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From c...@apache.org
Subject svn commit: r1594677 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
Date Wed, 14 May 2014 19:13:53 GMT
Author: clin
Date: Wed May 14 19:13:53 2014
New Revision: 1594677

URL: http://svn.apache.org/r1594677
Log:
Add an evaluation code to evaluate event-time and event-event relations at the same time.

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
  (with props)

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java?rev=1594677&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
(added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
Wed May 14 19:13:53 2014
@@ -0,0 +1,1089 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.temporal.eval;
+
+import java.io.File;
+import java.net.URI;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Deque;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
+import org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator;
+import org.apache.ctakes.temporal.ae.EventEventRelationAnnotator;
+import org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator;
+import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
+import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations.RemoveGoldAttributes;
+import org.apache.ctakes.temporal.utils.AnnotationIdCollection;
+import org.apache.ctakes.temporal.utils.TLinkTypeArray2;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+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.cas.CAS;
+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.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.util.FileUtils;
+import org.cleartk.classifier.jar.JarClassifierBuilder;
+import org.cleartk.classifier.libsvm.LIBSVMStringOutcomeDataWriter;
+import org.cleartk.classifier.tksvmlight.TKSVMlightStringOutcomeDataWriter;
+import org.cleartk.classifier.tksvmlight.model.CompositeKernel.ComboOperator;
+import org.cleartk.eval.AnnotationStatistics;
+import org.cleartk.util.ViewURIUtil;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.descriptor.ConfigurationParameter;
+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 com.google.common.base.Function;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.common.collect.Multimap;
+import com.google.common.collect.Sets;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+public class EvaluationOfTemporalRelations extends
+EvaluationOfTemporalRelations_ImplBase{
+	static interface TempRelOptions extends Evaluation_ImplBase.Options{
+		@Option
+		public boolean getPrintFormattedRelations();
+
+		@Option
+		public boolean getBaseline();
+
+		@Option
+		public boolean getClosure();
+
+		@Option
+		public boolean getUseTmp();
+
+		@Option
+		public boolean getUseGoldAttributes();
+		
+		@Option
+		public boolean getSkipTrain();
+	}
+
+	//  protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
+	//  protected static float DEFAULT_DOWNSAMPLE = 1.0f;
+	//  private static double DEFAULT_SVM_C = 1.0;
+	//  private static double DEFAULT_SVM_G = 1.0;
+	//  private static double DEFAULT_TK = 0.5;
+	//  private static double DEFAULT_LAMBDA = 0.5;
+
+	//  defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk",
+	//  		  DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
+	protected static ParameterSettings flatParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS,
DEFAULT_DOWNSAMPLE, "linear",
+			10.0, 1.0, "linear", ComboOperator.VECTOR_ONLY, DEFAULT_TK, DEFAULT_LAMBDA);
+	protected static ParameterSettings allBagsParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS,
DEFAULT_DOWNSAMPLE, "tk", 
+			100.0, 0.1, "radial basis function", ComboOperator.SUM, 0.5, 0.5);
+	protected static ParameterSettings allParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS,
DEFAULT_DOWNSAMPLE, "tk",
+			10.0, 1.0, "polynomial", ComboOperator.SUM, 0.1, 0.5);  // (0.3, 0.4 for tklibsvm)
+	protected static ParameterSettings ftParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS,
DEFAULT_DOWNSAMPLE, "tk", 
+			1.0, 0.1, "radial basis function", ComboOperator.SUM, 0.5, 0.5);
+
+	public static void main(String[] args) throws Exception {
+		TempRelOptions options = CliFactory.parseArguments(TempRelOptions.class, args);
+    List<Integer> trainItems = null;
+    List<Integer> devItems = null;
+    List<Integer> testItems = null;
+    
+    List<Integer> patientSets = options.getPatients().getList();
+    if(options.getXMLFormat() == XMLFormat.I2B2){
+      trainItems = I2B2Data.getTrainPatientSets(options.getXMLDirectory());
+      devItems = I2B2Data.getDevPatientSets(options.getXMLDirectory());
+      testItems = I2B2Data.getTestPatientSets(options.getXMLDirectory());
+    }else{
+      trainItems = THYMEData.getTrainPatientSets(patientSets);
+      devItems = THYMEData.getDevPatientSets(patientSets);
+      testItems = THYMEData.getTestPatientSets(patientSets);
+    }
+		ParameterSettings params = allParams;
+
+		//    possibleParams.add(defaultParams);
+
+		//    for(ParameterSettings params : possibleParams){
+		try{
+			File workingDir = new File("target/eval/temporal-relations/");
+			if(!workingDir.exists()) workingDir.mkdirs();
+			if(options.getUseTmp()){
+				File tempModelDir = File.createTempFile("temporal", null, workingDir);
+				tempModelDir.delete();
+				tempModelDir.mkdir();
+				workingDir = tempModelDir;
+			}
+			EvaluationOfTemporalRelations evaluation = new EvaluationOfTemporalRelations(
+					workingDir,
+					options.getRawTextDirectory(),
+					options.getXMLDirectory(),
+					options.getXMLFormat(),
+					options.getXMIDirectory(),
+					options.getTreebankDirectory(),
+					options.getClosure(),
+					options.getPrintErrors(),
+					options.getPrintFormattedRelations(),
+					options.getBaseline(),
+					options.getUseGoldAttributes(),
+					options.getKernelParams(),
+					params);
+			evaluation.prepareXMIsFor(patientSets);
+	    if(options.getI2B2Output()!=null) evaluation.setI2B2Output(options.getI2B2Output() +
"/temporal-relations/event-time");
+			List<Integer> training = trainItems;
+			List<Integer> testing = null;
+			if(options.getTest()){
+				training.addAll(devItems);
+				testing = testItems;
+			}else{
+				testing = devItems;
+			}
+			evaluation.skipTrain = options.getSkipTrain();
+			params.stats = evaluation.trainAndTest(training, testing);//training);//
+			//      System.err.println(options.getKernelParams() == null ? params : options.getKernelParams());
+			System.err.println(params.stats);
+			if(options.getUseTmp()){
+				// won't work because it's not empty. should we be concerned with this or is it responsibility
of 
+				// person invoking the tmp flag?
+				FileUtils.deleteRecursive(workingDir);
+			}
+		}catch(ResourceInitializationException e){
+			System.err.println("Error with parameter settings: " + params);
+			e.printStackTrace();
+		}
+	}
+
+	//  private ParameterSettings params;
+	private boolean baseline;
+	protected boolean useClosure;
+	protected boolean useGoldAttributes;
+	protected boolean skipTrain=false;
+	//  protected boolean printRelations = false;
+
+	public EvaluationOfTemporalRelations(
+			File baseDirectory,
+			File rawTextDirectory,
+			File xmlDirectory,
+			XMLFormat xmlFormat,
+			File xmiDirectory,
+			File treebankDirectory,
+			boolean useClosure,
+			boolean printErrors,
+			boolean printRelations,
+			boolean baseline,
+			boolean useGoldAttributes,
+			String kernelParams,
+			ParameterSettings params){
+		super(
+				baseDirectory,
+				rawTextDirectory,
+				xmlDirectory,
+				xmlFormat,
+				xmiDirectory,
+				treebankDirectory,
+				printErrors,
+				printRelations,
+				params);
+		this.params = params;
+		this.useClosure = useClosure;
+		this.printErrors = printErrors;
+		this.printRelations = printRelations;
+		this.useGoldAttributes = useGoldAttributes;
+		this.baseline = baseline;
+		this.kernelParams = kernelParams == null ? null : kernelParams.split(" ");
+	}
+
+	//  public EvaluationOfTemporalRelations(File baseDirectory, File rawTextDirectory,
+	//      File knowtatorXMLDirectory, File xmiDirectory) {
+	//
+	//    super(baseDirectory, rawTextDirectory, knowtatorXMLDirectory, xmiDirectory, null);
+	//    this.params = defaultParams;
+	//    this.printErrors = false;
+	//  }
+
+	@Override
+	protected void train(CollectionReader collectionReader, File directory) throws Exception
{
+		//	  if(this.baseline) return;
+	  if(this.skipTrain) return;
+		AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+		aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class,
BinaryTextRelation.class));
+		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveCrossSentenceRelations.class));
+		if(!this.useGoldAttributes){
+			aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveGoldAttributes.class));
+		}
+		if (this.useClosure) {
+			aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddClosure.class));//aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class));
+//			aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddContain2Overlap.class));
+			//			aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveBeforeAndOnRelations.class));
+		}
+//		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveNonContainsRelations.class));
+		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddFlippedOverlap.class));//add
flipped overlap instances to training data
+		
+//		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEventEventRelations.class));
+		aggregateBuilder.add(EventTimeRelationAnnotator.createDataWriterDescription(
+				//                LIBSVMStringOutcomeDataWriter.class,
+				TKSVMlightStringOutcomeDataWriter.class,
+				//        TKLIBSVMStringOutcomeDataWriter.class,
+				//        SVMlightStringOutcomeDataWriter.class,        
+				new File(directory,"event-time"),
+				params.probabilityOfKeepingANegativeExample));
+		aggregateBuilder.add(EventEventRelationAnnotator.createDataWriterDescription(
+				LIBSVMStringOutcomeDataWriter.class,
+				new File(directory,"event-event"), 
+				params.probabilityOfKeepingANegativeExample));
+		SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
+		String[] optArray;
+
+		if(this.kernelParams == null){
+			ArrayList<String> svmOptions = new ArrayList<>();
+			svmOptions.add("-c"); svmOptions.add(""+params.svmCost);        // svm cost
+			svmOptions.add("-t"); svmOptions.add(""+params.svmKernelIndex); // kernel index 
+			svmOptions.add("-d"); svmOptions.add("3");                      // degree parameter for
polynomial
+			svmOptions.add("-g"); svmOptions.add(""+params.svmGamma);
+			if(params.svmKernelIndex==ParameterSettings.SVM_KERNELS.indexOf("tk")){
+				svmOptions.add("-S"); svmOptions.add(""+params.secondKernelIndex);   // second kernel
index (similar to -t) for composite kernel
+				String comboFlag = (params.comboOperator == ComboOperator.SUM ? "+" : params.comboOperator
== ComboOperator.PRODUCT ? "*" : params.comboOperator == ComboOperator.TREE_ONLY ? "T" : "V");
+				svmOptions.add("-C"); svmOptions.add(comboFlag);
+				svmOptions.add("-L"); svmOptions.add(""+params.lambda);
+				svmOptions.add("-T"); svmOptions.add(""+params.tkWeight);
+				svmOptions.add("-N"); svmOptions.add("3");   // normalize trees and features
+			}
+			optArray = svmOptions.toArray(new String[]{});
+		}else{
+			optArray = this.kernelParams;
+			for(int i = 0; i < optArray.length; i+=2){
+				optArray[i] = "-" + optArray[i];
+			}
+		}
+
+		//    HideOutput hider = new HideOutput();
+		JarClassifierBuilder.trainAndPackage(new File(directory,"event-time"), optArray);
+		JarClassifierBuilder.trainAndPackage(new File(directory,"event-event"), "-h","0","-c",
"1000");
+		//    hider.restoreOutput();
+		//    hider.close();
+	}
+
+	@Override
+	protected AnnotationStatistics<String> test(CollectionReader collectionReader, File
directory)
+			throws Exception {
+		AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+		aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class));
+		
+		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+				RemoveCrossSentenceRelations.class,
+				RemoveCrossSentenceRelations.PARAM_SENTENCE_VIEW,
+				CAS.NAME_DEFAULT_SOFA,
+				RemoveCrossSentenceRelations.PARAM_RELATION_VIEW,
+				GOLD_VIEW_NAME));
+		if (this.useClosure) {
+			aggregateBuilder.add(
+					AnalysisEngineFactory.createPrimitiveDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
+					CAS.NAME_DEFAULT_SOFA,
+					GOLD_VIEW_NAME);
+					
+//			aggregateBuilder.add(
+//					AnalysisEngineFactory.createPrimitiveDescription(AddContain2Overlap.class),
+//					CAS.NAME_DEFAULT_SOFA,
+//					GOLD_VIEW_NAME);
+			//			aggregateBuilder.add(
+			//					AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveBeforeAndOnRelations.class),
+			//					CAS.NAME_DEFAULT_SOFA,
+			//					GOLD_VIEW_NAME);
+		}
+		
+//		aggregateBuilder.add(
+//				AnalysisEngineFactory.createPrimitiveDescription(RemoveNonContainsRelations.class,
+//						RemoveNonContainsRelations.PARAM_RELATION_VIEW,
+//						GOLD_VIEW_NAME));
+//		aggregateBuilder.add(
+//				AnalysisEngineFactory.createPrimitiveDescription(RemoveEventEventRelations.class),
+//				CAS.NAME_DEFAULT_SOFA,
+//				GOLD_VIEW_NAME);
+
+		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveRelations.class));
+		aggregateBuilder.add(this.baseline ? RecallBaselineEventTimeRelationAnnotator.createAnnotatorDescription(directory)
:
+			EventTimeRelationAnnotator.createAnnotatorDescription(new File(directory,"event-time")));
+		aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(new File(directory,"event-event")));
+    if(this.i2b2Output != null){
+      aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(WriteI2B2XML.class,
WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
+    }
+		if (this.useClosure) {//add closure for system output
+			aggregateBuilder.add(
+					AnalysisEngineFactory.createPrimitiveDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
+					GOLD_VIEW_NAME,
+					CAS.NAME_DEFAULT_SOFA
+					);
+		}
+		Function<BinaryTextRelation, ?> getSpan = new Function<BinaryTextRelation, HashableArguments>()
{
+			public HashableArguments apply(BinaryTextRelation relation) {
+				return new HashableArguments(relation);
+			}
+		};
+		Function<BinaryTextRelation, String> getOutcome = AnnotationStatistics.annotationToFeatureValue("category");
+
+		AnnotationStatistics<String> stats = new AnnotationStatistics<>();
+		JCasIterable jcasIter =new JCasIterable(collectionReader, aggregateBuilder.createAggregate());
+		JCas jCas = null;
+		while(jcasIter.hasNext()) {
+			jCas = jcasIter.next();
+			JCas goldView = jCas.getView(GOLD_VIEW_NAME);
+			JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+			Collection<BinaryTextRelation> goldRelations = JCasUtil.select(
+					goldView,
+					BinaryTextRelation.class);
+			Collection<BinaryTextRelation> systemRelations = JCasUtil.select(
+					systemView,
+					BinaryTextRelation.class);
+
+			//newly add
+//			systemRelations = removeNonGoldRelations(systemRelations, goldRelations);//for removing
non-gold pairs
+			systemRelations = correctArgOrder(systemRelations, goldRelations);//change the argument
order of "OVERLAP" relation, if the order is flipped
+			//find duplicates in gold relations:
+			//			Collection<BinaryTextRelation> duplicateGoldRelations = getDuplicateRelations(goldRelations,
getSpan);
+			//			if(!duplicateGoldRelations.isEmpty()){
+			//				System.err.println("******Duplicate gold relations in : " + ViewURIUtil.getURI(jCas).toString());
+			//				for (BinaryTextRelation rel : duplicateGoldRelations){
+			//					System.err.println("Duplicate : "+ formatRelation(rel));
+			//				}
+			//			}
+			//end newly add
+
+			stats.add(goldRelations, systemRelations, getSpan, getOutcome);
+			if(this.printRelations){
+				URI uri = ViewURIUtil.getURI(jCas);
+				String[] path = uri.getPath().split("/");
+				printRelationAnnotations(path[path.length - 1], systemRelations);
+			}
+			if(this.printErrors){
+				Map<HashableArguments, BinaryTextRelation> goldMap = Maps.newHashMap();
+				for (BinaryTextRelation relation : goldRelations) {
+					goldMap.put(new HashableArguments(relation), relation);
+				}
+				Map<HashableArguments, BinaryTextRelation> systemMap = Maps.newHashMap();
+				for (BinaryTextRelation relation : systemRelations) {
+					systemMap.put(new HashableArguments(relation), relation);
+				}
+				Set<HashableArguments> all = Sets.union(goldMap.keySet(), systemMap.keySet());
+				List<HashableArguments> sorted = Lists.newArrayList(all);
+				Collections.sort(sorted);
+				for (HashableArguments key : sorted) {
+					BinaryTextRelation goldRelation = goldMap.get(key);
+					BinaryTextRelation systemRelation = systemMap.get(key);
+					if (goldRelation == null) {
+						System.out.println("System added: " + formatRelation(systemRelation));
+					} else if (systemRelation == null) {
+						System.out.println("System dropped: " + formatRelation(goldRelation));
+					} else if (!systemRelation.getCategory().equals(goldRelation.getCategory())) {
+						String label = systemRelation.getCategory();
+						System.out.printf("System labeled %s for %s\n", label, formatRelation(goldRelation));
+					} else{
+						System.out.println("Nailed it! " + formatRelation(systemRelation));
+					}
+				}
+			}
+		}
+		return stats;
+	}
+
+	/*
+  private static String formatRelation(BinaryTextRelation relation) {
+	  IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
+	  IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
+	  String text = arg1.getCAS().getDocumentText();
+	  int begin = Math.min(arg1.getBegin(), arg2.getBegin());
+	  int end = Math.max(arg1.getBegin(), arg2.getBegin());
+	  begin = Math.max(0, begin - 50);
+	  end = Math.min(text.length(), end + 50);
+	  return String.format(
+			  "%s(%s(type=%d), %s(type=%d)) in ...%s...",
+			  relation.getCategory(),
+			  arg1.getCoveredText(),
+			  arg1.getTypeID(),
+			  arg2.getCoveredText(),
+			  arg2.getTypeID(),
+			  text.substring(begin, end).replaceAll("[\r\n]", " "));
+  }
+
+  private static void printRelationAnnotations(String fileName, Collection<BinaryTextRelation>
relations) {
+
+	  for(BinaryTextRelation binaryTextRelation : relations) {
+
+		  Annotation arg1 = binaryTextRelation.getArg1().getArgument();
+		  Annotation arg2 = binaryTextRelation.getArg2().getArgument();
+
+		  String arg1Type = arg1.getClass().getSimpleName();
+		  String arg2Type = arg2.getClass().getSimpleName();
+
+		  int arg1Begin = arg1.getBegin();
+		  int arg1End = arg1.getEnd();
+		  int arg2Begin = arg2.getBegin();
+		  int arg2End = arg2.getEnd();
+
+		  String category = binaryTextRelation.getCategory();
+
+		  System.out.format("%s\t%s\t%s\t%d\t%d\t%s\t%d\t%d\n", 
+				  fileName, category, arg1Type, arg1Begin, arg1End, arg2Type, arg2Begin, arg2End);
+	  }
+  }
+	 */
+
+//		private static <SPAN_TYPE> Collection<BinaryTextRelation> removeNonGoldRelations(
+//				Collection<BinaryTextRelation> systemRelations,
+//				Collection<BinaryTextRelation> goldRelations, Function<BinaryTextRelation,
?> getSpan) {
+//			//remove non-gold pairs from system relations:
+//			Set<BinaryTextRelation> goodSys = Sets.newHashSet();
+//			Set<SPAN_TYPE> goldspans = new HashSet<SPAN_TYPE>();
+//			
+//			for (BinaryTextRelation relation : goldRelations) {
+//				goldspans.add(((SPAN_TYPE) getSpan.apply(relation)));			
+//			}
+//			
+//			for (BinaryTextRelation relation : systemRelations) {
+//				if (goldspans.contains(((SPAN_TYPE) getSpan.apply(relation)))) {
+//					goodSys.add(relation);
+//				}
+//			}
+//			
+//			return goodSys;
+//		}
+	
+	private static boolean matchSpan(Annotation arg1, Annotation arg2) {
+		boolean result = false;
+		result = arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd();
+		return result;
+	}
+	
+	private static Collection<BinaryTextRelation> correctArgOrder(
+			Collection<BinaryTextRelation> systemRelations,
+			Collection<BinaryTextRelation> goldRelations) {
+		Set<BinaryTextRelation> goodSys = Sets.newHashSet();
+
+		for(BinaryTextRelation sysrel : systemRelations){
+			Annotation sysArg1 = sysrel.getArg1().getArgument();
+			Annotation sysArg2 = sysrel.getArg2().getArgument();
+			for(BinaryTextRelation goldrel : goldRelations){
+				Annotation goldArg1 = goldrel.getArg1().getArgument();
+				Annotation goldArg2 = goldrel.getArg2().getArgument();
+				if (matchSpan(sysArg2, goldArg1) && matchSpan(sysArg1, goldArg2)){//the order
of system pair was flipped 
+					if(sysrel.getCategory().equals("OVERLAP")){ //if the relation is overlap, and the arg
order was flipped, then change back the order
+						RelationArgument tempArg = (RelationArgument) sysrel.getArg1().clone();
+						sysrel.setArg1((RelationArgument) sysrel.getArg2().clone());
+						sysrel.setArg2(tempArg);
+					}//for other types of relation, still maintain the type.
+					continue;
+				}
+			}
+			goodSys.add(sysrel);
+		}
+
+		return goodSys;
+	}
+
+
+//	@SuppressWarnings("unchecked")
+//	private static <SPAN> Collection<BinaryTextRelation> getDuplicateRelations(
+//			Collection<BinaryTextRelation> goldRelations,
+//			Function<BinaryTextRelation, ?> getSpan) {
+//		Set<BinaryTextRelation> duplicateRelations = Sets.newHashSet();
+//		//build a multimap that map gold span to gold relation
+//		Multimap<SPAN, BinaryTextRelation> spanToRelation = HashMultimap.create();
+//		for (BinaryTextRelation relation : goldRelations) {
+//			spanToRelation.put((SPAN) getSpan.apply(relation), relation);			
+//		}
+//		for (SPAN span: spanToRelation.keySet()){
+//			Collection<BinaryTextRelation> relations = spanToRelation.get(span);
+//			if(relations.size()>1){//if same span maps to multiple relations
+//				duplicateRelations.addAll(relations);
+//			}
+//		}
+//		return duplicateRelations;
+//	}
+
+//	private static Collection<BinaryTextRelation> removeNonGoldRelations(
+//			Collection<BinaryTextRelation> systemRelations, Collection<BinaryTextRelation>
goldRelations) {
+//		//remove non-gold pairs from system relations:
+//		Set<BinaryTextRelation> goodSys = Sets.newHashSet();
+//
+//		for(BinaryTextRelation sysrel : systemRelations){
+//			Annotation sysArg1 = sysrel.getArg1().getArgument();
+//			Annotation sysArg2 = sysrel.getArg2().getArgument();
+//			for(BinaryTextRelation goldrel : goldRelations){
+//				Annotation goldArg1 = goldrel.getArg1().getArgument();
+//				Annotation goldArg2 = goldrel.getArg2().getArgument();
+//				if(matchSpan(sysArg1, goldArg1) && matchSpan(sysArg2, goldArg2)){
+//					goodSys.add(sysrel);
+//					continue;
+//				}else if (matchSpan(sysArg2, goldArg1) && matchSpan(sysArg1, goldArg2)){//the
order of system pair was flipped 
+//					if(sysrel.getCategory().equals("OVERLAP")){ //if the relation is overlap, and the
arg order was flipped, then change back the order
+//						RelationArgument tempArg = (RelationArgument) sysrel.getArg1().clone();
+//						sysrel.setArg1((RelationArgument) sysrel.getArg2().clone());
+//						sysrel.setArg2(tempArg);
+//					}//for other types of relation, still maintain the type.
+//					goodSys.add(sysrel);
+//					continue;
+//				}
+//			}
+//		}
+//
+//		return goodSys;
+//	}
+
+
+	public static class RemoveEventEventRelations extends JCasAnnotator_ImplBase {
+		public static final String PARAM_RELATION_VIEW = "RelationView";
+		@ConfigurationParameter(name = PARAM_RELATION_VIEW)
+		private String relationViewName = CAS.NAME_DEFAULT_SOFA;
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			JCas relationView;
+			try {
+				relationView = jCas.getView(this.relationViewName);
+			} catch (CASException e) {
+				throw new AnalysisEngineProcessException(e);
+			}
+
+			for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(relationView, BinaryTextRelation.class))){
+				//	    	  if(relation.getCategory().equals("CONTAINS")){
+				RelationArgument arg1 = relation.getArg1();
+				RelationArgument arg2 = relation.getArg2();
+				if(arg1.getArgument() instanceof TimeMention && arg2.getArgument() instanceof
EventMention ||
+						arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof
TimeMention){
+					// these are the kind we keep.
+					continue;
+				}
+				//	    		  if(arg1.getArgument() instanceof EventMention && arg2.getArgument()
instanceof EventMention){
+				arg1.removeFromIndexes();
+				arg2.removeFromIndexes();
+				relation.removeFromIndexes();
+			}
+			//	      }
+
+		}
+	}
+
+	/*  public static class RemoveNonTLINKRelations extends JCasAnnotator_ImplBase {
+    @Override
+    public void process(JCas jCas) throws AnalysisEngineProcessException {
+      for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+          jCas,
+          BinaryTextRelation.class))) {
+        if (!(relation instanceof TemporalTextRelation)) {
+          relation.getArg1().removeFromIndexes();
+          relation.getArg2().removeFromIndexes();
+          relation.removeFromIndexes();
+        }
+      }
+    }
+  }*/
+
+	public static class RemoveCrossSentenceRelations extends JCasAnnotator_ImplBase {
+
+		public static final String PARAM_SENTENCE_VIEW = "SentenceView";
+
+		@ConfigurationParameter(name = PARAM_SENTENCE_VIEW)
+		private String sentenceViewName = CAS.NAME_DEFAULT_SOFA;
+
+		public static final String PARAM_RELATION_VIEW = "RelationView";
+
+		@ConfigurationParameter(name = PARAM_RELATION_VIEW)
+		private String relationViewName = CAS.NAME_DEFAULT_SOFA;
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			JCas sentenceView, relationView;
+			try {
+				sentenceView = jCas.getView(this.sentenceViewName);
+				relationView = jCas.getView(this.relationViewName);
+			} catch (CASException e) {
+				throw new AnalysisEngineProcessException(e);
+			}
+
+			// map events and times to the sentences that contain them
+			Map<IdentifiedAnnotation, Integer> sentenceIndex = Maps.newHashMap();
+			int index = -1;
+			for (Sentence sentence : JCasUtil.select(sentenceView, Sentence.class)) {
+				++index;
+				for (EventMention event : JCasUtil.selectCovered(relationView, EventMention.class, sentence))
{
+					sentenceIndex.put(event, index);
+				}
+				for (TimeMention time : JCasUtil.selectCovered(relationView, TimeMention.class, sentence))
{
+					sentenceIndex.put(time, index);
+				}
+			}
+
+			// remove any relations that are in different sentences.
+			for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+					relationView,
+					BinaryTextRelation.class))) {
+				Integer sent1 = sentenceIndex.get(relation.getArg1().getArgument());
+				Integer sent2 = sentenceIndex.get(relation.getArg2().getArgument());
+				if (sent1 == null || sent2 == null || !sent1.equals(sent2)) {
+					relation.getArg1().removeFromIndexes();
+					relation.getArg2().removeFromIndexes();
+					relation.removeFromIndexes();
+				}
+			}
+		}
+	}
+
+
+	public static class RemoveRelations extends JCasAnnotator_ImplBase {
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+					jCas,
+					BinaryTextRelation.class))) {
+				relation.getArg1().removeFromIndexes();
+				relation.getArg2().removeFromIndexes();
+				relation.removeFromIndexes();
+			}
+		}
+	}
+
+	/**
+	 * Holds a set of parameters for a relation extraction model
+	 */
+//	public static class ParameterSettings {
+//		public boolean classifyBothDirections;
+//
+//		public float probabilityOfKeepingANegativeExample;
+//
+//		public String svmKernel;
+//
+//		public int svmKernelIndex;
+//
+//		public double svmCost;
+//
+//		public double svmGamma;
+//
+//		public String secondKernel;
+//		public int secondKernelIndex;
+//		public CompositeKernel.ComboOperator comboOperator;
+//		public double tkWeight;
+//		public double lambda;
+//
+//		public AnnotationStatistics<String> stats;
+//
+//		static List<String> SVM_KERNELS = Arrays.asList(
+//				"linear",
+//				"polynomial",
+//				"radial basis function",
+//				"sigmoid",
+//				"user",
+//				"tk");
+//
+//		public ParameterSettings(
+//				boolean classifyBothDirections,
+//				float probabilityOfKeepingANegativeExample,
+//				String svmKernel,
+//				double svmCost,
+//				double svmGamma,
+//				String secondKernel,
+//				CompositeKernel.ComboOperator comboOperator,
+//				double tkWeight,
+//				double lambda) {
+//			super();
+//			this.classifyBothDirections = classifyBothDirections;
+//			this.probabilityOfKeepingANegativeExample = probabilityOfKeepingANegativeExample;
+//			this.svmKernel = svmKernel;
+//			this.svmKernelIndex = SVM_KERNELS.indexOf(this.svmKernel);
+//			if (this.svmKernelIndex == -1) {
+//				throw new IllegalArgumentException("Unrecognized kernel: " + this.svmKernel);
+//			}
+//			this.svmCost = svmCost;
+//			this.svmGamma = svmGamma;
+//			this.secondKernel = secondKernel;
+//			this.secondKernelIndex = SVM_KERNELS.indexOf(this.secondKernel);
+//			this.comboOperator = comboOperator;
+//			this.tkWeight = tkWeight;
+//			this.lambda = lambda;
+//		}
+//
+//		@Override
+//		public String toString() {
+//			StringBuffer buff = new StringBuffer();
+//			//      buff.append("Bothdirections=");
+//			//      buff.append(classifyBothDirections);
+//			//      buff.append(",downsamplingratio=");
+//			//      buff.append(probabilityOfKeepingANegativeExample);
+//			buff.append(",Kernel=");
+//			buff.append(svmKernel);
+//			buff.append(",Cost=");
+//			buff.append(svmCost);
+//			buff.append(",Gamma=");
+//			buff.append(svmGamma);
+//			buff.append(",secondKernel=");
+//			buff.append(secondKernel);
+//			buff.append(",operator=");
+//			buff.append(comboOperator);
+//			buff.append(",tkWeight=");
+//			buff.append(tkWeight);
+//			buff.append(",lambda=");
+//			buff.append(lambda);
+//			return buff.toString();
+//		}
+//	}
+
+	public static class AddTransitiveContainsRelations extends JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+			// collect many-to-many mappings of containment relations 
+			Multimap<Annotation, Annotation> isContainedIn = HashMultimap.create();
+			Multimap<Annotation, Annotation> contains = HashMultimap.create();
+			Set<BinaryTextRelation> containsRelations = Sets.newHashSet();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+				if (relation.getCategory().equals("CONTAINS")) {
+					containsRelations.add(relation);
+					Annotation arg1 = relation.getArg1().getArgument();
+					Annotation arg2 = relation.getArg2().getArgument();
+					contains.put(arg1, arg2);
+					isContainedIn.put(arg2, arg1);
+				}
+			}
+
+			// look for X -> Y -> Z containment chains and add X -> Z relations
+			Deque<Annotation> todo = new ArrayDeque<>(isContainedIn.keySet());
+			while (!todo.isEmpty()) {
+				Annotation next = todo.removeFirst();
+				for (Annotation parent : Lists.newArrayList(isContainedIn.get(next))) {
+					for (Annotation grandParent : Lists.newArrayList(isContainedIn.get(parent))) {
+						if (!isContainedIn.containsEntry(next, grandParent)) {
+							isContainedIn.put(next, grandParent);
+							contains.put(grandParent, next);
+
+							// once X -> Z has been added, we need to re-do all W where W -> X
+							for (Annotation child : contains.get(next)) {
+								todo.add(child);
+							}
+						}
+					}
+				}
+			}
+
+			// remove old relations
+			for (BinaryTextRelation relation : containsRelations) {
+				relation.getArg1().removeFromIndexes();
+				relation.getArg2().removeFromIndexes();
+				relation.removeFromIndexes();
+			}
+
+			// add new, transitive relations
+			for (Annotation contained : isContainedIn.keySet()) {
+				for (Annotation container : isContainedIn.get(contained)) {
+					RelationArgument arg1 = new RelationArgument(jCas);
+					arg1.setArgument(container);
+					RelationArgument arg2 = new RelationArgument(jCas);
+					arg2.setArgument(contained);
+					BinaryTextRelation relation = new BinaryTextRelation(jCas);
+					relation.setArg1(arg1);
+					relation.setArg2(arg2);
+					relation.setCategory("CONTAINS");
+					arg1.addToIndexes();
+					arg2.addToIndexes();
+					relation.addToIndexes();
+				}
+			}
+		}
+
+	}
+	
+	public static class AddContain2Overlap extends JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+			Set<BinaryTextRelation> containsRelations = Sets.newHashSet();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+				if (relation.getCategory().equals("CONTAINS")) {
+					containsRelations.add(relation);
+				}
+			}
+
+			for (BinaryTextRelation relation : containsRelations) {
+				RelationArgument arg1 = (RelationArgument) relation.getArg1().clone();
+				RelationArgument arg2 = (RelationArgument) relation.getArg2().clone();
+				BinaryTextRelation newrelation = new BinaryTextRelation(jCas);
+				newrelation.setArg1(arg1);
+				newrelation.setArg2(arg2);
+				newrelation.setCategory("OVERLAP");
+				arg1.addToIndexes();
+				arg2.addToIndexes();
+				newrelation.addToIndexes();
+			}
+		}
+	}
+	
+	public static class AddFlippedOverlap extends JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+			Set<BinaryTextRelation> overlapRelations = Sets.newHashSet();
+			Multimap<Annotation, Annotation> overlaps = HashMultimap.create();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+				if (relation.getCategory().equals("OVERLAP")) {
+					overlapRelations.add(relation);
+					Annotation arg1 = relation.getArg1().getArgument();
+					Annotation arg2 = relation.getArg2().getArgument();
+					overlaps.put(arg1, arg2);
+				}
+			}
+
+			for (BinaryTextRelation orelation : overlapRelations) {
+				Annotation argA = orelation.getArg1().getArgument();
+				Annotation argB = orelation.getArg2().getArgument();
+				//add overlap 
+				if (!overlaps.containsEntry(argB, argA)) {
+					//create a new flipped relation:
+					RelationArgument arg1 = new RelationArgument(jCas);
+					arg1.setArgument(argB);
+					RelationArgument arg2 = new RelationArgument(jCas);
+					arg2.setArgument(argA);
+					BinaryTextRelation relation = new BinaryTextRelation(jCas);
+					relation.setArg1(arg1);
+					relation.setArg2(arg2);
+					relation.setCategory("OVERLAP");
+					arg1.addToIndexes();
+					arg2.addToIndexes();
+					relation.addToIndexes();
+					overlaps.put(argB, argA);
+				}
+
+			}
+		}
+	}
+	
+	public static class AddClosure extends JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			
+			Multimap<List<Annotation>, BinaryTextRelation> annotationsToRelation = HashMultimap.create();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)){
+				String relationType = relation.getCategory();
+				if(validTemporalType(relationType)){
+					Annotation arg1 = relation.getArg1().getArgument();
+			        Annotation arg2 = relation.getArg2().getArgument();
+			        annotationsToRelation.put(Arrays.asList(arg1, arg2), relation);
+				}
+			}
+			for (List<Annotation> span: Lists.newArrayList(annotationsToRelation.keySet())){
+				Collection<BinaryTextRelation> relations = annotationsToRelation.get(span);
+				if(relations.size()>1){//if same span maps to multiple relations
+					Set<String> types = Sets.newHashSet();
+					for(BinaryTextRelation relation: relations){
+						types.add(relation.getCategory());
+					}
+					if(types.size()>1){
+						for(BinaryTextRelation relation: Lists.newArrayList(relations)){
+							annotationsToRelation.remove(span, relation);
+							relation.getArg1().removeFromIndexes();
+							relation.getArg2().removeFromIndexes();
+							relation.removeFromIndexes();
+						}
+					}else if(types.size()==1){
+						for (int i =1; i< relations.size(); i++){
+							BinaryTextRelation relation = (BinaryTextRelation) relations.toArray()[i];
+							annotationsToRelation.remove(span, relation);
+							relation.getArg1().removeFromIndexes();
+							relation.getArg2().removeFromIndexes();
+							relation.removeFromIndexes();
+						}
+					}
+				}
+			}
+
+			ArrayList<BinaryTextRelation> temporalRelation = new ArrayList<>(annotationsToRelation.values());//new
ArrayList<BinaryTextRelation>();
+//			Map<List<Annotation>, BinaryTextRelation> temporalRelationLookup = new HashMap<List<Annotation>,
BinaryTextRelation>();
+//
+//			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)){
+//				String relationType = relation.getCategory();
+//				if(validTemporalType(relationType)){
+//					Annotation arg1 = relation.getArg1().getArgument();
+//			        Annotation arg2 = relation.getArg2().getArgument();
+//			        BinaryTextRelation tempRelation = temporalRelationLookup.get(Arrays.asList(arg1,
arg2));
+//					if( tempRelation == null){
+//						temporalRelation.add(relation);					
+//				        temporalRelationLookup.put(Arrays.asList(arg1, arg2), relation);
+//					}else{//if there is duplicate
+//						relation.getArg1().removeFromIndexes();
+//						relation.getArg2().removeFromIndexes();
+//						relation.removeFromIndexes();
+//					}
+//					
+//				}
+//			}
+
+			if (!temporalRelation.isEmpty()){
+				TLinkTypeArray2 relationArray = new TLinkTypeArray2(temporalRelation, new AnnotationIdCollection(temporalRelation));
+
+				int addedCount = 0;
+				for (BinaryTextRelation relation : relationArray.getClosedTlinks(jCas)) {
+					RelationArgument arg1 = relation.getArg1();
+					RelationArgument arg2 = relation.getArg2();
+					String relationType = relation.getCategory();
+					if(relationType.equals("CONTAINED-BY")||relationType.equals("AFTER")){//ignore these
two categories, because their reciprocal already exist.
+						continue;
+					}
+					//check if the inferred relation new:
+					Collection<BinaryTextRelation> relations = annotationsToRelation.get(Arrays.asList(arg1.getArgument(),
arg2.getArgument()));
+					if(relations.isEmpty()){ //if haven't seen this inferred relation before, then add this
relation
+						arg1.addToIndexes();
+						arg2.addToIndexes();
+						relation.addToIndexes();
+						addedCount++;
+					}		
+				}
+				
+				System.out.println( "**************************************************************");
+			    System.out.println( "Finally added closure relations: " + addedCount );
+			    System.out.println( "**************************************************************");
+			}			
+
+		}
+
+		private static boolean validTemporalType(String relationType) {
+			if(relationType.equals("CONTAINS")||relationType.equals("OVERLAP")||relationType.equals("BEFORE")||relationType.equals("ENDS-ON")||relationType.equals("BEGINS-ON"))
+				return true;
+			return false;
+		}
+	}
+
+//	public static class AddTransitiveBeforeAndOnRelations extends JCasAnnotator_ImplBase {
+//
+//		@Override
+//		public void process(JCas jCas) throws AnalysisEngineProcessException {
+//
+//			// collect many-to-many mappings of containment relations 
+//			Multimap<Annotation, Annotation> contains = HashMultimap.create();
+//			Multimap<Annotation, Annotation> before = HashMultimap.create();
+//			Multimap<Annotation, Annotation> endson = HashMultimap.create();
+//			Multimap<Annotation, Annotation> beginson = HashMultimap.create();
+//			Set<BinaryTextRelation> beforeRel = Sets.newHashSet();
+//
+//			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class))
{
+//				if (relation.getCategory().equals("CONTAINS")) {
+//					Annotation arg1 = relation.getArg1().getArgument();
+//					Annotation arg2 = relation.getArg2().getArgument();
+//					contains.put(arg1, arg2);
+//				}else if (relation.getCategory().equals("BEFORE")) {
+//					Annotation arg1 = relation.getArg1().getArgument();
+//					Annotation arg2 = relation.getArg2().getArgument();
+//					before.put(arg1, arg2);
+//					beforeRel.add(relation);
+//				}else if (relation.getCategory().equals("ENDS-ON")) {
+//					Annotation arg1 = relation.getArg1().getArgument();
+//					Annotation arg2 = relation.getArg2().getArgument();
+//					endson.put(arg1, arg2);
+//					if (!endson.containsEntry(arg2, arg1)) {
+//						endson.put(arg2, arg1);
+//					}
+//				}else if (relation.getCategory().equals("BEGINS-ON")) {
+//					Annotation arg1 = relation.getArg1().getArgument();
+//					Annotation arg2 = relation.getArg2().getArgument();
+//					beginson.put(arg1, arg2);
+//					if (!beginson.containsEntry(arg2, arg1)) {
+//						beginson.put(arg2, arg1);
+//					}
+//				}
+//			}
+//
+//			// for A BEFORE B, check if A and B Contain anything
+//			for (BinaryTextRelation brelation : beforeRel) {
+//				Annotation argA = brelation.getArg1().getArgument();
+//				Annotation argB = brelation.getArg2().getArgument();
+//				//add contained before
+//				for (Annotation childA : contains.get(argA)) {
+//					for (Annotation childB : contains.get(argB)) {
+//						if (!before.containsEntry(childA, childB)) {
+//							//create a new before relation:
+//							RelationArgument arg1 = new RelationArgument(jCas);
+//							arg1.setArgument(childA);
+//							RelationArgument arg2 = new RelationArgument(jCas);
+//							arg2.setArgument(childB);
+//							BinaryTextRelation relation = new BinaryTextRelation(jCas);
+//							relation.setArg1(arg1);
+//							relation.setArg2(arg2);
+//							relation.setCategory("BEFORE");
+//							arg1.addToIndexes();
+//							arg2.addToIndexes();
+//							relation.addToIndexes();
+//							before.put(childA, childB);
+//						}
+//					}
+//				}
+//				//add ends-on A
+//				for (Annotation endsOnA : endson.get(argA)) {
+//					if (!before.containsEntry(endsOnA, argB)) {
+//						//create a new before relation:
+//						RelationArgument arg1 = new RelationArgument(jCas);
+//						arg1.setArgument(endsOnA);
+//						RelationArgument arg2 = new RelationArgument(jCas);
+//						arg2.setArgument(argB);
+//						BinaryTextRelation relation = new BinaryTextRelation(jCas);
+//						relation.setArg1(arg1);
+//						relation.setArg2(arg2);
+//						relation.setCategory("BEFORE");
+//						arg1.addToIndexes();
+//						arg2.addToIndexes();
+//						relation.addToIndexes();
+//						before.put(endsOnA, argB);
+//					}
+//				}
+//				//add begins-on B
+//				for (Annotation beginsOnB : beginson.get(argB)) {
+//					if (!before.containsEntry(argA, beginsOnB)) {
+//						//create a new before relation:
+//						RelationArgument arg1 = new RelationArgument(jCas);
+//						arg1.setArgument(argA);
+//						RelationArgument arg2 = new RelationArgument(jCas);
+//						arg2.setArgument(beginsOnB);
+//						BinaryTextRelation relation = new BinaryTextRelation(jCas);
+//						relation.setArg1(arg1);
+//						relation.setArg2(arg2);
+//						relation.setCategory("BEFORE");
+//						arg1.addToIndexes();
+//						arg2.addToIndexes();
+//						relation.addToIndexes();
+//						before.put(argA, beginsOnB);
+//					}
+//				}
+//			}
+//		}
+//
+//	}
+}

Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
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