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From tm...@apache.org
Subject svn commit: r1625365 [2/10] - 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-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java Tue Sep 16 19:57:19 2014
@@ -73,6 +73,17 @@ import org.apache.uima.cas.CASException;
 import org.apache.uima.cas.Feature;
 import org.apache.uima.cas.text.AnnotationIndex;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+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.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.ConfigurationParameterFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.CasIOUtil;
+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;
@@ -80,31 +91,20 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.uima.util.CasCopier;
 import org.apache.uima.util.FileUtils;
-import org.cleartk.classifier.DataWriter;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.transform.InstanceDataWriter;
-import org.cleartk.classifier.feature.transform.InstanceStream;
-import org.cleartk.classifier.jar.DefaultDataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.cleartk.classifier.jar.JarClassifierBuilder;
-import org.cleartk.classifier.libsvm.LIBSVMStringOutcomeDataWriter;
 import org.cleartk.eval.Evaluation_ImplBase;
-//import org.cleartk.ml.libsvm.tk.TKLIBSVMStringOutcomeDataWriter;
+import org.cleartk.ml.DataWriter;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.InstanceDataWriter;
+import org.cleartk.ml.feature.transform.InstanceStream;
+import org.cleartk.ml.jar.DefaultDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.jar.JarClassifierBuilder;
+import org.cleartk.ml.libsvm.LibSvmStringOutcomeDataWriter;
+//import org.cleartk.ml.libsvm.tk.TKLibSvmStringOutcomeDataWriter;
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 import org.kohsuke.args4j.spi.BooleanOptionHandler;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.component.NoOpAnnotator;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
 
 import com.google.common.base.Objects;
 import com.google.common.collect.Lists;
@@ -362,7 +362,7 @@ private static Logger logger = Logger.ge
 
     // determine the type of classifier to be trained
 //    Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = DefaultMaxentDataWriterFactory.class;
-//    Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = DefaultMultiClassLIBSVMDataWriterFactory.class;
+//    Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = DefaultMultiClassLibSvmDataWriterFactory.class;
     
     // TODO Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = DefaultDataWriterFactory.class;
     //
@@ -392,10 +392,10 @@ private static Logger logger = Logger.ge
     }
     Class<? extends DataWriter<String>> dw = null;
     if(options.featConfig == FEATURE_CONFIG.STK || options.featConfig == FEATURE_CONFIG.PTK){ 
-//        dw = TKLIBSVMStringOutcomeDataWriter.class;
+//        dw = TKLibSvmStringOutcomeDataWriter.class;
       throw new UnsupportedOperationException("This requires cleartk-2.0 which");
     }
-    dw = LIBSVMStringOutcomeDataWriter.class;
+    dw = LibSvmStringOutcomeDataWriter.class;
     
     AssertionEvaluation evaluation = new AssertionEvaluation(
         modelsDir,
@@ -406,7 +406,7 @@ private static Logger logger = Logger.ge
         kernelParams
 //        "-t",
 //        "0",
-//       TKLIBSVMStringOutcomeDataWriter.class,
+//       TKLibSvmStringOutcomeDataWriter.class,
 //        "-c",
 //        "1"
 //        "-t",
@@ -627,7 +627,7 @@ public static void printScore(Map<String
     for (int i = 0; i < paths.length; ++i) {
       paths[i] = items.get(i).getPath();
     }
-    return CollectionReaderFactory.createCollectionReader(
+    return CollectionReaderFactory.createReader(
         XMIReader.class,
         TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(),
         XMIReader.PARAM_FILES,
@@ -663,32 +663,32 @@ public static void printScore(Map<String
   public void train(CollectionReader collectionReader, File directory) throws Exception {
     AggregateBuilder builder = new AggregateBuilder();
     
-    //builder.add(AnalysisEngineFactory.createPrimitiveDescription(ReplaceCTakesEntityMentionsAndModifiersWithGold.class));
+    //builder.add(AnalysisEngineFactory.createEngineDescription(ReplaceCTakesEntityMentionsAndModifiersWithGold.class));
 
 //    AnalysisEngineDescription assertionDescription = AssertionCleartkAnalysisEngine.getDescription(
 //        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
-//        //MultiClassLIBSVMDataWriterFactory.class.getName(),
+//        //MultiClassLibSvmDataWriterFactory.class.getName(),
 //        MaxentStringOutcomeDataWriter.class.getName(),
 //        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
 //        directory.getPath());
 //    builder.add(assertionDescription);
     
-    AnalysisEngineDescription documentIdPrinterAnnotator = AnalysisEngineFactory.createPrimitiveDescription(DocumentIdPrinterAnalysisEngine.class);
+    AnalysisEngineDescription documentIdPrinterAnnotator = AnalysisEngineFactory.createEngineDescription(DocumentIdPrinterAnalysisEngine.class);
     builder.add(documentIdPrinterAnnotator);
     
-    AnalysisEngineDescription goldCopierIdentifiedAnnotsAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
+    AnalysisEngineDescription goldCopierIdentifiedAnnotsAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
     builder.add(goldCopierIdentifiedAnnotsAnnotator);
     
-    AnalysisEngineDescription goldCopierSupportingAnnotsAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceSupportingAnnotationsSystemToGoldCopier.class);
+    AnalysisEngineDescription goldCopierSupportingAnnotsAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceSupportingAnnotationsSystemToGoldCopier.class);
     builder.add(goldCopierSupportingAnnotsAnnotator);
     
-    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
+    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceAnnotationsSystemAssertionClearer.class);
     builder.add(assertionAttributeClearerAnnotator);
     
 //    String generalSectionRegexFileUri =
 //        "org/mitre/medfacts/zoner/section_regex.xml";
 //    AnalysisEngineDescription zonerAnnotator =
-//        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+//        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
 //            ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
 //            generalSectionRegexFileUri
 //            );
@@ -697,7 +697,7 @@ public static void printScore(Map<String
 //    String mayoSectionRegexFileUri =
 //        "org/mitre/medfacts/uima/mayo_sections.xml";
 //    AnalysisEngineDescription mayoZonerAnnotator =
-//        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+//        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
 //            ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
 //            mayoSectionRegexFileUri
 //            );
@@ -710,7 +710,7 @@ public static void printScore(Map<String
 //
 //    
 //    AnalysisEngineDescription cuePhraseLookupAnnotator =
-//        AnalysisEngineFactory.createAnalysisEngineDescription("org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator");
+//        AnalysisEngineFactory.createEngineDescription("org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator");
 //    builder.add(cuePhraseLookupAnnotator);
 
     // Set up Feature Selection parameters
@@ -721,16 +721,16 @@ public static void printScore(Map<String
     }
     
     // Add each assertion Analysis Engine to the pipeline!
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(AlternateCuePhraseAnnotator.class, new Object[]{}));
+    builder.add(AnalysisEngineFactory.createEngineDescription(AlternateCuePhraseAnnotator.class, new Object[]{}));
     
     if (!options.ignorePolarity)
     {
     	AnalysisEngineDescription polarityAnnotator;
     	if (options.useYtexNegation) {
-    		 polarityAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription(YTEX_NEGATION_DESCRIPTOR);
+    		 polarityAnnotator = AnalysisEngineFactory.createEngineDescription(YTEX_NEGATION_DESCRIPTOR);
     	} else {
     		if (options.feda) {
-    			polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityFedaCleartkAnalysisEngine.class);
+    			polarityAnnotator = AnalysisEngineFactory.createEngineDescription(PolarityFedaCleartkAnalysisEngine.class);
 
       			ConfigurationParameterFactory.addConfigurationParameters(
         				polarityAnnotator,
@@ -739,7 +739,7 @@ public static void printScore(Map<String
         				);
     		} else {
     			// default: cleartk-based polarity, no domain adaptation
-    			polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    			polarityAnnotator = AnalysisEngineFactory.createEngineDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
       		}
     		ConfigurationParameterFactory.addConfigurationParameters(
     				polarityAnnotator,
@@ -764,7 +764,7 @@ public static void printScore(Map<String
 
     if (!options.ignoreConditional)
     {
-	    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+	    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createEngineDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
 	    ConfigurationParameterFactory.addConfigurationParameters(
 	        conditionalAnnotator,
 	        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -785,7 +785,7 @@ public static void printScore(Map<String
 
     if (!options.ignoreUncertainty)
     {
-	    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+	    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createEngineDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
 	    ConfigurationParameterFactory.addConfigurationParameters(
 	        uncertaintyAnnotator,
 	        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -808,7 +808,7 @@ public static void printScore(Map<String
 
     if (!options.ignoreSubject)
     {
-	    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createPrimitiveDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+	    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createEngineDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
 	    ConfigurationParameterFactory.addConfigurationParameters(
 	        subjectAnnotator,
 	        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -829,7 +829,7 @@ public static void printScore(Map<String
 
     if (!options.ignoreGeneric)
     {
-		AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createPrimitiveDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+		AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createEngineDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
 		    genericAnnotator,
 		    AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -850,7 +850,7 @@ public static void printScore(Map<String
     
     // 2/20/13 srh adding
     if (!options.ignoreHistory) {
-    	AnalysisEngineDescription historyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(HistoryCleartkAnalysisEngine.class);
+    	AnalysisEngineDescription historyAnnotator = AnalysisEngineFactory.createEngineDescription(HistoryCleartkAnalysisEngine.class);
     	ConfigurationParameterFactory.addConfigurationParameters(
     			historyAnnotator,
     			AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -870,7 +870,7 @@ public static void printScore(Map<String
     }
 
 /*
-    AnalysisEngineDescription classifierAnnotator = AnalysisEngineFactory.createPrimitiveDescription(
+    AnalysisEngineDescription classifierAnnotator = AnalysisEngineFactory.createEngineDescription(
         this.classifierAnnotatorClass,
         this.additionalParameters);
     ConfigurationParameterFactory.addConfigurationParameters(
@@ -898,7 +898,7 @@ public static void printScore(Map<String
   @Override
   protected Map<String, AnnotationStatisticsCompact> test(CollectionReader collectionReader, File directory)
       throws Exception {
-//    AnalysisEngine classifierAnnotator = AnalysisEngineFactory.createPrimitive(AssertionCleartkAnalysisEngine.getDescription(
+//    AnalysisEngine classifierAnnotator = AnalysisEngineFactory.createEngine(AssertionCleartkAnalysisEngine.getDescription(
 //        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
 //        new File(directory, "model.jar").getPath()));
 
@@ -906,10 +906,10 @@ public static void printScore(Map<String
     
     // directory is such as /cTAKES/workspaces/Apache-cTAKES-trunk/ctakes/ctakes-assertion/sharp_data/model/eval.model
     
-    AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
+    AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
     builder.add(goldCopierAnnotator);
     
-    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
+    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceAnnotationsSystemAssertionClearer.class);
     builder.add(assertionAttributeClearerAnnotator);
     
     if ( options.noCleartk ) {
@@ -926,31 +926,18 @@ public static void printScore(Map<String
     	TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescription();
     	
         AnalysisEngineDescription noOp =
-    		AnalysisEngineFactory.createPrimitiveDescription(
+    		AnalysisEngineFactory.createEngineDescription(
 	            NoOpAnnotator.class,
 	            typeSystemDescription);
     	builder.add(noOp);
     	
         AnalysisEngineDescription mergeGold =
-    		AnalysisEngineFactory.createPrimitiveDescription(org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.class, typeSystemDescription);
-    	builder.add(mergeGold);
-    	
-    } else if (evaluationOutputDirectory!=null)  {
-        AnalysisEngineDescription xwriter =
-    		AnalysisEngineFactory.createPrimitiveDescription(
-	            XWriter.class,
-	            AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION,
-	            XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-	            evaluationOutputDirectory,
-	            XWriter.PARAM_XML_SCHEME_NAME,
-	            XWriter.XMI,
-	            XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-	            CtakesFileNamer.class.getName());
-        builder.add(xwriter);
+    		AnalysisEngineFactory.createEngineDescription(org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.class, typeSystemDescription);
+    	builder.add(mergeGold); 	
     }
     
-    //SimplePipeline.runPipeline(collectionReader,  builder.createAggregateDescription());
-    //AnalysisEngineDescription aggregateDescription = builder.createAggregateDescription();
+    //SimplePipeline.runPipeline(collectionReader,  builder.createEngineDescription());
+    //AnalysisEngineDescription aggregateDescription = builder.createEngineDescription();
     
     AnalysisEngine aggregate = builder.createAggregate();
     
@@ -994,7 +981,8 @@ public static void printScore(Map<String
     }
 
     // run on existing output that has both system (or instance gathering) and gold
-    for (JCas jCas : new JCasIterable(collectionReader, aggregate)) {
+    for (Iterator<JCas> casIter = new JCasIterator(collectionReader, aggregate); casIter.hasNext();) {
+      JCas jCas = casIter.next();
     	
 //    	printViewNames("Views found by JCasIterable:", jCas);
     	
@@ -1037,6 +1025,11 @@ public static void printScore(Map<String
       systemEntitiesAndEvents.addAll(systemEvents);
 //      System.out.format("system entities: %d%nsystem events: %d%n%n", systemEntities.size(), systemEvents.size());
       
+      if (evaluationOutputDirectory != null){
+          String sourceFileName = DocumentIDAnnotationUtil.getDocumentID(jCas);
+          CasIOUtil.writeXmi(jCas, new File(evaluationOutputDirectory, sourceFileName + ".xmi"));
+      }
+      
       if (!options.ignorePolarity)
       {
 	      polarityStats.add(goldEntitiesAndEvents, systemEntitiesAndEvents,
@@ -1155,7 +1148,7 @@ public static void printScore(Map<String
 
 
 	      // now write in the libsvm format
-//	      LIBLINEARStringOutcomeDataWriter dataWriter = new LIBLINEARStringOutcomeDataWriter(directory);
+//	      LibLinearStringOutcomeDataWriter dataWriter = new LibLinearStringOutcomeDataWriter(directory);
 		  Constructor c = this.dataWriterClass.getConstructor(File.class);
 	      DataWriter dataWriter = (DataWriter) c.newInstance(directory);
 	      
@@ -1501,7 +1494,7 @@ public static class HashableAnnotation i
 private void addExternalAttributeAnnotatorsToAggregate(AggregateBuilder builder)
 		throws UIMAException, IOException {
 	// RUN ALL THE OLD (non-ClearTK) CLASSIFIERS
-	AnalysisEngineDescription oldAssertionAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription("desc/assertionAnalysisEngine"); 
+	AnalysisEngineDescription oldAssertionAnnotator = AnalysisEngineFactory.createEngineDescription("desc/assertionAnalysisEngine"); 
 	ConfigurationParameterFactory.addConfigurationParameters(
 			oldAssertionAnnotator,
 			AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -1509,7 +1502,7 @@ private void addExternalAttributeAnnotat
 	);
 	builder.add(oldAssertionAnnotator);
 
-	AnalysisEngineDescription oldConversionAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription("desc/conceptConverterAnalysisEngine"); 
+	AnalysisEngineDescription oldConversionAnnotator = AnalysisEngineFactory.createEngineDescription("desc/conceptConverterAnalysisEngine"); 
 	ConfigurationParameterFactory.addConfigurationParameters(
 			oldConversionAnnotator,
 			AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -1517,7 +1510,7 @@ private void addExternalAttributeAnnotat
 	);
 	builder.add(oldConversionAnnotator);
 
-	AnalysisEngineDescription oldSubjectAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription("desc/SubjectAttributeAnalysisEngine"); 
+	AnalysisEngineDescription oldSubjectAnnotator = AnalysisEngineFactory.createEngineDescription("desc/SubjectAttributeAnalysisEngine"); 
 	ConfigurationParameterFactory.addConfigurationParameters(
 			oldSubjectAnnotator,
 			AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -1525,7 +1518,7 @@ private void addExternalAttributeAnnotat
 	);
 	builder.add(oldSubjectAnnotator);
 
-	AnalysisEngineDescription oldGenericAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription("desc/GenericAttributeAnalysisEngine"); 
+	AnalysisEngineDescription oldGenericAnnotator = AnalysisEngineFactory.createEngineDescription("desc/GenericAttributeAnalysisEngine"); 
 	ConfigurationParameterFactory.addConfigurationParameters(
 			oldGenericAnnotator,
 			AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -1538,14 +1531,14 @@ private void addCleartkAttributeAnnotato
 		AggregateBuilder builder) throws UIMAException, IOException,
 		ResourceInitializationException {
 //	AnalysisEngineDescription cuePhraseLookupAnnotator =
-//		AnalysisEngineFactory.createAnalysisEngineDescription("org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator");
+//		AnalysisEngineFactory.createEngineDescription("org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator");
 //	builder.add(cuePhraseLookupAnnotator);
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(AlternateCuePhraseAnnotator.class, new Object[]{}));
+    builder.add(AnalysisEngineFactory.createEngineDescription(AlternateCuePhraseAnnotator.class, new Object[]{}));
 
 //	String generalSectionRegexFileUri =
 //		"org/mitre/medfacts/zoner/section_regex.xml";
 //	AnalysisEngineDescription zonerAnnotator =
-//		AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+//		AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
 //				ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
 //				generalSectionRegexFileUri
 //		);
@@ -1554,7 +1547,7 @@ private void addCleartkAttributeAnnotato
 //	String mayoSectionRegexFileUri =
 //		"org/mitre/medfacts/uima/mayo_sections.xml";
 //	AnalysisEngineDescription mayoZonerAnnotator =
-//		AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+//		AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
 //				ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
 //				mayoSectionRegexFileUri
 //		);
@@ -1565,11 +1558,11 @@ private void addCleartkAttributeAnnotato
 	{
 		AnalysisEngineDescription polarityAnnotator;
     	if (options.useYtexNegation) {
-    		polarityAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription(YTEX_NEGATION_DESCRIPTOR);
+    		polarityAnnotator = AnalysisEngineFactory.createEngineDescription(YTEX_NEGATION_DESCRIPTOR);
     		builder.add(polarityAnnotator);
     	} else {
     		if (options.feda) {
-    			polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityFedaCleartkAnalysisEngine.class);
+    			polarityAnnotator = AnalysisEngineFactory.createEngineDescription(PolarityFedaCleartkAnalysisEngine.class);
 
       			ConfigurationParameterFactory.addConfigurationParameters(
         				polarityAnnotator,
@@ -1578,7 +1571,7 @@ private void addCleartkAttributeAnnotato
         				);
     		} else {
     			// default: cleartk-based polarity, no domain adaptation
-    			polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    			polarityAnnotator = AnalysisEngineFactory.createEngineDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
       		}
     		ConfigurationParameterFactory.addConfigurationParameters(
     				polarityAnnotator,
@@ -1596,7 +1589,7 @@ private void addCleartkAttributeAnnotato
 	// Add the rest of the ClearTk classifiers
 	if (!options.ignoreConditional)
 	{
-		AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+		AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createEngineDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
 				conditionalAnnotator,
 				AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -1609,7 +1602,7 @@ private void addCleartkAttributeAnnotato
 
 	if (!options.ignoreUncertainty)
 	{
-		AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+		AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createEngineDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
 				uncertaintyAnnotator,
 				AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -1622,7 +1615,7 @@ private void addCleartkAttributeAnnotato
 
 	if (!options.ignoreSubject)
 	{
-		AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createPrimitiveDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+		AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createEngineDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
 				subjectAnnotator,
 				AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -1635,7 +1628,7 @@ private void addCleartkAttributeAnnotato
 
 	if (!options.ignoreGeneric)
 	{
-		AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createPrimitiveDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+		AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createEngineDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
 		ConfigurationParameterFactory.addConfigurationParameters(
 				genericAnnotator,
 				AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -1647,7 +1640,7 @@ private void addCleartkAttributeAnnotato
 	}
 	
 	if(!options.ignoreHistory){
-		AnalysisEngineDescription historyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(HistoryCleartkAnalysisEngine.class);
+		AnalysisEngineDescription historyAnnotator = AnalysisEngineFactory.createEngineDescription(HistoryCleartkAnalysisEngine.class);
 		ConfigurationParameterFactory.addConfigurationParameters(
 				historyAnnotator,
 				AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java Tue Sep 16 19:57:19 2014
@@ -44,14 +44,14 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.metadata.ResourceMetaData;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.uima.util.CasCreationUtils;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.component.NoOpAnnotator;
-import org.uimafit.component.ViewCreatorAnnotator;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.component.NoOpAnnotator;
+import org.apache.uima.fit.component.ViewCreatorAnnotator;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * 
@@ -95,7 +95,7 @@ public class MergeGoldViewFromOneCasInto
 		viewWithPreexistingGoldAnnotations = getViewWithGoldAnnotations(correspondingCasThatHasGoldAnnotations);
 
 		// Create the new view in the current CAS so the current CAS has both views
-		// org.uimafit.util.ViewNames.INITIAL_VIEW; // org.uimafit.examples.experiment.pos.ViewNames
+		// org.apache.uima.fit.util.ViewNames.INITIAL_VIEW; // org.apache.uima.fit.examples.experiment.pos.ViewNames
 
 
 		//newGoldView = jCas.createView(AssertionEvaluation.GOLD_VIEW_NAME);
@@ -231,14 +231,14 @@ public class MergeGoldViewFromOneCasInto
 			// uimafit find available type systems on classpath
 			TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescription();
 
-			AnalysisEngineDescription noOp = AnalysisEngineFactory.createPrimitiveDescription(NoOpAnnotator.class, typeSystemDescription);
+			AnalysisEngineDescription noOp = AnalysisEngineFactory.createEngineDescription(NoOpAnnotator.class, typeSystemDescription);
 			builder.add(noOp);
 		} catch (ResourceInitializationException e) {
 			throw new RuntimeException(e);
 		}
 
 		try {
-			//SimplePipeline.runPipeline(cr, builder.createAggregate());
+			//SimplePipeline.runPipeline(cr, builder.createEngine());
 			AnalysisEngine engine = builder.createAggregate();
 
 			final List<ResourceMetaData> metaData = new ArrayList<ResourceMetaData>();
@@ -272,7 +272,7 @@ public class MergeGoldViewFromOneCasInto
 		    for (int i = 0; i < paths.length; ++i) {
 		      paths[i] = items.get(i).getPath();
 		    }
-		    return CollectionReaderFactory.createCollectionReader(
+		    return CollectionReaderFactory.createReader(
 		        XMIReader.class,
 		        TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(),
 		        XMIReader.PARAM_FILES,

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java Tue Sep 16 19:57:19 2014
@@ -20,11 +20,9 @@ package org.apache.ctakes.assertion.eval
 
 import java.io.File;
 
-import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
-import org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.transform.InstanceDataWriter;
-import org.cleartk.classifier.feature.transform.InstanceStream;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.transform.InstanceDataWriter;
+import org.cleartk.ml.feature.transform.InstanceStream;
 
 public class TestFeatureSelection {
 

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

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java Tue Sep 16 19:57:19 2014
@@ -34,9 +34,9 @@ import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-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.util.JCasUtil;
 
 public class AlternateCuePhraseAnnotator extends JCasAnnotator_ImplBase {
 

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -34,7 +34,6 @@ import org.apache.ctakes.assertion.attri
 import org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction;
 import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.ctakes.typesystem.type.constants.CONST;
-import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
@@ -46,22 +45,22 @@ import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CASException;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.ConfigurationParameterFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.TreeFeature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-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.feature.function.FeatureFunctionExtractor;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.TreeFeature;
+import org.cleartk.ml.feature.extractor.CleartkExtractor;
+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.FeatureFunctionExtractor;
 
 import scala.actors.threadpool.Arrays;
 //import org.chboston.cnlp.ctakes.relationextractor.ae.ModifierExtractorAnnotator;
@@ -162,14 +161,14 @@ public abstract class AssertionCleartkAn
   
 	
 	
-//private SimpleFeatureExtractor tokenFeatureExtractor;
+//private FeatureExtractor1 tokenFeatureExtractor;
 //  protected List<ContextExtractor<IdentifiedAnnotation>> contextFeatureExtractors;
 //  protected List<ContextExtractor<BaseToken>> tokenContextFeatureExtractors;
   protected List<CleartkExtractor> contextFeatureExtractors;
   protected List<CleartkExtractor> tokenContextFeatureExtractors;
   protected List<CleartkExtractor> tokenCleartkExtractors;
-  protected List<SimpleFeatureExtractor> entityFeatureExtractors;
-  protected List<SimpleFeatureExtractor> entityTreeExtractors;
+  protected List<FeatureExtractor1> entityFeatureExtractors;
+  protected List<FeatureExtractor1> entityTreeExtractors;
   protected CleartkExtractor cuePhraseInWindowExtractor;
   
   protected List<FeatureFunctionExtractor> featureFunctionExtractors;
@@ -216,7 +215,7 @@ public abstract class AssertionCleartkAn
     // a list of feature extractors that require only the token:
     // the stem of the word, the text of the word itself, plus
     // features created from the word text like character ngrams
-    this.entityFeatureExtractors = new ArrayList<SimpleFeatureExtractor>();
+    this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
     
     // a list of feature extractors that require the token and the sentence
 //    this.contextFeatureExtractors = new ArrayList<CleartkExtractor>();
@@ -263,8 +262,8 @@ public abstract class AssertionCleartkAn
     //List<Feature> features = new ArrayList<Feature>();
     //ConllDependencyNode node1 = findAnnotationHead(jCas, arg1);
 
-    CombinedExtractor baseExtractorCuePhraseCategory =
-        new CombinedExtractor
+    CombinedExtractor1 baseExtractorCuePhraseCategory =
+        new CombinedExtractor1
           (
            new CoveredTextExtractor(),
            new TypePathExtractor(AssertionCuePhraseAnnotation.class, "cuePhrase"),
@@ -290,7 +289,7 @@ public abstract class AssertionCleartkAn
     	// set up FeatureFunction for all the laggard, non-Extractor features
     	ffDomainAdaptor = new FedaFeatureFunction( new ArrayList<String>(new HashSet<String>(fileToDomain.values())) );
     }
-    entityTreeExtractors =  new ArrayList<SimpleFeatureExtractor>();
+    entityTreeExtractors =  new ArrayList<FeatureExtractor1>();
   }
 
   @Override
@@ -461,12 +460,12 @@ public abstract class AssertionCleartkAn
       
       // only extract these features if not doing domain adaptation
       if (ffDomainAdaptor==null) {
-    	  for (SimpleFeatureExtractor extractor : this.entityFeatureExtractors) {
+    	  for (FeatureExtractor1 extractor : this.entityFeatureExtractors) {
     		  instance.addAll(extractor.extract(jCas, entityOrEventMention));
     	  }
       }
 
-      for (SimpleFeatureExtractor extractor : this.entityTreeExtractors) {
+      for (FeatureExtractor1 extractor : this.entityTreeExtractors) {
         instance.addAll(extractor.extract(jCas, entityOrEventMention));
       }
 
@@ -541,7 +540,7 @@ public abstract class AssertionCleartkAn
 
   public static AnalysisEngineDescription getDescription(Object... additionalConfiguration)
 	      throws ResourceInitializationException {
-	    AnalysisEngineDescription desc = AnalysisEngineFactory.createPrimitiveDescription(AssertionCleartkAnalysisEngine.class);
+	    AnalysisEngineDescription desc = AnalysisEngineFactory.createEngineDescription(AssertionCleartkAnalysisEngine.class);
 	    if (additionalConfiguration.length > 0) {
 	      ConfigurationParameterFactory.addConfigurationParameters(desc, additionalConfiguration);
 	    }

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionComponents.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionComponents.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionComponents.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionComponents.java Tue Sep 16 19:57:19 2014
@@ -19,7 +19,7 @@
 package org.apache.ctakes.assertion.medfacts.cleartk;
 
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
 
 /**
  * <br>

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionSampleFeatureGenerator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionSampleFeatureGenerator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionSampleFeatureGenerator.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionSampleFeatureGenerator.java Tue Sep 16 19:57:19 2014
@@ -18,19 +18,10 @@
  */
 package org.apache.ctakes.assertion.medfacts.cleartk;
 
-import java.util.Arrays;
-
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.feature.extractor.simple.CoveredTextExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SpannedTextExtractor;
-import org.cleartk.classifier.feature.proliferate.CapitalTypeProliferator;
-import org.cleartk.classifier.feature.proliferate.CharacterNGramProliferator;
-import org.cleartk.classifier.feature.proliferate.LowerCaseProliferator;
-import org.cleartk.classifier.feature.proliferate.NumericTypeProliferator;
-import org.cleartk.classifier.feature.proliferate.ProliferatingExtractor;
 import org.cleartk.util.cr.XReader;
-import org.uimafit.factory.CollectionReaderFactory;
 
 public class AssertionSampleFeatureGenerator
 {
@@ -50,7 +41,7 @@ public class AssertionSampleFeatureGener
 	{
 		String filename = "/work/medfacts/sharp/data/2012-10-16_full_data_set_updated/Seed_Corpus/clean_dirs/splits/official/train";
 		
-	    CollectionReader reader = CollectionReaderFactory.createCollectionReader(
+	    CollectionReader reader = CollectionReaderFactory.createReader(
 		        XReader.class,
 		        XReader.PARAM_ROOT_FILE,
 		        filename,

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -19,17 +19,15 @@
 package org.apache.ctakes.assertion.medfacts.cleartk;
 
 import java.io.File;
-import java.io.IOException;
 import java.net.URI;
 
-import org.apache.uima.UimaContext;
-import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Instance;
-
 import org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection;
 import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.cleartk.ml.Instance;
 
 public class ConditionalCleartkAnalysisEngine extends
 		AssertionCleartkAnalysisEngine {

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java Tue Sep 16 19:57:19 2014
@@ -21,34 +21,29 @@ package org.apache.ctakes.assertion.medf
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
-import java.io.IOException;
-import java.net.URI;
 import java.net.URISyntaxException;
 
 import org.apache.ctakes.assertion.eval.AssertionEvaluation;
 import org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer;
 import org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier;
 import org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier;
-import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.ConfigurationParameterFactory;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.DataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.cleartk.classifier.opennlp.DefaultMaxentDataWriterFactory;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.DataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.opennlp.maxent.MaxentStringOutcomeDataWriter;
 import org.mitre.medfacts.uima.ZoneAnnotator;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.xml.sax.SAXException;
 
 public class CreateAssertionDescriptor
 {
   
-  public static final Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = DefaultMaxentDataWriterFactory.class;
+//  public static final Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = MaxentStringOutcomeDataWriter.class;
 
   /**
    * @param args
@@ -77,19 +72,19 @@ public class CreateAssertionDescriptor
     AggregateBuilder builder = new AggregateBuilder();
 
 ////
-    AnalysisEngineDescription goldCopierIdentifiedAnnotsAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
+    AnalysisEngineDescription goldCopierIdentifiedAnnotsAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
     builder.add(goldCopierIdentifiedAnnotsAnnotator);
     
-    AnalysisEngineDescription goldCopierSupportingAnnotsAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceSupportingAnnotationsSystemToGoldCopier.class);
+    AnalysisEngineDescription goldCopierSupportingAnnotsAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceSupportingAnnotationsSystemToGoldCopier.class);
     builder.add(goldCopierSupportingAnnotsAnnotator);
     
-    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
+    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceAnnotationsSystemAssertionClearer.class);
     builder.add(assertionAttributeClearerAnnotator);
     
     String generalSectionRegexFileUri =
         "org/mitre/medfacts/zoner/section_regex.xml";
     AnalysisEngineDescription zonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             generalSectionRegexFileUri
             );
@@ -98,68 +93,68 @@ public class CreateAssertionDescriptor
     String mayoSectionRegexFileUri =
         "org/mitre/medfacts/uima/mayo_sections.xml";
     AnalysisEngineDescription mayoZonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             mayoSectionRegexFileUri
             );
     builder.add(mayoZonerAnnotator);
     
     
-    AnalysisEngineDescription polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription polarityAnnotator = AnalysisEngineFactory.createEngineDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         polarityAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
         AssertionEvaluation.GOLD_VIEW_NAME,
-        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
-        this.dataWriterFactoryClass.getName(),
+//        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
+//        this.dataWriterFactoryClass.getName(),
         DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
         new File(directory, "polarity").getPath()
         );
     builder.add(polarityAnnotator);
 
-    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createEngineDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         conditionalAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
         AssertionEvaluation.GOLD_VIEW_NAME,
-        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
-        this.dataWriterFactoryClass.getName(),
+//        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
+//        this.dataWriterFactoryClass.getName(),
         DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
         new File(directory, "conditional").getPath()
         );
     builder.add(conditionalAnnotator);
 
-    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createEngineDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         uncertaintyAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
         AssertionEvaluation.GOLD_VIEW_NAME,
-        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
-        this.dataWriterFactoryClass.getName(),
+//        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
+//        this.dataWriterFactoryClass.getName(),
         DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
         new File(directory, "uncertainty").getPath()
         );
     builder.add(uncertaintyAnnotator);
 
-    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createPrimitiveDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createEngineDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         subjectAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
         AssertionEvaluation.GOLD_VIEW_NAME,
         CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
-        this.dataWriterFactoryClass.getName(),
-        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
+//        this.dataWriterFactoryClass.getName(),
+//        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
         new File(directory, "subject").getPath()
         );
     builder.add(subjectAnnotator);
 
-    AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createPrimitiveDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createEngineDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         genericAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
         AssertionEvaluation.GOLD_VIEW_NAME,
-        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
-        this.dataWriterFactoryClass.getName(),
+//        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
+//        this.dataWriterFactoryClass.getName(),
         DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
         new File(directory, "generic").getPath()
         );
@@ -182,16 +177,16 @@ public class CreateAssertionDescriptor
     AggregateBuilder builder = new AggregateBuilder();
 
 ////
-    AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
+    AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
     builder.add(goldCopierAnnotator);
     
-    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
+    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceAnnotationsSystemAssertionClearer.class);
     builder.add(assertionAttributeClearerAnnotator);
     
     String generalSectionRegexFileUri =
       "org/mitre/medfacts/zoner/section_regex.xml";
     AnalysisEngineDescription zonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             generalSectionRegexFileUri
             );
@@ -200,13 +195,13 @@ public class CreateAssertionDescriptor
     String mayoSectionRegexFileUri =
       "org/mitre/medfacts/uima/mayo_sections.xml";
     AnalysisEngineDescription mayoZonerAnnotator =
-        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
+        AnalysisEngineFactory.createEngineDescription(ZoneAnnotator.class,
             ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
             mayoSectionRegexFileUri
             );
     builder.add(mayoZonerAnnotator);
     
-    AnalysisEngineDescription polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription polarityAnnotator = AnalysisEngineFactory.createEngineDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         polarityAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -216,7 +211,7 @@ public class CreateAssertionDescriptor
         );
     builder.add(polarityAnnotator);
 
-    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createEngineDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         conditionalAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -226,7 +221,7 @@ public class CreateAssertionDescriptor
         );
     builder.add(conditionalAnnotator);
   
-    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createEngineDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         uncertaintyAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -236,7 +231,7 @@ public class CreateAssertionDescriptor
         );
     builder.add(uncertaintyAnnotator);
 
-    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createPrimitiveDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createEngineDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         subjectAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -246,7 +241,7 @@ public class CreateAssertionDescriptor
         );
     builder.add(subjectAnnotator);
 
-    AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createPrimitiveDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
+    AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createEngineDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
     ConfigurationParameterFactory.addConfigurationParameters(
         genericAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
@@ -257,13 +252,11 @@ public class CreateAssertionDescriptor
     builder.add(genericAnnotator);
 
     AnalysisEngineDescription xwriter =
-    AnalysisEngineFactory.createPrimitiveDescription(
-          XWriter.class,
+    AnalysisEngineFactory.createEngineDescription(
+          XmiWriterCasConsumerCtakes.class,
           AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION,
-          XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-          testOutputDirectory,
-          XWriter.PARAM_XML_SCHEME_NAME,
-          XWriter.XMI);
+          XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+          testOutputDirectory);
     builder.add(xwriter);
 ////
     

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -19,7 +19,6 @@
 package org.apache.ctakes.assertion.medfacts.cleartk;
 
 import java.io.File;
-import java.io.IOException;
 import java.net.URI;
 import java.util.ArrayList;
 
@@ -31,9 +30,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 public class GenericCleartkAnalysisEngine extends
 		AssertionCleartkAnalysisEngine {
@@ -67,7 +65,7 @@ public class GenericCleartkAnalysisEngin
 //				new CleartkExtractor(
 //						IdentifiedAnnotation.class, new GenericFeaturesExtractor()) );
 		if(this.entityFeatureExtractors == null){
-			this.entityFeatureExtractors = new ArrayList<SimpleFeatureExtractor>();
+			this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
 		}
 		this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/generic.txt"));
 		this.entityFeatureExtractors.add(new GenericFeaturesExtractor());

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -19,7 +19,6 @@
 package org.apache.ctakes.assertion.medfacts.cleartk;
 
 import java.io.File;
-import java.io.IOException;
 import java.net.URI;
 import java.util.ArrayList;
 
@@ -32,9 +31,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 public class HistoryCleartkAnalysisEngine extends
 		AssertionCleartkAnalysisEngine {
@@ -69,7 +67,7 @@ public class HistoryCleartkAnalysisEngin
 //						IdentifiedAnnotation.class, new HistoryFeaturesExtractor()) );
 //		
 		if(this.entityFeatureExtractors == null){
-			this.entityFeatureExtractors = new ArrayList<SimpleFeatureExtractor>();
+			this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
 		}
 		this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/history.txt"));
 		this.entityFeatureExtractors.add(new HistoryFeaturesExtractor());

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -35,11 +35,11 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.uimafit.factory.AnalysisEngineFactory;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
 
 
 public class PolarityCleartkAnalysisEngine extends AssertionCleartkAnalysisEngine {
@@ -54,7 +54,7 @@ public class PolarityCleartkAnalysisEngi
 		probabilityOfKeepingADefaultExample = 1.0; //0.1;
 		
 		if(this.entityFeatureExtractors == null){
-			this.entityFeatureExtractors = new ArrayList<SimpleFeatureExtractor>();
+			this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
 		}
 		
 		// polarity keyword list:
@@ -154,7 +154,7 @@ public class PolarityCleartkAnalysisEngi
 	}
 	
 	public static AnalysisEngineDescription createAnnotatorDescription(String modelPath) throws ResourceInitializationException {
-	  return AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class,
+	  return AnalysisEngineFactory.createEngineDescription(PolarityCleartkAnalysisEngine.class,
 	      AssertionCleartkAnalysisEngine.PARAM_FEATURE_CONFIG,
         AssertionCleartkAnalysisEngine.FEATURE_CONFIG.DEP_REGEX,
 	      GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -21,27 +21,21 @@ package org.apache.ctakes.assertion.medf
 import java.io.File;
 import java.net.URI;
 import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
 
 import org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection;
 import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
 import org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveLeftFragmentExtractor;
-import org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveRightFragmentExtractor;
 import org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor;
 import org.apache.ctakes.assertion.medfacts.cleartk.extractors.ExtractorListFeatureFunctionConverter;
-import org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction;
 import org.apache.ctakes.assertion.medfacts.cleartk.extractors.NegationDependencyFeatureExtractor;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.cleartk.classifier.feature.function.FeatureFunctionExtractor;
-import org.uimafit.descriptor.ConfigurationParameter;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+import org.cleartk.ml.feature.function.FeatureFunctionExtractor;
 
 
 public class PolarityFedaCleartkAnalysisEngine extends PolarityCleartkAnalysisEngine {
@@ -55,7 +49,7 @@ public class PolarityFedaCleartkAnalysis
 		probabilityOfKeepingADefaultExample = 1.0; //0.1;
 
 		if(this.entityFeatureExtractors == null){
-			this.entityFeatureExtractors = new ArrayList<SimpleFeatureExtractor>();
+			this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
 		}
 		this.entityFeatureExtractors.add(new NegationDependencyFeatureExtractor());
 		this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/polarity.txt"));

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -19,9 +19,7 @@
 package org.apache.ctakes.assertion.medfacts.cleartk;
 
 import java.io.File;
-import java.io.IOException;
 import java.net.URI;
-import java.util.ArrayList;
 
 import org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor;
 import org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection;
@@ -31,9 +29,7 @@ import org.apache.log4j.Level;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.ContextExtractor;
+import org.cleartk.ml.Instance;
 
 public class SubjectCleartkAnalysisEngine extends
 		AssertionCleartkAnalysisEngine {

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java Tue Sep 16 19:57:19 2014
@@ -19,7 +19,6 @@
 package org.apache.ctakes.assertion.medfacts.cleartk;
 
 import java.io.File;
-import java.util.Locale;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -32,35 +31,25 @@ import org.apache.commons.cli.ParseExcep
 import org.apache.ctakes.assertion.eval.AssertionEvaluation;
 import org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer;
 import org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
 import org.apache.log4j.Logger;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
-
 import org.apache.uima.collection.CollectionReader;
-import org.apache.uima.collection.CollectionReaderDescription;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.CleartkAnnotatorDescriptionFactory;
-import org.cleartk.classifier.DataWriterFactory;
-import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
-import org.cleartk.classifier.opennlp.DefaultMaxentDataWriterFactory;
-import org.cleartk.classifier.opennlp.MaxentDataWriter;
-import org.cleartk.classifier.opennlp.MaxentStringOutcomeDataWriter;
-import org.cleartk.util.cr.FilesCollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.ConfigurationParameterFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.testing.util.HideOutput;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.DataWriterFactory;
+import org.cleartk.ml.jar.DefaultDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.opennlp.maxent.MaxentStringOutcomeDataWriter;
 import org.cleartk.util.cr.XReader;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.testing.util.HideOutput;
 //import org.junit.Test;
-import org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine;
-import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 //import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.cleartk.classifier.jar.DefaultDataWriterFactory;
 
 
 public class TrainAssertionModel {
@@ -87,11 +76,11 @@ public class TrainAssertionModel {
 		try {
 		CollectionReader reader = FilesCollectionReader.getCollectionReader(trainDir);
 		AggregateBuilder builder = new AggregateBuilder();
-		//builder.add(AnalysisEngineFactory.createAnalysisEngineDescription("desc/AssertionMiniPipelineAnalysisEngine.xml", null));
-		//builder.add(AnalysisEngineFactory.createPrimitiveDescription(IdentifiedAnnotation.class));
-		//builder.add(AnalysisEngineFactory.createAnalysisEngineDescription("edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation"));
+		//builder.add(AnalysisEngineFactory.createEngineDescription("desc/AssertionMiniPipelineAnalysisEngine.xml", null));
+		//builder.add(AnalysisEngineFactory.createEngineDescription(IdentifiedAnnotation.class));
+		//builder.add(AnalysisEngineFactory.createEngineDescription("edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation"));
 	    builder.add(AssertionCleartkAnalysisEngine.getWriterDescription(outputDir));
-	    SimplePipeline.runPipeline(reader, builder.createAggregateDescription());
+	    SimplePipeline.runPipeline(reader, builder.createEngineDescription());
 	    org.cleartk.classifier.jar.Train.main(outputDir);
 		} catch (Exception e) {
 			System.err.println("Exception: " + e);
@@ -113,7 +102,7 @@ public class TrainAssertionModel {
     String evaluationOutputDataDirectory = "/work/medfacts/cleartk/data/eval2.output";
 
     String maxentModelOutputDirectory = modelOutputDirectory + "/maxent";
-    AnalysisEngineDescription dataWriter = AnalysisEngineFactory.createPrimitiveDescription(
+    AnalysisEngineDescription dataWriter = AnalysisEngineFactory.createEngineDescription(
         AssertionCleartkAnalysisEngine.class,
         AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION,
         DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
@@ -233,7 +222,7 @@ public class TrainAssertionModel {
     String maxentModelOutputDirectory = modelDirectory + "/maxent";
     try
     {
-      AnalysisEngineDescription dataWriter = AnalysisEngineFactory.createPrimitiveDescription(
+      AnalysisEngineDescription dataWriter = AnalysisEngineFactory.createEngineDescription(
           AssertionCleartkAnalysisEngine.class,
           AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION,
           DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
@@ -266,13 +255,13 @@ public class TrainAssertionModel {
       String... trainingArgs) throws Exception
   {
     
-    CollectionReader trainingCollectionReader = CollectionReaderFactory.createCollectionReader(
+    CollectionReader trainingCollectionReader = CollectionReaderFactory.createReader(
         XReader.class,
         XReader.PARAM_ROOT_FILE,
         trainingDataInputDirectory,
         XReader.PARAM_XML_SCHEME,
         XReader.XMI);
-    CollectionReader evaluationCollectionReader = CollectionReaderFactory.createCollectionReader(
+    CollectionReader evaluationCollectionReader = CollectionReaderFactory.createReader(
         XReader.class,
         XReader.PARAM_ROOT_FILE,
         decodingInputDirectory,
@@ -282,15 +271,15 @@ public class TrainAssertionModel {
     
     AggregateBuilder trainingBuilder = new AggregateBuilder();
     
-    AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
+    AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
     trainingBuilder.add(goldCopierAnnotator);
     
-    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
+    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceAnnotationsSystemAssertionClearer.class);
     trainingBuilder.add(assertionAttributeClearerAnnotator);
     
-    Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = DefaultMaxentDataWriterFactory.class;
+//    Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = DefaultMaxentDataWriterFactory.class;
     AnalysisEngineDescription trainingAssertionAnnotator = 
-        AnalysisEngineFactory.createPrimitiveDescription(
+        AnalysisEngineFactory.createEngineDescription(
             AssertionCleartkAnalysisEngine.class,
             AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION
             );
@@ -298,8 +287,8 @@ public class TrainAssertionModel {
         trainingAssertionAnnotator,
         AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
         AssertionEvaluation.GOLD_VIEW_NAME,
-        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
-        dataWriterFactoryClass.getName(),
+//        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
+//        dataWriterFactoryClass.getName(),
         DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
         modelOutputDirectory
         );
@@ -336,20 +325,20 @@ public class TrainAssertionModel {
 
     HideOutput hider = new HideOutput();
     logger.info("starting training...");
-    org.cleartk.classifier.jar.Train.main(args);
+    org.cleartk.ml.jar.Train.main(args);
     logger.info("finished training.");
     hider.restoreOutput();
 
     AggregateBuilder decodingBuilder = new AggregateBuilder();
     
-    //AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
+    //AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
     decodingBuilder.add(goldCopierAnnotator);
     
-    //AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
+    //AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createEngineDescription(ReferenceAnnotationsSystemAssertionClearer.class);
     decodingBuilder.add(assertionAttributeClearerAnnotator);
     
     AnalysisEngineDescription decodingAssertionAnnotator =
-      AnalysisEngineFactory.createPrimitiveDescription(
+      AnalysisEngineFactory.createEngineDescription(
         AssertionCleartkAnalysisEngine.class,
         AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION
         );
@@ -362,12 +351,12 @@ public class TrainAssertionModel {
         );
     decodingBuilder.add(decodingAssertionAnnotator);
     
-    //SimplePipeline.runPipeline(collectionReader,  builder.createAggregateDescription());
+    //SimplePipeline.runPipeline(collectionReader,  builder.createEngineDescription());
     AnalysisEngineDescription decodingAggregateDescription = decodingBuilder.createAggregateDescription();
     
     
     
-//    AnalysisEngineDescription taggerDescription = AnalysisEngineFactory.createPrimitiveDescription(
+//    AnalysisEngineDescription taggerDescription = AnalysisEngineFactory.createEngineDescription(
 //        AssertionCleartkAnalysisEngine.class,
 //        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
 //        //AssertionComponents.TYPE_SYSTEM_DESCRIPTION,
@@ -381,13 +370,11 @@ public class TrainAssertionModel {
 //        DefaultSnowballStemmer.getDescription("English"),
         //taggerDescription,
         decodingAggregateDescription,
-        AnalysisEngineFactory.createPrimitiveDescription(
-            XWriter.class,
+        AnalysisEngineFactory.createEngineDescription(
+            XmiWriterCasConsumerCtakes.class,
             AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION,
-            XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-            decodingOutputDirectory,
-            XWriter.PARAM_XML_SCHEME_NAME,
-            XWriter.XMI));
+            XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+            decodingOutputDirectory));
     logger.info("finished decoding.");
 
   }

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -19,7 +19,6 @@
 package org.apache.ctakes.assertion.medfacts.cleartk;
 
 import java.io.File;
-import java.io.IOException;
 import java.net.URI;
 import java.util.ArrayList;
 
@@ -31,8 +30,8 @@ import org.apache.ctakes.typesystem.type
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Instance;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Instance;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 public class UncertaintyCleartkAnalysisEngine extends AssertionCleartkAnalysisEngine {
 
@@ -41,7 +40,7 @@ public class UncertaintyCleartkAnalysisE
 		super.initialize(context);
 		probabilityOfKeepingADefaultExample = 0.1;
 		if(this.entityFeatureExtractors == null){
-			this.entityFeatureExtractors = new ArrayList<SimpleFeatureExtractor>();
+			this.entityFeatureExtractors = new ArrayList<FeatureExtractor1>();
 		}
 		this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/uncertainty.txt"));
 		this.entityFeatureExtractors.add(new AboveLeftFragmentExtractor("ALUncertainty", "org/apache/ctakes/assertion/models/sharpUncertaintyFrags.txt"));

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveLeftFragmentExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveLeftFragmentExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveLeftFragmentExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveLeftFragmentExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,7 +27,7 @@ import org.apache.ctakes.constituency.pa
 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.ml.Feature;
 import org.cleartk.util.CleartkInitializationException;
 
 public class AboveLeftFragmentExtractor extends TreeFragmentFeatureExtractor {

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveRightFragmentExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveRightFragmentExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveRightFragmentExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveRightFragmentExtractor.java Tue Sep 16 19:57:19 2014
@@ -27,7 +27,7 @@ import org.apache.ctakes.constituency.pa
 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.ml.Feature;
 import org.cleartk.util.CleartkInitializationException;
 
 public class AboveRightFragmentExtractor extends TreeFragmentFeatureExtractor {



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