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From c...@apache.org
Subject svn commit: r1632167 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/
Date Wed, 15 Oct 2014 19:29:44 GMT
Author: clin
Date: Wed Oct 15 19:29:44 2014
New Revision: 1632167

URL: http://svn.apache.org/r1632167
Log:
Added more cleartk2.0 compliant feature extractors for within-sentence event-event event-time relations

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ConjunctionRelationFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoordinateFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependingVerbsFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DeterminerRelationFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPositionRelationFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventsInTheSameSentenceExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/OverlappedHeadFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SpecialAnnotationRelationExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalPETFlatExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXPropertyRelationFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXRelationFeaturesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TokenPropertyFeaturesExtractor.java
Modified:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ConjunctionRelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ConjunctionRelationFeaturesExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ConjunctionRelationFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ConjunctionRelationFeaturesExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,61 @@
+package org.apache.ctakes.temporal.ae.feature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+public class ConjunctionRelationFeaturesExtractor implements
+RelationFeaturesExtractor {
+	
+	private String name = "ConjunctionFeature";
+	@Override
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		ArrayList<Feature> feats = new ArrayList<>();
+		
+		int begin = arg1.getEnd();
+		int end   = arg2.getBegin();
+		
+		if ( begin > end ){
+			begin = arg2.getEnd();
+			end   = arg1.getBegin();
+		}
+		
+		if ( begin >= end ){
+			return feats;
+		}
+		
+		List<BaseToken> betweenTokens = JCasUtil.selectCovered(jCas, BaseToken.class, begin, end);
+		List<EventMention> eventsInBetween = JCasUtil.selectCovered(jCas, EventMention.class, begin, end);
+		//filter events:
+		List<EventMention> realEvents = new ArrayList<>();
+		//filtering events
+		for(EventMention event : eventsInBetween){
+			// filter out ctakes events
+			if(event.getClass().equals(EventMention.class)){
+				realEvents.add(event);
+			}
+		}
+		eventsInBetween = realEvents;
+		if(eventsInBetween.size() ==0 ){
+			for (BaseToken token: betweenTokens){
+				String pos = token.getPartOfSpeech();
+				if(pos.startsWith("CC")||pos.equals(",")||pos.startsWith("IN")){
+					feats.add(new Feature(this.name, "Contain_Conjunction_inBetween"));
+					feats.add(new Feature(this.name, pos));
+				}
+			}
+		}
+		
+		return feats;
+	}
+
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoordinateFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoordinateFeaturesExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoordinateFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoordinateFeaturesExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,68 @@
+package org.apache.ctakes.temporal.ae.feature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+public class CoordinateFeaturesExtractor implements
+RelationFeaturesExtractor {
+
+	@SuppressWarnings("null")
+	@Override
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		ArrayList<Feature> feats = new ArrayList<>();
+		
+		List<BaseToken> arg1Tokens = JCasUtil.selectCovered(jCas, BaseToken.class, arg1);
+		List<BaseToken> arg2Tokens = JCasUtil.selectCovered(jCas, BaseToken.class, arg2);
+		
+		int arg1Length = arg1Tokens == null ? 0 : arg1Tokens.size();
+		int arg2Length = arg2Tokens == null ? 0 : arg2Tokens.size();
+		
+		if(arg1Length != arg2Length || arg1Length == 0 || arg2Length == 0){
+			return feats;
+		}
+		
+		for (int i=0; i<arg1Length; i++){
+			if(!arg1Tokens.get(i).getPartOfSpeech().equals(arg2Tokens.get(i).getPartOfSpeech())){
+				return feats;
+			}
+		}
+		
+		int begin = arg1.getEnd();
+		int end   = arg2.getBegin();
+		
+		if ( begin > end ){
+			begin = arg2.getEnd();
+			end   = arg1.getBegin();
+		}
+		
+		if ( begin >= end ){
+			return feats;
+		}
+		
+		List<EventMention> betweenEvents = JCasUtil.selectCovered(jCas, EventMention.class, begin, end);
+		int eventInBetween  = betweenEvents == null ? 0 : betweenEvents.size();
+		if(eventInBetween >0) return feats;
+		
+		List<BaseToken> betweenTokens = JCasUtil.selectCovered(jCas, BaseToken.class, begin, end);
+		for (BaseToken token: betweenTokens){
+			String tokenwd = token.getCoveredText();
+			if(token.getPartOfSpeech().startsWith("CC")||tokenwd.equals(",")||tokenwd.equals(";")||tokenwd.equals("/")||tokenwd.equals("w")||tokenwd.equals("&")||tokenwd.equalsIgnoreCase("versus")||tokenwd.equalsIgnoreCase("vs")||tokenwd.equalsIgnoreCase("with")){
+				feats.add(new Feature("Coordinate_feature", "Coordinate"));
+				break;
+			}
+		}
+		
+		return feats;
+	}
+
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependingVerbsFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependingVerbsFeatureExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependingVerbsFeatureExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependingVerbsFeatureExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,97 @@
+package org.apache.ctakes.temporal.ae.feature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+public class DependingVerbsFeatureExtractor implements RelationFeaturesExtractor {
+
+	private static final String FEAT_NAME = "Depending_Verb"; 
+
+	@Override
+	public List<Feature> extract(JCas jcas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		List<Feature> features = new ArrayList<>();
+		// first get the common ancestor of both arguments...
+		ConllDependencyNode ancestor = null;
+		boolean hasCommonVerb = false;
+		outerloop:
+		for (ConllDependencyNode firstNode : JCasUtil.selectCovered(jcas, ConllDependencyNode.class, arg1)) {//get the covered conll nodes within the first extent
+			String pos = firstNode.getPostag();
+			if(pos!=null && pos.startsWith("NN")){//get the head node
+				for(ConllDependencyNode nextNode : JCasUtil.selectCovered(jcas, ConllDependencyNode.class, arg2)){//get the covered conll nodes within the next extent
+					pos = nextNode.getPostag();
+					if(pos!=null && pos.startsWith("NN")){//get the head node
+						ancestor = DependencyParseUtils.getCommonAncestor(firstNode, nextNode);
+						if(ancestor!=null && ancestor.getPostag().startsWith("VB")){
+							features.add(new Feature(FEAT_NAME, "both_events_governed_by_the_same_verb"));
+							features.add(new Feature(FEAT_NAME, ancestor.getDeprel()+"_"+ancestor.getCoveredText().toLowerCase()));
+							hasCommonVerb = true;
+							break outerloop;
+						}
+					}
+				}
+			}
+		}
+
+		if(!hasCommonVerb){//if arg1 and arg2 don't depend on the same verb, get their independent depending verbs
+			features.addAll(getDependingVerbFeature(jcas, arg1));
+			features.addAll(getDependingVerbFeature(jcas, arg2));
+		}
+		
+		return features;
+	}
+
+	private static List<Feature> getDependingVerbFeature(JCas jcas, IdentifiedAnnotation arg) {
+		List<Feature> feats = new ArrayList<>();
+		
+		for (ConllDependencyNode dnode : JCasUtil.selectCovered(jcas, ConllDependencyNode.class, arg)) {//get the covered conll nodes within the first extent
+			String pos = dnode.getPostag();
+			if(pos!=null && pos.startsWith("NN")){//get the head node
+				ConllDependencyNode verbNode = getVerbAncestor(dnode);
+				if(verbNode != null){//get verb node features
+					Integer typeId = -1;
+					if(arg instanceof EventMention){
+						EventMention mention = (EventMention) arg;
+						if(mention.getEvent() != null && mention.getEvent().getProperties() != null){
+							typeId = mention.getEvent().getProperties().getTypeIndexID();
+						}
+					}
+					feats.add(new Feature(FEAT_NAME, typeId+"_"+ verbNode.getPostag()));
+					String depRelation = dnode.getDeprel();
+					if(depRelation.startsWith("nsubj"))
+						feats.add(new Feature(FEAT_NAME, typeId+"_isASubject"));
+					else if(depRelation.startsWith("dobj"))
+						feats.add(new Feature(FEAT_NAME, typeId+"_isAnObject"));
+					
+					break;
+				}
+			}
+		}
+		return feats;
+	}
+
+	private static ConllDependencyNode getVerbAncestor(ConllDependencyNode dnode) {
+		ConllDependencyNode verbNode = null;
+		ConllDependencyNode currNode = dnode;
+	    while (currNode != null && currNode.getHead() != null) { 
+	      currNode = currNode.getHead();
+	      String nodepos = currNode == null ? null : currNode.getPostag();
+	      if(nodepos != null && nodepos.startsWith("VB")){
+	    	  verbNode = currNode;
+	    	  return verbNode;
+	      }
+	    }
+		return verbNode;
+	}
+
+	
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DeterminerRelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DeterminerRelationFeaturesExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DeterminerRelationFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DeterminerRelationFeaturesExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,63 @@
+/**
+ * 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.ae.feature;
+
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+import com.google.common.collect.Lists;
+/**
+ * extract the nearby nearest time, date information for any event 
+ * @author CH151862
+ *
+ */
+public class DeterminerRelationFeaturesExtractor implements RelationFeaturesExtractor {
+
+	private String name="Determiner";
+
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		List<Feature> features = Lists.newArrayList();
+
+		List<IdentifiedAnnotation> arguments = Lists.newArrayList();
+		arguments.add(arg1);
+		arguments.add(arg2);
+		
+		for(IdentifiedAnnotation arg: arguments){
+			List<WordToken> tokens = JCasUtil.selectCovered(jCas, WordToken.class, arg);
+			for(WordToken word : tokens){
+				String pos = word.getPartOfSpeech();
+				if(pos.startsWith("DT")||pos.startsWith("PRP$")){
+//					features.add(new Feature(this.name, "contains_DT"));
+					features.add(new Feature(this.name, pos));
+					break;
+				}
+			}
+		}
+
+		return features;
+	}
+}

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java?rev=1632167&r1=1632166&r2=1632167&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java Wed Oct 15 19:29:44 2014
@@ -20,7 +20,9 @@ package org.apache.ctakes.temporal.ae.fe
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
@@ -32,52 +34,78 @@ import org.cleartk.ml.Feature;
 import org.apache.uima.fit.util.JCasUtil;
 
 public class EventArgumentPropertyExtractor implements
-    RelationFeaturesExtractor {
+RelationFeaturesExtractor {
 
-  @Override
-  public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
-      IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
-    List<Feature> feats = new ArrayList<Feature>();
-    
-    Sentence coveringSent = JCasUtil.selectCovering(jCas, Sentence.class, arg1.getBegin(), arg1.getEnd()).get(0);
-    List<EventMention> events = JCasUtil.selectCovered(EventMention.class, coveringSent);
-    List<EventMention> realEvents = new ArrayList<EventMention>();
-    for(EventMention event : events){
-    	// filter out ctakes events
-    	if(event.getClass().equals(EventMention.class)){
-    		realEvents.add(event);
-    	}
-    }
-    events = realEvents;
-    EventMention anchor = events.get(0);
-    
-    if(arg1.getBegin() == anchor.getBegin() && arg1.getEnd() == anchor.getEnd()){
-    	feats.add(new Feature("Arg1LeftmostEvent"));
-    }else if(arg2.getBegin() == anchor.getBegin() && arg2.getEnd() == anchor.getEnd()){
-    	feats.add(new Feature("Arg2LeftmostEvent"));
-    }
-    
-    if(arg1 instanceof EventMention){
-      feats.addAll(getEventFeats("mention1property", (EventMention)arg1));
-    }
-    if(arg2 instanceof EventMention){
-      feats.addAll(getEventFeats("mention2property", (EventMention)arg2));
-    }
-    return feats;
-   }
-
-  private static Collection<? extends Feature> getEventFeats(String name, EventMention mention) {
-    List<Feature> feats = new ArrayList<Feature>();
-    
-    feats.add(new Feature(name + "_modality", mention.getEvent().getProperties().getContextualModality()));
-    feats.add(new Feature(name + "_aspect", mention.getEvent().getProperties().getContextualAspect()));
-    feats.add(new Feature(name + "_permanence", mention.getEvent().getProperties().getPermanence()));
-    feats.add(new Feature(name + "_polarity", mention.getEvent().getProperties().getPolarity()));
-    feats.add(new Feature(name + "_category", mention.getEvent().getProperties().getCategory()));
-    feats.add(new Feature(name + "_degree", mention.getEvent().getProperties().getDegree()));
-    feats.add(new Feature(name + "_doctimerel", mention.getEvent().getProperties().getDocTimeRel()));
-    
-    return feats;
-  }
+	@Override
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		List<Feature> feats = new ArrayList<>();
+
+		Set<Sentence> coveringSents = new HashSet<>();
+		if( arg1 instanceof EventMention){
+			coveringSents.addAll(JCasUtil.selectCovering(jCas, Sentence.class, arg1.getBegin(), arg1.getEnd()));
+		}else if(arg2 instanceof EventMention){
+			coveringSents.addAll(JCasUtil.selectCovering(jCas, Sentence.class, arg2.getBegin(), arg2.getEnd()));
+		}else{
+			return feats;
+		}
+
+		for(Sentence coveringSent : coveringSents){
+			List<EventMention> events = JCasUtil.selectCovered(EventMention.class, coveringSent);
+			List<EventMention> realEvents = new ArrayList<>();
+			for(EventMention event : events){
+				// filter out ctakes events
+				if(event.getClass().equals(EventMention.class)){
+					realEvents.add(event);
+				}
+			}
+			events = realEvents;
+			if( events.size()>0){
+				EventMention anchor = events.get(0);
+				if(arg1 == anchor){
+					feats.add(new Feature("Arg1LeftmostEvent"));
+				}else if(arg2 == anchor){
+					feats.add(new Feature("Arg2LeftmostEvent"));
+				}
+			}
+		}
+		
+		if(arg1 instanceof EventMention){
+			feats.addAll(getEventFeats("mention1property", (EventMention)arg1));
+		}
+		if(arg2 instanceof EventMention){
+			feats.addAll(getEventFeats("mention2property", (EventMention)arg2));
+		}
+
+		return feats;
+	}
+
+	private static Collection<? extends Feature> getEventFeats(String name, EventMention mention) {
+		List<Feature> feats = new ArrayList<>();
+		//add contextual modality as a feature
+		if(mention.getEvent()==null || mention.getEvent().getProperties() == null){
+			return feats;
+		}
+		String contextualModality = mention.getEvent().getProperties().getContextualModality();
+		if (contextualModality != null)
+			feats.add(new Feature(name + "_modality", contextualModality));
+
+		//    feats.add(new Feature(name + "_aspect", mention.getEvent().getProperties().getContextualAspect()));//null
+		//    feats.add(new Feature(name + "_permanence", mention.getEvent().getProperties().getPermanence()));//null
+		Integer polarity = mention.getEvent().getProperties().getPolarity();
+		if(polarity!=null )
+			feats.add(new Feature(name + "_polarity", polarity));
+		//    feats.add(new Feature(name + "_category", mention.getEvent().getProperties().getCategory()));//null
+		//    feats.add(new Feature(name + "_degree", mention.getEvent().getProperties().getDegree()));//null
+		String docTimeRel = mention.getEvent().getProperties().getDocTimeRel();
+		if(docTimeRel!=null)
+			feats.add(new Feature(name + "_doctimerel", docTimeRel));
+
+		Integer typeId = mention.getEvent().getProperties().getTypeIndexID();
+		if(typeId != null)
+			feats.add(new Feature(name + "_typeId", typeId));
+
+		return feats;
+	}
 
 }

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPositionRelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPositionRelationFeaturesExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPositionRelationFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPositionRelationFeaturesExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,141 @@
+/**
+ * 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.ae.feature;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+import com.google.common.collect.Lists;
+/**
+ * extract the nearby nearest time, date information for any event 
+ * @author CH151862
+ *
+ */
+public class EventPositionRelationFeaturesExtractor implements RelationFeaturesExtractor {
+
+	private String name="EventRelaionPosition";
+
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		List<Feature> features = Lists.newArrayList();
+
+		List<EventMention> events = Lists.newArrayList();
+		if(arg1 instanceof EventMention) events.add((EventMention)arg1);
+		if(arg2 instanceof EventMention) events.add((EventMention)arg2);
+		
+		Collection<Sentence> sentences = JCasUtil.select(jCas, Sentence.class);
+		List<Sentence> sentList = Lists.newArrayList();
+		sentList.addAll(sentences);
+		int sentSize = sentList.size();
+		
+		//get covering segment:
+		Map<EventMention, Collection<Segment>> coveringMap =
+				JCasUtil.indexCovering(jCas, EventMention.class, Segment.class);
+		
+		Collection<EventMention> allevents = JCasUtil.select(jCas, EventMention.class);
+		List<EventMention> eventList = Lists.newArrayList();
+		//filter events
+		for(EventMention eventa : allevents){
+			// filter out ctakes events
+			if(eventa.getClass().equals(EventMention.class)){
+				eventList.add(eventa);
+			}
+		}
+		int eventSize = eventList.size();
+
+		for(EventMention event: events){
+			//check if it within the last/first 5 sentences			
+			if( sentSize >= 5){
+				if( containEvent(sentList.get(0), sentList.get(4), event)){
+					Feature feature = new Feature(this.name, "Within_Top_5_sentences");
+					features.add(feature);
+				}
+				if( containEvent(sentList.get(sentSize-5), sentList.get(sentSize-1), event)){
+					Feature feature = new Feature(this.name, "Within_Last_5_sentences");
+					features.add(feature);
+				}
+			}
+
+			//check if it within the last/first 5 events
+			if(eventSize >= 5){
+				if( containEvent(eventList.get(0), eventList.get(4), event)){
+					Feature feature = new Feature(this.name, "Within_Top_5_events");
+					features.add(feature);
+				}
+				if( containEvent(eventList.get(eventSize-5), eventList.get(eventSize-1), event)){
+					Feature feature = new Feature(this.name, "Within_Last_5_events");
+					features.add(feature);
+				}
+			}
+
+			
+			Collection<Segment> segList = coveringMap.get(event);
+
+			//if an event is the first/last 3 events in its section
+			for(Segment seg : segList) {
+				String segname = seg.getId();
+				if (!segname.equals("SIMPLE_SEGMENT")){//remove simple segment
+					List<EventMention> segEvents = JCasUtil.selectCovered(jCas, EventMention.class, seg);
+					List<EventMention> realEvents = new ArrayList<>();
+					//filtering events
+					for(EventMention segevent : segEvents){
+						// filter out ctakes events
+						if(segevent.getClass().equals(EventMention.class)){
+							realEvents.add(segevent);
+						}
+					}
+					segEvents = realEvents;
+					int segEventSize = segEvents.size();
+					if(segEventSize >= 3){
+						if( containEvent(segEvents.get(0), segEvents.get(2), event)){
+							Feature feature = new Feature(this.name, "Within_Top_3_events_of"+segname);
+							features.add(feature);
+						}
+						if( containEvent(segEvents.get(segEventSize-3), segEvents.get(segEventSize-1), event)){
+							Feature feature = new Feature(this.name, "Within_Last_3_events_of"+segname);
+							features.add(feature);
+						}
+					}
+				}
+			}
+		}
+
+		return features;
+	}
+
+	private static boolean containEvent(Annotation arg1, Annotation arg2,
+			Annotation target) {
+		if(target.getBegin()>=arg1.getBegin() && target.getEnd()<= arg2.getEnd())
+			return true;
+		return false;
+	}
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,139 @@
+/**
+ * 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.ae.feature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
+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.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.ml.Feature;
+import org.cleartk.util.ViewUriUtil;
+import org.apache.uima.fit.util.JCasUtil;
+
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Multimap;
+/**
+ * Given a pair of arguments, if any one of them is an event, get the related event-sectiontime as features 
+ * @author CH151862
+ *
+ */
+public class EventTimeRelationFeatureExtractor implements
+RelationFeaturesExtractor {
+
+	private String cachedDocID = null;
+	private Multimap<EventMention, String> eventSectionTimeRelationLookup;
+	
+	@SuppressWarnings("null")
+	@Override
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		
+		String docId=null;
+		try{
+			docId = ViewUriUtil.getURI(jCas).toString();// get docID
+		}catch(Exception e){
+			docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+		}
+		if(!docId.equals(cachedDocID)){
+			// rebuild cache
+			cachedDocID = docId;
+			rebuildCache(jCas);
+		}
+		
+		ArrayList<Feature> feats = new ArrayList<>();
+		
+		List<EventMention> events = Lists.newArrayList();
+		if(arg1 instanceof EventMention) events.add((EventMention)arg1);
+		if(arg2 instanceof EventMention) events.add((EventMention)arg2);
+		for(EventMention event: events){
+			for(String value : eventSectionTimeRelationLookup.get(event)){
+				feats.add(new Feature("hasEventTimeRelation_", value));
+			}
+		}
+
+		return feats;
+	}
+
+	private void rebuildCache(JCas jCas){
+		//get admission Time:
+		TimeMention admissionTime = null;
+		//may need better way to identify Discharge Time other than relative span information:
+		for (TimeMention time : JCasUtil.selectCovered(jCas, TimeMention.class, 15, 30)) {
+			if(time.getTimeClass().equals("DATE")){
+				admissionTime = time;
+				break;
+			}
+		}
+		//get discharge Time id: T1:
+		TimeMention dischargeTime = null;
+		//may need better way to identify Discharge Time other than relative span information:
+		for (TimeMention time : JCasUtil.selectCovered(jCas, TimeMention.class, 40, 60)) {
+			if(time.getTimeClass().equals("DATE")){
+				dischargeTime = time;
+				break;
+			}
+		}
+		
+		eventSectionTimeRelationLookup = HashMultimap.create();
+		for (TemporalTextRelation relation : JCasUtil.select(jCas, TemporalTextRelation.class)) {
+//			Annotation potentialSectTime = relation.getArg2().getArgument();
+//			String relationTo = "";
+//			if(potentialSectTime==admissionTime){
+//				relationTo="admissionTime";
+//			}else if(potentialSectTime == dischargeTime){
+//				relationTo="dischargeTime";
+//			}
+			Annotation arg1 = relation.getArg1().getArgument();
+			Annotation arg2 = relation.getArg2().getArgument();
+			Annotation event = null;
+			TimeMention time  = null;
+			if( arg1 instanceof EventMention && arg2 instanceof TimeMention){
+				event = arg1;
+				time  = (TimeMention)arg2;
+			}else if(arg2 instanceof EventMention && arg1 instanceof TimeMention){
+				event = arg2;
+				time  = (TimeMention)arg1;
+			}
+			if(event != null && time !=null){
+				if(time == admissionTime){
+					eventSectionTimeRelationLookup.put((EventMention)event, "admissionTime_"+relation.getCategory());
+				}else if(time == dischargeTime){
+					eventSectionTimeRelationLookup.put((EventMention)event, "dischargeTime_"+relation.getCategory());
+				}else{
+					eventSectionTimeRelationLookup.put((EventMention)event, time.getTimeClass()+"_"+relation.getCategory());
+				}
+//				Annotation potentialEvent = relation.getArg1().getArgument();
+//				if(potentialEvent instanceof EventMention){
+//					eventSectionTimeRelationLookup.put((EventMention)potentialEvent, relationTo+"_"+relation.getCategory());
+//				}
+			} 
+		}
+
+	}
+}

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java?rev=1632167&r1=1632166&r2=1632167&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java Wed Oct 15 19:29:44 2014
@@ -38,14 +38,14 @@ public class NearbyVerbTenseRelationExtr
 	@Override
 	public List<Feature> extract(JCas jcas, IdentifiedAnnotation arg1,
 			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
-		List<Feature> feats = new ArrayList<Feature>();
+		List<Feature> feats = new ArrayList<>();
 
 		//find event
-		EventMention event = null;
+		List<EventMention> events = new ArrayList<>();
 		if(arg1 instanceof EventMention){
-			event = (EventMention) arg1;
-		}else if(arg1 instanceof EventMention){
-			event = (EventMention) arg2;
+			events.add((EventMention) arg1);
+		}else if(arg2 instanceof EventMention){
+			events.add((EventMention) arg2);
 		}else{
 			return feats;
 		}
@@ -53,25 +53,40 @@ public class NearbyVerbTenseRelationExtr
 		//1 get covering sentence:
 		Map<EventMention, Collection<Sentence>> coveringMap =
 				JCasUtil.indexCovering(jcas, EventMention.class, Sentence.class);
-		Collection<Sentence> sentList = coveringMap.get(event);
-
-		//2 get Verb Tense
-		if (sentList != null && !sentList.isEmpty()){
-			for(Sentence sent : sentList) {
-				String verbTP ="";
-				for ( WordToken wt : JCasUtil.selectCovered(jcas, WordToken.class, sent)) {
-					if (wt != null){
-						String pos = wt.getPartOfSpeech();
-						if (pos.startsWith("VB")){
-							verbTP = verbTP + "_" + pos;
+		
+		Sentence knowSentence = null;
+		String seenVbPattern = null;
+
+		for(EventMention event: events){
+			Collection<Sentence> sentList = coveringMap.get(event);
+
+			//2 get Verb Tense
+			if (sentList != null && !sentList.isEmpty()){
+				for(Sentence sent : sentList) {
+					String verbTP ="";
+					for ( WordToken wt : JCasUtil.selectCovered(jcas, WordToken.class, sent)) {
+						if (wt != null){
+							String pos = wt.getPartOfSpeech();
+							if (pos.startsWith("VB")){
+								verbTP = verbTP + "_" + pos;
+							}
 						}
 					}
+					Feature feature = new Feature("VerbTenseFeature", verbTP);
+					feats.add(feature);
+					//logger.info("found nearby verb's pos tag: "+ verbTP);
+					
+					//check if the verb pattern is different from the old
+					if(knowSentence == null && !verbTP.equals("")){
+						knowSentence = sent;
+						seenVbPattern = verbTP;
+					}else if(knowSentence != null && knowSentence != sent && verbTP.equals(seenVbPattern)){
+						feature = new Feature("TwoSentenceShareTheSameVerbPattern", verbTP);
+						feats.add(feature);
+					}
 				}
-				Feature feature = new Feature("VerbTenseFeature", verbTP);
-				feats.add(feature);
-				//logger.info("found nearby verb's pos tag: "+ verbTP);
-			}
 
+			}
 		}
 		return feats;
 	}

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java?rev=1632167&r1=1632166&r2=1632167&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java Wed Oct 15 19:29:44 2014
@@ -22,14 +22,23 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.NumToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 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.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
 
+/**
+ * Count the number of EventMention and TimeMention in between two arguments as features
+ * @author CH151862
+ *
+ */
 public class NumberOfEventTimeBetweenCandidatesExtractor implements
 RelationFeaturesExtractor {
 
@@ -55,21 +64,46 @@ RelationFeaturesExtractor {
 		
 		int eventsInBetween = 0;
 		int timesInBetween  = 0;
+		int wordsInBetween  = 0;
+		int puncsInBetween  = 0;
+//		int numsInBetween   = 0;
+//		int newlineInBetween= 0;
 		
 		List<EventMention> events = JCasUtil.selectCovered(jCas, EventMention.class, begin, end);
 		List<TimeMention> times   = JCasUtil.selectCovered(jCas, TimeMention.class, begin, end);
+		List<WordToken> words 	  = JCasUtil.selectCovered(jCas, WordToken.class, begin, end);
+		List<PunctuationToken>punc= JCasUtil.selectCovered(jCas, PunctuationToken.class, begin, end);
+//		List<NumToken> numTokens  = JCasUtil.selectCovered(jCas, NumToken.class, begin, end);
+//		List<NewlineToken> newline= JCasUtil.selectCovered(jCas, NewlineToken.class, begin, end);
+		
+		//filter out ctakes events
+//		List<EventMention> realEvents = new ArrayList<>();
+//		for(EventMention event : events){
+//			// filter out ctakes events
+//			if(event.getClass().equals(EventMention.class)){
+//				realEvents.add(event);
+//			}
+//		}
+//		events = realEvents;
 		eventsInBetween = events==null? 0: events.size();
+//		if(eventsInBetween > 10) eventsInBetween = 10;
 		timesInBetween  = times==null? 0: times.size();
+		wordsInBetween  = words==null? 0 : words.size();
+		if(wordsInBetween > 20) wordsInBetween = 20;
+		puncsInBetween   = punc == null? 0 : punc.size();
+		if(puncsInBetween > 5) puncsInBetween = 5;
+//		numsInBetween   = numTokens == null? 0 : numTokens.size();
+//		newlineInBetween= newline == null? 0 : newline.size();
+		
+		
 		feats.add(new Feature("NumOfEvents_InBetween", eventsInBetween));
 		feats.add(new Feature("NumOfTimes_InBetween", timesInBetween));
 		feats.add(new Feature("NumOfEventsAndTimes_InBetween", timesInBetween+eventsInBetween));
+		feats.add(new Feature("NumOfWords_InBetween", wordsInBetween));
+		feats.add(new Feature("NumOfPunctuation_InBetween", puncsInBetween));
+//		feats.add(new Feature("NumOfNumberToken_InBetween", numsInBetween));
+//		feats.add(new Feature("NumOfNewLine_InBetween", newlineInBetween));
 		
-//		//print long distances
-//		if (eventsInBetween >= 200){
-//			System.out.println("++++++++++Long Distance Relation in "+ ViewUriUtil.getURI(jCas).toString() + "+++++++");
-//			System.out.println("["+arg1.getCoveredText()+"] "+ jCas.getDocumentText().substring(arg1.getEnd(), arg2.getBegin()) +" ["+arg2.getCoveredText()+"]");
-//		}
-
 		return feats;
 	}
 

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventsInTheSameSentenceExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventsInTheSameSentenceExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventsInTheSameSentenceExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventsInTheSameSentenceExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,110 @@
+/**
+ * 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.ae.feature;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+import com.google.common.collect.Lists;
+/**
+ * Count the number of EventMentions in the same sentence as the two arguments, used for features for within sentence event-event relation discovery
+ * @author CH151862
+ *
+ */
+public class NumberOfEventsInTheSameSentenceExtractor implements
+RelationFeaturesExtractor {
+
+	@SuppressWarnings("null")
+	@Override
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		ArrayList<Feature> feats = new ArrayList<>();
+
+		//get the sentence that covers the first argument, suppose arg1 and arg2 are within the same sentence
+		Map<IdentifiedAnnotation, Collection<Sentence>> coveringMap =
+				JCasUtil.indexCovering(jCas, IdentifiedAnnotation.class, Sentence.class);
+		Collection<Sentence> sentList = coveringMap.get(arg1);
+		if (sentList == null && sentList.isEmpty()) return feats;
+
+		for(Sentence sent : sentList) {
+			List<EventMention> events = JCasUtil.selectCovered(jCas, EventMention.class, sent);
+
+			//filter out ctakes events:
+			List<EventMention> realEvents = Lists.newArrayList();
+			for( EventMention event : events){
+				if(event.getClass().equals(EventMention.class)){
+					realEvents.add(event);
+				}
+			}
+			events = realEvents;
+
+			int eventsNum = events==null? 0: events.size();
+			
+			//find the two arguments indices in the event list
+			int arg1Index = -1;
+			int arg2Index = -1;
+			for(int i=0; i< eventsNum; i++){
+				EventMention currentEvent = events.get(i);
+				if(currentEvent==arg1){
+					arg1Index = i;
+				}
+				if(currentEvent==arg2){
+					arg2Index = i;
+				}
+				if(arg1Index!=-1 && arg2Index!=-1){
+					break;
+				}
+			}
+//			feats.add(new Feature("NumOfEvents_InTheSentence", eventsNum)); //tried this feature, but it is not helpful.
+			if(arg1Index!=-1 && arg2Index!=-1){
+//				feats.add(new Feature("arg1_index", arg1Index));
+//				feats.add(new Feature("arg2_index", arg2Index)); //tried these two features, but not helpful
+//				if(arg1Index == 0 || arg2Index == 0){
+//					feats.add(new Feature("EventPair_", "ContainsTheFirstEvent"));
+//				}// tried this feature, but not helpful
+//				if(arg1Index == eventsNum-1 || arg2Index == eventsNum-1){
+//					feats.add(new Feature("EventPair_", "ContainsTheLastEvent"));
+//				}// tired, not helpful
+				int dis = Math.abs(arg1Index-arg2Index);
+				feats.add(new Feature("EventPair_Distance", dis));
+				if(dis == eventsNum-1){
+					feats.add(new Feature("EventPair_", "Major"));
+				}
+				if(dis==1){
+					feats.add(new Feature("EventPair_", "Consecutive"));
+				}
+			}else{
+				System.out.println("Same sentence events matching error.");
+			}
+		}
+		return feats;
+	}
+
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/OverlappedHeadFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/OverlappedHeadFeaturesExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/OverlappedHeadFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/OverlappedHeadFeaturesExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,79 @@
+package org.apache.ctakes.temporal.ae.feature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+/**
+ * Extract the overlapping head words of two arguments. Head words: the NNs of NP + the VBs of VP
+ * @author CH151862
+ *
+ */
+public class OverlappedHeadFeaturesExtractor extends TokenFeaturesExtractor {
+
+	@Override
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation mention1, IdentifiedAnnotation mention2)
+			throws AnalysisEngineProcessException {
+		List<Feature> features = new ArrayList<>();
+		Annotation arg1 = mention1;
+		Annotation arg2 = mention2;
+		
+		String featName = "overlappingHeadTerms";
+
+		//iterate through the tokens of two arguments
+		List<WordToken> currentTokens = JCasUtil.selectCovered(jCas, WordToken.class, arg1);
+		List<WordToken> nextTokens = JCasUtil.selectCovered(jCas, WordToken.class, arg2);
+		
+		int headSize1 = 0;
+		int headSize2 = 0;
+		int headSize  = 0;
+		int longHeadSize = 0;
+		int matches = 0;
+		for(WordToken t1: currentTokens){
+			String t1_pos = t1.getPartOfSpeech();
+			if(t1_pos.startsWith("NN")||t1_pos.startsWith("VB")){
+				headSize1 ++;
+				for(WordToken t2: nextTokens){
+					String t2_pos = t2.getPartOfSpeech();
+					if(t2_pos.startsWith("NN")||t2_pos.startsWith("VB")){
+						headSize2 ++;
+						String t1str = t1.getCanonicalForm();
+						String t2str = t2.getCanonicalForm();
+						if(t1str.equals(t2str)){
+							features.add(new Feature(featName+"_CanoticalForm", t1str));
+							features.add(new Feature(featName+"_length", t1str.length()));
+							features.add(new Feature(featName+"_POS", t1_pos));
+							matches++;
+						}
+					}
+				}
+			}
+		}
+		if(matches > 0){
+			headSize = Math.min(headSize1, headSize2);
+			longHeadSize = Math.max(headSize1, headSize2);
+			
+			//feature of counting times of matches
+			features.add(new Feature(featName+"_count", matches));
+			
+			//ratio of the count of matches to the shorter length of tokens between the two arguments
+			float matchShortRatio = (float)matches/headSize;
+			features.add(new Feature(featName+"_shortRatio", matchShortRatio));
+			
+			//ratio of the count of matches to the longer length of tokens between the two arguments
+			float matchLongRatio  = (float)matches/longHeadSize;
+			features.add(new Feature(featName+"_longRatio", matchLongRatio));
+		}
+		
+		return features;
+	}
+
+}

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java?rev=1632167&r1=1632166&r2=1632167&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java Wed Oct 15 19:29:44 2014
@@ -32,36 +32,71 @@ import org.apache.uima.jcas.JCas;
 import org.cleartk.ml.Feature;
 import org.apache.uima.fit.util.JCasUtil;
 
+import com.google.common.collect.Lists;
+
 public class SectionHeaderRelationExtractor implements RelationFeaturesExtractor{
 
 	@Override
 	public List<Feature> extract(JCas jcas, IdentifiedAnnotation arg1,
 			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
-		List<Feature> feats = new ArrayList<Feature>();
+		List<Feature> feats = new ArrayList<>();
 
 		//find event
-		EventMention event = null;
+		EventMention eventA = null;
+		EventMention eventB = null;
 		if(arg1 instanceof EventMention){
-			event = (EventMention) arg1;
-		}else if(arg1 instanceof EventMention){
-			event = (EventMention) arg2;
-		}else{
+			eventA = (EventMention) arg1;
+		}
+		if(arg2 instanceof EventMention){
+			eventB = (EventMention) arg2;
+		}
+		
+		if(eventA==null && eventB==null){
 			return feats;
 		}
 
 		//get covering segment set:
 		Map<EventMention, Collection<Segment>> coveringMap =
 				JCasUtil.indexCovering(jcas, EventMention.class, Segment.class);
-		Collection<Segment> segList = coveringMap.get(event);
-
+		List<Segment> segListA = Lists.newArrayList();
+		List<Segment> segListB = Lists.newArrayList();
+		if(eventA != null){
+			for ( Segment seg : coveringMap.get(eventA)){
+				if (!seg.getId().equals("SIMPLE_SEGMENT")){//remove simple segment
+					segListA.add(seg);
+				}
+			}
+		}
+		if(eventB != null){
+			for ( Segment seg : coveringMap.get(eventB)){
+				if (!seg.getId().equals("SIMPLE_SEGMENT")){//remove simple segment
+					segListB.add(seg);
+				}
+			}
+		}
+		
 		//get segment id
-		if (segList != null && !segList.isEmpty()){
-			for(Segment seg : segList) {
-				String segname = seg.getId();
-				Feature feature = new Feature("SegmentID", segname);
-				feats.add(feature);
+		List<String> segANames = Lists.newArrayList();
+		List<String> segBNames = Lists.newArrayList();
+		for(Segment seg : segListA) {
+			String segname = seg.getId();
+			Feature feature = new Feature("SegmentID_arg1", segname);
+			feats.add(feature);
+			segANames.add(segname);
+		}
+		for(Segment seg : segListB) {
+			String segname = seg.getId();
+			Feature feature = new Feature("SegmentID_arg2", segname);
+			feats.add(feature);
+			segBNames.add(segname);
+		}
+		for(String segA : segANames){
+			for(String segB : segBNames){
+				if(segA.equals(segB)){
+					Feature feature = new Feature("InTheSameSegment_", segA);
+					feats.add(feature);
+				}
 			}
-
 		}
 		return feats;
 	}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SpecialAnnotationRelationExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SpecialAnnotationRelationExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SpecialAnnotationRelationExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SpecialAnnotationRelationExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,157 @@
+/**
+ * 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.ae.feature;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.FractionAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.RangeAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+public class SpecialAnnotationRelationExtractor implements RelationFeaturesExtractor{
+
+	@Override
+	public List<Feature> extract(JCas jcas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		List<Feature> feats = new ArrayList<>();
+		EventMention eventA = null;
+		EventMention eventB = null;
+
+		//find event
+		if(arg1 instanceof EventMention){
+			eventA = (EventMention) arg1;
+		}else if(arg2 instanceof EventMention){
+			eventB = (EventMention) arg2;
+		}else{
+			return feats;
+		}
+
+		//1 get covering sentence:
+		Map<EventMention, Collection<Sentence>> coveringMap =
+				JCasUtil.indexCovering(jcas, EventMention.class, Sentence.class);
+
+		Sentence sentenceA = getCoveringSentence(eventA, coveringMap);
+		Sentence sentenceB = getCoveringSentence(eventB, coveringMap);
+
+		//get all special annotation that is in sentence A
+		List<RangeAnnotation> rangeInA = new ArrayList<>();
+		List<FractionAnnotation> fracInA = new ArrayList<>();
+		List<RomanNumeralAnnotation> romanInA = new ArrayList<>();
+		List<MeasurementAnnotation> measureInA = new ArrayList<>();
+		if(sentenceA != null){
+			rangeInA.addAll(JCasUtil.selectCovered(jcas, RangeAnnotation.class, sentenceA));
+			if(!rangeInA.isEmpty()) feats.add(new Feature("arg1_has_nearby_", "RangeAnnotation"));
+			fracInA.addAll(JCasUtil.selectCovered(jcas, FractionAnnotation.class, sentenceA));
+			if(!fracInA.isEmpty()) feats.add(new Feature("arg1_has_nearby_", "FractionAnnotation"));
+			romanInA.addAll(JCasUtil.selectCovered(jcas, RomanNumeralAnnotation.class, sentenceA));
+			if(!romanInA.isEmpty()) feats.add(new Feature("arg1_has_nearby_", "RomanNumeralAnnotation"));
+			measureInA.addAll(JCasUtil.selectCovered(jcas, MeasurementAnnotation.class, sentenceA));
+			if(!measureInA.isEmpty()) feats.add(new Feature("arg1_has_nearby_", "MeasurementAnnotation"));
+		}
+
+		//get all special annotation that is in sentence B
+		List<RangeAnnotation> rangeInB = new ArrayList<>();
+		List<FractionAnnotation> fracInB = new ArrayList<>();
+		List<RomanNumeralAnnotation> romanInB = new ArrayList<>();
+		List<MeasurementAnnotation> measureInB = new ArrayList<>();
+		if(sentenceB != null){
+			rangeInB.addAll(JCasUtil.selectCovered(jcas, RangeAnnotation.class, sentenceB));
+			if(!rangeInB.isEmpty()) feats.add(new Feature("arg2_has_nearby_", "RangeAnnotation"));
+			fracInB.addAll(JCasUtil.selectCovered(jcas, FractionAnnotation.class, sentenceB));
+			if(!fracInB.isEmpty()) feats.add(new Feature("arg2_has_nearby_", "FractionAnnotation"));
+			romanInB.addAll(JCasUtil.selectCovered(jcas, RomanNumeralAnnotation.class, sentenceB));
+			if(!romanInB.isEmpty()) feats.add(new Feature("arg2_has_nearby_", "RomanNumeralAnnotation"));
+			measureInB.addAll(JCasUtil.selectCovered(jcas, MeasurementAnnotation.class, sentenceB));
+			if(!measureInB.isEmpty()) feats.add(new Feature("arg2_has_nearby_", "MeasurementAnnotation"));
+		}
+
+		//check if annotation matches
+		if(sentenceA != null && sentenceB != null && sentenceA != sentenceB){
+			range:
+			for(RangeAnnotation rangeA: rangeInA){
+				for(RangeAnnotation rangeB: rangeInB){
+					if(rangeA.getCoveredText().equalsIgnoreCase(rangeB.getCoveredText())){
+						feats.add(new Feature("shareCommonRange_", rangeB.getCoveredText().toLowerCase()));
+						break range;
+					}
+				}
+			}
+
+		    fraction:
+			for(FractionAnnotation fracA: fracInA){
+				for(FractionAnnotation fracB: fracInB){
+					if(fracA.getCoveredText().equalsIgnoreCase(fracB.getCoveredText())){
+						feats.add(new Feature("shareCommonFraction_", fracB.getCoveredText().toLowerCase()));
+						break fraction;
+					}
+				}
+			}
+
+		    number:
+			for(RomanNumeralAnnotation numA: romanInA){
+				for(RomanNumeralAnnotation numB: romanInB){
+					if(numA.getCoveredText().equalsIgnoreCase(numB.getCoveredText())){
+						feats.add(new Feature("shareCommonFraction_", numB.getCoveredText().toLowerCase()));
+						break number;
+					}
+				}
+			}
+			
+			measure:
+			for(MeasurementAnnotation meaA: measureInA){
+				for(MeasurementAnnotation meaB: measureInB){
+					if(meaA.getCoveredText().equalsIgnoreCase(meaB.getCoveredText())){
+						feats.add(new Feature("shareCommonFraction_", meaB.getCoveredText().toLowerCase()));
+						break measure;
+					}
+				}
+			}
+		}
+
+
+
+		return feats;
+	}
+
+	private static Sentence getCoveringSentence(EventMention event,
+			Map<EventMention, Collection<Sentence>> coveringMap) {
+		List<Sentence> sentList = new ArrayList<>();
+		if(event != null){
+			sentList.addAll(coveringMap.get(event));			
+			if(!sentList.isEmpty()){
+				return(sentList.get(0));
+			}
+		}
+		return null;
+	}
+
+
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalPETFlatExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalPETFlatExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalPETFlatExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalPETFlatExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,175 @@
+package org.apache.ctakes.temporal.ae.feature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.constituency.parser.treekernel.TreeExtractor;
+import org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils;
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+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.utils.tree.SimpleTree;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+public class TemporalPETFlatExtractor implements RelationFeaturesExtractor {
+
+	private static final String FEAT_NAME = "Flat_DPK"; 
+
+	@Override
+	public List<Feature> extract(JCas jcas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		List<Feature> features = new ArrayList<>();
+		// first get the root and print it out...
+		TopTreebankNode root = AnnotationTreeUtils.getTreeCopy(jcas, AnnotationTreeUtils.getAnnotationTree(jcas, arg1));
+
+		if(root == null){
+			SimpleTree fakeTree = new SimpleTree("(S (NN null))");
+			features.add(new Feature(FEAT_NAME, fakeTree.toString()));
+			return features;
+		}
+
+		// swap the order if necessary:
+		if(arg2.getBegin() <= arg1.getBegin() && arg2.getEnd() <= arg1.getEnd()){
+			IdentifiedAnnotation temp = arg1;
+			arg1 = arg2;
+			arg2 = temp;
+		}
+
+		String a1type="", a2type="";
+		String eventModality="";
+		String timeClass;
+
+		if(arg1 instanceof EventMention){
+			EventMention mention = (EventMention) arg1;
+			if(mention.getEvent() != null && mention.getEvent().getProperties() != null){
+				eventModality = mention.getEvent().getProperties().getContextualModality();
+			}
+			a1type = "EVENT-"+eventModality;
+		}else if(arg1 instanceof TimeMention){
+			timeClass = ((TimeMention)arg1).getTimeClass();	
+			a1type = "TIMEX-"+timeClass;
+		}
+
+		if(arg2 instanceof EventMention){
+			EventMention mention = (EventMention) arg2;
+			if(mention.getEvent() != null && mention.getEvent().getProperties() != null){
+				eventModality = mention.getEvent().getProperties().getContextualModality();
+			}
+			a2type = "EVENT-"+eventModality;		  
+		}else if(arg2 instanceof TimeMention){
+			timeClass = ((TimeMention)arg2).getTimeClass();
+			a2type = "TIMEX-"+timeClass;		  
+		}
+
+		TreebankNode t1 = AnnotationTreeUtils.insertAnnotationNode(jcas, root, arg1, "ARG1-"+a1type);
+		TreebankNode t2 = AnnotationTreeUtils.insertAnnotationNode(jcas, root, arg2, "ARG2-"+a2type);
+
+		//		addOtherTimes(jcas,root, arg1, arg2);
+
+		SimpleTree tree = null;
+		if(t1.getBegin() <= t2.getBegin() && t1.getEnd() >= t2.getEnd()){
+			// t1 encloses t2
+			tree = TreeExtractor.getSimpleClone(t1);
+		}else if(t2.getBegin() <= t1.getBegin() && t2.getEnd() >= t1.getEnd()){
+			// t2 encloses t1
+			tree = TreeExtractor.getSimpleClone(t2);
+		}else{
+			tree = TreeExtractor.extractPathEnclosedTree(t1, t2, jcas);
+		}
+
+		tree.setGeneralizeLeaf(true);
+		moveTimexDownToNP(tree);
+		simplifyGCG(tree);
+
+		features.addAll(traverseTreeForDPath(tree));
+		return features;
+	}
+
+	private List<Feature> traverseTreeForDPath(SimpleTree tree) {
+		List<Feature> features = new ArrayList<>();
+		String rootStr = tree.cat;
+		features.add(new Feature(FEAT_NAME, rootStr));//add length 0 DPK
+		if(tree.children.size() == 1 && tree.children.get(0).children.size() == 0){//if tree is a leaf
+			features.add(new Feature(FEAT_NAME, rootStr + "-" + tree.children.get(0).cat));
+		}else{//if tree is not a leaf
+			for(SimpleTree subtree: tree.children){
+				features.addAll(traverseTreeForDPath(subtree));
+				for(String str: getSubTreeStrings(subtree)){
+					features.add(new Feature(FEAT_NAME, rootStr+"-"+str));
+				}
+			}
+		}
+		return features;
+	}
+
+	private List<String> getSubTreeStrings(SimpleTree subtree) {
+		List<String> subTreeStrings = new ArrayList<>();
+		subTreeStrings.add(subtree.cat);
+		if(subtree.children.size() == 1 && subtree.children.get(0).children.size() == 0){//if subtree is a leaf
+			subTreeStrings.add(subtree.cat + "-" + subtree.children.get(0).cat);
+		}else{ //if subtree is not a leaf
+			for(SimpleTree subsubTree: subtree.children){
+				for(String str: getSubTreeStrings(subsubTree)){
+					subTreeStrings.add(subtree.cat+"-"+str);
+				}
+			}
+		}
+		return subTreeStrings;
+	}
+
+	public static void addOtherTimes(JCas jcas, TopTreebankNode root, IdentifiedAnnotation arg1, IdentifiedAnnotation arg2) {
+		List<TimeMention> timexes = JCasUtil.selectCovered(TimeMention.class, root);
+
+		for(TimeMention timex : timexes){
+			// don't want the same timex that we are looking at the argument for...
+			if(timex.getBegin() == arg1.getBegin() && timex.getEnd() == arg1.getEnd() ||
+					timex.getBegin() == arg2.getBegin() && timex.getEnd() == arg2.getEnd()) continue;
+			// but make sure it is in the correct span...
+			if(timex.getBegin() > arg1.getBegin() && timex.getEnd() <= arg2.getBegin()){
+				AnnotationTreeUtils.insertAnnotationNode(jcas, root, timex, "TIMEX");
+			}
+		}
+	}
+
+	public static void moveTimexDownToNP(SimpleTree tree) {
+		if(tree.cat.contains("-TIMEX-")){
+			SimpleTree child = tree.children.get(0);
+			// we've found the correct node: only correct clear violations: PP -> IN NP
+			if(child.cat.contains("PP") && child.children.size() == 2 && child.children.get(0).cat.equals("IN") && child.children.get(1).cat.startsWith("NP")){
+				// swap labels
+				String fullCat = tree.cat;
+				tree.cat = "PP";
+				child.cat = fullCat;
+
+				// now point the new PP at the preposition and stop the new TIMEX from pointing at it:
+				tree.children.add(0, child.children.get(0));
+				child.children.remove(0);
+			}
+			return;
+		}else if(tree.children == null || tree.children.size() == 0){
+			return;
+		}
+		// if we are not there we have to return
+		for(SimpleTree child : tree.children){
+			moveTimexDownToNP(child);
+		}
+	}
+
+	public static void simplifyGCG(SimpleTree tree){
+		if(tree.children == null || tree.children.size() == 0) return;
+
+		int ampInd = tree.cat.indexOf('+');
+		if(ampInd > 0){
+			tree.cat = tree.cat.substring(0, ampInd);
+		}
+		for(SimpleTree child : tree.children){
+			simplifyGCG(child);
+		}
+	}
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXPropertyRelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXPropertyRelationFeaturesExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXPropertyRelationFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXPropertyRelationFeaturesExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,85 @@
+/**
+ * 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.ae.feature;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+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.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+import com.google.common.collect.Lists;
+/**
+ * Check is an timex argument is in the begining/end of a sentence 
+ * @author CH151862
+ *
+ */
+public class TimeXPropertyRelationFeaturesExtractor implements RelationFeaturesExtractor {
+
+	private String name="TimeXProperty";
+
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		List<Feature> features = Lists.newArrayList();
+
+		List<TimeMention> times = Lists.newArrayList();
+		if(arg1 instanceof TimeMention) times.add((TimeMention)arg1);
+		if(arg2 instanceof TimeMention) times.add((TimeMention)arg2);
+
+		Map<TimeMention, Collection<Sentence>> coveringMap =
+				JCasUtil.indexCovering(jCas, TimeMention.class, Sentence.class);
+
+		for(TimeMention time : times){
+			Collection<Sentence> sentList = coveringMap.get(time);
+
+			//get time class
+			String timeclass = time.getTimeClass();
+			if(timeclass != null) features.add(new Feature("TimeClass", timeclass));
+			
+			//check if it contains only one word
+			List<WordToken> timewords = Lists.newArrayList();
+			timewords.addAll(JCasUtil.selectCovered(jCas, WordToken.class, time));
+			if(timewords.size()==1){
+				features.add(new Feature(name, "one_word"));
+			}
+			
+			//get position in sentence
+			for(Sentence sent : sentList) {
+				if(sent.getBegin()==time.getBegin() && time.getEnd()>=(sent.getEnd()-2)){
+					features.add(new Feature(name, "entire_sentence"));
+				}else if(sent.getBegin()==time.getBegin()){
+					features.add(new Feature(name, "beginning_of_sentence"));
+				}else if(time.getEnd()>=(sent.getEnd()-2)){//allow a sentence to have a space and a period.
+					features.add(new Feature(name, "end_of_sentence"));
+				}
+			}
+		}
+
+		return features;
+	}
+
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXRelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXRelationFeaturesExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXRelationFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXRelationFeaturesExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,114 @@
+/**
+ * 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.ae.feature;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.TimeAnnotation;
+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.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+import com.google.common.collect.Lists;
+/**
+ * extract the nearby nearest time, date information for any event 
+ * @author CH151862
+ *
+ */
+public class TimeXRelationFeaturesExtractor implements RelationFeaturesExtractor {
+
+	private String name="TimeXRelatioinFeature";
+
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		List<Feature> features = Lists.newArrayList();
+
+		List<EventMention> events = Lists.newArrayList();
+		if(arg1 instanceof EventMention) events.add((EventMention)arg1);
+		if(arg2 instanceof EventMention) events.add((EventMention)arg2);
+
+		Map<EventMention, Collection<Sentence>> coveringMap =
+				JCasUtil.indexCovering(jCas, EventMention.class, Sentence.class);
+
+		for(EventMention event : events){
+			Collection<Sentence> sentList = coveringMap.get(event);
+
+			//2 get TimeX
+			Map<Integer, IdentifiedAnnotation> timeDistMap = new TreeMap<>();
+
+			for(Sentence sent : sentList) {
+				for (TimeMention time : JCasUtil.selectCovered(jCas, TimeMention.class, sent)) {
+					timeDistMap.put(Math.abs(time.getBegin() - event.getBegin()), time);
+				}
+				for (TimeAnnotation time : JCasUtil.selectCovered(jCas, TimeAnnotation.class, sent)) {
+					timeDistMap.put(Math.abs(time.getBegin() - event.getBegin()), time);
+				}
+				for (DateAnnotation time : JCasUtil.selectCovered(jCas, DateAnnotation.class, sent)) {
+					timeDistMap.put(Math.abs(time.getBegin() - event.getBegin()), time);
+				}
+			}
+
+			//get the closest Time Expression feature
+			for (Map.Entry<Integer, IdentifiedAnnotation> entry : timeDistMap.entrySet()) {
+				Feature feature = new Feature(this.name, entry.getValue().getCoveredText());
+				features.add(feature);
+				//			  logger.info("add time feature: "+ entry.getValue().getCoveredText() + entry.getValue().getTimeClass());
+				Feature indicator = new Feature("TimeXNearby", this.name);
+				features.add(indicator);
+				Feature type = new Feature("TimeXType", entry.getValue().getClass());
+				features.add(type);
+
+				//add PP get Heading preposition
+				for(TreebankNode treebankNode : JCasUtil.selectCovering(
+						jCas, 
+						TreebankNode.class, 
+						entry.getValue().getBegin(), 
+						entry.getValue().getEnd())) {
+
+					if(treebankNode.getNodeType().equals("PP")) {
+						Feature PPNodeType = new Feature("Timex_PPNodeType", treebankNode.getNodeType());
+						features.add(PPNodeType);
+						String value = treebankNode.getNodeValue();
+						if(value != null)
+							features.add(new Feature("Timex_PPNodeValue_", value));
+						features.add(new Feature("PP_Timex_", entry.getValue().getClass().getCanonicalName()));
+						break;
+					}
+				}
+
+				break;
+
+			}
+		}
+
+		return features;
+	}
+
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TokenPropertyFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TokenPropertyFeaturesExtractor.java?rev=1632167&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TokenPropertyFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TokenPropertyFeaturesExtractor.java Wed Oct 15 19:29:44 2014
@@ -0,0 +1,126 @@
+package org.apache.ctakes.temporal.ae.feature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
+import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
+import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
+import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
+
+public class TokenPropertyFeaturesExtractor implements
+RelationFeaturesExtractor {
+
+	@SuppressWarnings("null")
+	@Override
+	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+		ArrayList<Feature> feats = new ArrayList<>();
+
+		List<BaseToken> arg1Tokens = JCasUtil.selectCovered(jCas, BaseToken.class, arg1);
+		List<BaseToken> arg2Tokens = JCasUtil.selectCovered(jCas, BaseToken.class, arg2);
+
+		int arg1Length = arg1Tokens == null ? 0 : arg1Tokens.size();
+		int arg2Length = arg2Tokens == null ? 0 : arg2Tokens.size();
+
+		//get token size feature:
+		feats.add(new Feature("arg1_tokenSize", arg1Length));
+		feats.add(new Feature("arg2_tokenSize", arg2Length));
+
+		for(BaseToken bt : arg1Tokens){
+			if(bt.getPartOfSpeech().startsWith("VB")){
+				feats.add(new Feature("arg1_contains", "VB"));
+				break;
+			}
+		}
+		for(BaseToken bt : arg2Tokens){
+			if(bt.getPartOfSpeech().startsWith("VB")){
+				feats.add(new Feature("arg2_contains", "VB"));
+				break;
+			}
+		}
+
+		if(arg1Length == 0 || arg2Length == 0){
+			return feats;
+		}
+
+		//check if the last token match:
+		String arg1last = arg1Tokens.get(arg1Length-1).getCoveredText().toLowerCase();
+		String arg2last = arg2Tokens.get(arg2Length-1).getCoveredText().toLowerCase();
+		if(arg1last.equals(arg2last)){
+			feats.add(new Feature("contain_matching_last_token", true));
+			feats.add(new Feature("matching_last_token_", arg1last));
+		}
+
+		//check if contains the same anatomical sites:
+		List<AnatomicalSiteMention> arg1anaSites = JCasUtil.selectCovered(jCas, AnatomicalSiteMention.class, arg1);
+		List<AnatomicalSiteMention> arg2anaSites = JCasUtil.selectCovered(jCas, AnatomicalSiteMention.class, arg2);
+		for(AnatomicalSiteMention siteA : arg1anaSites){
+			for(AnatomicalSiteMention siteB : arg2anaSites){
+				if(siteA.getCoveredText().equalsIgnoreCase(siteB.getCoveredText())){
+					feats.add(new Feature("contain_matching_anatomicalSite", true));
+					feats.add(new Feature("matching_anatomicalSite_", siteA.getCoveredText().toLowerCase()));
+				}
+			}
+		}
+
+		//check if contains the same procedure:
+		List<ProcedureMention> arg1procedure = JCasUtil.selectCovered(jCas, ProcedureMention.class, arg1);
+		List<ProcedureMention> arg2procedure = JCasUtil.selectCovered(jCas, ProcedureMention.class, arg2);
+		for(ProcedureMention proA : arg1procedure){
+			for(ProcedureMention proB : arg2procedure){
+				if(proA.getCoveredText().equalsIgnoreCase(proB.getCoveredText())){
+					feats.add(new Feature("contain_matching_Procedure", true));
+					feats.add(new Feature("matching_Procedure_", proA.getCoveredText().toLowerCase()));
+				}
+			}
+		}
+
+		//check if contains the same Sign and Symptom:
+		List<SignSymptomMention> arg1ss = JCasUtil.selectCovered(jCas, SignSymptomMention.class, arg1);
+		List<SignSymptomMention> arg2ss = JCasUtil.selectCovered(jCas, SignSymptomMention.class, arg2);
+		for(SignSymptomMention ssA : arg1ss){
+			for(SignSymptomMention ssB : arg2ss){
+				if(ssA.getCoveredText().equalsIgnoreCase(ssB.getCoveredText())){
+					feats.add(new Feature("contain_matching_SignSymptom", true));
+					feats.add(new Feature("matching_SignSymptom_", ssA.getCoveredText().toLowerCase()));
+				}
+			}
+		}
+
+		//check if contains the same Disease Disorder:
+		List<DiseaseDisorderMention> arg1dd = JCasUtil.selectCovered(jCas, DiseaseDisorderMention.class, arg1);
+		List<DiseaseDisorderMention> arg2dd = JCasUtil.selectCovered(jCas, DiseaseDisorderMention.class, arg2);
+		for(DiseaseDisorderMention ddA : arg1dd){
+			for(DiseaseDisorderMention ddB : arg2dd){
+				if(ddA.getCoveredText().equalsIgnoreCase(ddB.getCoveredText())){
+					feats.add(new Feature("contain_matching_DiseaseDisorder", true));
+					feats.add(new Feature("matching_DiseaseDisorder_", ddA.getCoveredText().toLowerCase()));
+				}
+			}
+		}
+
+		//check if contains the same Medication:
+		List<MedicationMention> arg1med = JCasUtil.selectCovered(jCas, MedicationMention.class, arg1);
+		List<MedicationMention> arg2med = JCasUtil.selectCovered(jCas, MedicationMention.class, arg2);
+		for(MedicationMention medA : arg1med){
+			for(MedicationMention medB : arg2med){
+				if(medA.getCoveredText().equalsIgnoreCase(medB.getCoveredText())){
+					feats.add(new Feature("contain_matching_Medication", true));
+					feats.add(new Feature("matching_Medication_", medA.getCoveredText().toLowerCase()));
+				}
+			}
+		}
+
+		return feats;
+	}
+
+}



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