
+    for(Iterator<JCas> casIter = new JCasIterator(reader, ae); casIter.hasNext();){
+      JCas jcas = casIter.next();
       numDocs++;
       // print out document name
-      System.out.println("######### Document id: " + ViewURIUtil.getURI(jcas).toString());
+      System.out.println("######### Document id: " + ViewUriUtil.getURI(jcas).toString());
       JCas goldView = jcas.getView(GOLD_VIEW_NAME);
       
       Map<Markable,Integer> markable2par = new HashMap<>();

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java Tue Sep 16 19:57:19 2014
@@ -35,12 +35,12 @@ import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+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.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -79,7 +79,7 @@ public class EventContextAnalysisPipelin
 		List<File> trainFiles = Arrays.asList(options.getInputDirectory().listFiles());
     CollectionReader collectionReader = getCollectionReader(trainFiles);
 		
-    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(
     		EventAndTokenContextWriter.class,
     		"TokenOutputFile",
     		options.getTokenOutputFile(),
@@ -200,7 +200,7 @@ public class EventContextAnalysisPipelin
     String[] paths = new String[fileNames.size()];
     fileNames.toArray(paths);
     
-    return CollectionReaderFactory.createCollectionReader(
+    return CollectionReaderFactory.createReader(
         XMIReader.class,
         XMIReader.PARAM_FILES,
         paths);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java Tue Sep 16 19:57:19 2014
@@ -39,12 +39,12 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.jcas.JCas;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+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.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.base.Functions;
@@ -81,7 +81,7 @@ public class EventPrinterPipeline {
 		List<File> trainFiles = Arrays.asList(options.getInputDirectory().listFiles());
     CollectionReader collectionReader = getCollectionReader(trainFiles);
 		
-    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(
     		EventWriter.class,
     		"UmlsSemanticType",
     		options.getUmlsSemanticType(),
@@ -183,7 +183,7 @@ public class EventPrinterPipeline {
 	  String[] paths = new String[fileNames.size()];
 	  fileNames.toArray(paths);
 
-	  return CollectionReaderFactory.createCollectionReader(
+	  return CollectionReaderFactory.createReader(
 	      XMIReader.class,
 	      XMIReader.PARAM_FILES,
 	      paths);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java Tue Sep 16 19:57:19 2014
@@ -38,11 +38,11 @@ import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.util.ViewURIUtil;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.util.ViewUriUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -72,7 +72,7 @@ public class GoldRelationViewer {
 		List<File> trainFiles = Utils.getFilesFor(trainItems, options.getInputDirectory());
     CollectionReader collectionReader = Utils.getCollectionReader(trainFiles);
 		
-    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(
     		RelationContextPrinter.class);
     		
 		SimplePipeline.runPipeline(collectionReader, annotationConsumer);
@@ -111,7 +111,7 @@ public class GoldRelationViewer {
         relationLookup.put(Arrays.asList(arg1, arg2), relation);
       }
 
-      File noteFile = new File(ViewURIUtil.getURI(jCas).toString());
+      File noteFile = new File(ViewUriUtil.getURI(jCas).toString());
       String fileName = noteFile.getName();
       
       for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintFailedTimeNormalizations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintFailedTimeNormalizations.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintFailedTimeNormalizations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintFailedTimeNormalizations.java Tue Sep 16 19:57:19 2014
@@ -24,6 +24,7 @@ import info.bethard.timenorm.TimeSpan;
 
 import java.io.File;
 import java.net.URL;
+import java.util.Iterator;
 import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -34,13 +35,13 @@ import org.apache.ctakes.temporal.eval.T
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.cleartk.util.ae.UriToDocumentTextAnnotator;
 import org.cleartk.util.cr.UriCollectionReader;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 import scala.util.Try;
 
@@ -70,7 +71,7 @@ public class PrintFailedTimeNormalizatio
     CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(files);
     AggregateBuilder aggregateBuilder = new AggregateBuilder();
     aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
         XMIReader.class,
         XMIReader.PARAM_XMI_DIRECTORY,
         options.getXMIDirectory()));
@@ -78,7 +79,8 @@ public class PrintFailedTimeNormalizatio
     String grammarPath = "/org/apache/ctakes/temporal/timenorm.en.grammar";
     URL grammarURL = PrintFailedTimeNormalizations.class.getResource(grammarPath);
     TemporalExpressionParser parser = new TemporalExpressionParser(grammarURL);
-    for (JCas jCas : new JCasIterable(reader, aggregateBuilder.createAggregate())) {
+    for (Iterator<JCas> casIter = new JCasIterator(reader, aggregateBuilder.createAggregate()); casIter.hasNext();) {
+      JCas jCas = casIter.next();
       JCas goldView = jCas.getView("GoldView");
 
       Matcher matcher = DOC_TIME_PATTERN.matcher(goldView.getDocumentText());

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java Tue Sep 16 19:57:19 2014
@@ -20,6 +20,7 @@ package org.apache.ctakes.temporal.data.
 
 import java.io.File;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
@@ -31,15 +32,15 @@ import org.apache.ctakes.temporal.eval.T
 import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-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.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.collect.HashMultimap;
@@ -73,14 +74,15 @@ public class PrintInconsistentAnnotation
     CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(files);
     AggregateBuilder aggregateBuilder = new AggregateBuilder();
     aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
         XMIReader.class,
         XMIReader.PARAM_XMI_DIRECTORY,
         options.getXMIDirectory()));
 
     int totalDocTimeRels = 0;
     int totalInconsistentDocTimeRels = 0;
-    for (JCas jCas : new JCasIterable(reader, aggregateBuilder.createAggregate())) {
+    for (Iterator<JCas> casIter = new JCasIterator(reader, aggregateBuilder.createAggregate()); casIter.hasNext();) {
+      JCas jCas = casIter.next();
       String text = jCas.getDocumentText();
       JCas goldView = jCas.getView("GoldView");
 
@@ -149,7 +151,7 @@ public class PrintInconsistentAnnotation
           int end = Math.min(offsets.get(offsets.size() - 1) + windowSize, text.length());
           System.err.printf(
               "Inconsistent DocTimeRels in %s, ...%s...\n",
-              new File(ViewURIUtil.getURI(jCas)).getName(),
+              new File(ViewUriUtil.getURI(jCas)).getName(),
               text.substring(begin, end).replaceAll("([\r\n])[\r\n]+", "$1"));
           if (container instanceof EventMention) {
             System.err.printf(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintNormalizedTemporalExpressions.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintNormalizedTemporalExpressions.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintNormalizedTemporalExpressions.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintNormalizedTemporalExpressions.java Tue Sep 16 19:57:19 2014
@@ -24,8 +24,8 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.CASException;
 import org.apache.uima.jcas.JCas;
 import org.threeten.bp.temporal.TemporalUnit;
-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 scala.collection.immutable.Set;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextViewerPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextViewerPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextViewerPipeline.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextViewerPipeline.java Tue Sep 16 19:57:19 2014
@@ -37,12 +37,12 @@ import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+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.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -75,7 +75,7 @@ public class RelationContextViewerPipeli
 		List<File> trainFiles = getFilesFor(trainItems, options.getInputDirectory());
     CollectionReader collectionReader = getCollectionReader(trainFiles);
 		
-    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(
     		RelationContextPrinter.class,
     		"OutputFile",
     		options.getOutputFile());
@@ -95,7 +95,7 @@ public class RelationContextViewerPipeli
 	  String[] paths = new String[fileNames.size()];
 	  fileNames.toArray(paths);
 
-	  return CollectionReaderFactory.createCollectionReader(
+	  return CollectionReaderFactory.createReader(
 	      XMIReader.class,
 	      XMIReader.PARAM_FILES,
 	      paths);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/TimexTreeAlignmentStatistics.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/TimexTreeAlignmentStatistics.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/TimexTreeAlignmentStatistics.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/TimexTreeAlignmentStatistics.java Tue Sep 16 19:57:19 2014
@@ -21,6 +21,7 @@ package org.apache.ctakes.temporal.data.
 import java.io.File;
 import java.io.IOException;
 import java.util.Collection;
+import java.util.Iterator;
 import java.util.List;
 
 import org.apache.ctakes.constituency.parser.util.TreeUtils;
@@ -33,13 +34,13 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.cleartk.util.ae.UriToDocumentTextAnnotator;
 import org.cleartk.util.cr.UriCollectionReader;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -71,7 +72,7 @@ public class TimexTreeAlignmentStatistic
     CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(THYMEData.getFilesFor(trainItems, options.getRawTextDirectory()));
     AggregateBuilder aggregateBuilder = new AggregateBuilder();
     aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
         XMIReader.class,
         XMIReader.PARAM_XMI_DIRECTORY,
         options.getXMIDirectory()));
@@ -79,10 +80,11 @@ public class TimexTreeAlignmentStatistic
     int numMentions=0;
     int numMatches=0;
     
-    for(JCas jCas : new JCasIterable(reader, ae)){
+    for(Iterator<JCas> casIter = new JCasIterator(reader, ae); casIter.hasNext();){
       //      String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
       //      String docId = jCas.
       //      System.out.println("Document: " + docId);
+      JCas jCas = casIter.next();
       for(Segment segment : JCasUtil.select(jCas, Segment.class)){
     	  if(THYMEData.SEGMENTS_TO_SKIP.contains(segment.getId())) continue;
         Collection<TimeMention> mentions = JCasUtil.selectCovered(jCas.getView("GoldView"), TimeMention.class, segment);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventDurationDistribution.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventDurationDistribution.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventDurationDistribution.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventDurationDistribution.java Tue Sep 16 19:57:19 2014
@@ -46,12 +46,12 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.apache.uima.resource.ResourceInitializationException;
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+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.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.google.common.base.Charsets;
 import com.google.common.base.Joiner;
@@ -93,7 +93,7 @@ public class EventDurationDistribution {
 		List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
     CollectionReader collectionReader = getCollectionReader(trainFiles);
 		
-    AnalysisEngine temporalDurationExtractor = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine temporalDurationExtractor = AnalysisEngineFactory.createEngine(
     		TemporalDurationExtractor.class,
     		"OutputFile",
     		options.outputFile);
@@ -283,7 +283,7 @@ public class EventDurationDistribution {
       paths[i] = items.get(i).getPath();
     }
     
-    return CollectionReaderFactory.createCollectionReader(
+    return CollectionReaderFactory.createReader(
         XMIReader.class,
         XMIReader.PARAM_FILES,
         paths);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventEventDurationStatistics.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventEventDurationStatistics.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventEventDurationStatistics.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventEventDurationStatistics.java Tue Sep 16 19:57:19 2014
@@ -33,11 +33,11 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.jcas.JCas;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+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.fit.util.JCasUtil;
 
 import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;
@@ -73,7 +73,7 @@ public class EventEventDurationStatistic
     List<File> trainFiles = Utils.getFilesFor(trainItems, options.getInputDirectory());
     CollectionReader collectionReader = Utils.getCollectionReader(trainFiles);
 
-    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(
         AnalyseRelationArgumentDuration.class,
         "OutputFile",
         options.getOutputFile());

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventTimeDurationStatistics.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventTimeDurationStatistics.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventTimeDurationStatistics.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventTimeDurationStatistics.java Tue Sep 16 19:57:19 2014
@@ -35,11 +35,11 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.jcas.JCas;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+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.fit.util.JCasUtil;
 
 import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;
@@ -75,7 +75,7 @@ public class EventTimeDurationStatistics
     List<File> trainFiles = Utils.getFilesFor(trainItems, options.getInputDirectory());
     CollectionReader collectionReader = Utils.getCollectionReader(trainFiles);
 
-    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(
         AnalyseRelationArgumentDuration.class,
         "OutputFile",
         options.getOutputFile());

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/ExtractDurationsUsingContainsRelation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/ExtractDurationsUsingContainsRelation.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/ExtractDurationsUsingContainsRelation.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/ExtractDurationsUsingContainsRelation.java Tue Sep 16 19:57:19 2014
@@ -39,12 +39,12 @@ import org.apache.uima.collection.Collec
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.threeten.bp.temporal.TemporalUnit;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+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.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 import scala.collection.immutable.Set;
 
@@ -80,7 +80,7 @@ public class ExtractDurationsUsingContai
     List<File> files = Arrays.asList(options.getInputDirectory().listFiles());
     CollectionReader collectionReader = getCollectionReader(files);
 
-    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(
         ProcessRelations.class,
         "EventOutputFile",
         options.getEventOutputFile());
@@ -193,7 +193,7 @@ public class ExtractDurationsUsingContai
     String[] paths = new String[fileNames.size()];
     fileNames.toArray(paths);
 
-    return CollectionReaderFactory.createCollectionReader(
+    return CollectionReaderFactory.createReader(
         XMIReader.class,
         XMIReader.PARAM_FILES,
         paths);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventEventRelationsInGold.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventEventRelationsInGold.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventEventRelationsInGold.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventEventRelationsInGold.java Tue Sep 16 19:57:19 2014
@@ -28,8 +28,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CASException;
 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.Charsets;
 import com.google.common.collect.Lists;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventTimeRelationsInGold.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventTimeRelationsInGold.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventTimeRelationsInGold.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventTimeRelationsInGold.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.cas.CASException;
 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.Charsets;
 import com.google.common.collect.Lists;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventsInGold.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventsInGold.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventsInGold.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventsInGold.java Tue Sep 16 19:57:19 2014
@@ -26,8 +26,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CASException;
 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.Charsets;
 import com.google.common.collect.Lists;

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventEventRelationsInGold.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventEventRelationsInGold.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventEventRelationsInGold.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventEventRelationsInGold.java Tue Sep 16 19:57:19 2014
@@ -26,8 +26,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CASException;
 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.collect.Lists;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventTimeRelationsInGold.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventTimeRelationsInGold.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventTimeRelationsInGold.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventTimeRelationsInGold.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.cas.CASException;
 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.collect.Lists;
 

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/Utils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/Utils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/Utils.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/Utils.java Tue Sep 16 19:57:19 2014
@@ -48,11 +48,11 @@ import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 import org.threeten.bp.temporal.TemporalField;
 import org.threeten.bp.temporal.TemporalUnit;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import scala.collection.immutable.Set;
 import scala.util.Try;
@@ -393,7 +393,7 @@ public class Utils {
     String[] paths = new String[fileNames.size()];
     fileNames.toArray(paths);
 
-    return CollectionReaderFactory.createCollectionReader(
+    return CollectionReaderFactory.createReader(
         XMIReader.class,
         XMIReader.PARAM_FILES,
         paths);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java Tue Sep 16 19:57:19 2014
@@ -23,6 +23,7 @@ import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
@@ -36,16 +37,16 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+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.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.cleartk.eval.AnnotationStatistics;
-import org.cleartk.util.ViewURIUtil;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.util.ViewUriUtil;
 
 import com.google.common.base.Function;
 import com.google.common.collect.Ordering;
@@ -120,7 +121,7 @@ Evaluation_ImplBase<AnnotationStatistics
 		AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
 		aggregateBuilder.add(this.getAnnotatorDescription(directory), "TimexView", CAS.NAME_DEFAULT_SOFA);
 		if(this.i2b2Output != null){
-			aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
+			aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
 		}
 		AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
 		Ordering<Annotation> bySpans = Ordering.<Integer> natural().lexicographical().onResultOf(
@@ -130,7 +131,8 @@ Evaluation_ImplBase<AnnotationStatistics
 						return Arrays.asList(annotation.getBegin(), annotation.getEnd());
 					}
 				});
-		for (JCas jCas : new JCasIterable(collectionReader, aggregateBuilder.createAggregate())) {
+		for (Iterator<JCas> casIter = new JCasIterator(collectionReader, aggregateBuilder.createAggregate()); casIter.hasNext();) {
+			JCas jCas = casIter.next();
 			JCas goldView = jCas.getView(GOLD_VIEW_NAME);
 			JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
 			for (Segment segment : JCasUtil.select(jCas, Segment.class)) {
@@ -162,7 +164,7 @@ Evaluation_ImplBase<AnnotationStatistics
 
 					String text = jCas.getDocumentText().replaceAll("[\r\n]", " ");
 					if (!goldOnly.isEmpty() || !systemOnly.isEmpty()) {
-						this.logger.fine("Errors in : " + ViewURIUtil.getURI(jCas).toString());
+						this.logger.fine("Errors in : " + ViewUriUtil.getURI(jCas).toString());
 						Set<Annotation> errors = new TreeSet<Annotation>(bySpans);
 						errors.addAll(goldOnly);
 						errors.addAll(systemOnly);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java Tue Sep 16 19:57:19 2014
@@ -23,6 +23,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.logging.FileHandler;
@@ -31,9 +32,9 @@ import java.util.logging.Level;
 import java.util.logging.LogRecord;
 import java.util.logging.Logger;
 
-import org.apache.ctakes.temporal.ae.EventToClearTKEventAnnotator;
-import org.apache.ctakes.temporal.ae.ClearTKDocumentCreationTimeAnnotator;
 import org.apache.ctakes.temporal.ae.ClearTKDocTimeRelAnnotator;
+import org.apache.ctakes.temporal.ae.ClearTKDocumentCreationTimeAnnotator;
+import org.apache.ctakes.temporal.ae.EventToClearTKEventAnnotator;
 import org.apache.ctakes.typesystem.type.refsem.EventProperties;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
@@ -42,24 +43,24 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.CAS;
 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.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.eval.AnnotationStatistics;
-import org.cleartk.syntax.opennlp.ParserAnnotator;
-import org.cleartk.syntax.opennlp.PosTaggerAnnotator;
-import org.cleartk.syntax.opennlp.SentenceAnnotator;
+import org.cleartk.opennlp.tools.ParserAnnotator;
+import org.cleartk.opennlp.tools.PosTaggerAnnotator;
+import org.cleartk.opennlp.tools.SentenceAnnotator;
+import org.cleartk.snowball.DefaultSnowballStemmer;
 import org.cleartk.timeml.event.EventAspectAnnotator;
 import org.cleartk.timeml.event.EventClassAnnotator;
 import org.cleartk.timeml.event.EventModalityAnnotator;
 import org.cleartk.timeml.event.EventPolarityAnnotator;
 import org.cleartk.timeml.event.EventTenseAnnotator;
 import org.cleartk.timeml.tlink.TemporalLinkEventToDocumentCreationTimeAnnotator;
-import org.cleartk.token.stem.snowball.DefaultSnowballStemmer;
 import org.cleartk.token.tokenizer.TokenAnnotator;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.google.common.collect.Maps;
@@ -158,7 +159,8 @@ public class EvaluationOfClearTKEventPro
 
     Map<String, AnnotationStatistics<String>> statsMap = new HashMap<String, AnnotationStatistics<String>>();
     statsMap.put(DOC_TIME_REL, new AnnotationStatistics<String>());
-    for (JCas jCas : new JCasIterable(collectionReader, aggregateBuilder.createAggregate())) {
+    for (Iterator<JCas> casIter = new JCasIterator(collectionReader, aggregateBuilder.createAggregate()); casIter.hasNext();) {
+      JCas jCas = casIter.next();
       JCas goldView = jCas.getView(GOLD_VIEW_NAME);
       JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
       String text = goldView.getDocumentText();

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java Tue Sep 16 19:57:19 2014
@@ -27,21 +27,21 @@ import java.util.logging.Level;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.component.NoOpAnnotator;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+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.eval.AnnotationStatistics;
-import org.cleartk.syntax.opennlp.ParserAnnotator;
-import org.cleartk.syntax.opennlp.PosTaggerAnnotator;
-import org.cleartk.syntax.opennlp.SentenceAnnotator;
+import org.cleartk.opennlp.tools.ParserAnnotator;
+import org.cleartk.opennlp.tools.PosTaggerAnnotator;
+import org.cleartk.opennlp.tools.SentenceAnnotator;
+import org.cleartk.snowball.DefaultSnowballStemmer;
 import org.cleartk.timeml.event.EventAnnotator;
 import org.cleartk.timeml.type.Event;
-import org.cleartk.token.stem.snowball.DefaultSnowballStemmer;
 import org.cleartk.token.tokenizer.TokenAnnotator;
-import org.uimafit.component.NoOpAnnotator;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 
@@ -87,7 +87,7 @@ public class EvaluationOfClearTKEventSpa
   protected AnalysisEngineDescription getDataWriterDescription(File directory)
       throws ResourceInitializationException {
     // not training a model - just using the ClearTK one
-    return AnalysisEngineFactory.createPrimitiveDescription(NoOpAnnotator.class);
+    return AnalysisEngineFactory.createEngineDescription(NoOpAnnotator.class);
   }
 
   @Override

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java Tue Sep 16 19:57:19 2014
@@ -21,6 +21,7 @@ package org.apache.ctakes.temporal.eval;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Iterator;
 import java.util.List;
 
 import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
@@ -34,11 +35,16 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.cleartk.eval.AnnotationStatistics;
-import org.cleartk.syntax.opennlp.ParserAnnotator;
-import org.cleartk.syntax.opennlp.PosTaggerAnnotator;
-import org.cleartk.syntax.opennlp.SentenceAnnotator;
+import org.cleartk.opennlp.tools.ParserAnnotator;
+import org.cleartk.opennlp.tools.PosTaggerAnnotator;
+import org.cleartk.opennlp.tools.SentenceAnnotator;
+import org.cleartk.snowball.DefaultSnowballStemmer;
 import org.cleartk.timeml.event.EventAspectAnnotator;
 import org.cleartk.timeml.event.EventClassAnnotator;
 import org.cleartk.timeml.event.EventModalityAnnotator;
@@ -47,12 +53,7 @@ import org.cleartk.timeml.event.EventTen
 import org.cleartk.timeml.time.TimeTypeAnnotator;
 import org.cleartk.timeml.tlink.TemporalLinkEventToSameSentenceTimeAnnotator;
 import org.cleartk.timeml.tlink.TemporalLinkEventToSubordinatedEventAnnotator;
-import org.cleartk.token.stem.snowball.DefaultSnowballStemmer;
 import org.cleartk.token.tokenizer.TokenAnnotator;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 import com.google.common.base.Function;
 import com.lexicalscope.jewel.cli.CliFactory;
@@ -136,7 +137,7 @@ public class EvaluationOfClearTKRelation
       CollectionReader collectionReader, File directory) throws Exception {
     AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
     aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class));
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
         RemoveCrossSentenceRelations.class,
         RemoveCrossSentenceRelations.PARAM_SENTENCE_VIEW,
         CAS.NAME_DEFAULT_SOFA,
@@ -144,13 +145,13 @@ public class EvaluationOfClearTKRelation
         GOLD_VIEW_NAME));
     if(!this.doEventEvent){
       aggregateBuilder.add(
-          AnalysisEngineFactory.createPrimitiveDescription(RemoveEventEventRelations.class),
+          AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class),
           CAS.NAME_DEFAULT_SOFA,
           GOLD_VIEW_NAME);
     }
     if(!this.doEventTime){
       aggregateBuilder.add(
-          AnalysisEngineFactory.createPrimitiveDescription(PreserveEventEventRelations.class),
+          AnalysisEngineFactory.createEngineDescription(PreserveEventEventRelations.class),
           CAS.NAME_DEFAULT_SOFA,
           GOLD_VIEW_NAME);
     }
@@ -187,7 +188,8 @@ public class EvaluationOfClearTKRelation
     };
     Function<BinaryTextRelation, String> getOutcome = AnnotationStatistics.annotationToFeatureValue("category");
     AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
-    for (JCas jCas : new JCasIterable(collectionReader, aggregateBuilder.createAggregate())) {
+    for (Iterator<JCas> casIter = new JCasIterator(collectionReader, aggregateBuilder.createAggregate()); casIter.hasNext();) {
+      JCas jCas = casIter.next();
       JCas goldView = jCas.getView(GOLD_VIEW_NAME);
       JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
       Collection<BinaryTextRelation> goldRelations = JCasUtil.select(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java Tue Sep 16 19:57:19 2014
@@ -28,20 +28,20 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.TimeMention;
 import org.apache.ctakes.typesystem.type.textspan.Segment;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.component.NoOpAnnotator;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+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.eval.AnnotationStatistics;
-import org.cleartk.syntax.opennlp.PosTaggerAnnotator;
-import org.cleartk.syntax.opennlp.SentenceAnnotator;
+import org.cleartk.opennlp.tools.PosTaggerAnnotator;
+import org.cleartk.opennlp.tools.SentenceAnnotator;
+import org.cleartk.snowball.DefaultSnowballStemmer;
 import org.cleartk.timeml.time.TimeAnnotator;
 import org.cleartk.timeml.type.Time;
-import org.cleartk.token.stem.snowball.DefaultSnowballStemmer;
 import org.cleartk.token.tokenizer.TokenAnnotator;
-import org.uimafit.component.NoOpAnnotator;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 
@@ -88,7 +88,7 @@ public class EvaluationOfClearTKTimeSpan
   protected AnalysisEngineDescription getDataWriterDescription(File directory)
       throws ResourceInitializationException {
     // not training a model - just using the ClearTK one
-    return AnalysisEngineFactory.createPrimitiveDescription(NoOpAnnotator.class);
+    return AnalysisEngineFactory.createEngineDescription(NoOpAnnotator.class);
   }
 
   @Override



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