dl-learner-svn — DL-Learner Subversion commits

[DL-Learner SVN] SF.net SVN: dl-learner:[4285] trunk/components-core/src/main/java/org/ dllearner/reasoning/OWLPunningDetector.java

[<lor...@us...>]

Revision: 4285
          http://sourceforge.net/p/dl-learner/code/4285
Author:   lorenz_b
Date:     2014-08-06 12:19:49 +0000 (Wed, 06 Aug 2014)
Log Message:
-----------
Updated OWL API.

Added Paths:
-----------
    trunk/components-core/src/main/java/org/dllearner/reasoning/OWLPunningDetector.java

Added: trunk/components-core/src/main/java/org/dllearner/reasoning/OWLPunningDetector.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/OWLPunningDetector.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/OWLPunningDetector.java	2014-08-06 12:19:49 UTC (rev 4285)
@@ -0,0 +1,54 @@
+/**
+ * 
+ */
+package org.dllearner.reasoning;
+
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class OWLPunningDetector {
+	
+	/**
+	 * This object property is used to connect individuals with classes that are also individuals, thus, lead to punning.
+	 */
+	public static final ObjectProperty punningProperty = new ObjectProperty("http://dl-learner.org/punning/relatedTo");
+	
+	/**
+	 * Checks whether the same IRI denotes both a class and an individual in the ontology.
+	 * @param ontology
+	 * @param iri
+	 * @return
+	 */
+	public static boolean hasPunning(OWLOntology ontology, NamedClass cls){
+		return hasPunning(ontology, IRI.create(cls.getName()));
+	}
+	
+	/**
+	 * Checks whether the same IRI denotes both a class and an individual in the ontology.
+	 * @param ontology
+	 * @param iri
+	 * @return
+	 */
+	public static boolean hasPunning(OWLOntology ontology, IRI iri){
+		boolean isClass = ontology.getClassesInSignature().contains(ontology.getOWLOntologyManager().getOWLDataFactory().getOWLClass(iri));
+		boolean isIndividual = ontology.getIndividualsInSignature().contains(ontology.getOWLOntologyManager().getOWLDataFactory().getOWLNamedIndividual(iri));
+		return isClass && isIndividual;
+	}
+	
+	/**
+	 * Checks whether the same IRI denotes both a class and an individual in the ontology.
+	 * @param ontology
+	 * @param iri
+	 * @return
+	 */
+	public static boolean hasPunning(OWLOntology ontology, String iri){
+		return hasPunning(ontology, IRI.create(iri));
+	}
+
+}

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4284] trunk/scripts/pom.xml

[<lor...@us...>]

Revision: 4284
          http://sourceforge.net/p/dl-learner/code/4284
Author:   lorenz_b
Date:     2014-08-06 11:52:27 +0000 (Wed, 06 Aug 2014)
Log Message:
-----------
Updated OWL API.

Modified Paths:
--------------
    trunk/scripts/pom.xml

Modified: trunk/scripts/pom.xml
===================================================================
--- trunk/scripts/pom.xml	2014-08-06 11:41:26 UTC (rev 4283)
+++ trunk/scripts/pom.xml	2014-08-06 11:52:27 UTC (rev 4284)
@@ -129,7 +129,6 @@
 		<dependency>
 			<groupId>net.sourceforge.owlapi</groupId>
 			<artifactId>owlapi-distribution</artifactId>
-			<version>3.5.1-SNAPSHOT</version>
 		</dependency>
 		<!-- <dependency>
 			<groupId>net.sourceforge.owlapi</groupId>

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4283] trunk

[<lor...@us...>]

Revision: 4283
          http://sourceforge.net/p/dl-learner/code/4283
Author:   lorenz_b
Date:     2014-08-06 11:41:26 +0000 (Wed, 06 Aug 2014)
Log Message:
-----------
Updated OWL API.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/DatatypeProperty.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/Description.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/NamedClass.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyExpression.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyInverse.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectQuantorRestriction.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectSomeRestriction.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/PropertyExpression.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java
    trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLSyntaxObjectRenderer.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java
    trunk/components-core/src/test/java/org/dllearner/test/PunningTest.java
    trunk/components-core/src/test/resources/punning_example.ttl
    trunk/pom.xml

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -346,6 +346,9 @@
 			
 		if(writeSearchTree) {
 			File f = new File(searchTreeFile );
+			if(f.getParentFile() != null){
+				f.getParentFile().mkdirs();
+			}
 			Files.clearFile(f);
 		}
 		

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DatatypeProperty.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DatatypeProperty.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DatatypeProperty.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -52,6 +52,14 @@
     public URI getURI() {
     	return URI.create(name);
     }	
+    
+    /* (non-Javadoc)
+     * @see org.dllearner.core.owl.PropertyExpression#isAnonymous()
+     */
+    @Override
+    public boolean isAnonymous() {
+    	return false;
+    }
 	
 	@Override
 	public String toString() {

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/Description.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/Description.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/Description.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -25,6 +25,8 @@
 import java.util.Map;
 import java.util.Set;
 
+import org.semanticweb.owlapi.model.OWLRuntimeException;
+
 /**
  * A class description is sometimes also called "complex class" or "concept". 
  * 
@@ -216,8 +218,20 @@
 		return this instanceof NamedClass;
 	}
 	
+	/**
+     * Determines whether or not this expression represents an anonymous class
+     * expression.
+     * 
+     * @return {@code true} if this is an anonymous class expression, or
+     *         {@code false} if this is a named class ( {@code OWLClass})
+     */
+    public boolean isAnonymous(){
+    	return true;
+    };
+	
 	public NamedClass asNamedClass(){
-		return (NamedClass)this;
+		 throw new OWLRuntimeException(
+	                "Not an OWLClass.  This method should only be called if the isAnonymous method returns false!");
 	}
 	
 	/**

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/NamedClass.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/NamedClass.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/NamedClass.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -56,6 +56,22 @@
     	return URI.create(name);
     }
     
+    /* (non-Javadoc)
+     * @see org.dllearner.core.owl.Description#isAnonymous()
+     */
+    @Override
+    public boolean isAnonymous() {
+    	return false;
+    }
+    
+    /* (non-Javadoc)
+     * @see org.dllearner.core.owl.Description#asNamedClass()
+     */
+    @Override
+    public NamedClass asNamedClass() {
+    	return this;
+    }
+    
 	public int getLength() {
 		return 1;
 	}

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -46,7 +46,23 @@
 	
     public URI getURI() {
     	return URI.create(name);
-    }	
+    }
+    
+    /* (non-Javadoc)
+     * @see org.dllearner.core.owl.ObjectPropertyExpression#asObjectProperty()
+     */
+    @Override
+    public ObjectProperty asObjectProperty() {
+    	return this;
+    }
+    
+    /* (non-Javadoc)
+     * @see org.dllearner.core.owl.PropertyExpression#isAnonymous()
+     */
+    @Override
+    public boolean isAnonymous() {
+    	return false;
+    }
 	
 	@Override		
 	public String toString() {

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyExpression.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyExpression.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyExpression.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -21,6 +21,8 @@
 
 import java.io.Serializable;
 
+import org.semanticweb.owlapi.model.OWLRuntimeException;
+
 /**
  * An object property expression is an object property construct, which
  * can be used in axioms, e.g. complex class descriptions. It can be
@@ -52,7 +54,21 @@
 		result = prime * result + ((name == null) ? 0 : name.hashCode());
 		return result;
 	}
-
+	
+	 /**
+     * If the property is a named object property then this method will obtain
+     * the property as such. The general pattern of use is that the
+     * {@code isAnonymous} method should first be used to determine if the
+     * property is named (i.e. not an object property expression such as
+     * inv(p)). If the property is named then this method may be used to obtain
+     * the property as a named property without casting.
+     * 
+     * @return The property as an {@code ObjectProperty} if possible.
+     * @throws OWLRuntimeException
+     *         if the property is not a named property.
+     */
+	public abstract ObjectProperty asObjectProperty();
+	
 	@Override
 	public boolean equals(Object obj) {
 		if (this == obj)

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyInverse.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyInverse.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyInverse.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -22,6 +22,7 @@
 import java.util.Map;
 
 import org.dllearner.utilities.Helper;
+import org.semanticweb.owlapi.model.OWLRuntimeException;
 
 /**
  * Represents the inverse of a property expression. It can be used
@@ -49,6 +50,23 @@
 	public int getLength() {
 		return 2;
 	}
+	
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.owl.ObjectPropertyExpression#asObjectProperty()
+	 */
+	@Override
+	public ObjectProperty asObjectProperty() {
+		 throw new OWLRuntimeException(
+	                "Property is not a named property.  Check using the isAnonymous method before calling this method!");
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.owl.PropertyExpression#isAnonymous()
+	 */
+	@Override
+	public boolean isAnonymous() {
+		return true;
+	}
 		
 	public String toString(String baseURI, Map<String,String> prefixes) {
 		return Helper.getAbbreviatedString(name, baseURI, prefixes) + "-";

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectQuantorRestriction.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectQuantorRestriction.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectQuantorRestriction.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -19,6 +19,7 @@
 
 package org.dllearner.core.owl;
 
+
 /**
  * 
  * @author Jens Lehmann
@@ -26,9 +27,6 @@
  */
 public abstract class ObjectQuantorRestriction extends QuantorRestriction {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = -5482730659805823042L;
 
 	public ObjectQuantorRestriction(ObjectPropertyExpression role, Description c) {

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectSomeRestriction.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectSomeRestriction.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectSomeRestriction.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -29,9 +29,6 @@
  */
 public class ObjectSomeRestriction extends ObjectQuantorRestriction {
 
-    /**
-	 * 
-	 */
 	private static final long serialVersionUID = 858960420513908151L;
 
 	public ObjectSomeRestriction(ObjectPropertyExpression role, Description c) {

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/PropertyExpression.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/PropertyExpression.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/PropertyExpression.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -24,5 +24,14 @@
  *
  */
 public interface PropertyExpression extends KBElement {
+	
+	/**
+     * Determines if this property expression is anonymous.
+     * 
+     * @return {@code true} if the property expression is anonymous (because it
+     *         is the inverse of a property). {@code false} if this property is
+     *         a named object property or named data property.
+     */
+    boolean isAnonymous();
 
 }

Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -26,6 +26,7 @@
 import java.io.ObjectInputStream;
 import java.io.ObjectOutputStream;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -153,7 +154,7 @@
     private boolean materializeExistentialRestrictions = false;
 
 	private boolean useCaching = true;
-    
+    private boolean handlePunning = true;
 
     public enum ForallSemantics { 
     	Standard, // standard all quantor
@@ -271,6 +272,7 @@
 			HashFunction hf = Hashing.md5();
 			Hasher hasher = hf.newHasher();
 			hasher.putBoolean(materializeExistentialRestrictions);
+			hasher.putBoolean(handlePunning);
 			for (OWLOntology ont : rc.getOWLAPIOntologies()) {
 				hasher.putInt(ont.getLogicalAxioms().hashCode());
 				hasher.putInt(ont.getAxioms().hashCode());
@@ -373,6 +375,7 @@
 			sd.put(dp, rc.getStringDatatypeMembers(dp));
 		}			
 		
+		
 		if(materializeExistentialRestrictions){
 			ExistentialRestrictionMaterialization materialization = new ExistentialRestrictionMaterialization(rc.getReasoner().getRootOntology());
 			for (NamedClass cls : atomicConcepts) {
@@ -384,6 +387,42 @@
 			}
 		}
 		
+		//materialize facts based on OWL punning, i.e.:
+		//for each A in N_C
+		if(handlePunning){
+			OWLOntology ontology = rc.getReasoner().getRootOntology();
+			
+			Individual genericIndividual = new Individual("http://dl-learner.org/punning#genInd");
+			Map<Individual, SortedSet<Individual>> map = new HashMap<Individual, SortedSet<Individual>>();
+			for (Individual individual : individuals) {
+				SortedSet<Individual> objects = new TreeSet<Individual>();
+				objects.add(genericIndividual);
+				map.put(individual, objects);
+			}
+			for (NamedClass cls : atomicConcepts) {
+				classInstancesNeg.get(cls).add(genericIndividual);
+				if(OWLPunningDetector.hasPunning(ontology, cls)){
+					Individual clsAsInd = new Individual(cls.getName());
+					//for each x \in N_I with A(x) we add relatedTo(x,A)
+					SortedSet<Individual> individuals = classInstancesPos.get(cls);
+					for (Individual individual : individuals) {
+						SortedSet<Individual> objects = map.get(individual);
+						if(objects == null){
+							objects = new TreeSet<Individual>();
+							map.put(individual, objects);
+						}
+						objects.add(clsAsInd);
+						
+					}
+				}
+			}
+			opPos.put(OWLPunningDetector.punningProperty, map);
+			atomicRoles = new TreeSet<ObjectProperty>(atomicRoles);
+			atomicRoles.add(OWLPunningDetector.punningProperty);
+			atomicRoles = Collections.unmodifiableSet(atomicRoles);
+//			individuals.add(genericIndividual);
+		}
+		
 		long dematDuration = System.currentTimeMillis() - dematStartTime;
 		logger.debug("TBox dematerialised in " + dematDuration + " ms");
 	}
@@ -482,6 +521,9 @@
 			}
 			ObjectProperty op = (ObjectProperty) ope;
 			Description child = description.getChild(0);
+			if(handlePunning && op == OWLPunningDetector.punningProperty && child.equals(new NamedClass(Thing.uri.toString()))){
+				return true;
+			}
 			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
 
 			if (mapping == null) {
@@ -489,7 +531,8 @@
 						+ ").");
 				return false;
 			}
-			SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+			
+			SortedSet<Individual> roleFillers = mapping.get(individual);
 			if (roleFillers == null) {
 				return false;
 			}
@@ -565,7 +608,9 @@
 				return true;
 			}
 			// return false if there are none or not enough role fillers
-			if (roleFillers == null || roleFillers.size() < number) {
+			if (roleFillers == null
+					|| (roleFillers.size() < number && op != OWLPunningDetector.punningProperty)
+					) {
 				return false;
 			}
 
@@ -574,7 +619,9 @@
 				index++;
 				if (hasTypeImpl(child, roleFiller)) {
 					nrOfFillers++;
-					if (nrOfFillers == number) {
+					if (nrOfFillers == number 
+							|| (handlePunning && op == OWLPunningDetector.punningProperty)
+							) {
 						return true;
 					}
 					// early abort: e.g. >= 10 hasStructure.Methyl;
@@ -763,7 +810,7 @@
 						+ description + " unsupported. Inverse object properties not supported.");
 			}
 			ObjectProperty op = (ObjectProperty) ope;
-			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);			
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);	
 			
 			// each individual is connected to a set of individuals via the property;
 			// we loop through the complete mapping
@@ -1265,4 +1312,18 @@
 	public void setMaterializeExistentialRestrictions(boolean materializeExistentialRestrictions) {
 		this.materializeExistentialRestrictions = materializeExistentialRestrictions;
 	}
+	
+	/**
+	 * @param handlePunning the handlePunning to set
+	 */
+	public void setHandlePunning(boolean handlePunning) {
+		this.handlePunning = handlePunning;
+	}
+	
+	/**
+	 * @param useCaching the useCaching to set
+	 */
+	public void setUseMaterializationCaching(boolean useCaching) {
+		this.useCaching = useCaching;
+	}
 }

Modified: trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -75,6 +75,7 @@
 import org.dllearner.utilities.Helper;
 import org.dllearner.utilities.owl.ConceptComparator;
 import org.dllearner.utilities.owl.ConceptTransformation;
+import org.dllearner.utilities.owl.OWLAPIDescriptionConvertVisitor;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import com.google.common.collect.Sets;
@@ -499,15 +500,17 @@
 			}
 		
 		} else if (description instanceof Intersection) {
-				
+			
+				System.out.println("REFINING: " + OWLAPIDescriptionConvertVisitor.getOWLClassExpression(description));
 			// refine one of the elements
 			for(Description child : description.getChildren()) {
-				
+				System.out.println(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(child));
+				System.out.println(maxLength - description.getLength()+child.getLength());
 				// refine the child; the new max length is the current max length minus
 				// the currently considered concept plus the length of the child
 				// TODO: add better explanation
 				tmp = refine(child, maxLength - description.getLength()+child.getLength(),null,currDomain);
-				
+				System.out.println(tmp);
 				// create new intersection
 				for(Description c : tmp) {
 					List<Description> newChildren = (List<Description>)((LinkedList<Description>)description.getChildren()).clone();

Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLSyntaxObjectRenderer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLSyntaxObjectRenderer.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLSyntaxObjectRenderer.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -254,6 +254,12 @@
 
 	@Override
 	public void visit(OWLAsymmetricObjectPropertyAxiom axiom) {
+		axiom.getProperty().accept(this);
+		writeSpace();
+		write(DISJOINT_WITH);
+		writeSpace();
+		axiom.getProperty().accept(this);
+		write(INVERSE);
 	}
 
 	@Override

Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -22,6 +22,10 @@
 import java.util.Comparator;
 
 import org.dllearner.core.EvaluatedDescription;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.reasoning.OWLPunningDetector;
 
 /**
  * Comparator for evaluated descriptions, which orders them by
@@ -47,8 +51,12 @@
 		else if(acc1 < acc2)
 			return -1;
 		else {
-			int length1 = ed1.getDescriptionLength();
-			int length2 = ed2.getDescriptionLength();
+			int length1 = 
+					getLength(ed1);
+//			ed1.getDescriptionLength();
+			int length2 = 
+					getLength(ed2);
+//			ed2.getDescriptionLength();
 			if(length1 < length2)
 				return 1;
 			else if(length1 > length2)
@@ -57,5 +65,20 @@
 				return cc.compare(ed1.getDescription(), ed2.getDescription());
 		}
 	}
+	
+	private int getLength(EvaluatedDescription ed){
+		int length = 0;
+		Description d = ed.getDescription();
+		if(d instanceof Intersection){
+			for (Description child : d.getChildren()) {
+				if(child instanceof ObjectSomeRestriction && ((ObjectSomeRestriction) child).getRole().asObjectProperty() == OWLPunningDetector.punningProperty){
+					length += child.getChild(0).getLength();
+				} else {
+					length += child.getLength();
+				}
+			}
+		}
+		return length;
+	}
 
 }
\ No newline at end of file

Modified: trunk/components-core/src/test/java/org/dllearner/test/PunningTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/PunningTest.java	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/test/java/org/dllearner/test/PunningTest.java	2014-08-06 11:41:26 UTC (rev 4283)
@@ -3,37 +3,48 @@
  */
 package org.dllearner.test;
 
-import java.io.ByteArrayInputStream;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
+import java.util.SortedSet;
 
 import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.algorithms.celoe.OEHeuristicRuntime;
 import org.dllearner.core.AbstractCELA;
-import org.dllearner.core.AbstractLearningProblem;
-import org.dllearner.core.AbstractReasonerComponent;
 import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.EvaluatedDescription;
 import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.owl.Description;
 import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.core.owl.Thing;
 import org.dllearner.kb.OWLAPIOntology;
 import org.dllearner.learningproblems.PosNegLPStandard;
-import org.dllearner.reasoning.FastInstanceChecker;
-import org.dllearner.utilities.owl.OWLAPIConverter;
+import org.dllearner.reasoning.MaterializableFastInstanceChecker;
+import org.dllearner.reasoning.OWLPunningDetector;
+import org.dllearner.refinementoperators.RhoDRDown;
+import org.dllearner.utilities.owl.DLSyntaxObjectRenderer;
 import org.dllearner.utilities.owl.OWLAPIDescriptionConvertVisitor;
 import org.junit.Assert;
 import org.junit.Test;
 import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLClass;
 import org.semanticweb.owlapi.model.OWLDataFactory;
-import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLEntity;
 import org.semanticweb.owlapi.model.OWLNamedIndividual;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.owllink.parser.OWLlinkDescriptionElementHandler;
 
 import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
 
 import com.google.common.collect.Sets;
+import com.google.common.collect.Sets.SetView;
 
 /**
  * @author Lorenz Buehmann
@@ -41,87 +52,35 @@
  */
 public class PunningTest {
 	
-	
-	public OWLOntology makeExampleKB() throws OWLOntologyCreationException{
-		String kb = "@prefix owl:<http://www.w3.org/2002/07/owl#> . @prefix :<http://foo.org/> .";
-		kb += ":p a owl:ObjectProperty .";
-		
-		for (int i = 1; i <= 5; i++) {
-			kb += ":r" + i + " a owl:ObjectProperty .";
-		}
-		
-		kb += ":A a owl:Class; :r1 :o1; :r2 :o2 .";
-		kb += ":B a owl:Class; :r1 :o3; :r3 :o2 .";
-		
-		for (int i = 1; i <= 10; i++) {
-			kb += ":x" + i + " a owl:NamedIndividual .";
-		}
-		
-		int m = 5;
-		int n = 5;
-		
-		//m instances of A
-		for (int i = 1; i <= m; i++) {
-			kb += ":x" + i + " a :A .";
-		}
-		
-		//n instances of B
-		for (int i = 1; i <= n; i++) {
-			kb += ":x" + i + " a :A .";
-		}
-		
-		OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new ByteArrayInputStream(kb.getBytes()));
-		return ontology;
-	}
-	
 	public OWLOntology loadExample() throws OWLOntologyCreationException{
 		OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(this.getClass().getClassLoader().getResourceAsStream("punning_example.ttl"));
 		return ontology;
 	}
 	
 	@Test
-	public void testPunning() throws OWLOntologyCreationException, ComponentInitException{
-		OWLOntology ontology = makeExampleKB();
-		OWLDataFactory df = new OWLDataFactoryImpl();
+	public void testPunningExists() throws OWLOntologyCreationException, ComponentInitException{
+		OWLOntology ontology = loadExample();
 		
-		//check that A and B are both, individual and class
-		OWLClass clsA = df.getOWLClass(IRI.create("http://foo.org/A"));
-		OWLClass clsB = df.getOWLClass(IRI.create("http://foo.org/B"));
-		OWLIndividual indA = df.getOWLNamedIndividual(IRI.create("http://foo.org/A"));
-		OWLIndividual indB = df.getOWLNamedIndividual(IRI.create("http://foo.org/B"));
-		
+		Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
 		Set<OWLClass> classes = ontology.getClassesInSignature();
-		Set<OWLObjectProperty> properties = ontology.getObjectPropertiesInSignature();
-		Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
 		
-		System.out.println("Classes:" + classes);
-		System.out.println("Properties:" + properties);
-		System.out.println("Individuals:" + individuals);
+		SetView<IRI> intersection = Sets.intersection(toIRI(individuals), toIRI(classes));
+		System.out.println("Entities that are class and individual:\n" + intersection);
+		Assert.assertTrue(!intersection.isEmpty());
 		
-		Assert.assertTrue(
-				ontology.getClassesInSignature().contains(clsA) && 
-				ontology.getClassesInSignature().contains(clsB) &&
-				ontology.getIndividualsInSignature().contains(indA) &&
-				ontology.getIndividualsInSignature().contains(indB)
-				);
-		
-		KnowledgeSource ks = new OWLAPIOntology(ontology);
-		ks.init();
-		
-		AbstractReasonerComponent rc = new FastInstanceChecker(ks);
-		rc.init();
-		
-		AbstractLearningProblem lp = new PosNegLPStandard(rc);
-		lp.init();
-		
-		AbstractCELA la = new CELOE(lp, rc);
-		la.init();
-		
-		la.start();
 	}
 	
+	private Set<IRI> toIRI(Set<? extends OWLEntity> entities){
+		Set<IRI> iris = new HashSet<IRI>();
+		for (OWLEntity e : entities) {
+			iris.add(e.getIRI());
+		}
+		return iris;
+	}
+	
 	@Test
-	public void testPunning2() throws OWLOntologyCreationException, ComponentInitException{
+	public void testPunning() throws OWLOntologyCreationException, ComponentInitException{
+		ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
 		OWLOntology ontology = loadExample();
 		OWLDataFactory df = new OWLDataFactoryImpl();
 		
@@ -138,18 +97,83 @@
 		KnowledgeSource ks = new OWLAPIOntology(ontology);
 		ks.init();
 		
-		AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+		MaterializableFastInstanceChecker rc = new MaterializableFastInstanceChecker(ks);
+//		rc.setUseMaterializationCaching(false);
+		rc.setHandlePunning(true);
+		rc.setUseMaterializationCaching(false);
 		rc.init();
+		rc.setBaseURI("http://ex.org/");
 		
 		PosNegLPStandard lp = new PosNegLPStandard(rc);
 		lp.setPositiveExamples(posExamples);
 		lp.setNegativeExamples(negExamples);
 		lp.init();
 		
-		AbstractCELA la = new CELOE(lp, rc);
+		CELOE la = new CELOE(lp, rc);
+		la.setWriteSearchTree(true);
+		la.setSearchTreeFile("log/punning_search_tree.txt");
+		la.setReplaceSearchTree(true);
+		la.setMaxNrOfResults(50);
+		la.setMaxExecutionTimeInSeconds(20);
+		la.setExpandAccuracy100Nodes(true);
+		OEHeuristicRuntime heuristic = new OEHeuristicRuntime();
+//		heuristic.setExpansionPenaltyFactor(0.001);
+//		la.setHeuristic(heuristic);
 		la.init();
+		((RhoDRDown)la.getOperator()).setUseNegation(false);
+//		la.start();
 		
-		la.start();
+		System.out.println("Classes: " + ontology.getClassesInSignature());
+		System.out.println("Individuals: " + ontology.getIndividualsInSignature());
+		
+		Description d = new Intersection(new NamedClass("http://ex.org/Fahrzeug"));
+		System.out.println(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(d));
+		SortedSet<Individual> individuals = rc.getIndividuals(d);
+		System.out.println(individuals);
+
+		d = new Intersection(new NamedClass("http://ex.org/Fahrzeug"), new ObjectSomeRestriction(
+				OWLPunningDetector.punningProperty, Thing.instance));
+		System.out.println(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(d));
+		individuals = rc.getIndividuals(d);
+		System.out.println(individuals);
+
+		d = new Intersection(new NamedClass("http://ex.org/Fahrzeug"), new ObjectSomeRestriction(
+				OWLPunningDetector.punningProperty, new ObjectSomeRestriction(new ObjectProperty(
+						"http://ex.org/bereifung"), Thing.instance)));
+		System.out.println(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(d));
+		individuals = rc.getIndividuals(d);
+		System.out.println(individuals);
+		
+		d = new Intersection(new NamedClass("http://ex.org/Fahrzeug"), new ObjectSomeRestriction(
+				OWLPunningDetector.punningProperty, 
+//				new ObjectSomeRestriction(new ObjectProperty("http://ex.org/bereifung"), 
+						Thing.instance));
+		System.out.println(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(d));
+		individuals = rc.getIndividuals(d);
+		System.out.println(individuals);
+		
+		//get some refinements
+		System.out.println("###############");
+		System.out.println("Refinements:");
+		Set<Description> refinements = la.getOperator().refine(d, d.getLength() + 4);
+		for (Description ref : refinements) {
+			System.out.println(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(ref));
+			System.out.println(lp.getAccuracyOrTooWeak(ref, 0d));
+		}
+		System.out.println("###############");
+		
+
+		d = new Intersection(new NamedClass("http://ex.org/Fahrzeug"), new ObjectSomeRestriction(
+				OWLPunningDetector.punningProperty, new ObjectSomeRestriction(new ObjectProperty(
+						"http://ex.org/bereifung"), new ObjectSomeRestriction(OWLPunningDetector.punningProperty,
+						Thing.instance))));
+		System.out.println(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(d));
+		individuals = rc.getIndividuals(d);
+		System.out.println(individuals);
+//		List<? extends EvaluatedDescription> currentlyBestEvaluatedDescriptions = la.getCurrentlyBestEvaluatedDescriptions(100);
+//		for (EvaluatedDescription ed : currentlyBestEvaluatedDescriptions) {
+//			System.out.println(ed);
+//		}
 	}
 
 }

Modified: trunk/components-core/src/test/resources/punning_example.ttl
===================================================================
--- trunk/components-core/src/test/resources/punning_example.ttl	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/components-core/src/test/resources/punning_example.ttl	2014-08-06 11:41:26 UTC (rev 4283)
@@ -57,11 +57,7 @@
 <http://ex.org/SIEMENS425#567> a ex:Bahn .
 <http://ex.org/TATRAT3#678> a ex:Tram .
 
-# punning workaround
-ex:p a owl:ObjectProperty .
-<http://ex.org/TRABANT601#1234> ex:p ex:Auto .
-<http://ex.org/S51#2345> ex:p ex:Moped .
-<http://ex.org/MIFA23#3456> ex:p ex:Fahrrad .
-<http://ex.org/CLIPSO90MG#4567> ex:p ex:Schubkarre .
-<http://ex.org/SIEMENS425#567> ex:p ex:Bahn .
-<http://ex.org/TATRAT3#678> ex:p ex:Tram .
\ No newline at end of file
+# punning of ex:Gummireifen
+ex:bestehtAus a owl:ObjectProperty .
+ex:Gummireifen ex:bestehtAus ex:GUMMI .
+ex:GUMMI a ex:Werkstoff .

Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml	2014-07-29 13:56:03 UTC (rev 4282)
+++ trunk/pom.xml	2014-08-06 11:41:26 UTC (rev 4283)
@@ -123,7 +123,7 @@
 			<dependency>
 			<groupId>net.sourceforge.owlapi</groupId>
 			<artifactId>owlapi-distribution</artifactId>
-			<version>3.4.5</version>
+			<version>3.5.1</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.owlapi</groupId>

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4282] trunk/components-core/src/main/java/org/ dllearner/kb/sparql/BlanknodeResolvingCBDGenerator.java

[<lor...@us...>]

Revision: 4282
          http://sourceforge.net/p/dl-learner/code/4282
Author:   lorenz_b
Date:     2014-07-29 13:56:03 +0000 (Tue, 29 Jul 2014)
Log Message:
-----------
Added punning test.

Added Paths:
-----------
    trunk/components-core/src/main/java/org/dllearner/kb/sparql/BlanknodeResolvingCBDGenerator.java

Added: trunk/components-core/src/main/java/org/dllearner/kb/sparql/BlanknodeResolvingCBDGenerator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/BlanknodeResolvingCBDGenerator.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/BlanknodeResolvingCBDGenerator.java	2014-07-29 13:56:03 UTC (rev 4282)
@@ -0,0 +1,100 @@
+/**
+ * 
+ */
+package org.dllearner.kb.sparql;
+
+import java.util.List;
+
+import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
+
+import com.hp.hpl.jena.query.ParameterizedSparqlString;
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.rdf.model.Model;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class BlanknodeResolvingCBDGenerator implements ConciseBoundedDescriptionGenerator{
+	
+	private QueryExecutionFactoryModel qef;
+	boolean resolveBlankNodes = true;
+
+	public BlanknodeResolvingCBDGenerator(Model model) {
+		String query = "prefix : <http://dl-learner.org/ontology/> "
+				+ "construct { ?s ?p ?o ; ?type ?s .} "
+				+ "where {  ?s ?p ?o .  bind( if(isIRI(?s),:sameIri,:sameBlank) as ?type )}";
+		qef = new QueryExecutionFactoryModel(model);
+		QueryExecution qe = qef.createQueryExecution(query);
+		Model extendedModel = qe.execConstruct();
+		qe.close();
+		
+		qef = new QueryExecutionFactoryModel(extendedModel);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator#getConciseBoundedDescription(java.lang.String)
+	 */
+	@Override
+	public Model getConciseBoundedDescription(String resourceURI) {
+		return getConciseBoundedDescription(resourceURI, 0);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator#getConciseBoundedDescription(java.lang.String, int)
+	 */
+	@Override
+	public Model getConciseBoundedDescription(String resourceURI, int depth) {
+		return getConciseBoundedDescription(resourceURI, depth, false);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator#getConciseBoundedDescription(java.lang.String, int, boolean)
+	 */
+	@Override
+	public Model getConciseBoundedDescription(String resourceURI, int depth, boolean withTypesForLeafs) {
+		StringBuilder constructTemplate = new StringBuilder("?s0 ?p0 ?o0 .");
+		for(int i = 1; i <= depth; i++){
+			constructTemplate.append("?o").append(i-1).append(" ?p").append(i).append(" ?o").append(i).append(" .");
+		}
+		
+		StringBuilder triplesTemplate = new StringBuilder("?s0 ?p0 ?o0 .");
+		for(int i = 1; i <= depth; i++){
+			triplesTemplate.append("OPTIONAL{").append("?o").append(i-1).append(" ?p").append(i).append(" ?o").append(i).append(" .");
+		}
+		if(resolveBlankNodes){
+			triplesTemplate.append("?o").append(depth).append("((!<x>|!<y>)/:sameBlank)* ?x . ?x ?px ?ox .filter(!(?p in (:sameIri, :sameBlank)))");
+		}
+		for(int i = 1; i <= depth; i++){
+			triplesTemplate.append("}");
+		}
+		
+		
+		StringBuilder queryString = new StringBuilder("prefix : <http://dl-learner.org/ontology/> ");
+		queryString.append("CONSTRUCT{").append(constructTemplate).append("}");
+		queryString.append(" WHERE {").append(triplesTemplate).append("}");
+		
+		ParameterizedSparqlString query = new ParameterizedSparqlString(queryString.toString());
+		query.setIri("s0", resourceURI);
+		System.out.println(query);
+		QueryExecution qe = qef.createQueryExecution(query.toString());
+		Model cbd = qe.execConstruct();
+		qe.close();
+		return cbd;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator#setRestrictToNamespaces(java.util.List)
+	 */
+	@Override
+	public void setRestrictToNamespaces(List<String> namespaces) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator#setRecursionDepth(int)
+	 */
+	@Override
+	public void setRecursionDepth(int maxRecursionDepth) {
+	}
+
+}

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4281] trunk/components-core/src

[<lor...@us...>]

Revision: 4281
          http://sourceforge.net/p/dl-learner/code/4281
Author:   lorenz_b
Date:     2014-07-29 13:55:31 +0000 (Tue, 29 Jul 2014)
Log Message:
-----------
Added punning test.

Added Paths:
-----------
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/ClassExpressionLiteralCombination.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/Materialization.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLSyntaxObjectRenderer.java
    trunk/components-core/src/test/java/org/dllearner/test/PunningTest.java
    trunk/components-core/src/test/java/org/dllearner/test/junit/PunningTest.java
    trunk/components-core/src/test/resources/log4j.properties
    trunk/components-core/src/test/resources/punning_example.ttl

Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/ClassExpressionLiteralCombination.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/ClassExpressionLiteralCombination.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/ClassExpressionLiteralCombination.java	2014-07-29 13:55:31 UTC (rev 4281)
@@ -0,0 +1,336 @@
+/**
+ * 
+ */
+package org.dllearner.algorithms.qtl.util;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.dllearner.algorithms.pattern.ManchesterOWLSyntaxOWLObjectRendererImpl;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx;
+import org.semanticweb.owlapi.model.OWLDataAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLDataComplementOf;
+import org.semanticweb.owlapi.model.OWLDataExactCardinality;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataHasValue;
+import org.semanticweb.owlapi.model.OWLDataIntersectionOf;
+import org.semanticweb.owlapi.model.OWLDataMaxCardinality;
+import org.semanticweb.owlapi.model.OWLDataMinCardinality;
+import org.semanticweb.owlapi.model.OWLDataOneOf;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLDataRange;
+import org.semanticweb.owlapi.model.OWLDataRangeVisitorEx;
+import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLDataUnionOf;
+import org.semanticweb.owlapi.model.OWLDatatype;
+import org.semanticweb.owlapi.model.OWLDatatypeRestriction;
+import org.semanticweb.owlapi.model.OWLFacetRestriction;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectComplementOf;
+import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
+import org.semanticweb.owlapi.model.OWLObjectHasSelf;
+import org.semanticweb.owlapi.model.OWLObjectHasValue;
+import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
+import org.semanticweb.owlapi.model.OWLObjectMaxCardinality;
+import org.semanticweb.owlapi.model.OWLObjectMinCardinality;
+import org.semanticweb.owlapi.model.OWLObjectOneOf;
+import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectUnionOf;
+import org.semanticweb.owlapi.model.PrefixManager;
+import org.semanticweb.owlapi.util.DefaultPrefixManager;
+import org.semanticweb.owlapi.vocab.OWLFacet;
+
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class ClassExpressionLiteralCombination implements OWLClassExpressionVisitorEx<Set<OWLClassExpression>>, OWLDataRangeVisitorEx<Set<OWLDataRange>>{
+	
+	private OWLDataFactory df =  new OWLDataFactoryImpl();
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLClass)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLClass ce) {
+		Set<OWLClassExpression> expressions = new HashSet<OWLClassExpression>(1);
+		expressions.add(ce);
+		return expressions;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectIntersectionOf)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectIntersectionOf ce) {
+		Set<OWLClassExpression> expressions = new HashSet<OWLClassExpression>();
+		Set<Set<OWLClassExpression>> combinations = new HashSet<Set<OWLClassExpression>>();
+		for (int i = 0; i < ce.getOperands().size(); i++) {
+			Set<OWLClassExpression> tmp = new HashSet<OWLClassExpression>();
+			combinations.add(tmp);
+		}
+		for (OWLClassExpression operand : ce.getOperands()) {
+			Set<Set<OWLClassExpression>> combinationsTmp = new HashSet<Set<OWLClassExpression>>();
+			Set<OWLClassExpression> newOperands = operand.accept(this);
+			for (Set<OWLClassExpression> set : combinations) {
+				for (OWLClassExpression newOp : newOperands) {
+					Set<OWLClassExpression> tmp = new HashSet<OWLClassExpression>();
+					tmp.addAll(set);
+					tmp.add(newOp);
+					combinationsTmp.add(tmp);
+				}
+			}
+			combinations = combinationsTmp;
+		}
+		for (Set<OWLClassExpression> combination : combinations) {
+			expressions.add(df.getOWLObjectIntersectionOf(combination));
+		}
+		return expressions;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectUnionOf)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectUnionOf ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectComplementOf)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectComplementOf ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectSomeValuesFrom ce) {
+		Set<OWLClassExpression> expressions = new HashSet<OWLClassExpression>();
+		Set<OWLClassExpression> newFillers = ce.getFiller().accept(this);
+		for (OWLClassExpression newFiller : newFillers) {
+			expressions.add(df.getOWLObjectSomeValuesFrom(ce.getProperty(), newFiller));
+		}
+		return expressions;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectAllValuesFrom)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectAllValuesFrom ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectHasValue)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectHasValue ce) {
+		Set<OWLClassExpression> expressions = new HashSet<OWLClassExpression>();
+		expressions.add(ce);
+		return expressions;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectMinCardinality)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectMinCardinality ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectExactCardinality)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectExactCardinality ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectMaxCardinality)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectMaxCardinality ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectHasSelf)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectHasSelf ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLObjectOneOf)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLObjectOneOf ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataSomeValuesFrom)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLDataSomeValuesFrom ce) {
+		Set<OWLClassExpression> expressions = new HashSet<OWLClassExpression>();
+		Set<OWLDataRange> newDataRanges = ce.getFiller().accept(this);
+		for (OWLDataRange newDataRange : newDataRanges) {
+			expressions.add(df.getOWLDataSomeValuesFrom(ce.getProperty(), newDataRange));
+		}
+		return expressions;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataAllValuesFrom)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLDataAllValuesFrom ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataHasValue)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLDataHasValue ce) {
+		Set<OWLClassExpression> expressions = new HashSet<OWLClassExpression>();
+		expressions.add(ce);
+		return expressions;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataMinCardinality)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLDataMinCardinality ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataExactCardinality)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLDataExactCardinality ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataMaxCardinality)
+	 */
+	@Override
+	public Set<OWLClassExpression> visit(OWLDataMaxCardinality ce) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitorEx#visit(org.semanticweb.owlapi.model.OWLDatatype)
+	 */
+	@Override
+	public Set<OWLDataRange> visit(OWLDatatype dr) {
+		Set<OWLDataRange> dataRanges = new HashSet<OWLDataRange>();
+		dataRanges.add(dr);
+		return dataRanges;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataOneOf)
+	 */
+	@Override
+	public Set<OWLDataRange> visit(OWLDataOneOf dr) {
+		Set<OWLDataRange> dataRanges = new HashSet<OWLDataRange>();
+		dataRanges.add(dr);
+		return dataRanges;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataComplementOf)
+	 */
+	@Override
+	public Set<OWLDataRange> visit(OWLDataComplementOf dr) {
+		Set<OWLDataRange> dataRanges = new HashSet<OWLDataRange>();
+		dataRanges.add(dr);
+		return dataRanges;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataIntersectionOf)
+	 */
+	@Override
+	public Set<OWLDataRange> visit(OWLDataIntersectionOf dr) {
+		Set<OWLDataRange> dataRanges = new HashSet<OWLDataRange>();
+		dataRanges.add(dr);
+		return dataRanges;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitorEx#visit(org.semanticweb.owlapi.model.OWLDataUnionOf)
+	 */
+	@Override
+	public Set<OWLDataRange> visit(OWLDataUnionOf dr) {
+		Set<OWLDataRange> dataRanges = new HashSet<OWLDataRange>();
+		dataRanges.add(dr);
+		return dataRanges;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitorEx#visit(org.semanticweb.owlapi.model.OWLDatatypeRestriction)
+	 */
+	@Override
+	public Set<OWLDataRange> visit(OWLDatatypeRestriction dr) {
+		Set<OWLDataRange> dataRanges = new HashSet<OWLDataRange>();
+		Set<OWLFacetRestriction> facetRestrictions = dr.getFacetRestrictions();
+		OWLLiteral min = null;
+		OWLLiteral max = null;
+		for (OWLFacetRestriction facetRestriction : facetRestrictions) {
+			OWLFacet facet = facetRestriction.getFacet();
+			if(facet == OWLFacet.MIN_INCLUSIVE){
+				min = facetRestriction.getFacetValue();
+			} else if(facet == OWLFacet.MAX_INCLUSIVE){
+				max = facetRestriction.getFacetValue();
+			} else {
+				throw new IllegalArgumentException("Facet not allowed for transformation.");
+			}
+		}
+//		dataRanges.add(dr);
+		dataRanges.add(df.getOWLDatatypeRestriction(dr.getDatatype(), df.getOWLFacetRestriction(OWLFacet.MIN_INCLUSIVE, min)));
+		dataRanges.add(df.getOWLDatatypeRestriction(dr.getDatatype(), df.getOWLFacetRestriction(OWLFacet.MAX_INCLUSIVE, max)));
+//		dataRanges.add(dr.getDatatype());
+		return dataRanges;
+	}
+	
+	
+	public static void main(String[] args) throws Exception {
+		ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
+		OWLDataFactoryImpl df = new OWLDataFactoryImpl();
+		PrefixManager pm = new DefaultPrefixManager(":");
+		OWLClass A = df.getOWLClass("A", pm );
+		OWLDataProperty s = df.getOWLDataProperty("s", pm);
+		OWLDataProperty t = df.getOWLDataProperty("t", pm);
+		OWLDatatypeRestriction dr1 = df.getOWLDatatypeMinMaxInclusiveRestriction(1.0, 2.0);
+		OWLDatatypeRestriction dr2 = df.getOWLDatatypeMinMaxInclusiveRestriction(15, 100);
+		OWLClassExpression ce = df.getOWLObjectIntersectionOf(A,
+				df.getOWLDataSomeValuesFrom(s, dr1),
+				df.getOWLDataSomeValuesFrom(t, dr2)						
+				);
+		Set<OWLClassExpression> expressions = ce.accept(new ClassExpressionLiteralCombination());
+		for (OWLClassExpression expr : expressions) {
+			System.out.println(expr);
+		}
+	}
+
+
+}

Added: trunk/components-core/src/main/java/org/dllearner/reasoning/Materialization.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/Materialization.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/Materialization.java	2014-07-29 13:55:31 UTC (rev 4281)
@@ -0,0 +1,37 @@
+package org.dllearner.reasoning;
+
+import java.io.Serializable;
+import java.util.Map;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import org.dllearner.core.owl.Constant;
+import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+
+class Materialization implements Serializable{
+		// we use sorted sets (map indices) here, because they have only log(n)
+		// complexity for checking whether an element is contained in them
+		// instances of classes
+		public Map<NamedClass, TreeSet<Individual>> classInstancesPos = new TreeMap<NamedClass, TreeSet<Individual>>();
+		public Map<NamedClass, TreeSet<Individual>> classInstancesNeg = new TreeMap<NamedClass, TreeSet<Individual>>();
+		// object property mappings
+		public Map<ObjectProperty, Map<Individual, SortedSet<Individual>>> opPos = new TreeMap<ObjectProperty, Map<Individual, SortedSet<Individual>>>();
+		// data property mappings
+		public Map<DatatypeProperty, Map<Individual, SortedSet<Constant>>> dpPos = new TreeMap<DatatypeProperty, Map<Individual, SortedSet<Constant>>>();
+			
+		
+		// datatype property mappings
+		// for boolean data properties we have one mapping for true and false for efficiency reasons
+		public Map<DatatypeProperty, TreeSet<Individual>> bdPos = new TreeMap<DatatypeProperty, TreeSet<Individual>>();
+		public Map<DatatypeProperty, TreeSet<Individual>> bdNeg = new TreeMap<DatatypeProperty, TreeSet<Individual>>();
+		//double datatype property mappings
+		public Map<DatatypeProperty, Map<Individual, SortedSet<Double>>> dd = new TreeMap<DatatypeProperty, Map<Individual, SortedSet<Double>>>();
+		//int datatype property
+		public Map<DatatypeProperty, Map<Individual, SortedSet<Integer>>> id = new TreeMap<DatatypeProperty, Map<Individual, SortedSet<Integer>>>();
+		//string datatype property
+		public Map<DatatypeProperty, Map<Individual, SortedSet<String>>> sd = new TreeMap<DatatypeProperty, Map<Individual, SortedSet<String>>>();
+	}
\ No newline at end of file

Added: trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLSyntaxObjectRenderer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLSyntaxObjectRenderer.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLSyntaxObjectRenderer.java	2014-07-29 13:55:31 UTC (rev 4281)
@@ -0,0 +1,903 @@
+package org.dllearner.utilities.owl;
+
+/*
+ * This file is part of the OWL API.
+ *
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ *
+ * Copyright (C) 2011, The University of Manchester
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see http://www.gnu.org/licenses/.
+ *
+ *
+ * Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0
+ * in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
+ *
+ * Copyright 2011, The University of Manchester
+ *
+ * Licensed 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.
+ */
+
+import static org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntax.FACET_RESTRICTION_SEPARATOR;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.AND;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.BOTTOM;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.COMMA;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.COMP;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.DISJOINT_WITH;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.EQUAL;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.EQUIVALENT_TO;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.EXISTS;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.FORALL;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.IMPLIES;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.IN;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.INVERSE;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.MAX;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.MIN;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.NOT;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.NOT_EQUAL;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.OR;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.SELF;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.SUBCLASS;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.TOP;
+import static uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax.WEDGE;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.TreeSet;
+
+import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.util.IRIShortFormProvider;
+import org.semanticweb.owlapi.util.ShortFormProvider;
+import org.semanticweb.owlapi.util.SimpleIRIShortFormProvider;
+import org.semanticweb.owlapi.util.SimpleShortFormProvider;
+
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntax;
+
+/**
+ * Extended version of the DLSyntaxObjectRenderer class in OWL API. Extension is
+ * done for data range facets, e.g. double[<=1.5].
+ * 
+ * Renders objects in unicode DL syntax.
+ * 
+ * @author Matthew Horridge, The University Of Manchester, Bio-Health
+ *         Informatics Group, Date: 10-Feb-2008
+ */
+public class DLSyntaxObjectRenderer implements OWLObjectRenderer, OWLObjectVisitor {
+
+	private ShortFormProvider shortFormProvider;
+	private IRIShortFormProvider iriShortFormProvider;
+	private StringBuilder buffer;
+	private OWLObject focusedObject;
+
+	/** default constructor */
+	public DLSyntaxObjectRenderer() {
+		shortFormProvider = new SimpleShortFormProvider();
+		iriShortFormProvider = new SimpleIRIShortFormProvider();
+		buffer = new StringBuilder();
+	}
+
+	/**
+	 * @param focusedObject
+	 *            focusedObject
+	 */
+	public void setFocusedObject(OWLObject focusedObject) {
+		this.focusedObject = focusedObject;
+	}
+
+	/**
+	 * @param obj
+	 *            obj
+	 * @return true if focused
+	 */
+	public boolean isFocusedObject(OWLObject obj) {
+		if (focusedObject == null) {
+			return false;
+		}
+		return focusedObject.equals(obj);
+	}
+
+	@Override
+	public void setShortFormProvider(ShortFormProvider shortFormProvider) {
+		this.shortFormProvider = shortFormProvider;
+	}
+
+	@Override
+	public String render(OWLObject object) {
+		buffer = new StringBuilder();
+		object.accept(this);
+		return buffer.toString();
+	}
+
+	@Override
+	public void visit(OWLOntology ontology) {
+		for (OWLAxiom ax : new TreeSet<OWLAxiom>(ontology.getLogicalAxioms())) {
+			ax.accept(this);
+			write("\n");
+		}
+	}
+
+	protected void write(String s) {
+		buffer.append(s);
+	}
+
+	protected String renderEntity(OWLEntity entity) {
+		return shortFormProvider.getShortForm(entity);
+	}
+
+	protected void writeEntity(OWLEntity entity) {
+		write(renderEntity(entity));
+	}
+
+	protected void write(DLSyntax keyword) {
+		write(keyword.toString());
+	}
+
+	protected void write(int i) {
+		write(Integer.toString(i));
+	}
+
+	protected void writeNested(OWLObject object) {
+		if (isBracketedIfNested(object)) {
+			write("(");
+		}
+		object.accept(this);
+		if (isBracketedIfNested(object)) {
+			write(")");
+		}
+	}
+
+	protected boolean isBracketedIfNested(OWLObject object) {
+		// if(object instanceof OWLObjectComplementOf) {
+		// if(!((OWLObjectComplementOf) object).getOperand().isAnonymous()) {
+		// return false;
+		// }
+		// }
+		// return object instanceof OWLClassExpression && !((OWLClassExpression)
+		// object).isClassExpressionLiteral();
+		return !(object instanceof OWLEntity);
+	}
+
+	private void writeObject(OWLObject object, boolean nest) {
+		if (nest) {
+			writeNested(object);
+		} else {
+			object.accept(this);
+		}
+	}
+
+	protected void write(Collection<? extends OWLObject> objects, DLSyntax delim, boolean nest) {
+		if (objects.size() == 2) {
+			Iterator<? extends OWLObject> it = objects.iterator();
+			OWLObject o1 = it.next();
+			OWLObject o2 = it.next();
+			if (isFocusedObject(o1) || !isFocusedObject(o2)) {
+				writeObject(o1, nest);
+				writeSpace();
+				write(delim);
+				writeSpace();
+				writeObject(o2, nest);
+			} else {
+				writeObject(o2, nest);
+				writeSpace();
+				write(delim);
+				writeSpace();
+				writeObject(o1, nest);
+			}
+		} else {
+			for (Iterator<? extends OWLObject> it = objects.iterator(); it.hasNext();) {
+				OWLObject o = it.next();
+				writeObject(o, nest);
+				if (it.hasNext()) {
+					writeSpace();
+					write(delim);
+					writeSpace();
+				}
+			}
+		}
+	}
+
+	// protected void write(Collection<? extends OWLObject> objects, DLSyntax
+	// keyword, boolean nest) {
+	// write(objects, keyword, nest);
+	// }
+	@Override
+	public void visit(OWLSubClassOfAxiom axiom) {
+		axiom.getSubClass().accept(this);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		axiom.getSuperClass().accept(this);
+	}
+
+	private void writePropertyAssertion(OWLPropertyAssertionAxiom<?, ?> ax) {
+		if (ax instanceof OWLNegativeObjectPropertyAssertionAxiom
+				|| ax instanceof OWLNegativeDataPropertyAssertionAxiom) {
+			write(NOT);
+		}
+		ax.getProperty().accept(this);
+		write("(");
+		ax.getSubject().accept(this);
+		write(", ");
+		ax.getObject().accept(this);
+		write(")");
+	}
+
+	@Override
+	public void visit(OWLNegativeObjectPropertyAssertionAxiom axiom) {
+		write(NOT);
+		writePropertyAssertion(axiom);
+	}
+
+	@Override
+	public void visit(OWLAsymmetricObjectPropertyAxiom axiom) {
+	}
+
+	@Override
+	public void visit(OWLReflexiveObjectPropertyAxiom axiom) {
+		write(TOP);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		write(EXISTS);
+		writeSpace();
+		axiom.getProperty().accept(this);
+		write(" .");
+		write(SELF);
+	}
+
+	@Override
+	public void visit(OWLDisjointClassesAxiom axiom) {
+		List<OWLClassExpression> descs = new ArrayList<OWLClassExpression>(axiom.getClassExpressions());
+		for (int i = 0; i < descs.size(); i++) {
+			for (int j = i + 1; j < descs.size(); j++) {
+				descs.get(i).accept(this);
+				writeSpace();
+				write(DISJOINT_WITH);
+				writeSpace();
+				descs.get(j).accept(this);
+				if (j < descs.size() - 1) {
+					write(", ");
+				}
+			}
+		}
+		// write(axiom.getClassExpressions(), DISJOINT_WITH, true);
+	}
+
+	private void writeDomainAxiom(OWLPropertyDomainAxiom<?> axiom) {
+		write(EXISTS);
+		writeSpace();
+		axiom.getProperty().accept(this);
+		writeRestrictionSeparator();
+		write(TOP);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		writeNested(axiom.getDomain());
+	}
+
+	private void writeRestrictionSeparator() {
+		write(".");
+	}
+
+	@Override
+	public void visit(OWLDataPropertyDomainAxiom axiom) {
+		writeDomainAxiom(axiom);
+	}
+
+	@Override
+	public void visit(OWLObjectPropertyDomainAxiom axiom) {
+		writeDomainAxiom(axiom);
+	}
+
+	@Override
+	public void visit(OWLEquivalentObjectPropertiesAxiom axiom) {
+		write(axiom.getProperties(), EQUIVALENT_TO, false);
+	}
+
+	@Override
+	public void visit(OWLNegativeDataPropertyAssertionAxiom axiom) {
+		write(NOT);
+		writePropertyAssertion(axiom);
+	}
+
+	@Override
+	public void visit(OWLDifferentIndividualsAxiom axiom) {
+		write(axiom.getIndividuals(), NOT_EQUAL, false);
+	}
+
+	@Override
+	public void visit(OWLDisjointDataPropertiesAxiom axiom) {
+		write(axiom.getProperties(), DISJOINT_WITH, false);
+	}
+
+	@Override
+	public void visit(OWLDisjointObjectPropertiesAxiom axiom) {
+		write(axiom.getProperties(), DISJOINT_WITH, false);
+	}
+
+	private void writeRangeAxiom(OWLPropertyRangeAxiom<?, ?> axiom) {
+		write(TOP);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		write(FORALL);
+		writeSpace();
+		axiom.getProperty().accept(this);
+		writeRestrictionSeparator();
+		writeNested(axiom.getRange());
+	}
+
+	@Override
+	public void visit(OWLObjectPropertyRangeAxiom axiom) {
+		writeRangeAxiom(axiom);
+	}
+
+	@Override
+	public void visit(OWLObjectPropertyAssertionAxiom axiom) {
+		writePropertyAssertion(axiom);
+	}
+
+	private void writeFunctionalProperty(OWLPropertyExpression<?, ?> property) {
+		write(TOP);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		write(MAX);
+		writeSpace();
+		write(1);
+		writeSpace();
+		property.accept(this);
+	}
+
+	@Override
+	public void visit(OWLFunctionalObjectPropertyAxiom axiom) {
+		writeFunctionalProperty(axiom.getProperty());
+	}
+
+	@Override
+	public void visit(OWLSubObjectPropertyOfAxiom axiom) {
+		axiom.getSubProperty().accept(this);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		axiom.getSuperProperty().accept(this);
+	}
+
+	@Override
+	public void visit(OWLDisjointUnionAxiom axiom) {
+		axiom.getOWLClass().accept(this);
+		write(EQUAL);
+		write(axiom.getClassExpressions(), OR, false);
+	}
+
+	@Override
+	public void visit(OWLDeclarationAxiom axiom) {
+	}
+
+	@Override
+	public void visit(OWLAnnotationAssertionAxiom axiom) {
+	}
+
+	@Override
+	public void visit(OWLSymmetricObjectPropertyAxiom axiom) {
+		axiom.getProperty().accept(this);
+		writeSpace();
+		write(EQUIVALENT_TO);
+		writeSpace();
+		axiom.getProperty().accept(this);
+		write(INVERSE);
+	}
+
+	private void writeSpace() {
+		write(" ");
+	}
+
+	@Override
+	public void visit(OWLDataPropertyRangeAxiom axiom) {
+		writeRangeAxiom(axiom);
+	}
+
+	@Override
+	public void visit(OWLFunctionalDataPropertyAxiom axiom) {
+		writeFunctionalProperty(axiom.getProperty());
+	}
+
+	@Override
+	public void visit(OWLEquivalentDataPropertiesAxiom axiom) {
+		write(axiom.getProperties(), EQUIVALENT_TO, false);
+	}
+
+	@Override
+	public void visit(OWLClassAssertionAxiom axiom) {
+		if (axiom.getClassExpression().isAnonymous()) {
+			write("(");
+		}
+		axiom.getClassExpression().accept(this);
+		if (axiom.getClassExpression().isAnonymous()) {
+			write(")");
+		}
+		write("(");
+		axiom.getIndividual().accept(this);
+		write(")");
+	}
+
+	@Override
+	public void visit(OWLEquivalentClassesAxiom axiom) {
+		write(axiom.getClassExpressions(), EQUIVALENT_TO, false);
+	}
+
+	@Override
+	public void visit(OWLDataPropertyAssertionAxiom axiom) {
+		writePropertyAssertion(axiom);
+	}
+
+	@Override
+	public void visit(OWLTransitiveObjectPropertyAxiom axiom) {
+		axiom.getProperty().accept(this);
+		writeSpace();
+		write(IN);
+		writeSpace();
+		write("R");
+		write("\u207A");
+	}
+
+	@Override
+	public void visit(OWLIrreflexiveObjectPropertyAxiom axiom) {
+		write(TOP);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		write(NOT);
+		write(EXISTS);
+		writeSpace();
+		axiom.getProperty().accept(this);
+		write(" .");
+		write(SELF);
+	}
+
+	@Override
+	public void visit(OWLSubDataPropertyOfAxiom axiom) {
+		axiom.getSubProperty().accept(this);
+		write(SUBCLASS);
+		axiom.getSuperProperty().accept(this);
+	}
+
+	@Override
+	public void visit(OWLInverseFunctionalObjectPropertyAxiom axiom) {
+		write(TOP);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		write(MAX);
+		writeSpace();
+		write(1);
+		writeSpace();
+		axiom.getProperty().accept(this);
+		write(INVERSE);
+	}
+
+	@Override
+	public void visit(OWLSameIndividualAxiom axiom) {
+		write(axiom.getIndividuals(), EQUAL, false);
+	}
+
+	@Override
+	public void visit(OWLSubPropertyChainOfAxiom axiom) {
+		write(axiom.getPropertyChain(), COMP, false);
+		writeSpace();
+		write(SUBCLASS);
+		writeSpace();
+		axiom.getSuperProperty().accept(this);
+	}
+
+	@Override
+	public void visit(OWLInverseObjectPropertiesAxiom axiom) {
+		OWLObject o1 = axiom.getFirstProperty();
+		OWLObject o2 = axiom.getSecondProperty();
+		OWLObject first, second;
+		if (isFocusedObject(o1) || !isFocusedObject(o2)) {
+			first = o1;
+			second = o2;
+		} else {
+			first = o2;
+			second = o1;
+		}
+		first.accept(this);
+		writeSpace();
+		write(EQUIVALENT_TO);
+		writeSpace();
+		second.accept(this);
+		write(INVERSE);
+	}
+
+	@Override
+	public void visit(SWRLRule rule) {
+		write(rule.getHead(), WEDGE, false);
+		writeSpace();
+		write(IMPLIES);
+		writeSpace();
+		write(rule.getBody(), WEDGE, false);
+	}
+
+	@Override
+	public void visit(OWLClass desc) {
+		if (desc.isOWLThing()) {
+			write(TOP);
+		} else if (desc.isOWLNothing()) {
+			write(BOTTOM);
+		} else {
+			writeEntity(desc);
+		}
+	}
+
+	@Override
+	public void visit(OWLObjectIntersectionOf desc) {
+		write(desc.getOperands(), AND, true);
+	}
+
+	@Override
+	public void visit(OWLObjectUnionOf desc) {
+		write(desc.getOperands(), OR, true);
+	}
+
+	@Override
+	public void visit(OWLObjectComplementOf desc) {
+		write(NOT);
+		writeNested(desc.getOperand());
+	}
+
+	private void writeCardinalityRestriction(OWLDataCardinalityRestriction restriction, DLSyntax keyword) {
+		write(keyword);
+		writeSpace();
+		write(restriction.getCardinality());
+		writeSpace();
+		restriction.getProperty().accept(this);
+		// if (restriction.isQualified()) {
+		writeRestrictionSeparator();
+		writeNested(restriction.getFiller());
+		// }
+	}
+
+	private void writeCardinalityRestriction(OWLObjectCardinalityRestriction restriction, DLSyntax keyword) {
+		write(keyword);
+		writeSpace();
+		write(restriction.getCardinality());
+		writeSpace();
+		restriction.getProperty().accept(this);
+		// if (restriction.isQualified()) {
+		writeRestrictionSeparator();
+		writeNested(restriction.getFiller());
+		// }
+	}
+
+	private void writeQuantifiedRestriction(OWLQuantifiedDataRestriction restriction, DLSyntax keyword) {
+		write(keyword);
+		writeSpace();
+		restriction.getProperty().accept(this);
+		writeRestrictionSeparator();
+		writeNested(restriction.getFiller());
+	}
+
+	private void writeQuantifiedRestriction(OWLQuantifiedObjectRestriction restriction, DLSyntax keyword) {
+		write(keyword);
+		writeSpace();
+		restriction.getProperty().accept(this);
+		writeRestrictionSeparator();
+		writeNested(restriction.getFiller());
+	}
+
+	@Override
+	public void visit(OWLObjectSomeValuesFrom desc) {
+		writeQuantifiedRestriction(desc, EXISTS);
+	}
+
+	@Override
+	public void visit(OWLObjectAllValuesFrom desc) {
+		writeQuantifiedRestriction(desc, FORALL);
+	}
+
+	private <R extends OWLPropertyRange, P extends OWLPropertyExpression<R, P>, V extends OWLObject> void writeValueRestriction(
+			OWLHasValueRestriction<R, P, V> restriction) {
+		write(EXISTS);
+		writeSpace();
+		restriction.getProperty().accept(this);
+		writeRestrictionSeparator();
+		write("{");
+		restriction.getValue().accept(this);
+		write("}");
+	}
+
+	@Override
+	public void visit(OWLObjectHasValue desc) {
+		writeValueRestriction(desc);
+	}
+
+	@Override
+	public void visit(OWLObjectMinCardinality desc) {
+		writeCardinalityRestriction(desc, MIN);
+	}
+
+	@Override
+	public void visit(OWLObjectExactCardinality desc) {
+		writeCardinalityRestriction(desc, EQUAL);
+	}
+
+	@Override
+	public void visit(OWLObjectMaxCardinality desc) {
+		writeCardinalityRestriction(desc, MAX);
+	}
+
+	@Override
+	public void visit(OWLObjectHasSelf desc) {
+		write(EXISTS);
+		writeSpace();
+		desc.getProperty().accept(this);
+		write(" .");
+		write(SELF);
+	}
+
+	@Override
+	public void visit(OWLObjectOneOf desc) {
+		for (Iterator<OWLIndividual> it = desc.getIndividuals().iterator(); it.hasNext();) {
+			write("{");
+			it.next().accept(this);
+			write("}");
+			if (it.hasNext()) {
+				write(" ");
+				write(OR);
+				write(" ");
+			}
+		}
+	}
+
+	@Override
+	public void visit(OWLDataSomeValuesFrom desc) {
+		writeQuantifiedRestriction(desc, EXISTS);
+	}
+
+	@Override
+	public void visit(OWLDataAllValuesFrom desc) {
+		writeQuantifiedRestriction(desc, FORALL);
+	}
+
+	@Override
+	public void visit(OWLDataHasValue desc) {
+		writeValueRestriction(desc);
+	}
+
+	@Override
+	public void visit(OWLDataMinCardinality desc) {
+		writeCardinalityRestriction(desc, MIN);
+	}
+
+	@Override
+	public void visit(OWLDataExactCardinality desc) {
+		writeCardinalityRestriction(desc, EQUAL);
+	}
+
+	@Override
+	public void visit(OWLDataMaxCardinality desc) {
+		writeCardinalityRestriction(desc, MAX);
+	}
+	
+	// /////////////////////////////////////////////////////////////////////////////////////////////
+		//
+		// Data stuff
+		//
+		// /////////////////////////////////////////////////////////////////////////////////////////////
+
+		public void visit(OWLDataIntersectionOf node) {
+			write("(");
+			write(node.getOperands(), AND, false);
+			write(")");
+		}
+
+		public void visit(OWLDataUnionOf node) {
+			write("(");
+			write(node.getOperands(), OR, false);
+			write(")");
+		}
+
+		public void visit(OWLDatatypeRestriction node) {
+			node.getDatatype().accept(this);
+	        write("[");
+	        for (OWLFacetRestriction facetRestriction : node.getFacetRestrictions()) {
+				facetRestriction.accept(this);
+				write(" " + FACET_RESTRICTION_SEPARATOR.toString() + " ");
+			}
+	        write("]");
+		}
+
+		public void visit(OWLFacetRestriction node) {
+			write(node.getFacet().getSymbolicForm());
+			writeSpace();
+			node.getFacetValue().accept(this);
+		}
+
+	@Override
+	public void visit(OWLDatatype node) {
+		write(shortFormProvider.getShortForm(node));
+	}
+
+	@Override
+	public void visit(OWLDataComplementOf node) {
+		write(NOT);
+		node.getDataRange().accept(this);
+	}
+
+	@Override
+	public void visit(OWLDataOneOf node) {
+		for (Iterator<OWLLiteral> it = node.getValues().iterator(); it.hasNext();) {
+			write("{");
+			it.next().accept(this);
+			write("}");
+			if (it.hasNext()) {
+				write(OR);
+			}
+		}
+	}
+
+	@Override
+	public void visit(OWLLiteral node) {
+		write(node.getLiteral());
+	}
+
+	@Override
+	public void visit(OWLObjectProperty property) {
+		writeEntity(property);
+	}
+
+	@Override
+	public void visit(OWLObjectInverseOf property) {
+		property.getInverse().accept(this);
+		write(INVERSE);
+	}
+
+	@Override
+	public void visit(OWLDataProperty property) {
+		writeEntity(property);
+	}
+
+	@Override
+	public void visit(OWLNamedIndividual individual) {
+		writeEntity(individual);
+	}
+
+	@Override
+	public void visit(OWLDatatypeDefinitionAxiom axiom) {
+	}
+
+	@Override
+	public void visit(OWLHasKeyAxiom axiom) {
+	}
+
+	@Override
+	public void visit(OWLAnnotationPropertyDomainAxiom axiom) {
+	}
+
+	@Override
+	public void visit(OWLAnnotationPropertyRangeAxiom axiom) {
+	}
+
+	@Override
+	public void visit(OWLSubAnnotationPropertyOfAxiom axiom) {
+	}
+
+	@Override
+	public void visit(OWLAnnotationProperty property) {
+	}
+
+	@Override
+	public void visit(OWLAnonymousIndividual individual) {
+	}
+
+	@Override
+	public void visit(IRI iri) {
+	}
+
+	@Override
+	public void visit(OWLAnnotation node) {
+	}
+
+	@Override
+	public void visit(SWRLClassAtom node) {
+		node.getPredicate().accept(this);
+		write("(");
+		node.getArgument().accept(this);
+		write(")");
+	}
+
+	@Override
+	public void visit(SWRLDataRangeAtom node) {
+		node.getPredicate().accept(this);
+		write("(");
+		node.getArgument().accept(this);
+		write(")");
+	}
+
+	@Override
+	public void visit(SWRLObjectPropertyAtom node) {
+		node.getPredicate().accept(this);
+		write("(");
+		node.getFirstArgument().accept(this);
+		write(", ");
+		node.getSecondArgument().accept(this);
+		write(")");
+	}
+
+	@Override
+	public void visit(SWRLDataPropertyAtom node) {
+		node.getPredicate().accept(this);
+		write("(");
+		node.getFirstArgument().accept(this);
+		write(", ");
+		node.getSecondArgument().accept(this);
+		write(")");
+	}
+
+	@Override
+	public void visit(SWRLBuiltInAtom node) {
+		write(node.getPredicate().toString());
+		write("(");
+		write(node.getArguments(), COMMA, true);
+		write(")");
+	}
+
+	@Override
+	public void visit(SWRLVariable node) {
+		write("?");
+		write(iriShortFormProvider.getShortForm(node.getIRI()));
+	}
+
+	@Override
+	public void visit(SWRLIndividualArgument node) {
+		node.getIndividual().accept(this);
+	}
+
+	@Override
+	public void visit(SWRLLiteralArgument node) {
+		node.getLiteral().accept(this);
+	}
+
+	@Override
+	public void visit(SWRLSameIndividualAtom node) {
+		write("sameAs(");
+		node.getFirstArgument().accept(this);
+		write(", ");
+		node.getSecondArgument().accept(this);
+		write(")");
+	}
+
+	@Override
+	public void visit(SWRLDifferentIndividualsAtom node) {
+		write("differentFrom(");
+		node.getFirstArgument().accept(this);
+		write(", ");
+		node.getSecondArgument().accept(this);
+		write(")");
+	}
+}

Added: trunk/components-core/src/test/java/org/dllearner/test/PunningTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/PunningTest.java	                        (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/test/PunningTest.java	2014-07-29 13:55:31 UTC (rev 4281)
@@ -0,0 +1,155 @@
+/**
+ * 
+ */
+package org.dllearner.test;
+
+import java.io.ByteArrayInputStream;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.AbstractLearningProblem;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.utilities.owl.OWLAPIConverter;
+import org.dllearner.utilities.owl.OWLAPIDescriptionConvertVisitor;
+import org.junit.Assert;
+import org.junit.Test;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
+import com.google.common.collect.Sets;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class PunningTest {
+	
+	
+	public OWLOntology makeExampleKB() throws OWLOntologyCreationException{
+		String kb = "@prefix owl:<http://www.w3.org/2002/07/owl#> . @prefix :<http://foo.org/> .";
+		kb += ":p a owl:ObjectProperty .";
+		
+		for (int i = 1; i <= 5; i++) {
+			kb += ":r" + i + " a owl:ObjectProperty .";
+		}
+		
+		kb += ":A a owl:Class; :r1 :o1; :r2 :o2 .";
+		kb += ":B a owl:Class; :r1 :o3; :r3 :o2 .";
+		
+		for (int i = 1; i <= 10; i++) {
+			kb += ":x" + i + " a owl:NamedIndividual .";
+		}
+		
+		int m = 5;
+		int n = 5;
+		
+		//m instances of A
+		for (int i = 1; i <= m; i++) {
+			kb += ":x" + i + " a :A .";
+		}
+		
+		//n instances of B
+		for (int i = 1; i <= n; i++) {
+			kb += ":x" + i + " a :A .";
+		}
+		
+		OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new ByteArrayInputStream(kb.getBytes()));
+		return ontology;
+	}
+	
+	public OWLOntology loadExample() throws OWLOntologyCreationException{
+		OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(this.getClass().getClassLoader().getResourceAsStream("punning_example.ttl"));
+		return ontology;
+	}
+	
+	@Test
+	public void testPunning() throws OWLOntologyCreationException, ComponentInitException{
+		OWLOntology ontology = makeExampleKB();
+		OWLDataFactory df = new OWLDataFactoryImpl();
+		
+		//check that A and B are both, individual and class
+		OWLClass clsA = df.getOWLClass(IRI.create("http://foo.org/A"));
+		OWLClass clsB = df.getOWLClass(IRI.create("http://foo.org/B"));
+		OWLIndividual indA = df.getOWLNamedIndividual(IRI.create("http://foo.org/A"));
+		OWLIndividual indB = df.getOWLNamedIndividual(IRI.create("http://foo.org/B"));
+		
+		Set<OWLClass> classes = ontology.getClassesInSignature();
+		Set<OWLObjectProperty> properties = ontology.getObjectPropertiesInSignature();
+		Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
+		
+		System.out.println("Classes:" + classes);
+		System.out.println("Properties:" + properties);
+		System.out.println("Individuals:" + individuals);
+		
+		Assert.assertTrue(
+				ontology.getClassesInSignature().contains(clsA) && 
+				ontology.getClassesInSignature().contains(clsB) &&
+				ontology.getIndividualsInSignature().contains(indA) &&
+				ontology.getIndividualsInSignature().contains(indB)
+				);
+		
+		KnowledgeSource ks = new OWLAPIOntology(ontology);
+		ks.init();
+		
+		AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+		rc.init();
+		
+		AbstractLearningProblem lp = new PosNegLPStandard(rc);
+		lp.init();
+		
+		AbstractCELA la = new CELOE(lp, rc);
+		la.init();
+		
+		la.start();
+	}
+	
+	@Test
+	public void testPunning2() throws OWLOntologyCreationException, ComponentInitException{
+		OWLOntology ontology = loadExample();
+		OWLDataFactory df = new OWLDataFactoryImpl();
+		
+		//check that A and B are both, individual and class
+		Set<Individual> posExamples = new HashSet<Individual>();
+		for (String uri : Sets.newHashSet("http://ex.org/TRABANT601#1234", "http://ex.org/S51#2345", "http://ex.org/MIFA23#3456")) {
+			posExamples.add(new Individual(uri));
+		}
+		Set<Individual> negExamples = new HashSet<Individual>();
+		for (String uri : Sets.newHashSet("http://ex.org/CLIPSO90MG#4567", "http://ex.org/SIEMENS425#567", "http://ex.org/TATRAT3#678")) {
+			negExamples.add(new Individual(uri));
+		}
+		
+		KnowledgeSource ks = new OWLAPIOntology(ontology);
+		ks.init();
+		
+		AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+		rc.init();
+		
+		PosNegLPStandard lp = new PosNegLPStandard(rc);
+		lp.setPositiveExamples(posExamples);
+		lp.setNegativeExamples(negExamples);
+		lp.init();
+		
+		AbstractCELA la = new CELOE(lp, rc);
+		la.init();
+		
+		la.start();
+	}
+
+}

Added: trunk/components-core/src/test/java/org/dllearner/test/junit/PunningTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/junit/PunningTest.java	                        (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/test/junit/PunningTest.java	2014-07-29 13:55:31 UTC (rev 4281)
@@ -0,0 +1,64 @@
+/**
+ * 
+ */
+package org.dllearner.test.junit;
+
+import static org.junit.Assert.*;
+
+import java.io.ByteArrayInputStream;
+
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.junit.Test;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class PunningTest {
+
+	@Test
+	public void test() throws Exception {
+		String triples = "@prefix owl:<http://www.w3.org/2002/07/owl#> . @prefix : <http://other.example.org/ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> ."
+				+ ":A a owl:NamedIndividual. :A a owl:Class. :A a :B . :B rdfs:subClassOf :A .";
+		System.out.println(triples);
+		ModelFactory.createDefaultModel().read(new ByteArrayInputStream(triples.getBytes()), null, "TURTLE");
+		
+		OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+		OWLDataFactory df = man.getOWLDataFactory();
+		OWLOntology ontology = man.loadOntologyFromOntologyDocument(new ByteArrayInputStream(triples.getBytes()));
+		System.out.println(ontology.getIndividualsInSignature());
+		System.out.println(ontology.getClassesInSignature());
+		OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance();
+		OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ontology);
+		OWLClass c = df.getOWLClass(IRI.create("http://other.example.org/ns#A"));
+		OWLNamedIndividual i = df.getOWLNamedIndividual(IRI.create("http://other.example.org/ns#A"));
+		System.out.println(reasoner.getInstances(c, false));
+		KnowledgeSource ks = new OWLAPIOntology(ontology);
+		AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+		rc.init();
+		NamedClass cls = new NamedClass("http://other.example.org/ns#A");
+		System.out.println(rc.getIndividuals(cls));
+		Individual ind = new Individual("http://other.example.org/ns#A");
+		System.out.println(rc.hasType(cls, ind));
+	}
+
+}

Added: trunk/components-core/src/test/resources/log4j.properties
===================================================================
--- trunk/components-core/src/test/resources/log4j.properties	                        (rev 0)
+++ trunk/components-core/src/test/resources/log4j.properties	2014-07-29 13:55:31 UTC (rev 4281)
@@ -0,0 +1,20 @@
+# Direct log messages to stdout
+# Root logger option
+log4j.rootLogger=INFO,stdout
+
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+#log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %p [%c] %L - %m%n
+log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} [%c] - %m%n
+
+#File Appender
+log4j.appender.FA=org.apache.log4j.FileAppender
+log4j.appender.FA.File=REX.log
+log4j.appender.FA.layout=org.apache.log4j.PatternLayout
+log4j.appender.FA.layout.ConversionPattern=%d{ABSOLUTE} %p [%c] %L - %m%n
+
+
+log4j.category.org.dllearner.algorithms=INFO
+log4j.category.org.dllearner.algorithms.isle=DEBUG
+log4j.category.org.dllearner.algorithms.qtl=INFO
+log4j.category.org.dllearner.algorithms.qtl.lgg=INFO


Property changes on: trunk/components-core/src/test/resources/log4j.properties
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: trunk/components-core/src/test/resources/punning_example.ttl
===================================================================
--- trunk/components-core/src/test/resources/punning_example.ttl	                        (rev 0)
+++ trunk/components-core/src/test/resources/punning_example.ttl	2014-07-29 13:55:31 UTC (rev 4281)
@@ -0,0 +1,67 @@
+#Solution \exists bereifung.\top \sqcap Fahrzeug
+
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix ex: <http://ex.org/> .
+
+ex:Gummireifen a owl:Class .
+ex:bereifung a owl:ObjectProperty .
+
+ex:Transporthilfe a owl:Class .
+
+ex:Schubkarre
+    a owl:Class ;
+    rdfs:subClassOf ex:Transporthilfe .
+
+ex:Fahrzeug a owl:Class .
+ex:Fahrzeug owl:disjointWith ex:Transporthilfe .
+
+ex:Tram
+    a owl:Class ;
+    rdfs:subClassOf ex:Fahrzeug .
+
+ex:Bahn
+    a owl:Class ;
+    rdfs:subClassOf ex:Fahrzeug .
+
+ex:Auto
+    a owl:Class ;
+    rdfs:subClassOf ex:Fahrzeug .
+
+ex:Moped
+    a owl:Class ;
+    rdfs:subClassOf ex:Fahrzeug .
+
+ex:Fahrrad
+    a owl:Class ;
+    rdfs:subClassOf ex:Fahrzeug .
+
+ex:BRIDGESTONE_XYZ a ex:Gummireifen .
+ex:PNEUMANT_4711 a ex:Gummireifen .
+ex:HEIDENAU_K36 a ex:Gummireifen .
+ex:DEMA_ABC23 a ex:Gummireifen .
+
+ex:Auto ex:bereifung ex:BRIDGESTONE_XYZ .
+ex:Moped ex:bereifung ex:HEIDENAU_K36 .
+ex:Fahrrad ex:bereifung ex:PNEUMANT_4711 .
+ex:Schubkarre ex:bereifung ex:DEMA_ABC23 .
+
+# positive individuals
+<http://ex.org/TRABANT601#1234> a ex:Auto .
+<http://ex.org/S51#2345> a ex:Moped .
+<http://ex.org/MIFA23#3456> a ex:Fahrrad .
+
+# negative individuals
+<http://ex.org/CLIPSO90MG#4567> a ex:Schubkarre .
+<http://ex.org/SIEMENS425#567> a ex:Bahn .
+<http://ex.org/TATRAT3#678> a ex:Tram .
+
+# punning workaround
+ex:p a owl:ObjectProperty .
+<http://ex.org/TRABANT601#1234> ex:p ex:Auto .
+<http://ex.org/S51#2345> ex:p ex:Moped .
+<http://ex.org/MIFA23#3456> ex:p ex:Fahrrad .
+<http://ex.org/CLIPSO90MG#4567> ex:p ex:Schubkarre .
+<http://ex.org/SIEMENS425#567> ex:p ex:Bahn .
+<http://ex.org/TATRAT3#678> ex:p ex:Tram .
\ No newline at end of file

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4280] trunk

[<lor...@us...>]

Revision: 4280
          http://sourceforge.net/p/dl-learner/code/4280
Author:   lorenz_b
Date:     2014-07-29 13:53:19 +0000 (Tue, 29 Jul 2014)
Log Message:
-----------
Added punning test.

Modified Paths:
--------------
    trunk/components-core/pom.xml
    trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2DisjunctiveMT.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java
    trunk/components-core/src/main/java/org/dllearner/core/AbstractCELA.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/Constant.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/DatatypeProperty.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMaxValue.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinValue.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/TypedConstant.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/ExistentialRestrictionMaterialization.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
    trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/ConceptComparator.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIDescriptionConvertVisitor.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/RoleComparator.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/isle/ISLETestCorpus.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/isle/ISLETestNoCorpus.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/isle/metrics/PMIRelevanceMetricTest.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/isle/metrics/RelevanceMetricsTest.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/GeneralisationTest.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/LGGTest.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/QTLTest.java
    trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java
    trunk/interfaces/pom.xml
    trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
    trunk/pom.xml
    trunk/scripts/pom.xml
    trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
    trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java

Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/pom.xml	2014-07-29 13:53:19 UTC (rev 4280)
@@ -100,10 +100,10 @@
 			<artifactId>mysql-connector-java</artifactId>
 		</dependency>
 
-		<dependency>
+		<!-- <dependency>
 			<groupId>net.sourceforge.owlapi</groupId>
 			<artifactId>owlapi-distribution</artifactId>
-		</dependency>
+		</dependency> -->
 
 		<dependency>
 			<groupId>com.clarkparsia</groupId>
@@ -152,10 +152,6 @@
 			<artifactId>hermit</artifactId>
 		</dependency>
 		
-		<dependency>
-			<groupId>eu.trowl</groupId>
-			<artifactId>trowl-core</artifactId>
-		</dependency>
 
 		<dependency>
 			<groupId>com.jamonapi</groupId>
@@ -249,6 +245,11 @@
         	<artifactId>jsexp</artifactId>
         	<version>0.1.0</version>
         </dependency>
+        <dependency>
+        	<groupId>eu.trowl</groupId>
+        	<artifactId>trowl-core</artifactId>
+        	<version>1.4.0</version>
+        </dependency>
 
          <dependency>
          	<groupId>xerces</groupId>
@@ -334,6 +335,16 @@
 				<artifactId>solr-solrj</artifactId>
 				<version>4.4.0</version>
 			</dependency>
+			<dependency>
+	<groupId>nz.ac.waikato.cms.weka</groupId>
+	<artifactId>weka-dev</artifactId>
+	<version>3.7.11</version>
+</dependency>
+			<!-- <dependency>
+				<groupId>nz.ac.waikato.cms.weka</groupId>
+				<artifactId>weka-stable</artifactId>
+				<version>3.6.9</version>
+			</dependency> -->
 	</dependencies>
 	<dependencyManagement>
 		<dependencies>

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -32,7 +32,6 @@
 import java.util.TreeSet;
 
 import org.apache.log4j.Logger;
-import org.dllearner.algorithms.elcopy.ELLearningAlgorithm;
 import org.dllearner.core.AbstractCELA;
 import org.dllearner.core.AbstractHeuristic;
 import org.dllearner.core.AbstractKnowledgeSource;
@@ -50,7 +49,6 @@
 import org.dllearner.core.owl.Restriction;
 import org.dllearner.core.owl.Thing;
 import org.dllearner.kb.OWLAPIOntology;
-import org.dllearner.kb.OWLFile;
 import org.dllearner.learningproblems.ClassLearningProblem;
 import org.dllearner.learningproblems.PosNegLP;
 import org.dllearner.learningproblems.PosOnlyLP;
@@ -92,7 +90,7 @@
  *
  */
 @ComponentAnn(name="CELOE", shortName="celoe", version=1.0, description="CELOE is an adapted and extended version of the OCEL algorithm applied for the ontology engineering use case. See http://jens-lehmann.org/files/2011/celoe.pdf for reference.")
-public class CELOE extends AbstractCELA {
+public class CELOE extends AbstractCELA implements Cloneable{
 
 	private static Logger logger = Logger.getLogger(CELOE.class);
 //	private CELOEConfigurator configurator;
@@ -224,6 +222,39 @@
 		
 	}
 	
+	public CELOE(CELOE celoe){
+		setReasoner(celoe.reasoner);
+		setLearningProblem(celoe.learningProblem);
+		setAllowedConcepts(celoe.getAllowedConcepts());
+		setExpandAccuracy100Nodes(celoe.expandAccuracy100Nodes);
+		setFilterDescriptionsFollowingFromKB(celoe.filterDescriptionsFollowingFromKB);
+		setHeuristic(celoe.heuristic);
+		setIgnoredConcepts(celoe.ignoredConcepts);
+		setLearningProblem(celoe.learningProblem);
+		setMaxClassExpressionTests(celoe.maxClassExpressionTests);
+		setMaxClassExpressionTestsAfterImprovement(celoe.maxClassExpressionTestsAfterImprovement);
+		setMaxDepth(celoe.maxDepth);
+		setMaxExecutionTimeInSeconds(celoe.maxExecutionTimeInSeconds);
+		setMaxExecutionTimeInSecondsAfterImprovement(celoe.maxExecutionTimeInSecondsAfterImprovement);
+		setMaxNrOfResults(celoe.maxNrOfResults);
+		setNoisePercentage(celoe.noisePercentage);
+		RhoDRDown op = new RhoDRDown((RhoDRDown)celoe.operator);
+		try {
+			op.init();
+		} catch (ComponentInitException e) {
+			e.printStackTrace();
+		}
+		setOperator(op);
+		setReplaceSearchTree(celoe.replaceSearchTree);
+		setReuseExistingDescription(celoe.reuseExistingDescription);
+		setSingleSuggestionMode(celoe.singleSuggestionMode);
+		setStartClass(celoe.startClass);
+		setStopOnFirstDefinition(celoe.stopOnFirstDefinition);
+		setTerminateOnNoiseReached(celoe.terminateOnNoiseReached);
+		setUseMinimizer(celoe.useMinimizer);
+		setWriteSearchTree(celoe.writeSearchTree);
+	}
+	
 	public CELOE(AbstractLearningProblem problem, AbstractReasonerComponent reasoner) {
 		super(problem, reasoner);
 //		configurator = new CELOEConfigurator(this);
@@ -529,7 +560,7 @@
 						treeString += "   " + n + "\n";
 					}
 				}
-				treeString += startNode.toTreeString(baseURI);
+				treeString += startNode.toTreeString(baseURI, prefixes);
 				treeString += "\n";
 
 				if (replaceSearchTree)
@@ -1134,6 +1165,14 @@
 	public void setExpandAccuracy100Nodes(boolean expandAccuracy100Nodes) {
 		this.expandAccuracy100Nodes = expandAccuracy100Nodes;
 	}
+	
+	/* (non-Javadoc)
+	 * @see java.lang.Object#clone()
+	 */
+	@Override
+	public Object clone() throws CloneNotSupportedException {
+		return new CELOE(this);
+	}
 
 	public static void main(String[] args) throws Exception{
 		String cls = "http://purl.org/procurement/public-contracts#Tender";

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -22,6 +22,7 @@
 import java.text.DecimalFormat;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 
 import org.dllearner.algorithms.SearchTreeNode;
 import org.dllearner.algorithms.isle.NLPHeuristic;
@@ -119,7 +120,11 @@
 	}
 	
 	public String getShortDescription(String baseURI) {
-		String ret = description.toString(baseURI,null) + " [";
+		return getShortDescription(baseURI, null);
+	}
+	
+	public String getShortDescription(String baseURI, Map<String, String> prefixes) {
+		String ret = description.toString(baseURI,prefixes) + " [";
 //		ret += "score" + NLPHeuristic.getNodeScore(this) + ",";
 		ret += "acc:" + dfPercent.format(accuracy) + ", ";
 		ret += "he:" + horizontalExpansion + ", ";
@@ -141,6 +146,10 @@
 		return toTreeString(0, baseURI).toString();
 	}	
 	
+	public String toTreeString(String baseURI, Map<String, String> prefixes) {
+		return toTreeString(0, baseURI, prefixes).toString();
+	}	
+	
 	private StringBuilder toTreeString(int depth, String baseURI) {
 		StringBuilder treeString = new StringBuilder();
 		for(int i=0; i<depth-1; i++)
@@ -153,6 +162,19 @@
 		}
 		return treeString;
 	}
+	
+	private StringBuilder toTreeString(int depth, String baseURI, Map<String, String> prefixes) {
+		StringBuilder treeString = new StringBuilder();
+		for(int i=0; i<depth-1; i++)
+			treeString.append("  ");
+		if(depth!=0)
+			treeString.append("|--> ");
+		treeString.append(getShortDescription(baseURI, prefixes)+"\n");
+		for(OENode child : children) {
+			treeString.append(child.toTreeString(depth+1,baseURI,prefixes));
+		}
+		return treeString;
+	}
 
 	/**
 	 * @return the refinementCount
@@ -166,5 +188,5 @@
 	 */
 	public void setRefinementCount(int refinementCount) {
 		this.refinementCount = refinementCount;
-	}	
+	}
 }

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -202,7 +202,7 @@
 	public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
 		EvaluatedQueryTree<String> bestSolution = solutions.first();
 		Description description = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
-				bestSolution.getTree().asOWLClassExpression(LiteralNodeConversionStrategy.FACET_RESTRICTION));
+				bestSolution.getTree().asOWLClassExpression(LiteralNodeConversionStrategy.MIN_MAX));
 		return new EvaluatedDescription(description, new AxiomScore(bestSolution.getScore()));
 	}
 	

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -19,7 +19,6 @@
 import org.apache.log4j.Logger;
 import org.dllearner.algorithms.qtl.cache.QueryTreeCache;
 import org.dllearner.algorithms.qtl.datastructures.QueryTree;
-import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
 import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.LiteralNodeConversionStrategy;
 import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.LiteralNodeSubsumptionStrategy;
 import org.dllearner.algorithms.qtl.operations.lgg.EvaluatedQueryTree;
@@ -42,8 +41,10 @@
 import org.dllearner.learningproblems.PosNegLP;
 import org.dllearner.learningproblems.QueryTreeScore;
 import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
+import org.dllearner.utilities.owl.DLSyntaxObjectRenderer;
 import org.dllearner.utilities.owl.OWLAPIConverter;
 import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLClassExpression;
 import org.semanticweb.owlapi.util.SimpleShortFormProvider;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -75,6 +76,7 @@
 	private Set<Individual> currentNegExamples;
 	
 	private Map<QueryTree<String>, Individual> tree2Individual;
+	private Map<Individual, QueryTree<String>> individual2Tree;
 	
 	private QueryTreeCache treeCache;
 
@@ -121,7 +123,15 @@
 	private long partialSolutionStartTime;
 	
 	private double startPosExamplesSize;
+	private int expressionTests = 0;
 	
+	LiteralNodeConversionStrategy[] strategies = new LiteralNodeConversionStrategy[]{
+			LiteralNodeConversionStrategy.MIN,
+			LiteralNodeConversionStrategy.MAX,
+			LiteralNodeConversionStrategy.MIN_MAX,
+			LiteralNodeConversionStrategy.DATATYPE
+	};
+	
 	public QTL2Disjunctive() {}
 	
 	public QTL2Disjunctive(PosNegLP learningProblem, AbstractReasonerComponent reasoner) throws LearningProblemUnsupportedException{
@@ -154,7 +164,7 @@
 	 */
 	@Override
 	public void init() throws ComponentInitException {
-		
+		ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
 		if(!(learningProblem instanceof PosNegLP)){
 			throw new IllegalArgumentException("Only PosNeg learning problems are supported");
 		}
@@ -170,6 +180,7 @@
 		logger.info("Initializing...");
 		treeCache = new QueryTreeCache(model);
 		tree2Individual = new HashMap<QueryTree<String>, Individual>(lp.getPositiveExamples().size()+lp.getNegativeExamples().size());
+		individual2Tree = new HashMap<Individual, QueryTree<String>>(lp.getPositiveExamples().size()+lp.getNegativeExamples().size());
 		
 		currentPosExampleTrees = new ArrayList<QueryTree<String>>(lp.getPositiveExamples().size());
 		currentNegExampleTrees = new ArrayList<QueryTree<String>>(lp.getNegativeExamples().size());
@@ -205,11 +216,13 @@
 		for (Individual ind : lp.getPositiveExamples()) {
 			queryTree = treeCache.getQueryTree(ind.getName());
 			tree2Individual.put(queryTree, ind);
+			individual2Tree.put(ind, queryTree);
 			currentPosExampleTrees.add(queryTree);
 		}
 		for (Individual ind : lp.getNegativeExamples()) {
 			queryTree = treeCache.getQueryTree(ind.getName());
 			tree2Individual.put(queryTree, ind);
+			individual2Tree.put(ind, queryTree);
 			currentNegExampleTrees.add(queryTree);
 		}
 		logger.info("...done.");
@@ -235,7 +248,7 @@
 			//compute best (partial) solution computed so far
 			EvaluatedQueryTree<String> bestPartialSolution = computeBestPartialSolution();
 			
-			//add if some criteria are satisfied
+			//add to partial solutions if criteria are satisfied
 			if(bestPartialSolution.getScore() >= minimumTreeScore){
 				
 				partialSolutions.add(bestPartialSolution);
@@ -244,14 +257,14 @@
 				QueryTree<String> tree;
 				for (Iterator<QueryTree<String>> iterator = currentPosExampleTrees.iterator(); iterator.hasNext();) {
 					tree = iterator.next();
-					if(tree.isSubsumedBy(bestPartialSolution.getTree())){
+					if(!bestPartialSolution.getFalseNegatives().contains(tree)){//a pos tree that is not covered
 						iterator.remove();
 						currentPosExamples.remove(tree2Individual.get(tree));
 					}
 				}
 				for (Iterator<QueryTree<String>> iterator = currentNegExampleTrees.iterator(); iterator.hasNext();) {
 					tree = iterator.next();
-					if(tree.isSubsumedBy(bestPartialSolution.getTree())){
+					if(bestPartialSolution.getFalsePositives().contains(tree)){//a neg example that is covered
 						iterator.remove();
 						currentNegExamples.remove(tree2Individual.get(tree));
 					}
@@ -272,8 +285,9 @@
 		
 		long endTime = System.currentTimeMillis();
 		logger.info("Finished in " + (endTime-startTime) + "ms.");
+		logger.info(expressionTests +" descriptions tested");
+		logger.info("Combined solution:" + OWLAPIConverter.getOWLAPIDescription(currentBestSolution.getDescription()).toString().replace("\n", ""));
 		
-		logger.info("Combined solution:" + OWLAPIConverter.getOWLAPIDescription(currentBestSolution.getDescription()).toString().replace("\n", ""));
 		logger.info(currentBestSolution.getScore());
 		
 	}
@@ -291,7 +305,9 @@
 			logger.trace("TODO list size: " + todoList.size());
 			//pick best element from todo list
 			currentElement = todoList.poll();
+			
 			currentTree = currentElement.getTree();
+			logger.info("Next tree: "  + currentElement.getTreeScore() + "\n" + OWLAPIConverter.getOWLAPIDescription(currentElement.getEvaluatedDescription().getDescription()));
 			//generate the LGG between the chosen tree and each uncovered positive example
 			Iterator<QueryTree<String>> it = currentElement.getFalseNegatives().iterator();
 			while (it.hasNext() && !isPartialSolutionTimeExpired() && !isTimeExpired()) {
@@ -302,26 +318,29 @@
 				lggMon.stop();
 				
 				//evaluate the LGG
-				Set<EvaluatedQueryTree<String>> solutions = evaluate(lgg, true);
+				Set<EvaluatedQueryTree<String>> solutions = evaluate2(lgg, true);
 				for (EvaluatedQueryTree<String> solution : solutions) {
+					expressionTests++;
 					double score = solution.getScore();
 					double mas = heuristic.getMaximumAchievableScore(solution);
 					
 					if(score >= bestCurrentScore){
-						//add to todo list, if not already contained in todo list or solution list
-						todo(solution);
 						if(score > bestCurrentScore){
 							logger.info("\tGot better solution:" + solution.getTreeScore());
+							logger.info(OWLAPIConverter.getOWLAPIDescription(solution.getEvaluatedDescription().getDescription()));
 							bestCurrentScore = score;
 							bestPartialSolutionTree = solution;
 						}
-						
+						//add to todo list, if not already contained in todo list or solution list
+						todo(solution);
 					} else if(mas >= bestCurrentScore){
 						todo(solution);
 					} else {
+						logger.info("Too weak:" + solution.getTreeScore());
 //						System.out.println("Too general");
 //						System.out.println("MAS=" + mas + "\nBest=" + bestCurrentScore);
 					}
+					
 					currentPartialSolutions.add(currentElement);
 				}
 			}
@@ -329,7 +348,7 @@
 		}
 		long endTime = System.currentTimeMillis();
 		logger.info("...finished in " + (endTime-partialSolutionStartTime) + "ms.");
-		EvaluatedDescription bestPartialSolution = bestPartialSolutionTree.asEvaluatedDescription(LiteralNodeConversionStrategy.SOME_VALUES_FROM);
+		EvaluatedDescription bestPartialSolution = bestPartialSolutionTree.getEvaluatedDescription();
 		
 		logger.info("Best partial solution: " + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()).toString().replace("\n", "") + "\n(" + bestPartialSolution.getScore() + ")");
 		
@@ -410,7 +429,12 @@
 		Set<EvaluatedQueryTree<String>> evaluatedTrees = new TreeSet<EvaluatedQueryTree<String>>();
 		
 		LiteralNodeSubsumptionStrategy[] strategies = LiteralNodeSubsumptionStrategy.values();
-		strategies = new LiteralNodeSubsumptionStrategy[]{LiteralNodeSubsumptionStrategy.DATATYPE, LiteralNodeSubsumptionStrategy.INTERVAL};
+		strategies = new LiteralNodeSubsumptionStrategy[]{
+				LiteralNodeSubsumptionStrategy.DATATYPE, 
+				LiteralNodeSubsumptionStrategy.INTERVAL, 
+				LiteralNodeSubsumptionStrategy.MIN,
+				LiteralNodeSubsumptionStrategy.MAX,
+				};
 		for (LiteralNodeSubsumptionStrategy strategy : strategies) {
 			//1. get a score for the coverage = recall oriented
 			List<QueryTree<String>> uncoveredPositiveExampleTrees = new ArrayList<QueryTree<String>>();
@@ -480,18 +504,27 @@
 	 * @param useSpecifity
 	 * @return
 	 */
-	private Set<EvaluatedDescription> evaluate2(QueryTree<String> tree, boolean useSpecifity){
-		Set<EvaluatedDescription> evaluatedDescriptions = new TreeSet<EvaluatedDescription>();
+	private Set<EvaluatedQueryTree<String>> evaluate2(QueryTree<String> tree, boolean useSpecifity){
+		Set<EvaluatedQueryTree<String>> evaluatedTrees = new TreeSet<EvaluatedQueryTree<String>>();
 		
-		LiteralNodeConversionStrategy[] strategies = LiteralNodeConversionStrategy.values();
-		strategies = new LiteralNodeConversionStrategy[]{LiteralNodeConversionStrategy.SOME_VALUES_FROM, LiteralNodeConversionStrategy.FACET_RESTRICTION};
+		//test different strategies on the conversion of literal nodes
+		Set<OWLClassExpression> combinations = new HashSet<OWLClassExpression>();
+		
 		for (LiteralNodeConversionStrategy strategy : strategies) {
-			Description d = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(tree.asOWLClassExpression(strategy));
+			OWLClassExpression ce = tree.asOWLClassExpression(strategy);
+			combinations.add(ce);
+		}
+		//compute all combinations of different types of facets
+//		OWLClassExpression ce = tree.asOWLClassExpression(LiteralNodeConversionStrategy.FACET_RESTRICTION);
+//		combinations = ce.accept(new ClassExpressionLiteralCombination());
+		for (OWLClassExpression c : combinations) {
+			Description d = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(c);
 			//convert to individuals
 			SortedSet<Individual> coveredExamples = reasoner.getIndividuals(d);
 			Set<Individual> coveredPosExamples = new TreeSet<Individual>(Sets.intersection(currentPosExamples, coveredExamples));
 			Set<Individual> uncoveredPosExamples = new TreeSet<Individual>(Sets.difference(currentPosExamples, coveredExamples));
 			Set<Individual> coveredNegExamples = new TreeSet<Individual>(Sets.intersection(currentNegExamples, coveredExamples));
+			Set<Individual> uncoveredNegExamples = new TreeSet<Individual>(Sets.difference(currentNegExamples, coveredExamples));
 			
 			//compute score
 			double recall = coveredPosExamples.size() / (double)currentPosExamples.size();
@@ -501,7 +534,7 @@
 			
 			double coverageScore = Heuristics.getFScore(recall, precision, beta);
 			
-			//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
+			//2. get a score for the specificity of the query, i.e. how many edges/nodes = precision oriented
 			int nrOfSpecificNodes = 0;
 			for (QueryTree<String> childNode : tree.getChildrenClosure()) {
 				if(!childNode.getUserObject().equals("?")){
@@ -516,33 +549,38 @@
 			//3.compute the total score
 			double score = coverageWeight * coverageScore + specifityWeight * specifityScore;
 			
-			QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
-					new TreeSet<Individual>(Sets.difference(currentPosExamples, uncoveredPosExamples)), uncoveredPosExamples,
-					coveredNegExamples, new TreeSet<Individual>(Sets.difference(currentNegExamples, coveredNegExamples)),
+			QueryTreeScore queryTreeScore = new QueryTreeScore(
+					score, coverageScore, 
+					coveredPosExamples, uncoveredPosExamples,
+					coveredNegExamples, uncoveredNegExamples,
 					specifityScore, nrOfSpecificNodes);
 			
 			//TODO use only the heuristic to compute the score
-//			score = heuristic.getScore(evaluatedTree);
-//			queryTreeScore.setScore(score);
-//			queryTreeScore.setAccuracy(score);
-//			
-//			EvaluatedDescription evaluatedDescription = new EvaluatedDescription(d, queryTreeScore);
-//			
-//			evaluatedDescriptions.add(evaluatedDescription);
+			EvaluatedQueryTree<String> evaluatedTree = new EvaluatedQueryTree<String>(tree, 
+					asQueryTrees(uncoveredPosExamples), asQueryTrees(coveredNegExamples), queryTreeScore);
+			score = heuristic.getScore(evaluatedTree);
+			queryTreeScore.setScore(score);
+			queryTreeScore.setAccuracy(score);
+			
+			
+			EvaluatedDescription evaluatedDescription = new EvaluatedDescription(d, queryTreeScore);
+			
+			evaluatedTree.setDescription(evaluatedDescription);
+			
+			evaluatedTrees.add(evaluatedTree);
 		}
-		
-		return evaluatedDescriptions;
+		return evaluatedTrees;
 	}
 	
 	private EvaluatedDescription buildCombinedSolution(){
 		EvaluatedDescription bestCombinedSolution = null;
 		double bestScore = Double.NEGATIVE_INFINITY;
 		LiteralNodeConversionStrategy[] strategies = LiteralNodeConversionStrategy.values();
-		strategies = new LiteralNodeConversionStrategy[]{LiteralNodeConversionStrategy.SOME_VALUES_FROM};
+		strategies = new LiteralNodeConversionStrategy[]{LiteralNodeConversionStrategy.DATATYPE};
 		for (LiteralNodeConversionStrategy strategy : strategies) {
 			EvaluatedDescription combinedSolution;
 			if(partialSolutions.size() == 1){
-				combinedSolution = partialSolutions.get(0).asEvaluatedDescription(strategy);
+				combinedSolution = partialSolutions.get(0).getEvaluatedDescription();
 			} else {
 				List<Description> disjuncts = new ArrayList<Description>();
 				
@@ -552,8 +590,7 @@
 				//build the union of all class expressions
 				Description partialDescription;
 				for (EvaluatedQueryTree<String> partialSolution : partialSolutions) {
-					partialDescription = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
-							partialSolution.getTree().asOWLClassExpression(strategy));
+					partialDescription = partialSolution.getEvaluatedDescription().getDescription();
 					disjuncts.add(partialDescription);
 					posCovered.addAll(partialSolution.getTreeScore().getCoveredPositives());
 					negCovered.addAll(partialSolution.getTreeScore().getCoveredNegatives());
@@ -679,11 +716,12 @@
 		return individuals;
 	}
 	
-	private void asTree(Description d){
-		QueryTree<String> tree = new QueryTreeImpl<String>("");
-		for (Description child : d.getChildren()) {
-			
+	private Set<QueryTree<String>> asQueryTrees(Collection<Individual> individuals){
+		Set<QueryTree<String>> trees = new HashSet<QueryTree<String>>(individuals.size());
+		for (Individual ind : individuals) {
+			trees.add(individual2Tree.get(ind));
 		}
+		return trees;
 	}
 
 	/**
@@ -802,16 +840,23 @@
 	private void todo(EvaluatedQueryTree<String> solution){
 		//check if not already contained in todo list
 		for (EvaluatedQueryTree<String> evTree : todoList) {
-			if(sameTrees(solution.getTree(), evTree.getTree())){
+			//this is a workaround as we have currently no equals method for trees based on the literal conversion strategy
+//			boolean sameTree = sameTrees(solution.getTree(), evTree.getTree());
+			boolean sameTree = OWLAPIConverter.getOWLAPIDescription(evTree.getEvaluatedDescription().getDescription()).toString()
+			.equals(OWLAPIConverter.getOWLAPIDescription(solution.getEvaluatedDescription().getDescription()).toString());
+			if(sameTree){
+				logger.warn("Not added to TODO list: Already contained in.");
 				return;
 			}
 		}
 		//check if not already contained in solutions
 		for (EvaluatedQueryTree<String> evTree : currentPartialSolutions) {
 			if(sameTrees(solution.getTree(), evTree.getTree())){
+				logger.warn("Not added to partial solutions list: Already contained in.");
 				return;
 			}
 		}
+		logger.info("Added to TODO list.");
 		todoList.add(solution);
 	}
 	

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2DisjunctiveMT.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2DisjunctiveMT.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2DisjunctiveMT.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -240,7 +240,7 @@
 	public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
 		EvaluatedQueryTree<String> bestSolution = solutions.first();
 		Description description = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
-				bestSolution.getTree().asOWLClassExpression(LiteralNodeConversionStrategy.FACET_RESTRICTION));
+				bestSolution.getTree().asOWLClassExpression(LiteralNodeConversionStrategy.MIN_MAX));
 		return new EvaluatedDescription(description, bestSolution.getTreeScore());
 	}
 	

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -118,11 +118,11 @@
 		/**
 		 * Literals as an interval on the datatype, e.g. [>= 5 <=10]
 		 */
-		FACET_RESTRICTION, 
+		MIN_MAX, 
 		/**
 		 * Literals as datatype, e.g. xsd:integer
 		 */
-		SOME_VALUES_FROM,
+		DATATYPE,
 		
 		MIN,
 		
@@ -207,7 +207,7 @@
         if(nodeType == NodeType.RESOURCE){
         	isResourceNode = true;
         } else if(nodeType == NodeType.LITERAL){
-        	isResourceNode = true;
+        	isLiteralNode = true;
         }
     }
     
@@ -1405,7 +1405,7 @@
      * are transformed into existential restrictions.
      */
     public OWLClassExpression asOWLClassExpression(){
-    	return asOWLClassExpression(LiteralNodeConversionStrategy.SOME_VALUES_FROM);
+    	return asOWLClassExpression(LiteralNodeConversionStrategy.DATATYPE);
     }
     
     /**
@@ -1430,7 +1430,7 @@
     	for(QueryTree<N> child : children){
     		String childLabel = (String) child.getUserObject();
     		String predicateString = (String) tree.getEdge(child);
-    		if(predicateString.equals(RDF.type.getURI())){
+    		if(predicateString.equals(RDF.type.getURI()) || predicateString.equals(RDFS.subClassOf.getURI())){//A
     			if(child.isVarNode()){
     				classExpressions.addAll(buildOWLClassExpressions(df, child, literalNodeConversionStrategy));
     			} else {
@@ -1438,25 +1438,17 @@
     					classExpressions.add(df.getOWLClass(IRI.create(childLabel)));
     				}
     			}
-    		} else if(predicateString.equals(RDFS.subClassOf.getURI())){
-    			if(child.isVarNode()){
-    				classExpressions.addAll(buildOWLClassExpressions(df, child, literalNodeConversionStrategy));
-    			} else {
-    				if(!childLabel.equals(OWL.Thing.getURI())){//avoid trivial owl:Thing statements
-    					classExpressions.add(df.getOWLClass(IRI.create(childLabel)));
-    				}
-    			}
     		} else {
     			if(child.isLiteralNode()){
     				OWLDataProperty p = df.getOWLDataProperty(IRI.create((String) tree.getEdge(child)));
-    				if(childLabel.equals("?")){
+    				if(childLabel.equals("?")){//p some int
     					Set<Literal> literals = child.getLiterals();
     					OWLDataRange dataRange = null;
     					if(literals.isEmpty()){//happens if there are heterogeneous datatypes
     						String datatypeURI = OWL2Datatype.RDFS_LITERAL.getURI().toString();
     						dataRange = df.getOWLDatatype(IRI.create(datatypeURI));
     					} else {
-    						if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.SOME_VALUES_FROM){
+    						if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.DATATYPE){
     							Literal lit = literals.iterator().next();
                     			RDFDatatype datatype = lit.getDatatype();
                     			String datatypeURI;
@@ -1468,7 +1460,7 @@
                     			dataRange = df.getOWLDatatype(IRI.create(datatypeURI));
     						} else if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.DATA_ONE_OF){
     							dataRange = asDataOneOf(df, literals);
-    						} else if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.FACET_RESTRICTION){
+    						} else if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.MIN_MAX){
     							dataRange = asFacet(df, literals);
     						} else if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.MIN){
     							dataRange = asMinFacet(df, literals);
@@ -1477,7 +1469,7 @@
     						}
     					}
             			classExpressions.add(df.getOWLDataSomeValuesFrom(p, dataRange));
-    				} else {
+    				} else {//p value 1.2
     					Set<Literal> literals = child.getLiterals();
             			Literal lit = literals.iterator().next();
             			OWLLiteral owlLiteral = asOWLLiteral(df, lit);
@@ -1486,7 +1478,7 @@
         		} else {
         			OWLObjectProperty p = df.getOWLObjectProperty(IRI.create((String) tree.getEdge(child)));
         			OWLClassExpression filler;
-        			if(child.isVarNode()){
+        			if(child.isVarNode()){//p some C
             			Set<OWLClassExpression> fillerClassExpressions = buildOWLClassExpressions(df, child, literalNodeConversionStrategy);
             			if(fillerClassExpressions.isEmpty()){
             				filler = df.getOWLThing();
@@ -1496,7 +1488,7 @@
             				filler = df.getOWLObjectIntersectionOf(fillerClassExpressions);
             			}
             			classExpressions.add(df.getOWLObjectSomeValuesFrom(p, filler));
-            		} else {
+            		} else {//p value {a}
             			classExpressions.add(df.getOWLObjectHasValue(p, df.getOWLNamedIndividual(IRI.create(childLabel))));
             		}
         		}

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -5,6 +5,7 @@
 import org.dllearner.algorithms.qtl.datastructures.QueryTree;
 import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.LiteralNodeConversionStrategy;
 import org.dllearner.core.EvaluatedDescription;
+import org.dllearner.core.owl.Description;
 import org.dllearner.learningproblems.QueryTreeScore;
 import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
 
@@ -18,6 +19,8 @@
 	private Collection<QueryTree<N>> falsePositives;
 	private QueryTreeScore score;
 //	private ScoreTwoValued score;
+	
+	private EvaluatedDescription description;
 
 	public EvaluatedQueryTree(QueryTree<N> tree, Collection<QueryTree<N>> falseNegatives, 
 			Collection<QueryTree<N>> falsePositives, QueryTreeScore score) {
@@ -61,7 +64,8 @@
 	@Override
 	public int compareTo(EvaluatedQueryTree<N> other) {
 		return ComparisonChain.start()
-		         .compare(this.getScore(), other.getScore())
+//		         .compare(this.getScore(), other.getScore())
+		         .compare(other.getScore(), this.getScore())
 		         .result();
 //		double diff = getScore() - other.getScore();
 //		if(diff == 0){
@@ -73,9 +77,26 @@
 //		}
 	}
 	
+	
+	/**
+	 * @return the description
+	 */
+	public EvaluatedDescription getEvaluatedDescription() {
+		return asEvaluatedDescription();
+	}
+	/**
+	 * @param description the description to set
+	 */
+	public void setDescription(EvaluatedDescription description) {
+		this.description = description;
+	}
+	
 	public EvaluatedDescription asEvaluatedDescription(){
-		return new EvaluatedDescription(DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
-				getTree().asOWLClassExpression(LiteralNodeConversionStrategy.FACET_RESTRICTION)), score);
+		if(description == null){
+			description = new EvaluatedDescription(DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
+					getTree().asOWLClassExpression(LiteralNodeConversionStrategy.MIN_MAX)), score);
+		}
+		return description;
 	}
 	
 	public EvaluatedDescription asEvaluatedDescription(LiteralNodeConversionStrategy strategy){

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -4,10 +4,17 @@
 package org.dllearner.algorithms.qtl.util;
 
 import java.util.Collection;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
 import java.util.Stack;
 
+import javax.xml.bind.DatatypeConverter;
+
 import org.dllearner.algorithms.qtl.datastructures.QueryTree;
 import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.LiteralNodeConversionStrategy;
 import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.NodeType;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.io.ToStringRenderer;
@@ -24,11 +31,15 @@
 import org.semanticweb.owlapi.model.OWLDataMaxCardinality;
 import org.semanticweb.owlapi.model.OWLDataMinCardinality;
 import org.semanticweb.owlapi.model.OWLDataOneOf;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLDataRange;
 import org.semanticweb.owlapi.model.OWLDataRangeVisitor;
 import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
 import org.semanticweb.owlapi.model.OWLDataUnionOf;
 import org.semanticweb.owlapi.model.OWLDatatype;
 import org.semanticweb.owlapi.model.OWLDatatypeRestriction;
+import org.semanticweb.owlapi.model.OWLFacetRestriction;
+import org.semanticweb.owlapi.model.OWLLiteral;
 import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
 import org.semanticweb.owlapi.model.OWLObjectComplementOf;
 import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
@@ -38,20 +49,24 @@
 import org.semanticweb.owlapi.model.OWLObjectMaxCardinality;
 import org.semanticweb.owlapi.model.OWLObjectMinCardinality;
 import org.semanticweb.owlapi.model.OWLObjectOneOf;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
 import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
 import org.semanticweb.owlapi.model.OWLObjectUnionOf;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyChange;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.PrefixManager;
-import org.semanticweb.owlapi.reasoner.OWLReasoner;
-import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 import org.semanticweb.owlapi.util.DefaultPrefixManager;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+import org.semanticweb.owlapi.vocab.OWLFacet;
 
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
 import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
 
-import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.hp.hpl.jena.datatypes.RDFDatatype;
+import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.RDFS;
 
 /**
  * Converts query trees into OWL class expressions and vice versa.
@@ -60,6 +75,8 @@
  */
 public class QueryTreeConverter implements OWLClassExpressionVisitor, OWLDataRangeVisitor{
 	
+	OWLDataFactory df = new OWLDataFactoryImpl();
+	
 	Stack<QueryTree<String>> stack = new Stack<QueryTree<String>>();
 	int id = 0;
 	
@@ -67,12 +84,213 @@
 	 * Returns a OWL class expression of the union of the given query trees.
 	 * @param queryTrees
 	 */
-	public void asOWLClassExpression(Collection<QueryTree<String>> queryTrees){
-		
-		//check for common paths
-		
+	public OWLClassExpression asOWLClassExpression(QueryTree<String> tree){
+		Set<OWLClassExpression> classExpressions = asOWLClassExpressions(tree);
+		OWLClassExpression expression;
+		if(classExpressions.isEmpty()){
+			expression = df.getOWLThing();
+		} else if(classExpressions.size() == 1){
+			expression = classExpressions.iterator().next();
+		} else {
+			expression = df.getOWLObjectIntersectionOf(classExpressions);
+		}
+		return expression;
 	}
 	
+	/**
+	 * Returns a OWL class expression representation of the given query tree.
+	 * @param queryTrees
+	 */
+	public Set<OWLClassExpression> asOWLClassExpressions(QueryTree<String> tree){
+		Set<OWLClassExpression> classExpressions = new HashSet<OWLClassExpression>();
+    	
+    	List<QueryTree<String>> children = tree.getChildren();
+    	for(QueryTree<String> child : children){
+    		String childLabel = (String) child.getUserObject();
+    		String predicateString = (String) tree.getEdge(child);
+    		if(predicateString.equals(RDF.type.getURI()) || predicateString.equals(RDFS.subClassOf.getURI())){//A
+    			if(child.isVarNode()){
+    				classExpressions.addAll(asOWLClassExpressions(child));
+    			} else {
+    				if(!childLabel.equals(OWL.Thing.getURI())){//avoid trivial owl:Thing statements
+    					classExpressions.add(df.getOWLClass(IRI.create(childLabel)));
+    				}
+    			}
+    		} else {
+    			if(child.isLiteralNode()){
+    				OWLDataProperty p = df.getOWLDataProperty(IRI.create((String) tree.getEdge(child)));
+    				if(childLabel.equals("?")){//p some int
+    					Set<Literal> literals = child.getLiterals();
+    					OWLDataRange dataRange = null;
+    					if(literals.isEmpty()){//happens if there are heterogeneous datatypes
+    						String datatypeURI = OWL2Datatype.RDFS_LITERAL.getURI().toString();
+    						dataRange = df.getOWLDatatype(IRI.create(datatypeURI));
+    					} else {
+    						for (LiteralNodeConversionStrategy strategy : LiteralNodeConversionStrategy.values()) {
+    							if(strategy == LiteralNodeConversionStrategy.DATATYPE){
+        							Literal lit = literals.iterator().next();
+                        			RDFDatatype datatype = lit.getDatatype();
+                        			String datatypeURI;
+                        			if(datatype == null){
+                        				datatypeURI = OWL2Datatype.RDF_PLAIN_LITERAL.getURI().toString();
+                        			} else {
+                        				datatypeURI = datatype.getURI();
+                        			}
+                        			dataRange = df.getOWLDatatype(IRI.create(datatypeURI));
+        						} else if(strategy == LiteralNodeConversionStrategy.DATA_ONE_OF){
+        							dataRange = asDataOneOf(df, literals);
+        						} else if(strategy == LiteralNodeConversionStrategy.MIN_MAX){
+        							dataRange = asFacet(df, literals);
+        						} else if(strategy == LiteralNodeConversionStrategy.MIN){
+        							dataRange = asMinFacet(df, literals);
+        						} else if(strategy == LiteralNodeConversionStrategy.MAX){
+        							dataRange = asMaxFacet(df, literals);
+        						}
+							}
+    					}
+            			classExpressions.add(df.getOWLDataSomeValuesFrom(p, dataRange));
+    				} else {//p value 1.2
+    					Set<Literal> literals = child.getLiterals();
+            			Literal lit = literals.iterator().next();
+            			OWLLiteral owlLiteral = asOWLLiteral(df, lit);
+            			classExpressions.add(df.getOWLDataHasValue(p, owlLiteral));
+    				}
+        		} else {
+        			OWLObjectProperty p = df.getOWLObjectProperty(IRI.create((String) tree.getEdge(child)));
+        			OWLClassExpression filler;
+        			if(child.isVarNode()){//p some C
+            			Set<OWLClassExpression> fillerClassExpressions = asOWLClassExpressions(child);
+            			if(fillerClassExpressions.isEmpty()){
+            				filler = df.getOWLThing();
+            			} else if(fillerClassExpressions.size() == 1){
+            				filler = fillerClassExpressions.iterator().next();
+            			} else {
+            				filler = df.getOWLObjectIntersectionOf(fillerClassExpressions);
+            			}
+            			classExpressions.add(df.getOWLObjectSomeValuesFrom(p, filler));
+            		} else {//p value {a}
+            			classExpressions.add(df.getOWLObjectHasValue(p, df.getOWLNamedIndividual(IRI.create(childLabel))));
+            		}
+        		}
+    		}
+    	}
+    	return classExpressions;
+	}
+	
+	private OWLDataRange asFacet(OWLDataFactory df, Set<Literal> literals){
+    	//return Boolean datatype because it doesn't make sense to return a facet of Boolean values
+    	if(getOWLDatatype(df, literals).equals(df.getBooleanOWLDatatype())){
+    		return df.getBooleanOWLDatatype();
+    	}
+    	Literal min = getMin(literals);
+    	Literal max = getMax(literals);
+    	
+    	OWLFacetRestriction minRestriction = df.getOWLFacetRestriction(OWLFacet.MIN_INCLUSIVE, asOWLLiteral(df, min));
+    	OWLFacetRestriction maxRestriction = df.getOWLFacetRestriction(OWLFacet.MAX_INCLUSIVE, asOWLLiteral(df, max));
+    	
+    	return df.getOWLDatatypeRestriction(getOWLDatatype(df, literals), minRestriction, maxRestriction);
+    }
+    
+    private OWLDataRange asMinFacet(OWLDataFactory df, Set<Literal> literals){
+    	//return Boolean datatype because it doesn't make sense to return a facet of Boolean values
+    	if(getOWLDatatype(df, literals).equals(df.getBooleanOWLDatatype())){
+    		return df.getBooleanOWLDatatype();
+    	}
+    	Literal min = getMin(literals);
+    	
+    	OWLFacetRestriction minRestriction = df.getOWLFacetRestriction(OWLFacet.MIN_INCLUSIVE, asOWLLiteral(df, min));
+    	
+    	return df.getOWLDatatypeRestriction(getOWLDatatype(df, literals), minRestriction);
+    }
+    
+    private OWLDataRange asMaxFacet(OWLDataFactory df, Set<Literal> literals){
+    	//return Boolean datatype because it doesn't make sense to return a facet of Boolean values
+    	if(getOWLDatatype(df, literals).equals(df.getBooleanOWLDatatype())){
+    		return df.getBooleanOWLDatatype();
+    	}
+    	Literal max = getMax(literals);
+    	
+    	OWLFacetRestriction maxRestriction = df.getOWLFacetRestriction(OWLFacet.MAX_INCLUSIVE, asOWLLiteral(df, max));
+    	
+    	return df.getOWLDatatypeRestriction(getOWLDatatype(df, literals), maxRestriction);
+    }
+    
+    private OWLDataRange asDataOneOf(OWLDataFactory df, Set<Literal> literals){
+    	//return Boolean datatype because it doesn't make sense to return a enumeration of Boolean values
+    	if(getOWLDatatype(df, literals).equals(df.getBooleanOWLDatatype())){
+    		return df.getBooleanOWLDatatype();
+    	}
+    	return df.getOWLDataOneOf(asOWLLiterals(df, literals));
+    }
+    
+    private Set<OWLLiteral> asOWLLiterals(OWLDataFactory df, Set<Literal> literals){
+    	Set<OWLLiteral> owlLiterals = new HashSet<OWLLiteral>(literals.size());
+    	for (Literal literal : literals) {
+			owlLiterals.add(asOWLLiteral(df, literal));
+		}
+    	return owlLiterals;
+    }
+    
+    private OWLLiteral asOWLLiteral(OWLDataFactory df, Literal literal){
+    	OWLLiteral owlLiteral;
+		if(literal.getDatatypeURI() == null){
+			owlLiteral = df.getOWLLiteral(literal.getLexicalForm(), literal.getLanguage());
+		} else {
+			owlLiteral = df.getOWLLiteral(literal.getLexicalForm(), df.getOWLDatatype(IRI.create(literal.getDatatypeURI())));
+		}
+    	return owlLiteral;
+    }
+    
+    private Literal getMin(Set<Literal> literals){
+    	Iterator<Literal> iter = literals.iterator();
+    	Literal min = iter.next();
+    	Literal l;
+    	while(iter.hasNext()){
+    		l = iter.next();
+    		if(l.getDatatype() == XSDDatatype.XSDinteger || l.getDatatype() == XSDDatatype.XSDint){
+    			min = (l.getInt() < min.getInt()) ? l : min;
+    		} else if(l.getDatatype() == XSDDatatype.XSDdouble || l.getDatatype() == XSDDatatype.XSDdecimal){
+    			min = (l.getDouble() < min.getDouble()) ? l : min;
+    		} else if(l.getDatatype() == XSDDatatype.XSDfloat){
+    			min = (l.getFloat() < min.getFloat()) ? l : min;
+    		} else if(l.getDatatype() == XSDDatatype.XSDdate){
+    			min = (DatatypeConverter.parseDate(l.getLexicalForm()).compareTo(DatatypeConverter.parseDate(min.getLexicalForm())) == -1) ? l : min;
+    		} 
+    	}
+    	return min;
+    }
+    
+    private Literal getMax(Set<Literal> literals){
+    	Iterator<Literal> iter = literals.iterator();
+    	Literal max = iter.next();
+    	Literal l;
+    	while(iter.hasNext()){
+    		l = iter.next();
+    		if(l.getDatatype() == XSDDatatype.XSDinteger || l.getDatatype() == XSDDatatype.XSDint){
+    			max = (l.getInt() > max.getInt()) ? l : max;
+    		} else if(l.getDatatype() == XSDDatatype.XSDdouble || l.getDatatype() == XSDDatatype.XSDdecimal){
+    			max = (l.getDouble() > max.getDouble()) ? l : max;
+    		} else if(l.getDatatype() == XSDDatatype.XSDfloat){
+    			max = (l.getFloat() > max.getFloat()) ? l : max;
+    		} else if(l.getDatatype() == XSDDatatype.XSDdate){
+    			max = (DatatypeConverter.parseDate(l.getLexicalForm()).compareTo(DatatypeConverter.parseDate(max.getLexicalForm())) == 1) ? l : max;
+    		} 
+    	}
+    	return max;
+    }
+    
+    private OWLDatatype getOWLDatatype(OWLDataFactory df, Set<Literal> literals){
+    	return df.getOWLDatatype(IRI.create(literals.iterator().next().getDatatypeURI()));
+    }
+	
+	
+	/**
+	 * Converts a OWL class expression into a query tree, if possible. Note that this is not possible
+	 * for all OWL constructs, e.g. universal restrictions are not allowed. An exceptions is thrown if the conversion
+	 * fails.
+	 * @param expression
+	 * @return
+	 */
 	public QueryTree<String> asQueryTree(OWLClassExpression expression){
 //		stack.push(new QueryTreeImpl<String>("?"));
 		reset();

Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractCELA.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractCELA.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractCELA.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -52,7 +52,7 @@
  * @author Jens Lehmann
  *
  */
-public abstract class AbstractCELA extends AbstractComponent implements ClassExpressionLearningAlgorithm, StoppableLearningAlgorithm, Cloneable {
+public abstract class AbstractCELA extends AbstractComponent implements ClassExpressionLearningAlgorithm, StoppableLearningAlgorithm {
 	
 	protected EvaluatedDescriptionSet bestEvaluatedDescriptions = new EvaluatedDescriptionSet(AbstractCELA.MAX_NR_OF_RESULTS);
 	protected DecimalFormat dfPercent = new DecimalFormat("0.00%");

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/Constant.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/Constant.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/Constant.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -19,17 +19,16 @@
 
 package org.dllearner.core.owl;
 
+import java.io.Serializable;
+
 /**
  * A constant value.
  * 
  * @author Jens Lehmann
  *
  */
-public abstract class Constant implements KBElement, Comparable<Constant> {
+public abstract class Constant implements KBElement, Comparable<Constant>, Serializable {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 2331790456049452753L;
 	String literal;
 	

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DatatypeProperty.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DatatypeProperty.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DatatypeProperty.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -31,9 +31,6 @@
  */
 public class DatatypeProperty implements Comparable<DatatypeProperty>, Property, NamedKBElement, Serializable {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 8452865438915671952L;
 	protected String name;
 	

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMaxValue.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMaxValue.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMaxValue.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -58,11 +58,11 @@
 	 * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
 	 */
 	public String toString(String baseURI, Map<String, String> prefixes) {
-		return " double[<= " + value + "]";
+		return "double[<= " + value + "]";
 	}
 	
 	public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " double[<= " + value + "]";
+		return "double[<= " + value + "]";
 	}
 	
 	public void accept(KBElementVisitor visitor) {
@@ -74,7 +74,7 @@
 	 */
 	@Override
 	public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " double[<= " + value + "]";
+		return "double[<= " + value + "]";
 	}
 
 	/* (non-Javadoc)

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -65,11 +65,11 @@
 	 * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
 	 */
 	public String toString(String baseURI, Map<String, String> prefixes) {
-		return " double[>= " + minValue + " <= " + maxValue + "]";
+		return "double[>= " + minValue + ", <= " + maxValue + "]";
 	}
 	
 	public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " double[>= " + minValue + " <= " + maxValue + "]";
+		return "double[>= " + minValue + ", <= " + maxValue + "]";
 	}
 	
 	public void accept(KBElementVisitor visitor) {
@@ -81,7 +81,7 @@
 	 */
 	@Override
 	public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " double[>= " + minValue + " <= " + maxValue + "]";
+		return "double[>= " + minValue + ", <= " + maxValue + "]";
 	}
 
 	/* (non-Javadoc)

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinValue.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinValue.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinValue.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -58,11 +58,11 @@
 	 * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
 	 */
 	public String toString(String baseURI, Map<String, String> prefixes) {
-		return " double[>= " + value + "]";
+		return "double[>= " + value + "]";
 	}	
 	
 	public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " double[>= " + value + "]";
+		return "double[>= " + value + "]";
 	}	
 	
 	public void accept(KBElementVisitor visitor) {
@@ -74,7 +74,7 @@
 	 */
 	@Override
 	public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " double[>= " + value + "]";
+		return "double[>= " + value + "]";
 	}
 
 	/* (non-Javadoc)

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -19,6 +19,7 @@
 
 package org.dllearner.core.owl;
 
+import java.io.Serializable;
 import java.net.URI;
 import java.util.Map;
 
@@ -31,7 +32,7 @@
  * @author Jens Lehmann
  *
  */
-public class ObjectProperty extends ObjectPropertyExpression implements Property, Comparable<ObjectProperty>{
+public class ObjectProperty extends ObjectPropertyExpression implements Property, Comparable<ObjectProperty>, Serializable{
 
 	private static final long serialVersionUID = -3343070247923446690L;
 

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/TypedConstant.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/TypedConstant.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/TypedConstant.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -29,9 +29,6 @@
  */
 public class TypedConstant extends Constant {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = -9135242138291085300L;
 	private Datatype datatype;
 	

Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/ExistentialRestrictionMaterialization.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/ExistentialRestrictionMaterialization.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/ExistentialRestrictionMaterialization.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -6,6 +6,7 @@
 import java.io.ByteArrayInputStream;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.Map;
 import java.util.Set;
 import java.util.Stack;
@@ -81,27 +82,55 @@
 		private Map<OWLClass, Set<OWLClassExpression>> map = new HashMap<>();
 		Stack<Set<OWLClassExpression>> stack = new Stack<Set<OWLClassExpression>>();
 		OWLDataFactory df;
+		boolean onlyIfExistentialOnPath = true;
+		
+		int indent = 0;
 
 		public SuperClassFinder() {
 			df = ontology.getOWLOntologyManager().getOWLDataFactory();
 		}
 		
 		public Set<OWLClassExpression> getSuperClasses(OWLClass cls){
+//			System.out.println("#################");
 			map.clear();
 			computeSuperClasses(cls);
 			Set<OWLClassExpression> superClasses = map.get(cls);
 			superClasses.remove(cls);
+			
+			//filter out non existential superclasses
+			if(onlyIfExistentialOnPath){
+				for (Iterator<OWLClassExpression> iterator = superClasses.iterator(); iterator.hasNext();) {
+					OWLClassExpression sup = iterator.next();
+					if (!(sup instanceof OWLObjectSomeValuesFrom || sup instanceof OWLDataAllValuesFrom)) {
+						iterator.remove();
+					}
+				}
+			}
 			return superClasses;
 		}
 		
 		private void computeSuperClasses(OWLClass cls){
+			String s = "";
+			for(int i = 0; i < indent; i++){
+				s += "   ";
+			}
+//			System.out.println(s + cls);
+			indent++;
 			Set<OWLClassExpression> superClasses = new HashSet<OWLClassExpression>();
 			superClasses.add(cls);
+			
+			//get the directly asserted super classes
 			Set<OWLClassExpression> superClassExpressions = cls.getSuperClasses(ontology);
+			
+			//omit trivial super class
+			superClassExpressions.remove(cls);
+			
+			//go subsumption hierarchy up for each directly asserted super class
 			for (OWLClassExpression sup : superClassExpressions) {
 				sup.accept(this);
 				superClasses.addAll(stack.pop());
 			}
+			
 			stack.push(superClasses);
 			map.put(cls, superClasses);
 		}

Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java	2014-07-02 06:31:52 UTC (rev 4279)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java	2014-07-29 13:53:19 UTC (rev 4280)
@@ -59,6 +59,7 @@
 import ...
 
[truncated message content]

[DL-Learner SVN] SF.net SVN: dl-learner:[4279] trunk/components-core/src/main/java/org/ dllearner/reasoning/SPARQLReasoner.java

[<lor...@us...>]

Revision: 4279
          http://sourceforge.net/p/dl-learner/code/4279
Author:   lorenz_b
Date:     2014-07-02 06:31:52 +0000 (Wed, 02 Jul 2014)
Log Message:
-----------
Added constructor.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java

Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java	2014-06-25 10:06:50 UTC (rev 4278)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java	2014-07-02 06:31:52 UTC (rev 4279)
@@ -54,14 +54,12 @@
 import org.dllearner.core.owl.DataRange;
 import org.dllearner.core.owl.Datatype;
 import org.dllearner.core.owl.DatatypeProperty;
-import org.dllearner.core.owl.DatatypePropertyHierarchy;
 import org.dllearner.core.owl.Description;
 import org.dllearner.core.owl.Individual;
 import org.dllearner.core.owl.Intersection;
 import org.dllearner.core.owl.NamedClass;
 import org.dllearner.core.owl.Nothing;
 import org.dllearner.core.owl.ObjectProperty;
-import org.dllearner.core.owl.ObjectPropertyHierarchy;
 import org.dllearner.core.owl.Property;
 import org.dllearner.core.owl.Thing;
 import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
@@ -82,7 +80,6 @@
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.RDFNode;
@@ -122,6 +119,15 @@
 		this(ks, (String)null);
 	}
 	
+	public SPARQLReasoner(QueryExecutionFactory qef) {
+		this.qef = qef;
+		
+		classPopularityMap = new HashMap<NamedClass, Integer>();
+		objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
+		dataPropertyPopularityMap = new HashMap<DatatypeProperty, Integer>();
+		individualPopularityMap = new HashMap<Individual, Integer>();
+	}
+	
 	public SPARQLReasoner(SparqlEndpointKS ks, String cacheDirectory) {
 		this.ks = ks;
 
@@ -140,9 +146,9 @@
 					CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
 					qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
 				} catch (ClassNotFoundException e) {
-					e.printStackTrace();
+					logger.error(e.getMessage(), e);
 				} catch (SQLException e) {
-					e.printStackTrace();
+					logger.error(e.getMessage(), e);
 				}
 			}
 //			qef = new QueryExecutionFactoryPaginated(qef, 10000);
@@ -177,7 +183,7 @@
 			qef = new QueryExecutionFactoryModel(((LocalModelBasedSparqlEndpointKS)ks).getModel());
 		}
 	}
-
+	
 	public SPARQLReasoner(SparqlEndpointKS ks, ExtractionDBCache cache) {
 		this(ks, cache.getCacheDirectory());
 	}
@@ -1871,6 +1877,10 @@
 	 */
 	@Override
 	public void init() throws ComponentInitException {
+		classPopularityMap = new HashMap<NamedClass, Integer>();
+		objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
+		dataPropertyPopularityMap = new HashMap<DatatypeProperty, Integer>();
+		individualPopularityMap = new HashMap<Individual, Integer>();
 	}
 
 	/* (non-Javadoc)

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4278] trunk/components-core/src/main/java/org/ dllearner/algorithms/qtl/QTL.java

[<ki...@us...>]

Revision: 4278
          http://sourceforge.net/p/dl-learner/code/4278
Author:   kirdie
Date:     2014-06-25 10:06:50 +0000 (Wed, 25 Jun 2014)
Log Message:
-----------
QTL bugfix and formatting improvement.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java	2014-06-24 09:35:44 UTC (rev 4277)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java	2014-06-25 10:06:50 UTC (rev 4278)
@@ -33,7 +33,6 @@
 import java.util.SortedSet;
 import java.util.TreeSet;
 import java.util.concurrent.TimeUnit;
-
 import org.aksw.jena_sparql_api.cache.core.QueryExecutionFactoryCacheEx;
 import org.aksw.jena_sparql_api.cache.extra.CacheCoreEx;
 import org.aksw.jena_sparql_api.cache.extra.CacheCoreH2;
@@ -54,6 +53,7 @@
 import org.dllearner.algorithms.qtl.operations.NBR;
 import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
 import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
+import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
 import org.dllearner.algorithms.qtl.util.SPARQLEndpointEx;
 import org.dllearner.core.AbstractCELA;
 import org.dllearner.core.AbstractLearningProblem;
@@ -101,39 +101,39 @@
  */
 @ComponentAnn(name="query tree learner", shortName="qtl", version=0.8)
 public class QTL extends AbstractCELA implements SparqlQueryLearningAlgorithm {
-	
+
 	private static final Logger logger = Logger.getLogger(QTL.class);
-	
+
 	private LearningProblem learningProblem;
 	private SparqlEndpointKS endpointKS;
-//	private QTLConfigurator configurator;
-	
+	//	private QTLConfigurator configurator;
+
 	private SparqlEndpoint endpoint;
 	private Model model;
-	private org.aksw.jena_sparql_api.core.QueryExecutionFactory qef;
+	private QueryExecutionFactory qef;
 	private String cacheDirectory;
-	
+
 	private QueryTreeCache treeCache;
-	
+
 	private LGGGenerator<String> lggGenerator;
 	private NBR<String> nbr;
-	
+
 	private List<String> posExamples;
 	private List<String> negExamples;
-	
+
 	private List<QueryTree<String>> posExampleTrees;
 	private List<QueryTree<String>> negExampleTrees;
-	
+
 	private QueryTreeFilter queryTreeFilter;
-	
+
 	private ConciseBoundedDescriptionGenerator cbdGenerator;
-	
+
 	private int maxExecutionTimeInSeconds = 60;
 	private int maxQueryTreeDepth = 2;
-	
+
 	private QueryTree<String> lgg;
 	private SortedSet<String> lggInstances;
-	
+
 	private Set<String> objectNamespacesToIgnore = new HashSet<String>();
 	private Set<String> allowedNamespaces = new HashSet<String>();
 	private Map<String, String> prefixes = new HashMap<String, String>();
@@ -145,14 +145,14 @@
 		options.add(new IntegerConfigOption("maxQueryTreeDepth", "recursion depth of query tree extraction", 2));
 		return options;
 	}
-	
-	public QTL() {
-	}
-	
+
+	//	public QTL() {
+	//	}
+
 	public QTL(AbstractLearningProblem learningProblem, SparqlEndpointKS endpointKS) throws LearningProblemUnsupportedException{
 		this(learningProblem, endpointKS, null);
 	}
-	
+
 	public QTL(AbstractLearningProblem learningProblem, SparqlEndpointKS endpointKS, String cacheDirectory) throws LearningProblemUnsupportedException{
 		if(!(learningProblem instanceof PosOnlyLP || learningProblem instanceof PosNegLP)){
 			throw new LearningProblemUnsupportedException(learningProblem.getClass(), getClass());
@@ -161,69 +161,69 @@
 		this.endpointKS = endpointKS;
 		this.cacheDirectory = cacheDirectory;
 	}
-	
+
 	public QTL(SPARQLEndpointEx endpoint, String cacheDirectory) {
 		this.endpoint = endpoint;
 		this.cacheDirectory = cacheDirectory;
-		
+
 		treeCache = new QueryTreeCache();
 		cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(endpoint, cacheDirectory));
 		cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
-		
+
 		lggGenerator = new LGGGeneratorImpl<String>();
 		nbr = new NBR<String>(endpoint, cacheDirectory);
 		nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
-		
+
 		posExampleTrees = new ArrayList<QueryTree<String>>();
 		negExampleTrees = new ArrayList<QueryTree<String>>();
 	}
-	
+
 	public QTL(SparqlEndpointKS endpointKS, String cacheDirectory) {
 		this.endpointKS = endpointKS;
 		this.cacheDirectory = cacheDirectory;
-		
+
 		treeCache = new QueryTreeCache();
 		cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(endpoint, cacheDirectory));
 		cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
-		
+
 		lggGenerator = new LGGGeneratorImpl<String>();
 		nbr = new NBR<String>(endpoint, cacheDirectory);
 		nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
-		
+
 		posExampleTrees = new ArrayList<QueryTree<String>>();
 		negExampleTrees = new ArrayList<QueryTree<String>>();
 	}
-	
+
 	public QTL(Model model) {
 		this.model = model;
-		
+
 		treeCache = new QueryTreeCache();
 		cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(model));
 		cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
-		
+
 		lggGenerator = new LGGGeneratorImpl<String>();
 		nbr = new NBR<String>(model);
 		nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
-		
+
 		posExampleTrees = new ArrayList<QueryTree<String>>();
 		negExampleTrees = new ArrayList<QueryTree<String>>();
 	}
-	
+
 	public String getQuestion(List<String> posExamples, List<String> negExamples) throws EmptyLGGException, NegativeTreeCoverageExecption, TimeOutException {
 		this.posExamples = posExamples;
 		this.negExamples = negExamples;
-		
+
 		generatePositiveExampleTrees();
 		generateNegativeExampleTrees();
-		
+
 		if(negExamples.isEmpty()){
 			QueryTree<String> dummyNegTree = new QueryTreeImpl<String>("?");
 			dummyNegTree.addChild(new QueryTreeImpl<String>("?"), "dummy");
 			negExampleTrees.add(dummyNegTree);
 		}
-		
+
 		lgg = lggGenerator.getLGG(posExampleTrees);
-		
+
 		if(queryTreeFilter != null){
 			lgg = queryTreeFilter.getFilteredQueryTree(lgg);
 		}
@@ -233,86 +233,86 @@
 		if(lgg.isEmpty()){
 			throw new EmptyLGGException();
 		}
-		
+
 		int index = coversNegativeQueryTree(lgg);
 		if(index != -1){
 			throw new NegativeTreeCoverageExecption(negExamples.get(index));
 		}
-		
+
 		lggInstances = getResources(lgg);
 		nbr.setLGGInstances(lggInstances);
-		
+
 		String question;
 		if(negExamples.isEmpty()){
 			question = nbr.getQuestion(lgg, negExampleTrees, getKnownResources());
 		} else {
 			question = nbr.getQuestion(lgg, negExampleTrees, getKnownResources());
 		}
-		
-		
+
+
 		return question;
 	}
-	
+
 	public void setExamples(List<String> posExamples, List<String> negExamples){
 		this.posExamples = posExamples;
 		this.negExamples = negExamples;
 	}
-	
+
 	public void addStatementFilter(Filter<Statement> filter){
 		treeCache.setStatementFilter(filter);
 	}
-	
+
 	public void addQueryTreeFilter(QueryTreeFilter queryTreeFilter){
 		this.queryTreeFilter = queryTreeFilter;
 	}
-	
+
 	public void setMaxExecutionTimeInSeconds(int maxExecutionTimeInSeconds){
 		this.maxExecutionTimeInSeconds = maxExecutionTimeInSeconds;
 		nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
 	}
-	
+
 	public void setMaxQueryTreeDepth(int maxQueryTreeDepth){
 		this.maxQueryTreeDepth = maxQueryTreeDepth;
-//		cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
+		//		cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
 	}
-	
+
 	public int getMaxQueryTreeDepth() {
 		return maxQueryTreeDepth;
 	}
-	
+
 	public void setPrefixes(Map<String, String> prefixes) {
 		this.prefixes = prefixes;
 	}
-	
+
 	public Map<String, String> getPrefixes() {
 		return prefixes;
 	}
-	
+
 	public String getSPARQLQuery(){
 		if(lgg == null){
 			lgg = lggGenerator.getLGG(getQueryTrees(posExamples));
 		}
 		return lgg.toSPARQLQueryString();
 	}
-	
+
 	public void setObjectNamespacesToIgnore(Set<String> namespacesToIgnore){
 		this.objectNamespacesToIgnore = namespacesToIgnore;
 	}
-	
+
 	public void setRestrictToNamespaces(List<String> namespaces){
 		cbdGenerator.setRestrictToNamespaces(namespaces);
 	}
-	
+
 	private void generatePositiveExampleTrees(){
 		posExampleTrees.clear();
 		posExampleTrees.addAll(getQueryTrees(posExamples));
 	}
-	
+
 	private void generateNegativeExampleTrees(){
 		negExampleTrees.clear();
 		negExampleTrees.addAll(getQueryTrees(negExamples));
 	}
-	
+
 	private List<QueryTree<String>> getQueryTrees(List<String> resources){
 		List<QueryTree<String>> trees = new ArrayList<QueryTree<String>>();
 		Model model;
@@ -326,7 +326,7 @@
 				if(logger.isDebugEnabled()){
 					logger.debug("Tree for resource " + resource);
 					logger.debug(tree.getStringRepresentation());
-					
+
 				}
 				trees.add(tree);
 			} catch (Exception e) {
@@ -335,7 +335,7 @@
 		}
 		return trees;
 	}
-	
+
 	private void applyFilters(Model model){
 		Statement st;
 		for(StmtIterator iter = model.listStatements(); iter.hasNext();){
@@ -348,20 +348,20 @@
 			}
 		}
 	}
-	
+
 	private List<String> getKnownResources(){
 		return ListUtils.union(posExamples, negExamples);
 	}
-	
-//	private boolean coversNegativeQueryTree(QueryTree<String> tree){
-//		for(QueryTree<String> negTree : negExampleTrees){
-//			if(negTree.isSubsumedBy(tree)){
-//				return true;
-//			}
-//		}
-//		return false;
-//	}
-	
+
+	//	private boolean coversNegativeQueryTree(QueryTree<String> tree){
+	//		for(QueryTree<String> negTree : negExampleTrees){
+	//			if(negTree.isSubsumedBy(tree)){
+	//				return true;
+	//			}
+	//		}
+	//		return false;
+	//	}
+
 	private int coversNegativeQueryTree(QueryTree<String> tree){
 		for(int i = 0; i < negExampleTrees.size(); i++){
 			if(negExampleTrees.get(i).isSubsumedBy(tree)){
@@ -370,13 +370,13 @@
 		}
 		return -1;
 	}
-	
+
 	private SortedSet<String> getResources(QueryTree<String> tree){
 		SortedSet<String> resources = new TreeSet<String>();
 		String query = getDistinctSPARQLQuery(tree);
 		QueryExecution qe = qef.createQueryExecution(query);
 		ResultSet rs = qe.execSelect();
-		
+
 		QuerySolution qs;
 		while(rs.hasNext()){
 			qs = rs.next();
@@ -385,35 +385,35 @@
 		qe.close();
 		return resources;
 	}
-	
+
 	private String getDistinctSPARQLQuery(QueryTree<String> tree){
 		String query = tree.toSPARQLQueryString();
-//		query = "SELECT DISTINCT " + query.substring(7);
+		//		query = "SELECT DISTINCT " + query.substring(7);
 		return query;
 	}
 
-//	@Override
-//	public void start(){
-//		generatePositiveExampleTrees();
-//		
-//		lgg = lggGenerator.getLGG(posExampleTrees);
-//		
-//		if(queryTreeFilter != null){
-//			lgg = queryTreeFilter.getFilteredQueryTree(lgg);
-//		}
-//		if(logger.isDebugEnabled()){
-//			logger.debug("LGG: \n" + lgg.getStringRepresentation());
-//		}
-//		if(logger.isInfoEnabled()){
-//			logger.info("Generated SPARQL query:\n" + lgg.toSPARQLQueryString(true, enableNumericLiteralFilters, prefixes));
-//		}
-//	}
-	
+	//	@Override
+	//	public void start(){
+	//		generatePositiveExampleTrees();
+	//		
+	//		lgg = lggGenerator.getLGG(posExampleTrees);
+	//		
+	//		if(queryTreeFilter != null){
+	//			lgg = queryTreeFilter.getFilteredQueryTree(lgg);
+	//		}
+	//		if(logger.isDebugEnabled()){
+	//			logger.debug("LGG: \n" + lgg.getStringRepresentation());
+	//		}
+	//		if(logger.isInfoEnabled()){
+	//			logger.info("Generated SPARQL query:\n" + lgg.toSPARQLQueryString(true, enableNumericLiteralFilters, prefixes));
+	//		}
+	//	}
+
 	@Override
 	public void start(){
 		//build the query trees for the positive examples
 		generatePositiveExampleTrees();
-		
+
 		//compute the LGG
 		lgg = lggGenerator.getLGG(posExampleTrees);
 		if(queryTreeFilter != null){
@@ -425,21 +425,21 @@
 		if(logger.isInfoEnabled()){
 			logger.info("Generated SPARQL query:\n" + lgg.toSPARQLQueryString(true, enableNumericLiteralFilters, prefixes));
 		}
-		
+
 		//build the query trees for the negative examples
 		if(!negExamples.isEmpty()){
 			generateNegativeExampleTrees();
-			
+
 			try {
 				//check if the LGG covers a negative example
 				int index = coversNegativeQueryTree(lgg);
 				if(index != -1){
 					throw new NegativeTreeCoverageExecption(negExamples.get(index));
 				}
-				
+
 				lggInstances = getResources(lgg);
 				nbr.setLGGInstances(lggInstances);
-				
+
 				String question;
 				if(negExamples.isEmpty()){
 					question = nbr.getQuestion(lgg, negExampleTrees, getKnownResources());
@@ -454,15 +454,15 @@
 			}
 		}
 	}
-	
+
 	public void setEnableNumericLiteralFilters(boolean enableNumericLiteralFilters) {
 		this.enableNumericLiteralFilters = enableNumericLiteralFilters;
 	}
-	
+
 	public boolean isEnableNumericLiteralFilters() {
 		return enableNumericLiteralFilters;
 	}
-	
+
 	@Override
 	public List<String> getCurrentlyBestSPARQLQueries(int nrOfSPARQLQueries) {
 		return Collections.singletonList(getBestSPARQLQuery());
@@ -473,29 +473,39 @@
 		return lgg.toSPARQLQueryString();
 	}
 
-	public void init() {
-		if(endpointKS.isRemote()){
-			SparqlEndpoint endpoint = endpointKS.getEndpoint();
-			qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
-			if(cacheDirectory != null){
-				try {
-					long timeToLive = TimeUnit.DAYS.toMillis(30);
-					CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDirectory, timeToLive, true);
-					CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
-					qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
-				} catch (ClassNotFoundException e) {
-					e.printStackTrace();
-				} catch (SQLException e) {
-					e.printStackTrace();
+	public void init() {// TODO: further improve code quality 
+		//	private QTL() {
+		if(endpointKS==null)
+		{
+			qef = new QueryExecutionFactoryModel(this.model);
+			cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(model));
+			nbr = new NBR<String>(model);
+		}
+		else
+		{	
+			if(endpointKS.isRemote())
+			{
+				SparqlEndpoint endpoint = endpointKS.getEndpoint();
+				QueryExecutionFactory qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+				if(cacheDirectory != null){
+					try {
+						long timeToLive = TimeUnit.DAYS.toMillis(30);
+						CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDirectory, timeToLive, true);
+						CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+						qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+					} catch (ClassNotFoundException e) {
+						e.printStackTrace();
+					} catch (SQLException e) {
+						e.printStackTrace();
+					}
 				}
+				//			qef = new QueryExecutionFactoryPaginated(qef, 10000);
+			} else
+			{
+				qef = new QueryExecutionFactoryModel(((LocalModelBasedSparqlEndpointKS)endpointKS).getModel());
 			}
-//			qef = new QueryExecutionFactoryPaginated(qef, 10000);
-			
-		} else {
-			qef = new QueryExecutionFactoryModel(((LocalModelBasedSparqlEndpointKS)endpointKS).getModel());
-		}
-		
-		
+		} 
+
 		if(learningProblem instanceof PosOnlyLP){
 			this.posExamples = convert(((PosOnlyLP)learningProblem).getPositiveExamples());
 			this.negExamples = new ArrayList<String>();
@@ -505,23 +515,30 @@
 		}
 		treeCache = new QueryTreeCache();
 		treeCache.addAllowedNamespaces(allowedNamespaces);
-		
-		if(endpointKS instanceof LocalModelBasedSparqlEndpointKS){
-			cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(((LocalModelBasedSparqlEndpointKS) endpointKS).getModel()));
-		} else {
-			endpoint = endpointKS.getEndpoint();
-			cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(endpoint, endpointKS.getCache()));
+
+		if(endpointKS==null) {}
+		else
+		{
+			nbr = new NBR<String>(endpoint);
+			nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+			
+			if(endpointKS instanceof LocalModelBasedSparqlEndpointKS){
+				cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(((LocalModelBasedSparqlEndpointKS) endpointKS).getModel()));
+			} else {
+				endpoint = endpointKS.getEndpoint();
+				cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(endpoint, endpointKS.getCache()));
+			}
 		}
 		cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
-		
+
 		lggGenerator = new LGGGeneratorImpl<String>();
-		nbr = new NBR<String>(endpoint);
-		nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+
 		
+
 		posExampleTrees = new ArrayList<QueryTree<String>>();
 		negExampleTrees = new ArrayList<QueryTree<String>>();
 	}
-	
+
 	private List<String> convert(Set<Individual> individuals){
 		List<String> list = new ArrayList<String>();
 		for(Individual ind : individuals){
@@ -529,11 +546,11 @@
 		}
 		return list;
 	}
-	
+
 	public QueryTree<String> getLgg() {
 		return lgg;
 	}
-	
+
 	@Autowired
 	public void setLearningProblem(LearningProblem learningProblem) {
 		this.learningProblem = learningProblem;
@@ -578,7 +595,7 @@
 	public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
 		return null;
 	}
-	
+
 	/**
 	 * @param allowedNamespaces the allowedNamespaces to set
 	 */
@@ -590,7 +607,7 @@
 		Set<String> positiveExamples = new HashSet<String>();
 		positiveExamples.add("http://dbpedia.org/resource/Liverpool_F.C.");
 		positiveExamples.add("http://dbpedia.org/resource/Chelsea_F.C.");
-		
+
 		SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia());
 		ks.init();
 		PosOnlyLP lp = new PosOnlyLP();	
@@ -604,5 +621,5 @@
 		System.out.println(query);
 		System.out.println(qtl.getCurrentlyBestDescription());
 	}
-	
+
 }

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4277] trunk/components-core/src/main/java/org/ dllearner

[<ki...@us...>]

Revision: 4277
          http://sourceforge.net/p/dl-learner/code/4277
Author:   kirdie
Date:     2014-06-24 09:35:44 +0000 (Tue, 24 Jun 2014)
Log Message:
-----------
dl-learner works again by removing plugin version. clearer exception message in one case. 

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/kb/SparqlEndpointKS.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java

Modified: trunk/components-core/src/main/java/org/dllearner/kb/SparqlEndpointKS.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/SparqlEndpointKS.java	2014-06-23 12:57:22 UTC (rev 4276)
+++ trunk/components-core/src/main/java/org/dllearner/kb/SparqlEndpointKS.java	2014-06-24 09:35:44 UTC (rev 4277)
@@ -154,6 +154,11 @@
 
 	public void setSupportsSPARQL_1_1(boolean supportsSPARQL_1_1) {
 		this.supportsSPARQL_1_1 = supportsSPARQL_1_1;
+	}
+
+	@Override public String toString()
+	{
+		return endpoint.toString();
 	}	
 	
 }

Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java	2014-06-23 12:57:22 UTC (rev 4276)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java	2014-06-24 09:35:44 UTC (rev 4277)
@@ -33,7 +33,6 @@
 import java.util.TreeMap;
 import java.util.TreeSet;
 import java.util.concurrent.TimeUnit;
-
 import org.aksw.jena_sparql_api.cache.core.QueryExecutionFactoryCacheEx;
 import org.aksw.jena_sparql_api.cache.extra.CacheCoreEx;
 import org.aksw.jena_sparql_api.cache.extra.CacheCoreH2;
@@ -75,7 +74,6 @@
 import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
 import com.clarkparsia.owlapiv3.XSD;
 import com.google.common.collect.HashMultimap;
 import com.google.common.collect.Multimap;
@@ -89,6 +87,7 @@
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.OWL2;
 import com.hp.hpl.jena.vocabulary.RDF;
@@ -1758,8 +1757,15 @@
 	private ResultSet executeSelectQuery(String query){
 		logger.trace("Sending query \n {}", query);
 		QueryExecution qe = qef.createQueryExecution(query);
+		try
+		{
 		ResultSet rs = qe.execSelect();
 		return rs;
+		}
+		catch(QueryExceptionHTTP e)
+		{
+			throw new QueryExceptionHTTP("Error sending query \""+query+"\" to endpoint "+ks,e);
+		}
 	}
 
 	private ResultSet executeSelectQuery(String query, long timeout){

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4276] trunk

[<ki...@us...>]

Revision: 4276
          http://sourceforge.net/p/dl-learner/code/4276
Author:   kirdie
Date:     2014-06-23 12:57:22 +0000 (Mon, 23 Jun 2014)
Log Message:
-----------
made components-core and -ext compile again by removing version number of maven exec plugin. also fixed some warnings in the poms about duplicate info which is already contained in the parent.

Modified Paths:
--------------
    trunk/components-core/pom.xml
    trunk/components-ext/pom.xml

Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml	2014-05-27 13:03:09 UTC (rev 4275)
+++ trunk/components-core/pom.xml	2014-06-23 12:57:22 UTC (rev 4276)
@@ -2,7 +2,7 @@
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
-	<groupId>org.dllearner</groupId>
+	<!-- <groupId>org.dllearner</groupId> -->
 	<artifactId>components-core</artifactId>
 
 	<name>DL Learner Core Components</name>

Modified: trunk/components-ext/pom.xml
===================================================================
--- trunk/components-ext/pom.xml	2014-05-27 13:03:09 UTC (rev 4275)
+++ trunk/components-ext/pom.xml	2014-06-23 12:57:22 UTC (rev 4276)
@@ -2,12 +2,12 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
-    <groupId>org.dllearner</groupId>
+    <!-- <groupId>org.dllearner</groupId> -->
     <artifactId>components-ext</artifactId>
     <packaging>jar</packaging>
 
     <name>components-ext</name>
-    <version>1.0-SNAPSHOT</version>
+    <!-- <version>1.0-SNAPSHOT</version> -->
     <url>http://aksw.org/Projects/DLLearner</url>
 
     <parent>
@@ -192,7 +192,7 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>
-                <version>1.2.1</version>
+                <!-- <version>1.2.1</version> -->
                 <executions>
 
                     <execution>

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4275] trunk/components-core/src/main/java/org/ dllearner/reasoning

[<lor...@us...>]

Revision: 4275
          http://sourceforge.net/p/dl-learner/code/4275
Author:   lorenz_b
Date:     2014-05-27 13:03:09 +0000 (Tue, 27 May 2014)
Log Message:
-----------
Added simple materialization util for existential restrictions that can be used in the FastInstanceChecker..

Added Paths:
-----------
    trunk/components-core/src/main/java/org/dllearner/reasoning/ExistentialRestrictionMaterialization.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java

Added: trunk/components-core/src/main/java/org/dllearner/reasoning/ExistentialRestrictionMaterialization.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/ExistentialRestrictionMaterialization.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/ExistentialRestrictionMaterialization.java	2014-05-27 13:03:09 UTC (rev 4275)
@@ -0,0 +1,290 @@
+/**
+ * 
+ */
+package org.dllearner.reasoning;
+
+import java.io.ByteArrayInputStream;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.Stack;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLDataExactCardinality;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataHasValue;
+import org.semanticweb.owlapi.model.OWLDataMaxCardinality;
+import org.semanticweb.owlapi.model.OWLDataMinCardinality;
+import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectComplementOf;
+import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
+import org.semanticweb.owlapi.model.OWLObjectHasSelf;
+import org.semanticweb.owlapi.model.OWLObjectHasValue;
+import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
+import org.semanticweb.owlapi.model.OWLObjectMaxCardinality;
+import org.semanticweb.owlapi.model.OWLObjectMinCardinality;
+import org.semanticweb.owlapi.model.OWLObjectOneOf;
+import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectUnionOf;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.semanticweb.owlapi.util.OWLClassExpressionVisitorAdapter;
+
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class ExistentialRestrictionMaterialization {
+	
+	
+	private OWLOntology ontology;
+	private OWLReasoner reasoner;
+	private OWLDataFactory df;
+
+	public ExistentialRestrictionMaterialization(OWLOntology ontology) {
+		this.ontology = ontology;
+		
+		OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance();
+		reasoner = reasonerFactory.createNonBufferingReasoner(ontology);
+		
+		df = ontology.getOWLOntologyManager().getOWLDataFactory();
+	}
+	
+	private Set<OWLClassExpression> getSuperClasses(OWLClass cls){
+		return new SuperClassFinder().getSuperClasses(cls);
+	}
+	
+	public Set<OWLClassExpression> materialize(String classIRI){
+		return materialize(df.getOWLClass(IRI.create(classIRI)));
+	}
+	
+	public Set<OWLClassExpression> materialize(OWLClass cls){
+		Set<OWLClassExpression> superClasses = getSuperClasses(cls);
+		return superClasses;
+	}
+	
+	class SuperClassFinder extends OWLClassExpressionVisitorAdapter{
+		
+		private Map<OWLClass, Set<OWLClassExpression>> map = new HashMap<>();
+		Stack<Set<OWLClassExpression>> stack = new Stack<Set<OWLClassExpression>>();
+		OWLDataFactory df;
+
+		public SuperClassFinder() {
+			df = ontology.getOWLOntologyManager().getOWLDataFactory();
+		}
+		
+		public Set<OWLClassExpression> getSuperClasses(OWLClass cls){
+			map.clear();
+			computeSuperClasses(cls);
+			Set<OWLClassExpression> superClasses = map.get(cls);
+			superClasses.remove(cls);
+			return superClasses;
+		}
+		
+		private void computeSuperClasses(OWLClass cls){
+			Set<OWLClassExpression> superClasses = new HashSet<OWLClassExpression>();
+			superClasses.add(cls);
+			Set<OWLClassExpression> superClassExpressions = cls.getSuperClasses(ontology);
+			for (OWLClassExpression sup : superClassExpressions) {
+				sup.accept(this);
+				superClasses.addAll(stack.pop());
+			}
+			stack.push(superClasses);
+			map.put(cls, superClasses);
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLClass)
+		 */
+		@Override
+		public void visit(OWLClass ce) {
+			computeSuperClasses(ce);
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectIntersectionOf)
+		 */
+		@Override
+		public void visit(OWLObjectIntersectionOf ce) {
+			Set<OWLClassExpression> newIntersections = new HashSet<OWLClassExpression>();
+			Set<OWLClassExpression> operands = ce.getOperands();
+			for (OWLClassExpression op : operands) {
+				op.accept(this);
+				Set<OWLClassExpression> operandSuperClassExpressions = stack.pop();
+				Set<OWLClassExpression> newOperands = new HashSet<OWLClassExpression>(operands);
+				newOperands.remove(op);
+				for (OWLClassExpression opSup : operandSuperClassExpressions) {
+					newOperands.add(opSup);
+					newIntersections.add(df.getOWLObjectIntersectionOf(newOperands));
+					newOperands.remove(opSup);
+				}
+			}
+			stack.push(newIntersections);
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectUnionOf)
+		 */
+		@Override
+		public void visit(OWLObjectUnionOf ce) {
+			Set<OWLClassExpression> operands = ce.getOperands();
+			for (OWLClassExpression op : operands) {
+				op.accept(this);
+			}
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectComplementOf)
+		 */
+		@Override
+		public void visit(OWLObjectComplementOf ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom)
+		 */
+		@Override
+		public void visit(OWLObjectSomeValuesFrom ce) {
+			Set<OWLClassExpression> newRestrictions = new HashSet<OWLClassExpression>();
+			newRestrictions.add(ce);
+			OWLClassExpression filler = ce.getFiller();
+			filler.accept(this);
+			Set<OWLClassExpression> fillerSuperClassExpressions = stack.pop();
+			for (OWLClassExpression fillerSup : fillerSuperClassExpressions) {
+				newRestrictions.add(df.getOWLObjectSomeValuesFrom(ce.getProperty(), fillerSup));
+			}
+			stack.push(newRestrictions);
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectAllValuesFrom)
+		 */
+		@Override
+		public void visit(OWLObjectAllValuesFrom ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectHasValue)
+		 */
+		@Override
+		public void visit(OWLObjectHasValue ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectMinCardinality)
+		 */
+		@Override
+		public void visit(OWLObjectMinCardinality ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectExactCardinality)
+		 */
+		@Override
+		public void visit(OWLObjectExactCardinality ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectMaxCardinality)
+		 */
+		@Override
+		public void visit(OWLObjectMaxCardinality ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectHasSelf)
+		 */
+		@Override
+		public void visit(OWLObjectHasSelf ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectOneOf)
+		 */
+		@Override
+		public void visit(OWLObjectOneOf ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataSomeValuesFrom)
+		 */
+		@Override
+		public void visit(OWLDataSomeValuesFrom ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataAllValuesFrom)
+		 */
+		@Override
+		public void visit(OWLDataAllValuesFrom ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataHasValue)
+		 */
+		@Override
+		public void visit(OWLDataHasValue ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataMinCardinality)
+		 */
+		@Override
+		public void visit(OWLDataMinCardinality ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataExactCardinality)
+		 */
+		@Override
+		public void visit(OWLDataExactCardinality ce) {
+		}
+
+		/* (non-Javadoc)
+		 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataMaxCardinality)
+		 */
+		@Override
+		public void visit(OWLDataMaxCardinality ce) {
+		}
+	}
+
+	
+	public static void main(String[] args) throws Exception{
+		ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
+		String s = "@prefix : <http://example.org/> ."
+				+ "@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> ."
+				+ "@prefix owl: <http://www.w3.org/2002/07/owl#> ."
+				+ "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> ."
+				+ ":A a owl:Class . "
+				+ ":B a owl:Class . "
+				+ ":C a owl:Class . "
+				+ ":D a owl:Class . "
+				+ ":r a owl:ObjectProperty . "
+				+ ":A rdfs:subClassOf [ a owl:Restriction; owl:onProperty :r; owl:someValuesFrom :B]."
+				+ ":B rdfs:subClassOf :C."
+				+ ":C rdfs:subClassOf [ a owl:Restriction; owl:onProperty :r; owl:someValuesFrom :D]."
+				+ ":a a :A.";
+		
+		OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+		OWLOntology ontology = man.loadOntologyFromOntologyDocument(new ByteArrayInputStream(s.getBytes()));
+		ExistentialRestrictionMaterialization mat = new ExistentialRestrictionMaterialization(ontology);
+		Set<OWLClassExpression> superClassExpressions = mat.materialize("http://example.org/A");
+		for (OWLClassExpression sup : superClassExpressions) {
+			System.out.println(sup);
+		}
+	}
+
+}

Added: trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/MaterializableFastInstanceChecker.java	2014-05-27 13:03:09 UTC (rev 4275)
@@ -0,0 +1,1237 @@
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.dllearner.reasoning;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.ReasoningMethodUnsupportedException;
+import org.dllearner.core.config.ConfigOption;
+import org.dllearner.core.owl.Axiom;
+import org.dllearner.core.owl.BooleanValueRestriction;
+import org.dllearner.core.owl.Constant;
+import org.dllearner.core.owl.DataRange;
+import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
+import org.dllearner.core.owl.DatatypeValueRestriction;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DoubleMaxValue;
+import org.dllearner.core.owl.DoubleMinValue;
+import org.dllearner.core.owl.Entity;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.Negation;
+import org.dllearner.core.owl.Nothing;
+import org.dllearner.core.owl.ObjectAllRestriction;
+import org.dllearner.core.owl.ObjectCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMaxCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyExpression;
+import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.core.owl.ObjectValueRestriction;
+import org.dllearner.core.owl.Thing;
+import org.dllearner.core.owl.Union;
+import org.dllearner.parser.ParseException;
+import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.owl.ConceptTransformation;
+import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
+import org.dllearner.utilities.owl.OWLAPIConverter;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.propertyeditors.StringTrimmerEditor;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+
+/**
+ * Reasoner for fast instance checks. It works by completely dematerialising the
+ * knowledge base to speed up later reasoning requests. It then continues by
+ * only considering one model of the knowledge base (TODO: more explanation),
+ * which is neither correct nor complete, but sufficient in many cases. A big
+ * advantage of the algorithm is that it does not need even need to perform any
+ * set modifications (union, intersection, difference), so it avoids any Java
+ * object creation, which makes it extremely fast compared to standard
+ * reasoners.
+ * 
+ * Meanwhile, the algorithm has been extended to also perform fast retrieval
+ * operations. However, those need write access to memory and potentially have
+ * to deal with all individuals in a knowledge base. For many knowledge bases,
+ * they should still be reasonably fast. 
+ * 
+ * @author Jens Lehmann
+ * 
+ */
+@ComponentAnn(name = "fast instance checker", shortName = "fic", version = 0.9)
+public class MaterializableFastInstanceChecker extends AbstractReasonerComponent {
+
+	private static Logger logger = Logger.getLogger(MaterializableFastInstanceChecker.class);
+
+//	private boolean defaultNegation = true;
+
+	private Set<NamedClass> atomicConcepts;
+	private Set<ObjectProperty> atomicRoles;
+	private SortedSet<DatatypeProperty> datatypeProperties;
+	private SortedSet<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
+	private SortedSet<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
+	private SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
+	private SortedSet<DatatypeProperty> stringDatatypeProperties = new TreeSet<DatatypeProperty>();	
+	private TreeSet<Individual> individuals;
+
+	// private ReasonerComponent rs;
+
+	private OWLAPIReasoner rc;
+
+	// we use sorted sets (map indices) here, because they have only log(n)
+	// complexity for checking whether an element is contained in them
+	// instances of classes
+	private Map<NamedClass, TreeSet<Individual>> classInstancesPos = new TreeMap<NamedClass, TreeSet<Individual>>();
+	private Map<NamedClass, TreeSet<Individual>> classInstancesNeg = new TreeMap<NamedClass, TreeSet<Individual>>();
+	// object property mappings
+	private Map<ObjectProperty, Map<Individual, SortedSet<Individual>>> opPos = new TreeMap<ObjectProperty, Map<Individual, SortedSet<Individual>>>();
+	// data property mappings
+	private Map<DatatypeProperty, Map<Individual, SortedSet<Constant>>> dpPos = new TreeMap<DatatypeProperty, Map<Individual, SortedSet<Constant>>>();
+		
+	
+	// datatype property mappings
+	// we have one mapping for true and false for efficiency reasons
+	private Map<DatatypeProperty, TreeSet<Individual>> bdPos = new TreeMap<DatatypeProperty, TreeSet<Individual>>();
+	private Map<DatatypeProperty, TreeSet<Individual>> bdNeg = new TreeMap<DatatypeProperty, TreeSet<Individual>>();
+	// for int and double we assume that a property can have several values,
+	// althoug this should be rare,
+	// e.g. hasValue(object,2) and hasValue(object,3)
+	private Map<DatatypeProperty, Map<Individual, SortedSet<Double>>> dd = new TreeMap<DatatypeProperty, Map<Individual, SortedSet<Double>>>();
+	private Map<DatatypeProperty, Map<Individual, SortedSet<Integer>>> id = new TreeMap<DatatypeProperty, Map<Individual, SortedSet<Integer>>>();
+	private Map<DatatypeProperty, Map<Individual, SortedSet<String>>> sd = new TreeMap<DatatypeProperty, Map<Individual, SortedSet<String>>>();
+
+    @ConfigOption(name="defaultNegation", description = "Whether to use default negation, i.e. an instance not being in a class means that it is in the negation of the class.", defaultValue = "true", required = false)
+    private boolean defaultNegation = true;
+
+    @ConfigOption(name = "forAllRetrievalSemantics", description = "This option controls how to interpret the all quantifier in forall r.C. The standard option is" +
+            "to return all those which do not have an r-filler not in C. The domain semantics is to use those" +
+            "which are in the domain of r and do not have an r-filler not in C. The forallExists semantics is to"+
+            "use those which have at least one r-filler and do not have an r-filler not in C.",defaultValue = "standard",propertyEditorClass = StringTrimmerEditor.class)
+    private ForallSemantics forallSemantics = ForallSemantics.Standard;
+    
+    private boolean materializeExistentialRestrictions = true;
+    
+
+    public enum ForallSemantics { 
+    	Standard, // standard all quantor
+    	NonEmpty, // p only C for instance a returns false if there is no fact p(a,x) for any x  
+    	SomeOnly  // p only C for instance a returns false if there is no fact p(a,x) with x \ in C  
+    }
+    
+	/**
+	 * Creates an instance of the fast instance checker.
+	 */
+	public MaterializableFastInstanceChecker() {
+	}
+
+    public MaterializableFastInstanceChecker(TreeSet<Individual> individuals,
+			Map<NamedClass, TreeSet<Individual>> classInstancesPos,
+			Map<ObjectProperty, Map<Individual, SortedSet<Individual>>> opPos,
+			Map<DatatypeProperty, Map<Individual, SortedSet<Integer>>> id,
+			Map<DatatypeProperty, TreeSet<Individual>> bdPos,
+			Map<DatatypeProperty, TreeSet<Individual>> bdNeg,
+			KnowledgeSource... sources) {
+		super(new HashSet<KnowledgeSource>(Arrays.asList(sources)));
+		this.individuals = individuals;
+		this.classInstancesPos = classInstancesPos;
+		this.opPos = opPos;
+		this.id = id;
+		this.bdPos = bdPos;
+		this.bdNeg = bdNeg;
+		
+		if(rc == null){
+            rc = new OWLAPIReasoner(new HashSet<KnowledgeSource>(Arrays.asList(sources)));
+            try {
+				rc.init();
+			} catch (ComponentInitException e) {
+				e.printStackTrace();
+			}
+        }
+		
+		atomicConcepts = rc.getNamedClasses();
+		datatypeProperties = rc.getDatatypeProperties();
+		booleanDatatypeProperties = rc.getBooleanDatatypeProperties();
+		doubleDatatypeProperties = rc.getDoubleDatatypeProperties();
+		intDatatypeProperties = rc.getIntDatatypeProperties();
+		stringDatatypeProperties = rc.getStringDatatypeProperties();
+		atomicRoles = rc.getObjectProperties();
+		
+		for (NamedClass atomicConcept : rc.getNamedClasses()) {
+			TreeSet<Individual> pos = classInstancesPos.get(atomicConcept);
+			if(pos != null){
+				classInstancesNeg.put(atomicConcept, (TreeSet<Individual>) Helper.difference(individuals, pos));
+			} else {
+				classInstancesPos.put(atomicConcept, new TreeSet<Individual>());
+				classInstancesNeg.put(atomicConcept, individuals);
+			}
+		}
+		for(ObjectProperty p : atomicRoles){
+			if(opPos.get(p) == null){
+				opPos.put(p, new HashMap<Individual, SortedSet<Individual>>());
+			}
+		}
+		
+		for (DatatypeProperty dp : booleanDatatypeProperties) {
+			if(bdPos.get(dp) == null){
+				bdPos.put(dp, new TreeSet<Individual>());
+			}
+			if(bdNeg.get(dp) == null){
+				bdNeg.put(dp, new TreeSet<Individual>());
+			}
+			
+		}
+	}
+
+	public MaterializableFastInstanceChecker(Set<KnowledgeSource> sources) {
+        super(sources);
+    }
+
+    public MaterializableFastInstanceChecker(KnowledgeSource... sources) {
+        super(new HashSet<KnowledgeSource>(Arrays.asList(sources)));
+    }
+    
+    /**
+	 * @return The name of this component.
+	 */
+	public static String getName() {
+		return "fast instance checker";
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.dllearner.core.Component#init()
+	 */
+	@Override
+	public void init() throws ComponentInitException {
+
+		if (rc == null) {
+			rc = new OWLAPIReasoner(sources);
+			rc.init();
+		}
+		atomicConcepts = rc.getNamedClasses();
+		datatypeProperties = rc.getDatatypeProperties();
+		booleanDatatypeProperties = rc.getBooleanDatatypeProperties();
+		doubleDatatypeProperties = rc.getDoubleDatatypeProperties();
+		intDatatypeProperties = rc.getIntDatatypeProperties();
+		stringDatatypeProperties = rc.getStringDatatypeProperties();
+		atomicRoles = rc.getObjectProperties();
+		individuals = (TreeSet<Individual>) rc.getIndividuals();
+
+		dematerialize();
+	}
+	
+	private void dematerialize(){
+		long dematStartTime = System.currentTimeMillis();
+
+		//atomic concepts
+		logger.debug("dematerialising concepts");
+		for (NamedClass atomicConcept : rc.getNamedClasses()) {
+			SortedSet<Individual> pos = rc.getIndividuals(atomicConcept);
+			classInstancesPos.put(atomicConcept, (TreeSet<Individual>) pos);
+
+			if (isDefaultNegation()) {
+				classInstancesNeg.put(atomicConcept, (TreeSet<Individual>) Helper.difference(individuals, pos));
+			} else {
+				// Pellet needs approximately infinite time to answer
+				// negated queries
+				// on the carcinogenesis data set (and probably others), so
+				// we have to
+				// be careful here
+				Negation negatedAtomicConcept = new Negation(atomicConcept);
+				classInstancesNeg.put(atomicConcept, (TreeSet<Individual>) rc.getIndividuals(negatedAtomicConcept));
+			}
+		}
+
+		//atomic object properties
+		logger.debug("dematerialising object properties");
+		for (ObjectProperty atomicRole : atomicRoles) {
+			opPos.put(atomicRole, rc.getPropertyMembers(atomicRole));
+		}
+		
+		//atomic datatype properties
+		logger.debug("dematerialising datatype properties");
+		for (DatatypeProperty atomicRole : datatypeProperties) {
+			dpPos.put(atomicRole, rc.getDatatypeMembers(atomicRole));
+		}
+
+		//boolean datatype properties
+		for (DatatypeProperty dp : booleanDatatypeProperties) {
+			bdPos.put(dp, (TreeSet<Individual>) rc.getTrueDatatypeMembers(dp));
+			bdNeg.put(dp, (TreeSet<Individual>) rc.getFalseDatatypeMembers(dp));
+		}
+
+		//integer datatype properties
+		for (DatatypeProperty dp : intDatatypeProperties) {
+			id.put(dp, rc.getIntDatatypeMembers(dp));
+		}
+
+		//double datatype properties
+		for (DatatypeProperty dp : doubleDatatypeProperties) {
+			dd.put(dp, rc.getDoubleDatatypeMembers(dp));
+		}
+
+		//String datatype properties
+		for (DatatypeProperty dp : stringDatatypeProperties) {
+			sd.put(dp, rc.getStringDatatypeMembers(dp));
+		}			
+		
+		if(materializeExistentialRestrictions){
+			ExistentialRestrictionMaterialization materialization = new ExistentialRestrictionMaterialization(rc.getReasoner().getRootOntology());
+			for (NamedClass cls : atomicConcepts) {
+				TreeSet<Individual> individuals = classInstancesPos.get(cls);
+				Set<OWLClassExpression> superClass = materialization.materialize(cls.getName());
+				for (OWLClassExpression sup : superClass) {
+					fill(individuals, DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(sup));
+				}
+			}
+		}
+		
+		long dematDuration = System.currentTimeMillis() - dematStartTime;
+		logger.debug("TBox dematerialised in " + dematDuration + " ms");
+	}
+	
+	private void fill(SortedSet<Individual> individuals, Description d){
+		if(d instanceof Intersection){
+			List<Description> children = d.getChildren();
+			for (Description child : children) {
+				fill(individuals, child);
+			}
+		} else if(d instanceof ObjectSomeRestriction){
+			ObjectProperty role = (ObjectProperty) ((ObjectSomeRestriction) d).getRole();
+			Map<Individual, SortedSet<Individual>> map = opPos.get(role);
+			//create new individual as object value for each individual
+			SortedSet<Individual> newIndividuals = new TreeSet<Individual>();
+			int i = 0;
+			for (Individual individual : individuals) {
+				Individual newIndividual = new Individual("http://dllearner.org#genInd_" + i++);
+				newIndividuals.add(newIndividual);
+				SortedSet<Individual> values = map.get(individual);
+				if(values == null){
+					values = new TreeSet<Individual>();
+					map.put(individual, values);
+				}
+				values.add(newIndividual);
+			}
+			fill(newIndividuals, d.getChild(0));
+			
+		} else if(d instanceof NamedClass){
+			classInstancesPos.get(d).addAll(individuals);
+		} else {
+			throw new UnsupportedOperationException("Should not happen.");
+		}
+	}
+
+	@Override
+	public boolean hasTypeImpl(Description description, Individual individual)
+			throws ReasoningMethodUnsupportedException {
+
+//		 System.out.println("FIC: " + description + " " + individual);
+
+		if (description instanceof NamedClass) {
+			if(((NamedClass) description).getURI().equals(Thing.instance.getURI())){
+				return true;
+			} else
+			if(!atomicConcepts.contains(description)) {
+				throw new ReasoningMethodUnsupportedException("Class " + description + " is not contained in knowledge base.");
+			}
+			return classInstancesPos.get((NamedClass) description).contains(individual);
+		} else if (description instanceof Negation) {
+			Description child = description.getChild(0);
+			if (child instanceof NamedClass) {
+				return classInstancesNeg.get((NamedClass) child).contains(individual);
+			} else {
+				// default negation
+				if(isDefaultNegation()) {
+					return !hasTypeImpl(child, individual);
+				} else {
+					logger.debug("Converting description to negation normal form in fast instance check (should be avoided if possible).");
+					Description nnf = ConceptTransformation.transformToNegationNormalForm(child);
+					return hasTypeImpl(nnf, individual);					
+				}
+//				throw new ReasoningMethodUnsupportedException("Instance check for description "
+//						+ description
+//						+ " unsupported. Description needs to be in negation normal form.");
+			}
+		} else if (description instanceof Thing) {
+			return true;
+		} else if (description instanceof Nothing) {
+			return false;
+		} else if (description instanceof Union) {
+			// if the individual is instance of any of the subdescription of
+			// the union, we return true
+			List<Description> children = description.getChildren();
+			for (Description child : children) {
+				if (hasTypeImpl(child, individual)) {
+					return true;
+				}
+			}
+			return false;
+		} else if (description instanceof Intersection) {
+			// if the individual is instance of all of the subdescription of
+			// the union, we return true
+			List<Description> children = description.getChildren();
+			for (Description child : children) {
+				if (!hasTypeImpl(child, individual)) {
+					return false;
+				}
+			}
+			return true;
+		} else if (description instanceof ObjectSomeRestriction) {
+			ObjectPropertyExpression ope = ((ObjectSomeRestriction) description).getRole();
+			if (!(ope instanceof ObjectProperty)) {
+				throw new ReasoningMethodUnsupportedException("Instance check for description "
+						+ description + " unsupported. Inverse object properties not supported.");
+			}
+			ObjectProperty op = (ObjectProperty) ope;
+			Description child = description.getChild(0);
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+
+			if (mapping == null) {
+				logger.warn("Instance check of a description with an undefined property (" + op
+						+ ").");
+				return false;
+			}
+			SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+			if (roleFillers == null) {
+				return false;
+			}
+			for (Individual roleFiller : roleFillers) {
+				if (hasTypeImpl(child, roleFiller)) {
+					return true;
+				}
+			}
+			return false;
+		} else if (description instanceof ObjectAllRestriction) {
+			ObjectPropertyExpression ope = ((ObjectAllRestriction) description).getRole();
+			if (!(ope instanceof ObjectProperty)) {
+				throw new ReasoningMethodUnsupportedException("Instance check for description "
+						+ description + " unsupported. Inverse object properties not supported.");
+			}
+			ObjectProperty op = (ObjectProperty) ope;
+			Description child = description.getChild(0);
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+
+			if (mapping == null) {
+				logger.warn("Instance check of a description with an undefinied property (" + op
+						+ ").");
+				return true;
+			}
+			SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+			
+			if (roleFillers == null) {
+				if(forallSemantics == ForallSemantics.Standard) {
+					return true;	
+				} else {
+					return false;
+				}
+			}
+			boolean hasCorrectFiller = false;
+			for (Individual roleFiller : roleFillers) {
+				if (hasTypeImpl(child, roleFiller)) {
+					hasCorrectFiller = true;
+				} else {
+					return false;
+				}				
+			}
+			
+			if(forallSemantics == ForallSemantics.SomeOnly) {
+				return hasCorrectFiller;
+			} else {
+				return true;
+			}
+		} else if (description instanceof ObjectMinCardinalityRestriction) {
+			ObjectPropertyExpression ope = ((ObjectCardinalityRestriction) description).getRole();
+			if (!(ope instanceof ObjectProperty)) {
+				throw new ReasoningMethodUnsupportedException("Instance check for description "
+						+ description + " unsupported. Inverse object properties not supported.");
+			}
+			ObjectProperty op = (ObjectProperty) ope;
+			Description child = description.getChild(0);
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+
+			if (mapping == null) {
+				logger.warn("Instance check of a description with an undefinied property (" + op
+						+ ").");
+				return true;
+			}
+
+			int number = ((ObjectCardinalityRestriction) description).getNumber();
+			int nrOfFillers = 0;
+
+//			SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+			SortedSet<Individual> roleFillers = mapping.get(individual);
+//			System.out.println(roleFillers);
+			
+			// special case: there are always at least zero fillers
+			if (number == 0) {
+				return true;
+			}
+			// return false if there are none or not enough role fillers
+			if (roleFillers == null || roleFillers.size() < number) {
+				return false;
+			}
+
+			int index = 0;
+			for (Individual roleFiller : roleFillers) {
+				index++;
+				if (hasTypeImpl(child, roleFiller)) {
+					nrOfFillers++;
+					if (nrOfFillers == number) {
+						return true;
+					}
+					// early abort: e.g. >= 10 hasStructure.Methyl;
+					// if there are 11 fillers and 2 are not Methyl, the result
+					// is false
+				} else {
+					if (roleFillers.size() - index < number) {
+						return false;
+					}
+				}
+			}
+			return false;
+		} else if (description instanceof ObjectMaxCardinalityRestriction) {
+			ObjectPropertyExpression ope = ((ObjectCardinalityRestriction) description).getRole();
+			if (!(ope instanceof ObjectProperty)) {
+				throw new ReasoningMethodUnsupportedException("Instance check for description "
+						+ description + " unsupported. Inverse object properties not supported.");
+			}
+			ObjectProperty op = (ObjectProperty) ope;
+			Description child = description.getChild(0);
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+
+			if (mapping == null) {
+				logger.warn("Instance check of a description with an undefinied property (" + op
+						+ ").");
+				return true;
+			}
+
+			int number = ((ObjectCardinalityRestriction) description).getNumber();
+			int nrOfFillers = 0;
+
+			SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+			// return true if there are none or not enough role fillers
+			if (roleFillers == null || roleFillers.size() < number) {
+				return true;
+			}
+
+			int index = 0;
+			for (Individual roleFiller : roleFillers) {
+				index++;
+				if (hasTypeImpl(child, roleFiller)) {
+					nrOfFillers++;
+					if (nrOfFillers > number) {
+						return false;
+					}
+					// early abort: e.g. <= 5 hasStructure.Methyl;
+					// if there are 6 fillers and 2 are not Methyl, the result
+					// is true
+				} else {
+					if (roleFillers.size() - index <= number) {
+						return true;
+					}
+				}
+			}
+			return true;
+		} else if (description instanceof ObjectValueRestriction) {
+			Individual i = ((ObjectValueRestriction)description).getIndividual();
+			ObjectProperty op = (ObjectProperty) ((ObjectValueRestriction)description).getRestrictedPropertyExpression();
+			
+			Set<Individual> inds = opPos.get(op).get(individual);
+			return inds == null ? false : inds.contains(i);
+		} else if (description instanceof BooleanValueRestriction) {
+			DatatypeProperty dp = ((BooleanValueRestriction) description)
+					.getRestrictedPropertyExpression();
+			boolean value = ((BooleanValueRestriction) description).getBooleanValue();
+
+			if (value) {
+				// check whether the individual is in the set of individuals
+				// mapped
+				// to true by this datatype property
+				return bdPos.get(dp).contains(individual);
+			} else {
+				return bdNeg.get(dp).contains(individual);
+			}
+		} else if (description instanceof DatatypeSomeRestriction) {
+			DatatypeSomeRestriction dsr = (DatatypeSomeRestriction) description;
+			DatatypeProperty dp = (DatatypeProperty) dsr.getRestrictedPropertyExpression();
+			DataRange dr = dsr.getDataRange();
+			if(dr.isDatatype() 
+//					&& ((Datatype)dr).isTopDatatype()
+					){
+				 if(dpPos.get(dp).containsKey(individual)){
+					 return true;
+				 } else {
+					 return false;
+				 }
+			}
+			SortedSet<Double> values = dd.get(dp).get(individual);
+
+			// if there is no filler for this individual and property we
+			// need to return false
+			if (values == null) {
+				return false;
+			}
+
+			if (dr instanceof DoubleMaxValue) {
+				return (values.first() <= ((DoubleMaxValue) dr).getValue());
+			} else if (dr instanceof DoubleMinValue) {
+				return (values.last() >= ((DoubleMinValue) dr).getValue());
+			}
+		} else if (description instanceof DatatypeValueRestriction) {
+			String i = ((DatatypeValueRestriction)description).getValue().getLiteral();
+			DatatypeProperty dp = ((DatatypeValueRestriction)description).getRestrictedPropertyExpression();
+			
+			Set<String> inds = sd.get(dp).get(individual);
+			return inds == null ? false : inds.contains(i);
+		}
+
+		throw new ReasoningMethodUnsupportedException("Instance check for description "
+				+ description + " unsupported.");
+	}
+
+	@Override
+	public SortedSet<Individual> getIndividualsImpl(Description concept) throws ReasoningMethodUnsupportedException {
+		return getIndividualsImplFast(concept);
+	}
+	
+	public SortedSet<Individual> getIndividualsImplStandard(Description concept)
+		throws ReasoningMethodUnsupportedException {
+		if (concept instanceof NamedClass) {
+	 		return classInstancesPos.get((NamedClass) concept);
+	 	} else if (concept instanceof Negation && concept.getChild(0) instanceof NamedClass) {
+	 		return classInstancesNeg.get((NamedClass) concept.getChild(0));
+	 	}
+	 
+	 	// return rs.retrieval(concept);
+	 	SortedSet<Individual> inds = new TreeSet<Individual>();
+	 	for (Individual i : individuals) {
+	 		if (hasType(concept, i)) {
+	 			inds.add(i);
+	 		}
+	 	}
+		return inds;
+	}
+	
+	@SuppressWarnings("unchecked")
+	public SortedSet<Individual> getIndividualsImplFast(Description description)
+			throws ReasoningMethodUnsupportedException {
+		// policy: returned sets are clones, i.e. can be modified
+		// (of course we only have to clone the leafs of a class description tree)
+		if (description instanceof NamedClass) {
+			if(classInstancesPos.containsKey((NamedClass) description)){
+				return (TreeSet<Individual>) classInstancesPos.get((NamedClass) description).clone();
+			} else {
+				return new TreeSet<Individual>();
+			}
+		} else if (description instanceof Negation) {
+			if(description.getChild(0) instanceof NamedClass) {
+				return (TreeSet<Individual>) classInstancesNeg.get((NamedClass) description.getChild(0)).clone();
+			}
+			// implement retrieval as default negation
+			return Helper.difference((TreeSet<Individual>) individuals.clone(), getIndividualsImpl(description.getChild(0)));
+		} else if (description instanceof Thing) {
+			return (TreeSet<Individual>) individuals.clone();
+		} else if (description instanceof Nothing) {
+			return new TreeSet<Individual>();
+		} else if (description instanceof Union) {
+			// copy instances of first element and then subtract all others
+			SortedSet<Individual> ret = getIndividualsImpl(description.getChild(0));
+			int childNr = 0;
+			for(Description child : description.getChildren()) {
+				if(childNr != 0) {
+					ret.addAll(getIndividualsImpl(child));
+				}
+				childNr++;
+			}
+			return ret;
+		} else if (description instanceof Intersection) {
+			// copy instances of first element and then subtract all others
+			SortedSet<Individual> ret = getIndividualsImpl(description.getChild(0));
+			int childNr = 0;
+			for(Description child : description.getChildren()) {
+				if(childNr != 0) {
+					ret.retainAll(getIndividualsImpl(child));
+				}
+				childNr++;
+			}
+			return ret;
+		} else if (description instanceof ObjectSomeRestriction) {
+			SortedSet<Individual> targetSet = getIndividualsImpl(description.getChild(0));
+			SortedSet<Individual> returnSet = new TreeSet<Individual>();
+			
+			ObjectPropertyExpression ope = ((ObjectSomeRestriction) description).getRole();
+			if (!(ope instanceof ObjectProperty)) {
+				throw new ReasoningMethodUnsupportedException("Retrieval for description "
+						+ description + " unsupported. Inverse object properties not supported.");
+			}
+			ObjectProperty op = (ObjectProperty) ope;
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);			
+			
+			// each individual is connected to a set of individuals via the property;
+			// we loop through the complete mapping
+			for(Entry<Individual, SortedSet<Individual>> entry : mapping.entrySet()) {
+				SortedSet<Individual> inds = entry.getValue();
+				for(Individual ind : inds) {
+					if(targetSet.contains(ind)) {
+						returnSet.add(entry.getKey());
+						// once we found an individual, we do not need to check the others
+						continue; 
+					}
+				}
+			}
+			return returnSet;
+		} else if (description instanceof ObjectAllRestriction) {
+			// \forall restrictions are difficult to handle; assume we want to check
+			// \forall hasChild.male with domain(hasChild)=Person; then for all non-persons
+			// this is satisfied trivially (all of their non-existing children are male)
+//			if(!configurator.getForallRetrievalSemantics().equals("standard")) {
+//				throw new Error("Only forallExists semantics currently implemented.");
+//			}
+			
+			// problem: we need to make sure that \neg \exists r.\top \equiv \forall r.\bot
+			// can still be reached in an algorithm (\forall r.\bot \equiv \bot under forallExists
+			// semantics)
+			
+			SortedSet<Individual> targetSet = getIndividualsImpl(description.getChild(0));
+						
+			ObjectPropertyExpression ope = ((ObjectAllRestriction) description).getRole();
+			if (!(ope instanceof ObjectProperty)) {
+				throw new ReasoningMethodUnsupportedException("Instance check for description "
+						+ description + " unsupported. Inverse object properties not supported.");
+			}
+			ObjectProperty op = (ObjectProperty) ope;
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+//			SortedSet<Individual> returnSet = new TreeSet<Individual>(mapping.keySet());
+			SortedSet<Individual> returnSet = (SortedSet<Individual>) individuals.clone();
+			
+			// each individual is connected to a set of individuals via the property;
+			// we loop through the complete mapping
+			for(Entry<Individual, SortedSet<Individual>> entry : mapping.entrySet()) {
+				SortedSet<Individual> inds = entry.getValue();
+				for(Individual ind : inds) {
+					if(!targetSet.contains(ind)) {
+						returnSet.remove(entry.getKey());
+						continue; 
+					}
+				}
+			}
+			return returnSet;
+		} else if (description instanceof ObjectMinCardinalityRestriction) {
+			ObjectPropertyExpression ope = ((ObjectCardinalityRestriction) description).getRole();
+			if (!(ope instanceof ObjectProperty)) {
+				throw new ReasoningMethodUnsupportedException("Instance check for description "
+						+ description + " unsupported. Inverse object properties not supported.");
+			}
+			ObjectProperty op = (ObjectProperty) ope;
+			Description child = description.getChild(0);
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+			SortedSet<Individual> targetSet = getIndividualsImpl(child);
+			SortedSet<Individual> returnSet = new TreeSet<Individual>();
+
+			int number = ((ObjectCardinalityRestriction) description).getNumber();			
+
+			for(Entry<Individual, SortedSet<Individual>> entry : mapping.entrySet()) {
+				int nrOfFillers = 0;
+				int index = 0;
+				SortedSet<Individual> inds = entry.getValue();
+				
+				// we do not need to run tests if there are not sufficiently many fillers
+				if(inds.size() < number) {
+					continue;
+				}
+				
+				for(Individual ind : inds) {
+					// stop inner loop when nr of fillers is reached
+					if(nrOfFillers >= number) {
+						returnSet.add(entry.getKey());
+						break;
+					}		
+					// early abort when too many instance checks failed
+					if (inds.size() - index < number) {
+						break;
+					}					
+					if(targetSet.contains(ind)) {
+						nrOfFillers++;
+					}
+					index++;
+				}
+			}			
+			
+			return returnSet;
+		} else if (description instanceof ObjectMaxCardinalityRestriction) {
+			ObjectPropertyExpression ope = ((ObjectCardinalityRestriction) description).getRole();
+			if (!(ope instanceof ObjectProperty)) {
+				throw new ReasoningMethodUnsupportedException("Instance check for description "
+						+ description + " unsupported. Inverse object properties not supported.");
+			}
+			ObjectProperty op = (ObjectProperty) ope;
+			Description child = description.getChild(0);
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);
+			SortedSet<Individual> targetSet = getIndividualsImpl(child);
+			// initially all individuals are in the return set and we then remove those
+			// with too many fillers			
+			SortedSet<Individual> returnSet = (SortedSet<Individual>) individuals.clone();
+
+			int number = ((ObjectCardinalityRestriction) description).getNumber();			
+
+			for(Entry<Individual, SortedSet<Individual>> entry : mapping.entrySet()) {
+				int nrOfFillers = 0;
+				int index = 0;
+				SortedSet<Individual> inds = entry.getValue();
+				
+				// we do not need to run tests if there are not sufficiently many fillers
+				if(number < inds.size()) {
+					returnSet.add(entry.getKey());
+					continue;
+				}
+				
+				for(Individual ind : inds) {
+					// stop inner loop when nr of fillers is reached
+					if(nrOfFillers >= number) {
+						break;
+					}		
+					// early abort when too many instance are true already
+					if (inds.size() - index < number) {
+						returnSet.add(entry.getKey());
+						break;
+					}					
+					if(targetSet.contains(ind)) {
+						nrOfFillers++;
+					}
+					index++;
+				}
+			}			
+			
+			return returnSet;
+		} else if (description instanceof ObjectValueRestriction) {
+			Individual i = ((ObjectValueRestriction)description).getIndividual();
+			ObjectProperty op = (ObjectProperty) ((ObjectValueRestriction)description).getRestrictedPropertyExpression();
+			
+			Map<Individual, SortedSet<Individual>> mapping = opPos.get(op);			
+			SortedSet<Individual> returnSet = new TreeSet<Individual>();
+			
+			for(Entry<Individual, SortedSet<Individual>> entry : mapping.entrySet()) {
+				if(entry.getValue().contains(i)) {
+					returnSet.add(entry.getKey());
+				}
+			}
+			return returnSet;
+		} else if (description instanceof BooleanValueRestriction) {
+			DatatypeProperty dp = ((BooleanValueRestriction) description)
+					.getRestrictedPropertyExpression();
+			boolean value = ((BooleanValueRestriction) description).getBooleanValue();
+
+			if (value) {
+				return (TreeSet<Individual>) bdPos.get(dp).clone();
+			} else {
+				return (TreeSet<Individual>) bdNeg.get(dp).clone();
+			}
+		} else if (description instanceof DatatypeSomeRestriction) {
+			DatatypeSomeRestriction dsr = (DatatypeSomeRestriction) description;
+			DatatypeProperty dp = (DatatypeProperty) dsr.getRestrictedPropertyExpression();
+			DataRange dr = dsr.getDataRange();
+
+			Map<Individual, SortedSet<Double>> mapping = dd.get(dp);			
+			SortedSet<Individual> returnSet = new TreeSet<Individual>();			
+
+			if (dr instanceof DoubleMaxValue) {
+				for(Entry<Individual, SortedSet<Double>> entry : mapping.entrySet()) {
+					if(entry.getValue().first() <= ((DoubleMaxValue)dr).getValue()) {
+						returnSet.add(entry.getKey());
+					}
+				}				
+			} else if (dr instanceof DoubleMinValue) {
+				for(Entry<Individual, SortedSet<Double>> entry : mapping.entrySet()) {
+					if(entry.getValue().last() >= ((DoubleMinValue)dr).getValue()) {
+						returnSet.add(entry.getKey());
+					}
+				}
+			}
+		}
+			
+		throw new ReasoningMethodUnsupportedException("Retrieval for description "
+					+ description + " unsupported.");		
+			
+		// return rs.retrieval(concept);
+//		SortedSet<Individual> inds = new TreeSet<Individual>();
+//		for (Individual i : individuals) {
+//			if (hasType(concept, i)) {
+//				inds.add(i);
+//			}
+//		}
+//		return inds;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.dllearner.core.Reasoner#getAtomicConcepts()
+	 */
+	@Override
+	public Set<NamedClass> getNamedClasses() {
+		return atomicConcepts;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.dllearner.core.Reasoner#getAtomicRoles()
+	 */
+	@Override
+	public Set<ObjectProperty> getObjectProperties() {
+		return atomicRoles;
+	}
+
+	@Override
+	public SortedSet<DatatypeProperty> getDatatypePropertiesImpl() {
+		return datatypeProperties;
+	}
+
+	@Override
+	public SortedSet<DatatypeProperty> getBooleanDatatypePropertiesImpl() {
+		return booleanDatatypeProperties;
+	}
+
+	@Override
+	public SortedSet<DatatypeProperty> getDoubleDatatypePropertiesImpl() {
+		return doubleDatatypeProperties;
+	}
+
+	@Override
+	public SortedSet<DatatypeProperty> getIntDatatypePropertiesImpl() {
+		return intDatatypeProperties;
+	}
+
+	@Override
+	public SortedSet<DatatypeProperty> getStringDatatypePropertiesImpl() {
+		return stringDatatypeProperties;
+	}	
+	
+	@Override
+	protected SortedSet<Description> getSuperClassesImpl(Description concept) throws ReasoningMethodUnsupportedException {
+		return rc.getSuperClassesImpl(concept);
+	}
+	
+	@Override
+	protected SortedSet<Description> getSubClassesImpl(Description concept) throws ReasoningMethodUnsupportedException {
+		return rc.getSubClassesImpl(concept);
+	}
+
+	@Override
+	protected SortedSet<ObjectProperty> getSuperPropertiesImpl(ObjectProperty role) throws ReasoningMethodUnsupportedException {
+		return rc.getSuperPropertiesImpl(role);
+	}	
+
+	@Override
+	protected SortedSet<ObjectProperty> getSubPropertiesImpl(ObjectProperty role) throws ReasoningMethodUnsupportedException {
+		return rc.getSubPropertiesImpl(role);
+	}
+	
+	@Override
+	protected SortedSet<DatatypeProperty> getSuperPropertiesImpl(DatatypeProperty role) throws ReasoningMethodUnsupportedException {
+		return rc.getSuperPropertiesImpl(role);
+	}	
+
+	@Override
+	protected SortedSet<DatatypeProperty> getSubPropertiesImpl(DatatypeProperty role) throws ReasoningMethodUnsupportedException {
+		return rc.getSubPropertiesImpl(role);
+	}	
+	
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.dllearner.core.Reasoner#getIndividuals()
+	 */
+	@Override
+	public SortedSet<Individual> getIndividuals() {
+		return individuals;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.dllearner.core.Reasoner#getReasonerType()
+	 */
+	@Override
+	public ReasonerType getReasonerType() {
+		return ReasonerType.FAST_INSTANCE_CHECKER;
+	}
+
+//	@Override
+//	public ClassHierarchy getClassHierarchy() {
+//		return rc.getClassHierarchy();
+//	}
+
+//	@Override
+//	public void prepareRoleHierarchyImpl(Set<ObjectProperty> allowedRoles) {
+//		rc.prepareRoleHierarchy(allowedRoles);
+//	}
+
+//	@Override
+//	public ObjectPropertyHierarchy getRoleHierarchy() {
+//		return rc.getRoleHierarchy();
+//	}
+
+//	@Override
+//	public void prepareDatatypePropertyHierarchyImpl(Set<DatatypeProperty> allowedRoles) {
+//		rc.prepareDatatypePropertyHierarchyImpl(allowedRoles);
+//	}
+
+//	@Override
+//	public DatatypePropertyHierarchy getDatatypePropertyHierarchy() {
+//		return rc.getDatatypePropertyHierarchy();
+//	}
+
+	@Override
+	public boolean isSuperClassOfImpl(Description superConcept, Description subConcept) {
+		// Negation neg = new Negation(subConcept);
+		// Intersection c = new Intersection(neg,superConcept);
+		// return fastRetrieval.calculateSets(c).getPosSet().isEmpty();
+		return rc.isSuperClassOfImpl(superConcept, subConcept);
+	}
+
+	/**
+	 * Test method for fast instance checker.
+	 * 
+	 * @param args
+	 *            No arguments supported.
+	 * @throws ComponentInitException Component cannot be initialised.
+	 * @throws ParseException File cannot be parsed.
+	 * @throws ReasoningMethodUnsupportedException Reasoning method not supported.
+	 */
+	public static void main(String[] args) throws Exception,
+			ReasoningMethodUnsupportedException {
+		
+		String ontologyURL = "/home/me/tools/pellet/test/data/modularity/koala.owl";
+		OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+		OWLDataFactory dataFactory = man.getOWLDataFactory();
+		OWLOntology ontology = man.loadOntologyFromOntologyDocument(new File(ontologyURL));
+		OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance();
+		OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ontology);
+		OWLClass cls = dataFactory.getOWLClass(IRI.create("http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#Koala"));
+		Set<OWLClassExpression> superClasses = cls.getSuperClasses(ontology);
+		System.out.println(superClasses);
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.dllearner.core.Reasoner#getBaseURI()
+	 */
+	@Override
+	public String getBaseURI() {
+		return rc.getBaseURI();
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.dllearner.core.Reasoner#getPrefixes()
+	 */
+	@Override
+	public Map<String, String> getPrefixes() {
+		return rc.getPrefixes();
+	}
+	
+	public void setPrefixes(Map<String, String> prefixes) {
+		rc.setPrefixes(prefixes);
+	}
+	
+	/**
+	 * @param baseURI the baseURI to set
+	 */
+	public void setBaseURI(String baseURI) {
+		rc.setBaseURI(baseURI);
+	}
+
+	@Override
+	public Description getDomainImpl(ObjectProperty objectProperty) {
+		return rc.getDomain(objectProperty);
+	}
+
+	@Override
+	public Description getDomainImpl(DatatypeProperty datatypeProperty) {
+		return rc.getDomain(datatypeProperty);
+	}
+
+	@Override
+	public Description getRangeImpl(ObjectProperty objectProperty) {
+		return rc.getRange(objectProperty);
+	}
+	
+	@Override
+	public DataRange getRangeImpl(DatatypeProperty datatypeProperty) {
+		return rc.getRange(datatypeProperty);
+	}
+
+	@Override
+	public Map<Individual, SortedSet<Individual>> getPropertyMembersImpl(ObjectProperty atomicRole) {
+		return opPos.get(atomicRole);
+	}
+
+	@Override
+	public final SortedSet<Individual> getTrueDatatypeMembersImpl(DatatypeProperty datatypeProperty) {
+		return bdPos.get(datatypeProperty);
+	}
+	
+	@Override
+	public final SortedSet<Individual> getFalseDatatypeMembersImpl(DatatypeProperty datatypeProperty) {
+		return bdNeg.get(datatypeProperty);
+	}
+	
+	@Override
+	public Map<Individual, SortedSet<Integer>> getIntDatatypeMembersImpl(
+			DatatypeProperty datatypeProperty) {
+		return id.get(datatypeProperty);
+	}		
+	
+	@Override
+	public Map<Individual, SortedSet<Double>> getDoubleDatatypeMembersImpl(
+			DatatypeProperty datatypeProperty) {
+		return dd.get(datatypeProperty);
+	}	
+	
+	@Override
+	public Map<Individual, SortedSet<Constant>> getDatatypeMembersImpl(
+			DatatypeProperty datatypeProperty) {
+		return dpPos.get(datatypeProperty);
+//		return rc.getDatatypeMembersImpl(datatypeProperty);
+	}		
+	
+	@Override
+	public Set<Individual> getRelatedIndividualsImpl(Individual individual, ObjectProperty objectProperty) throws ReasoningMethodUnsupportedException {
+		return rc.getRelatedIndividuals(individual, objectProperty);
+	}
+	
+	@Override
+	protected Map<ObjectProperty,Set<Individual>> getObjectPropertyRelationshipsImpl(Individual individual) {
+		return rc.getObjectPropertyRelationships(individual);
+	}	
+	
+	@Override
+	public Set<Constant> getRelatedValuesImpl(Individual individual, DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException {
+		return rc.getRelatedValues(individual, datatypeProperty);
+	}	
+	
+	@Override
+	public boolean isSatisfiableImpl() {
+		return rc.isSatisfiable();
+	}	
+	
+	@Override
+	public Set<Constant> getLabelImpl(Entity entity) throws ReasoningMethodUnsupportedException {
+		return rc.getLabel(entity);
+	}	
+	
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.dllearner.core.ReasonerComponent#releaseKB()
+	 */
+	@Override
+	public void releaseKB() {
+		rc.releaseKB();
+	}
+
+//	@Override
+//	public boolean hasDatatypeSupport() {
+//		return true;
+//	}
+
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.ReasonerComponent#getTypesImpl(org.dllearner.core.owl.Individual)
+	 */
+	@Override
+	protected Set<NamedClass> getTypesImpl(Individual individual) {
+		return rc.getTypesImpl(individual);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.BaseReasoner#remainsSatisfiable(org.dllearner.core.owl.Axiom)
+	 */
+	@Override
+	public boolean remainsSatisfiableImpl(Axiom axiom) {
+		return rc.remainsSatisfiableImpl(axiom);
+	}
+
+	@Override
+	protected Set<Description> getAssertedDefinitionsImpl(NamedClass nc) {
+		return rc.getAssertedDefinitionsImpl(nc);
+	}
+
+    public OWLAPIReasoner getReasonerComponent() {
+        return rc;
+    }
+
+    @Autowired(required = false)
+    public void setReasonerComponent(OWLAPIReasoner rc) {
+        this.rc = rc;
+    }
+
+    public boolean isDefaultNegation() {
+        return defaultNegation;
+    }
+
+    public void setDefaultNegation(boolean defaultNegation) {
+        this.defaultNegation = defaultNegation;
+    }
+
+	public ForallSemantics getForAllSemantics() {
+		return forallSemantics;
+	}
+
+	public void setForAllSemantics(ForallSemantics forallSemantics) {
+		this.forallSemantics = forallSemantics;
+	}
+	
+	/**
+	 * @param materializeExistentialRestrictions the materializeExistentialRestrictions to set
+	 */
+	public void setMaterializeExistentialRestrictions(boolean materializeExistentialRestrictions) {
+		this.materializeExistentialRestrictions = materializeExistentialRestrictions;
+	}
+}

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4274] trunk/components-core/src/main/java/org/ dllearner

[<lor...@us...>]

Revision: 4274
          http://sourceforge.net/p/dl-learner/code/4274
Author:   lorenz_b
Date:     2014-05-27 12:58:39 +0000 (Tue, 27 May 2014)
Log Message:
-----------
Added equals for complex descriptions.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/rendering/Edge.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/NamedClass.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectSomeRestriction.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectValueRestriction.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/Thing.java

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-05-27 12:57:42 UTC (rev 4273)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-05-27 12:58:39 UTC (rev 4274)
@@ -1581,7 +1581,7 @@
     	for (QueryTree<N> child : children) {
     		Vertex childVertex = new Vertex(child.getId(), prefixed(prefixes, child.getUserObject().toString()));
     		graph.addVertex(childVertex);
-    		Edge edge = new Edge(Integer.valueOf(parent.getId() + "000" + childVertex.getId()), prefixed(prefixes, tree.getEdge(child).toString()));
+    		Edge edge = new Edge(Long.valueOf(parent.getId() + "0" + childVertex.getId()), prefixed(prefixes, tree.getEdge(child).toString()));
 			graph.addEdge(parent, childVertex, edge);
 			buildGraph(graph, child);
 		}

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/rendering/Edge.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/rendering/Edge.java	2014-05-27 12:57:42 UTC (rev 4273)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/rendering/Edge.java	2014-05-27 12:58:39 UTC (rev 4274)
@@ -1,10 +1,10 @@
 package org.dllearner.algorithms.qtl.datastructures.rendering;
 
 public class Edge {
-	int id;
+	long id;
 	String label;
 
-	public Edge(int id, String label) {
+	public Edge(long id, String label) {
 		this.id = id;
 		this.label = label;
 	}
@@ -12,7 +12,7 @@
 	/**
 	 * @return the id
 	 */
-	public int getId() {
+	public long getId() {
 		return id;
 	}
 
@@ -27,7 +27,7 @@
 	public int hashCode() {
 		final int prime = 31;
 		int result = 1;
-		result = prime * result + id;
+		result = prime * result + (int) (id ^ (id >>> 32));
 		return result;
 	}
 
@@ -44,4 +44,6 @@
 			return false;
 		return true;
 	}
+
+	
 }
\ No newline at end of file

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/NamedClass.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/NamedClass.java	2014-05-27 12:57:42 UTC (rev 4273)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/NamedClass.java	2014-05-27 12:58:39 UTC (rev 4274)
@@ -111,6 +111,8 @@
 			return true;
 		if (obj == null)
 			return false;
+		if(obj==Thing.instance && name.equals(Thing.uri.toString()))
+			return true;
 		if (getClass() != obj.getClass())
 			return false;
 		NamedClass other = (NamedClass) obj;

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java	2014-05-27 12:57:42 UTC (rev 4273)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectProperty.java	2014-05-27 12:58:39 UTC (rev 4274)
@@ -33,9 +33,6 @@
  */
 public class ObjectProperty extends ObjectPropertyExpression implements Property, Comparable<ObjectProperty>{
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = -3343070247923446690L;
 
 	public ObjectProperty(String name) {

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectSomeRestriction.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectSomeRestriction.java	2014-05-27 12:57:42 UTC (rev 4273)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectSomeRestriction.java	2014-05-27 12:58:39 UTC (rev 4274)
@@ -61,5 +61,37 @@
 	
 	public void accept(KBElementVisitor visitor) {
 		visitor.visit(this);
+	}
+
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((getChild(0) == null) ? 0 : getChild(0).hashCode());
+		result = prime * result + ((getRole() == null) ? 0 : getRole().hashCode());
+		return result;
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		ObjectSomeRestriction other = (ObjectSomeRestriction) obj;
+		if (getChild(0) == null) {
+			if (other.getChild(0) != null)
+				return false;
+		} else if (!getChild(0).equals(other.getChild(0)))
+			return false;
+		if (getRole() == null) {
+			if (other.getRole() != null)
+				return false;
+		} else if (!getRole().equals(other.getRole()))
+			return false;
+		return true;
 	}	
+	
 }

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectValueRestriction.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectValueRestriction.java	2014-05-27 12:57:42 UTC (rev 4273)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ObjectValueRestriction.java	2014-05-27 12:58:39 UTC (rev 4274)
@@ -30,9 +30,6 @@
  */
 public class ObjectValueRestriction extends ValueRestriction {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 2437223709767096950L;
 
 	/**
@@ -87,5 +84,36 @@
 	
 	public void accept(KBElementVisitor visitor) {
 		visitor.visit(this);
+	}
+
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((getRestrictedPropertyExpression() == null) ? 0 : getRestrictedPropertyExpression().hashCode());
+		result = prime * result + ((getValue() == null) ? 0 : getValue().hashCode());
+		return result;
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		ObjectValueRestriction other = (ObjectValueRestriction) obj;
+		if (getRestrictedPropertyExpression() == null) {
+			if (other.getRestrictedPropertyExpression() != null)
+				return false;
+		} else if (!getRestrictedPropertyExpression().equals(other.getRestrictedPropertyExpression()))
+			return false;
+		if (getValue() == null) {
+			if (other.getValue() != null)
+				return false;
+		} else if (!getValue().equals(other.getValue()))
+			return false;
+		return true;
 	}	
 }

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/Thing.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/Thing.java	2014-05-27 12:57:42 UTC (rev 4273)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/Thing.java	2014-05-27 12:58:39 UTC (rev 4274)
@@ -37,9 +37,6 @@
  */
 public class Thing extends Description {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = -880276915058868775L;
 	public static final Thing instance = new Thing();
 	
@@ -87,5 +84,25 @@
 		visitor.visit(this);
 	}
 
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((uri == null) ? 0 : uri.hashCode());
+		return result;
+	}
 
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if(obj.getClass() == getClass()){
+			return true;
+		}
+		if (obj.getClass() == NamedClass.class && ((NamedClass)obj).getName().equals(uri.toString()))
+			return true;
+		return false;
+	}
 }

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4273] trunk/components-core/src/main/java/org/ dllearner/utilities/owl/DescriptionMinimizer.java

[<lor...@us...>]

Revision: 4273
          http://sourceforge.net/p/dl-learner/code/4273
Author:   lorenz_b
Date:     2014-05-27 12:57:42 +0000 (Tue, 27 May 2014)
Log Message:
-----------
Added some trivial subclass checks.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java

Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java	2014-05-23 13:20:53 UTC (rev 4272)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java	2014-05-27 12:57:42 UTC (rev 4273)
@@ -30,6 +30,7 @@
 import org.dllearner.core.owl.IntMaxValue;
 import org.dllearner.core.owl.IntMinValue;
 import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.NamedClass;
 import org.dllearner.core.owl.Negation;
 import org.dllearner.core.owl.Nothing;
 import org.dllearner.core.owl.ObjectAllRestriction;
@@ -50,6 +51,8 @@
  * 
  */
 public class DescriptionMinimizer {
+	
+	private static final NamedClass OWL_THING = new NamedClass(Thing.uri);
 
 	private AbstractReasonerComponent reasoner;
 	private ConceptComparator conceptComparator = new ConceptComparator();
@@ -152,7 +155,16 @@
 			
 			if(description instanceof Intersection) {
 				for(int i=0; i<children.size(); i++) {
-					for(int j=0; j<children.size(); j++) {						
+					for(int j=0; j<children.size(); j++) {
+//						if(children.get(j) instanceof ObjectSomeRestriction && children.get(i) instanceof ObjectSomeRestriction){
+//							System.out.println(children.get(j) + "::::" + children.get(i));
+////							System.out.println(children.get(j).getClass().getSimpleName() + "::::" + children.get(i).getClass().getSimpleName());
+//							System.out.println(children.get(j).getChild(0).getClass().getSimpleName() + "::::" + children.get(i).getChild(0).getClass().getSimpleName());
+//							Description d1 = children.get(j);
+//							Description d2 = children.get(i);
+//							boolean subclassOf = isSubclassOf(d1, d2);
+//							System.out.println(subclassOf);
+//						}
 						if(i != j && isSubclassOf(children.get(j), children.get(i))) {
 							// remove element because it is super class of another element
 							children.remove(i);
@@ -253,6 +265,8 @@
 				return ((IntMaxValue)dr1).getValue() <= ((IntMaxValue)dr2).getValue();
 			}
 		} 
+		if(d1.equals(d2)) return true;
+		if(d2 == Thing.instance || d2.equals(OWL_THING)) return true;
 		if(!(d1.isNamedClass() && d2.isNamedClass())) return false;
 		// check whether we have cached this query
 		Map<Description,Boolean> tmp = cachedSubclassOf.get(d1);
@@ -275,4 +289,11 @@
 			return tmp2;
 		}
 	}	
+	
+	public static void main(String[] args) throws Exception {
+		Description d1 = new ObjectSomeRestriction(new ObjectProperty("r"), Thing.instance);
+		Description d2 = new ObjectSomeRestriction(new ObjectProperty("r"), new NamedClass(Thing.uri.toString()));
+		
+		System.out.println(d1.equals(d2));
+	}
 }

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4272] trunk/scripts/src/main/java/org/dllearner/ scripts/RAChallenge.java

[<lor...@us...>]

Revision: 4272
          http://sourceforge.net/p/dl-learner/code/4272
Author:   lorenz_b
Date:     2014-05-23 13:20:53 +0000 (Fri, 23 May 2014)
Log Message:
-----------
Updated RA Challenge script.

Modified Paths:
--------------
    trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java	2014-05-23 12:03:39 UTC (rev 4271)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java	2014-05-23 13:20:53 UTC (rev 4272)
@@ -14,12 +14,15 @@
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.SortedSet;
 import java.util.TreeSet;
 
+import org.apache.jena.riot.Lang;
+import org.apache.jena.riot.RDFDataMgr;
 import org.dllearner.algorithms.celoe.CELOE;
 import org.dllearner.algorithms.celoe.OEHeuristicRuntime;
 import org.dllearner.algorithms.elcopy.ELLearningAlgorithm;
@@ -50,6 +53,9 @@
 
 import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
 
+import com.hp.hpl.jena.graph.Triple;
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.DatasetFactory;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QuerySolution;
@@ -59,9 +65,8 @@
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.vocabulary.OWL;
-import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.sparql.core.Quad;
+import com.hp.hpl.jena.sparql.util.ModelUtils;
 
 /**
  * @author Lorenz Buehmann
@@ -96,16 +101,32 @@
 		File[] files = dataDir.listFiles(new FilenameFilter() {
 			@Override
 			public boolean accept(File dir, String name) {
-				return name.endsWith(".nt") || name.endsWith(".ttl") || name.endsWith(".rdf") || name.endsWith(".owl");
+				return name.endsWith(".nt") || name.endsWith(".ttl") || name.endsWith(".rdf") || name.endsWith(".owl") || name.endsWith(".nq");
 			}
 		});
 		System.out.println("loading data...");
 		Model model = ModelFactory.createDefaultModel();
 		for (File file : files) {
-			model.read(new FileInputStream(file), null, "TURTLE");
+			if(file.getName().endsWith(".nq")){
+				Dataset ds = DatasetFactory.createMem() ;
+		        RDFDataMgr.read(ds, new FileInputStream(file), Lang.NQUADS) ;
+//				Model subModel = ds.getNamedModel("http://bio2rdf.org/bio2rdf.dataset:bio2rdf-ra.challenge-R3");
+//				model.add(subModel);
+				Iterator<Quad> find = ds.asDatasetGraph().find();
+				Triple t;
+				while(find.hasNext()){
+					t = find.next().asTriple();
+					Statement st = model.asStatement(t);
+					model.add(st);
+				}
+			} else {
+				model.read(new FileInputStream(file), null, "TURTLE");
+			}
+			
 		}
+		System.out.println("done. loaded " + model.size() + " triples.");
 		
-		analyzeData(model);
+//		analyzeData(model);
 		
 		//get the positive and negative examples via SPARQL
 		//<http://bio2rdf.org/ra.challenge:1877000> <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> "true"^^<http://www.w3.org/2001/XMLSchema#boolean>  .
@@ -132,7 +153,12 @@
 		System.out.println("#neg examples: " + negExamples.size());
 		
 		//remove triples with property non-responder
+		System.out.println("Pruning data...");
 		model.remove(model.listStatements(null, model.createProperty("http://bio2rdf.org/ra.challenge_vocabulary:non-responder"), (RDFNode)null));
+		model.remove(model.listStatements(null, model.createProperty("http://rdfs.org/ns/void#inDataset"), (RDFNode)null));
+		model.remove(model.listStatements(null, model.createProperty("http://purl.org/dc/terms/description"), (RDFNode)null));
+		model.remove(model.listStatements(null, model.createProperty("http://www.w3.org/2000/01/rdf-schema#label"), (RDFNode)null));
+		System.out.println("done. remaining " + model.size() + " triples.");
 		
 		//enrich with additional data
 		enrich(model);
@@ -177,7 +203,7 @@
 		} else {
 			OEHeuristicRuntime heuristic = new OEHeuristicRuntime();
 			heuristic.setExpansionPenaltyFactor(0.1);
-			la = new CELOE(lp, rc);
+			la = new CELOE(lp, baseReasoner);
 			((CELOE) la).setHeuristic(heuristic);
 			((CELOE) la).setMaxExecutionTimeInSeconds(100);
 			((CELOE) la).setNoisePercentage(50);
@@ -188,7 +214,7 @@
 			RhoDRDown op = new RhoDRDown();
 			op.setUseHasValueConstructor(true);
 			op.setUseObjectValueNegation(true);
-			op.setReasoner(rc);
+			op.setReasoner(baseReasoner);
 			op.init();
 //			((CELOE) la).setOperator(op);
 		}
@@ -239,6 +265,12 @@
 		qe = QueryExecutionFactory.create(query, model);
 		rs = qe.execSelect();
 		System.out.println(ResultSetFormatter.asText(rs));
+		
+		query = "SELECT * WHERE {<http://bio2rdf.org/ra.challenge:825000> ?p ?o. "
+				+ "OPTIONAL{?o ?p1 ?o1.OPTIONAL{?o1 ?p2 ?o2. OPTIONAL{?o2 ?p3 ?o3.OPTIONAL{?o3 ?p4 ?o4.}}}}}";
+		qe = QueryExecutionFactory.create(query, model);
+		rs = qe.execSelect();
+		System.out.println(ResultSetFormatter.asText(rs));
 	}
 	
 	private static void computeLGG(Model model, SortedSet<Individual> posExamples){
@@ -293,7 +325,7 @@
 		
 		drugbankData.write(new FileOutputStream("drugbank.ttl"), "TURTLE", null);
 		model.add(drugbankData);
+		System.out.println("done. remaining " + model.size() + " triples.");
 		
-		
 	}
 }

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4271] trunk/components-core/src/main/java/org/ dllearner

[<lor...@us...>]

Revision: 4271
          http://sourceforge.net/p/dl-learner/code/4271
Author:   lorenz_b
Date:     2014-05-23 12:03:39 +0000 (Fri, 23 May 2014)
Log Message:
-----------
Added support for inter min max datarange.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/core/owl/IntMaxValue.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/IntMinValue.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
    trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/IntMaxValue.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/IntMaxValue.java	2014-05-22 11:04:32 UTC (rev 4270)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/IntMaxValue.java	2014-05-23 12:03:39 UTC (rev 4271)
@@ -58,11 +58,11 @@
 	 * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
 	 */
 	public String toString(String baseURI, Map<String, String> prefixes) {
-		return " <= " + value;
+		return "integer[<= " + value + "]";
 	}
 	
 	public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " <= " + value;
+		return "integer[<= " + value + "]";
 	}
 	
 	public void accept(KBElementVisitor visitor) {
@@ -74,7 +74,7 @@
 	 */
 	@Override
 	public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " <= " + value;
+		return "integer[<= " + value + "]";
 	}
 
 	/* (non-Javadoc)
@@ -85,4 +85,12 @@
 		return false;
 	}	
 	
+	/* (non-Javadoc)
+	 * @see java.lang.Object#toString()
+	 */
+	@Override
+	public String toString() {
+		return toString(null, null);
+	}
+	
 }

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/IntMinValue.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/IntMinValue.java	2014-05-22 11:04:32 UTC (rev 4270)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/IntMinValue.java	2014-05-23 12:03:39 UTC (rev 4271)
@@ -58,11 +58,11 @@
 	 * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
 	 */
 	public String toString(String baseURI, Map<String, String> prefixes) {
-		return " >= " + value;
+		return "integer[>= " + value + "]";
 	}	
 	
 	public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " >= " + value;
+		return "integer[>= " + value + "]";
 	}	
 	
 	public void accept(KBElementVisitor visitor) {
@@ -74,7 +74,7 @@
 	 */
 	@Override
 	public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " >= " + value;
+		return "integer[>= " + value + "]";
 	}
 
 	/* (non-Javadoc)
@@ -84,4 +84,12 @@
 	public boolean isDatatype() {
 		return false;
 	}	
+	
+	/* (non-Javadoc)
+	 * @see java.lang.Object#toString()
+	 */
+	@Override
+	public String toString() {
+		return toString(null, null);
+	}
 }

Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java	2014-05-22 11:04:32 UTC (rev 4270)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java	2014-05-23 12:03:39 UTC (rev 4271)
@@ -53,6 +53,8 @@
 import org.dllearner.core.owl.DoubleMinValue;
 import org.dllearner.core.owl.Entity;
 import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.IntMaxValue;
+import org.dllearner.core.owl.IntMinValue;
 import org.dllearner.core.owl.Intersection;
 import org.dllearner.core.owl.NamedClass;
 import org.dllearner.core.owl.Negation;
@@ -73,8 +75,6 @@
 import org.dllearner.parser.ParseException;
 import org.dllearner.utilities.Helper;
 import org.dllearner.utilities.owl.ConceptTransformation;
-import org.semanticweb.owlapi.owllink.builtin.requests.IsDataPropertySatisfiable;
-import org.semanticweb.owlapi.vocab.OWL2Datatype;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.propertyeditors.StringTrimmerEditor;
 
@@ -563,22 +563,39 @@
 				 } else {
 					 return false;
 				 }
-			}
-			SortedSet<Double> values = dd.get(dp).get(individual);
+			} else {
+				if(dr instanceof IntMaxValue || dr instanceof IntMinValue){
+					SortedSet<Integer> values = id.get(dp).get(individual);
 
-			// if there is no filler for this individual and property we
-			// need to return false
-			if (values == null) {
-				return false;
-			}
+					// if there is no filler for this individual and property we
+					// need to return false
+					if (values == null) {
+						return false;
+					}
+					if (dr instanceof IntMaxValue) {
+						return (values.first() <= ((IntMaxValue) dr).getValue());
+					} else if (dr instanceof IntMinValue) {
+						return (values.last() >= ((IntMinValue) dr).getValue());
+					}
+				} else {
+					SortedSet<Double> values = dd.get(dp).get(individual);
 
-			if (dr instanceof DoubleMaxValue) {
-				return (values.first() <= ((DoubleMaxValue) dr).getValue());
-			} else if (dr instanceof DoubleMinValue) {
-				return (values.last() >= ((DoubleMinValue) dr).getValue());
-			} else if (dr instanceof DoubleMinMaxRange){
-				return (values.first() <= ((DoubleMinMaxRange) dr).getMaxValue()) && (values.last() >= ((DoubleMinMaxRange) dr).getMinValue());
+					// if there is no filler for this individual and property we
+					// need to return false
+					if (values == null) {
+						return false;
+					}
+					if (dr instanceof DoubleMaxValue) {
+						return (values.first() <= ((DoubleMaxValue) dr).getValue());
+					} else if (dr instanceof DoubleMinValue) {
+						return (values.last() >= ((DoubleMinValue) dr).getValue());
+					} else if (dr instanceof DoubleMinMaxRange){
+						return (values.first() <= ((DoubleMinMaxRange) dr).getMaxValue()) && (values.last() >= ((DoubleMinMaxRange) dr).getMinValue());
+					}
+				}
+				
 			}
+			
 		} else if (description instanceof DatatypeValueRestriction) {
 			Constant value = ((DatatypeValueRestriction)description).getValue();
 			DatatypeProperty dp = ((DatatypeValueRestriction)description).getRestrictedPropertyExpression();

Modified: trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java	2014-05-22 11:04:32 UTC (rev 4270)
+++ trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java	2014-05-23 12:03:39 UTC (rev 4271)
@@ -53,6 +53,8 @@
 import org.dllearner.core.owl.DoubleMaxValue;
 import org.dllearner.core.owl.DoubleMinValue;
 import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.IntMaxValue;
+import org.dllearner.core.owl.IntMinValue;
 import org.dllearner.core.owl.Intersection;
 import org.dllearner.core.owl.NamedClass;
 import org.dllearner.core.owl.Negation;
@@ -96,8 +98,10 @@
 public class RhoDRDown extends RefinementOperatorAdapter implements Component, CustomHierarchyRefinementOperator, CustomStartRefinementOperator, ReasoningBasedRefinementOperator {
 
 	private static Logger logger = Logger
-	.getLogger(RhoDRDown.class);	
+	.getLogger(RhoDRDown.class);
 	
+	private static final NamedClass OWL_THING = new NamedClass(Thing.uri);
+	
 	private AbstractReasonerComponent reasoner;
 	
 	// hierarchies
@@ -152,18 +156,21 @@
 	private Map<NamedClass, Set<DatatypeProperty>> appBD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
 	private Map<NamedClass, Set<DatatypeProperty>> appDD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
 	private Map<NamedClass, Set<DatatypeProperty>> appSD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
+	private Map<NamedClass, Set<DatatypeProperty>> appID = new TreeMap<NamedClass, Set<DatatypeProperty>>();
 	
 	// most general applicable properties
 	private Map<NamedClass,Set<ObjectProperty>> mgr = new TreeMap<NamedClass,Set<ObjectProperty>>();
 	private Map<NamedClass,Set<DatatypeProperty>> mgbd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
 	private Map<NamedClass,Set<DatatypeProperty>> mgdd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
 	private Map<NamedClass,Set<DatatypeProperty>> mgsd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
+	private Map<NamedClass,Set<DatatypeProperty>> mgid = new TreeMap<NamedClass,Set<DatatypeProperty>>();
 	
 	// concept comparator
 	private ConceptComparator conceptComparator = new ConceptComparator();
 	
-	// splits for double datatype properties in ascening order
+	// splits for double datatype properties in ascending order
 	private Map<DatatypeProperty,List<Double>> splits = new TreeMap<DatatypeProperty,List<Double>>();
+	private Map<DatatypeProperty,List<Integer>> splitsInt = new TreeMap<DatatypeProperty,List<Integer>>();
 	private int maxNrOfSplits = 10;
 	
 	// data structure for a simple frequent pattern matching preprocessing phase
@@ -330,6 +337,11 @@
 			computeSplits(dp);
 		}
 		
+		// compute splits for integer datatype properties
+		for (DatatypeProperty dp : reasoner.getIntDatatypeProperties()) {
+			computeSplitsInt(dp);
+		}
+		
 		// determine the maximum number of fillers for each role
 		// (up to a specified cardinality maximum)
 		if(useCardinalityRestrictions) {
@@ -457,7 +469,7 @@
 			tmp = subHierarchy.getSuperClasses(description.getChild(0));
 				
 			for(Description c : tmp) {
-				if(!(c instanceof Thing))
+				if(!(c instanceof Thing) && !c.equals(OWL_THING))
 					refinements.add(new Negation(c));
 			}
 		
@@ -674,6 +686,31 @@
 					DatatypeSomeRestriction newDSR = new DatatypeSomeRestriction(dp,min);
 					refinements.add(newDSR);
 				}
+			} if(dr instanceof IntMaxValue) {
+				int value = ((IntMaxValue)dr).getValue();
+				// find out which split value was used
+				int splitIndex = splitsInt.get(dp).lastIndexOf(value);
+				if(splitIndex == -1)
+					throw new Error("split error");
+				int newSplitIndex = splitIndex - 1;
+				if(newSplitIndex >= 0) {
+					IntMaxValue max = new IntMaxValue(splitsInt.get(dp).get(newSplitIndex));
+					DatatypeSomeRestriction newDSR = new DatatypeSomeRestriction(dp,max);
+					refinements.add(newDSR);
+//					System.out.println(description + " => " + newDSR);
+				}
+			} else if(dr instanceof IntMinValue) {
+				int value = ((IntMinValue)dr).getValue();
+				// find out which split value was used
+				int splitIndex = splitsInt.get(dp).lastIndexOf(value);
+				if(splitIndex == -1)
+					throw new Error("split error");
+				int newSplitIndex = splitIndex + 1;
+				if(newSplitIndex < splitsInt.get(dp).size()) {
+					IntMinValue min = new IntMinValue(splitsInt.get(dp).get(newSplitIndex));
+					DatatypeSomeRestriction newDSR = new DatatypeSomeRestriction(dp,min);
+					refinements.add(newDSR);
+				}
 			}
 		} else if (description instanceof StringValueRestriction) {
 			StringValueRestriction svr = (StringValueRestriction) description;
@@ -786,6 +823,10 @@
 		TreeSet<DatatypeProperty> occuredDP = new TreeSet<DatatypeProperty>();
 		// rule 4: no double occurences of hasValue restrictions
 		TreeSet<ObjectProperty> occuredVR = new TreeSet<ObjectProperty>();
+		// rule 5: max. restrictions at most once
+				boolean maxIntOccurence = false;
+				// rule 6: min restrictions at most once
+				boolean minIntOccurence = false;
 		
 		for(Description child : intersection.getChildren()) {
 			if(child instanceof DatatypeSomeRestriction) {
@@ -800,6 +841,16 @@
 						return false;
 					else
 						minDoubleOccurence = true;
+				} else if(dr instanceof IntMaxValue) {
+					if(maxIntOccurence)
+						return false;
+					else
+						maxIntOccurence = true;
+				} else if(dr instanceof IntMinValue) {
+					if(minIntOccurence)
+						return false;
+					else
+						minIntOccurence = true;
 				}		
 			} else if(child instanceof BooleanValueRestriction) {
 				DatatypeProperty dp = (DatatypeProperty) ((BooleanValueRestriction)child).getRestrictedPropertyExpression();
@@ -978,7 +1029,7 @@
 		if(useNegation) {
 			Set<Description> m2tmp = subHierarchy.getSuperClasses(new Nothing());
 			for(Description c : m2tmp) {
-				if(!(c instanceof Thing)) {
+				if(!(c instanceof Thing) && !c.equals(OWL_THING)) {
 					m2.add(new Negation(c));	
 				}
 			}
@@ -1024,6 +1075,18 @@
 			}
 		}		
 		
+		if(useIntDatatypes) {
+			Set<DatatypeProperty> intDPs = reasoner.getIntDatatypeProperties();
+			for(DatatypeProperty dp : intDPs) {
+				if(splitsInt.get(dp).size() > 0) {
+					IntMaxValue max = new IntMaxValue(splitsInt.get(dp).get(splitsInt.get(dp).size()-1));
+					IntMinValue min = new IntMinValue(splitsInt.get(dp).get(0));
+					m3.add(new DatatypeSomeRestriction(dp,max));
+					m3.add(new DatatypeSomeRestriction(dp,min));
+				}
+			}
+		}
+		
 		if(useDataHasValueConstructor) {
 			Set<DatatypeProperty> stringDPs = reasoner.getStringDatatypeProperties();
 			for(DatatypeProperty dp : stringDPs) {
@@ -1161,8 +1224,21 @@
 					m3.add(new DatatypeSomeRestriction(dp,min));
 				}
 			}
-		}			
+		}
 		
+		if(useIntDatatypes) {
+			Set<DatatypeProperty> intDPs = mgid.get(nc);
+			
+			for(DatatypeProperty dp : intDPs) {
+				if(splitsInt.get(dp).size() > 0) {
+					IntMaxValue max = new IntMaxValue(splitsInt.get(dp).get(splitsInt.get(dp).size()-1));
+					IntMinValue min = new IntMinValue(splitsInt.get(dp).get(0));
+					m3.add(new DatatypeSomeRestriction(dp,max));
+					m3.add(new DatatypeSomeRestriction(dp,min));
+				}
+			}
+		}
+		
 		if(useDataHasValueConstructor) {
 			Set<DatatypeProperty> stringDPs = mgsd.get(nc);
 			for(DatatypeProperty dp : stringDPs) {
@@ -1257,7 +1333,7 @@
 //		System.out.println("index " + index + " lower class " + lowerClass);
 		
 		for(Description candidate :  subHierarchy.getSuperClasses(lowerClass)) {
-			if(!(candidate instanceof Thing)) {
+			if(!(candidate instanceof Thing) && !candidate.equals(OWL_THING)) {
 //				System.out.println("candidate: " + candidate);
 				// check disjointness with index/range (should not be disjoint otherwise not useful)
 				if(!isDisjoint(new Negation(candidate),index)) {
@@ -1293,6 +1369,7 @@
 		mgbd.put(domain, new TreeSet<DatatypeProperty>());
 		mgdd.put(domain, new TreeSet<DatatypeProperty>());
 		mgsd.put(domain, new TreeSet<DatatypeProperty>());
+		mgid.put(domain, new TreeSet<DatatypeProperty>());
 		
 		SortedSet<ObjectProperty> mostGeneral = reasoner.getMostGeneralProperties();
 		computeMgrRecursive(domain, mostGeneral, mgr.get(domain));
@@ -1302,9 +1379,11 @@
 		Set<DatatypeProperty> mostGeneralBDP = Helper.intersection(mostGeneralDP, reasoner.getBooleanDatatypeProperties());
 		Set<DatatypeProperty> mostGeneralDDP = Helper.intersection(mostGeneralDP, reasoner.getDoubleDatatypeProperties());
 		Set<DatatypeProperty> mostGeneralSDP = Helper.intersection(mostGeneralDP, reasoner.getStringDatatypeProperties());
+		Set<DatatypeProperty> mostGeneralIDP = Helper.intersection(mostGeneralDP, reasoner.getIntDatatypeProperties());
 		computeMgbdRecursive(domain, mostGeneralBDP, mgbd.get(domain));	
 		computeMgddRecursive(domain, mostGeneralDDP, mgdd.get(domain));
 		computeMgsdRecursive(domain, mostGeneralSDP, mgsd.get(domain));
+		computeMgidRecursive(domain, mostGeneralIDP, mgid.get(domain));
 	}
 	
 	private void computeMgrRecursive(NamedClass domain, Set<ObjectProperty> currProperties, Set<ObjectProperty> mgrTmp) {
@@ -1343,6 +1422,15 @@
 		}
 	}	
 	
+	private void computeMgidRecursive(NamedClass domain, Set<DatatypeProperty> currProperties, Set<DatatypeProperty> mgidTmp) {
+		for(DatatypeProperty prop : currProperties) {
+			if(appID.get(domain).contains(prop))
+				mgidTmp.add(prop);
+			else
+				computeMgidRecursive(domain, reasoner.getSubProperties(prop), mgidTmp);
+		}
+	}	
+	
 	// computes the set of applicable properties for a given class
 	private void computeApp(NamedClass domain) {
 		// object properties
@@ -1390,7 +1478,19 @@
 			if(!isDisjoint(domain,d))
 				applicableSDPs.add(role);
 		}
-		appSD.put(domain, applicableSDPs);		
+		appSD.put(domain, applicableSDPs);	
+		
+		// integer datatype properties
+				Set<DatatypeProperty> mostGeneralIDPs = reasoner.getIntDatatypeProperties();
+				Set<DatatypeProperty> applicableIDPs = new TreeSet<DatatypeProperty>();
+				for(DatatypeProperty role : mostGeneralIDPs) {
+//					Description d = (NamedClass) rs.getDomain(role);
+					Description d = reasoner.getDomain(role);
+//					System.out.println("domain: " + d);
+					if(!isDisjoint(domain,d))
+						applicableIDPs.add(role);
+				}
+				appID.put(domain, applicableIDPs);
 	}
 	
 	// returns true of the intersection contains elements disjoint
@@ -1541,6 +1641,37 @@
 //		System.out.println(splits);
 //		System.exit(0);
 	}
+	
+	private void computeSplitsInt(DatatypeProperty dp) {
+		Set<Integer> valuesSet = new TreeSet<Integer>();
+//		Set<Individual> individuals = rs.getIndividuals();
+		Map<Individual,SortedSet<Integer>> valueMap = reasoner.getIntDatatypeMembers(dp);
+		// add all values to the set (duplicates will be remove automatically)
+		for(Entry<Individual,SortedSet<Integer>> e : valueMap.entrySet())
+			valuesSet.addAll(e.getValue());
+		// convert set to a list where values are sorted
+		List<Integer> values = new LinkedList<Integer>(valuesSet);
+		Collections.sort(values);
+		
+		int nrOfValues = values.size();
+		// create split set
+		List<Integer> splitsDP = new LinkedList<Integer>();
+		for(int splitNr=0; splitNr < Math.min(maxNrOfSplits,nrOfValues-1); splitNr++) {
+			int index;
+			if(nrOfValues<=maxNrOfSplits)
+				index = splitNr;
+			else
+				index = (int) Math.floor(splitNr * (double)nrOfValues/(maxNrOfSplits+1));
+			
+			int value = values.get(index);
+			splitsDP.add(value);
+		}
+		splitsInt.put(dp, splitsDP);
+		
+//		System.out.println(values);
+//		System.out.println(splits);
+//		System.exit(0);
+	}
 
 	public int getFrequencyThreshold() {
 		return frequencyThreshold;

Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java	2014-05-22 11:04:32 UTC (rev 4270)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java	2014-05-23 12:03:39 UTC (rev 4271)
@@ -24,9 +24,12 @@
 import java.util.TreeMap;
 
 import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.owl.DataRange;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
 import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.IntMaxValue;
+import org.dllearner.core.owl.IntMinValue;
 import org.dllearner.core.owl.Intersection;
-import org.dllearner.core.owl.NamedClass;
 import org.dllearner.core.owl.Negation;
 import org.dllearner.core.owl.Nothing;
 import org.dllearner.core.owl.ObjectAllRestriction;
@@ -59,7 +62,7 @@
 	}
 
 	/**
-	 * Method which minimzes the input description. The algorithm does not 
+	 * Method which minimizes the input description. The algorithm does not 
 	 * replace subdescriptions with named classes, e.g.
 	 * if the description "male \sqcap \exists hasChild.\top" is passed to the
 	 * algorithm and a class "father" is defined in the obvious way 
@@ -241,6 +244,15 @@
 	}
 	
 	private boolean isSubclassOf(Description d1, Description d2) {
+		if(beautify && (d1 instanceof DatatypeSomeRestriction) && (d2 instanceof DatatypeSomeRestriction)){
+			DataRange dr1 = ((DatatypeSomeRestriction)d1).getDataRange();
+			DataRange dr2 = ((DatatypeSomeRestriction)d2).getDataRange();
+			if(dr1 instanceof IntMinValue && dr2 instanceof IntMinValue){
+				return ((IntMinValue)dr1).getValue() >= ((IntMinValue)dr2).getValue();
+			} else if(dr1 instanceof IntMaxValue && dr2 instanceof IntMaxValue){
+				return ((IntMaxValue)dr1).getValue() <= ((IntMaxValue)dr2).getValue();
+			}
+		} 
 		if(!(d1.isNamedClass() && d2.isNamedClass())) return false;
 		// check whether we have cached this query
 		Map<Description,Boolean> tmp = cachedSubclassOf.get(d1);
@@ -249,7 +261,8 @@
 			tmp2 = tmp.get(d2);
 		
 		if(tmp2==null) {
-			Boolean result = reasoner.isSuperClassOf(d2, d1);	
+			
+			Boolean result = reasoner.isSuperClassOf(d2, d1);
 						
 			// create new entry if necessary
 			Map<Description,Boolean> map1 = new TreeMap<Description,Boolean>(conceptComparator);

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4270] trunk/test/qtl

[<lor...@us...>]

Revision: 4270
          http://sourceforge.net/p/dl-learner/code/4270
Author:   lorenz_b
Date:     2014-05-22 11:04:32 +0000 (Thu, 22 May 2014)
Log Message:
-----------
Added QTL example.

Added Paths:
-----------
    trunk/test/qtl/heart/
    trunk/test/qtl/heart/files/
    trunk/test/qtl/heart/files/heart.dat
    trunk/test/qtl/heart/heart.owl
    trunk/test/qtl/heart/train.conf

Added: trunk/test/qtl/heart/files/heart.dat
===================================================================
--- trunk/test/qtl/heart/files/heart.dat	                        (rev 0)
+++ trunk/test/qtl/heart/files/heart.dat	2014-05-22 11:04:32 UTC (rev 4270)
@@ -0,0 +1,270 @@
+70.0,1.0,4.0,130.0,322.0,0.0,2.0,109.0,0.0,2.4,2.0,3.0,3.0,2
+67.0,0.0,3.0,115.0,564.0,0.0,2.0,160.0,0.0,1.6,2.0,0.0,7.0,1
+57.0,1.0,2.0,124.0,261.0,0.0,0.0,141.0,0.0,0.3,1.0,0.0,7.0,2
+64.0,1.0,4.0,128.0,263.0,0.0,0.0,105.0,1.0,0.2,2.0,1.0,7.0,1
+74.0,0.0,2.0,120.0,269.0,0.0,2.0,121.0,1.0,0.2,1.0,1.0,3.0,1
+65.0,1.0,4.0,120.0,177.0,0.0,0.0,140.0,0.0,0.4,1.0,0.0,7.0,1
+56.0,1.0,3.0,130.0,256.0,1.0,2.0,142.0,1.0,0.6,2.0,1.0,6.0,2
+59.0,1.0,4.0,110.0,239.0,0.0,2.0,142.0,1.0,1.2,2.0,1.0,7.0,2
+60.0,1.0,4.0,140.0,293.0,0.0,2.0,170.0,0.0,1.2,2.0,2.0,7.0,2
+63.0,0.0,4.0,150.0,407.0,0.0,2.0,154.0,0.0,4.0,2.0,3.0,7.0,2
+59.0,1.0,4.0,135.0,234.0,0.0,0.0,161.0,0.0,0.5,2.0,0.0,7.0,1
+53.0,1.0,4.0,142.0,226.0,0.0,2.0,111.0,1.0,0.0,1.0,0.0,7.0,1
+44.0,1.0,3.0,140.0,235.0,0.0,2.0,180.0,0.0,0.0,1.0,0.0,3.0,1
+61.0,1.0,1.0,134.0,234.0,0.0,0.0,145.0,0.0,2.6,2.0,2.0,3.0,2
+57.0,0.0,4.0,128.0,303.0,0.0,2.0,159.0,0.0,0.0,1.0,1.0,3.0,1
+71.0,0.0,4.0,112.0,149.0,0.0,0.0,125.0,0.0,1.6,2.0,0.0,3.0,1
+46.0,1.0,4.0,140.0,311.0,0.0,0.0,120.0,1.0,1.8,2.0,2.0,7.0,2
+53.0,1.0,4.0,140.0,203.0,1.0,2.0,155.0,1.0,3.1,3.0,0.0,7.0,2
+64.0,1.0,1.0,110.0,211.0,0.0,2.0,144.0,1.0,1.8,2.0,0.0,3.0,1
+40.0,1.0,1.0,140.0,199.0,0.0,0.0,178.0,1.0,1.4,1.0,0.0,7.0,1
+67.0,1.0,4.0,120.0,229.0,0.0,2.0,129.0,1.0,2.6,2.0,2.0,7.0,2
+48.0,1.0,2.0,130.0,245.0,0.0,2.0,180.0,0.0,0.2,2.0,0.0,3.0,1
+43.0,1.0,4.0,115.0,303.0,0.0,0.0,181.0,0.0,1.2,2.0,0.0,3.0,1
+47.0,1.0,4.0,112.0,204.0,0.0,0.0,143.0,0.0,0.1,1.0,0.0,3.0,1
+54.0,0.0,2.0,132.0,288.0,1.0,2.0,159.0,1.0,0.0,1.0,1.0,3.0,1
+48.0,0.0,3.0,130.0,275.0,0.0,0.0,139.0,0.0,0.2,1.0,0.0,3.0,1
+46.0,0.0,4.0,138.0,243.0,0.0,2.0,152.0,1.0,0.0,2.0,0.0,3.0,1
+51.0,0.0,3.0,120.0,295.0,0.0,2.0,157.0,0.0,0.6,1.0,0.0,3.0,1
+58.0,1.0,3.0,112.0,230.0,0.0,2.0,165.0,0.0,2.5,2.0,1.0,7.0,2
+71.0,0.0,3.0,110.0,265.0,1.0,2.0,130.0,0.0,0.0,1.0,1.0,3.0,1
+57.0,1.0,3.0,128.0,229.0,0.0,2.0,150.0,0.0,0.4,2.0,1.0,7.0,2
+66.0,1.0,4.0,160.0,228.0,0.0,2.0,138.0,0.0,2.3,1.0,0.0,6.0,1
+37.0,0.0,3.0,120.0,215.0,0.0,0.0,170.0,0.0,0.0,1.0,0.0,3.0,1
+59.0,1.0,4.0,170.0,326.0,0.0,2.0,140.0,1.0,3.4,3.0,0.0,7.0,2
+50.0,1.0,4.0,144.0,200.0,0.0,2.0,126.0,1.0,0.9,2.0,0.0,7.0,2
+48.0,1.0,4.0,130.0,256.0,1.0,2.0,150.0,1.0,0.0,1.0,2.0,7.0,2
+61.0,1.0,4.0,140.0,207.0,0.0,2.0,138.0,1.0,1.9,1.0,1.0,7.0,2
+59.0,1.0,1.0,160.0,273.0,0.0,2.0,125.0,0.0,0.0,1.0,0.0,3.0,2
+42.0,1.0,3.0,130.0,180.0,0.0,0.0,150.0,0.0,0.0,1.0,0.0,3.0,1
+48.0,1.0,4.0,122.0,222.0,0.0,2.0,186.0,0.0,0.0,1.0,0.0,3.0,1
+40.0,1.0,4.0,152.0,223.0,0.0,0.0,181.0,0.0,0.0,1.0,0.0,7.0,2
+62.0,0.0,4.0,124.0,209.0,0.0,0.0,163.0,0.0,0.0,1.0,0.0,3.0,1
+44.0,1.0,3.0,130.0,233.0,0.0,0.0,179.0,1.0,0.4,1.0,0.0,3.0,1
+46.0,1.0,2.0,101.0,197.0,1.0,0.0,156.0,0.0,0.0,1.0,0.0,7.0,1
+59.0,1.0,3.0,126.0,218.0,1.0,0.0,134.0,0.0,2.2,2.0,1.0,6.0,2
+58.0,1.0,3.0,140.0,211.0,1.0,2.0,165.0,0.0,0.0,1.0,0.0,3.0,1
+49.0,1.0,3.0,118.0,149.0,0.0,2.0,126.0,0.0,0.8,1.0,3.0,3.0,2
+44.0,1.0,4.0,110.0,197.0,0.0,2.0,177.0,0.0,0.0,1.0,1.0,3.0,2
+66.0,1.0,2.0,160.0,246.0,0.0,0.0,120.0,1.0,0.0,2.0,3.0,6.0,2
+65.0,0.0,4.0,150.0,225.0,0.0,2.0,114.0,0.0,1.0,2.0,3.0,7.0,2
+42.0,1.0,4.0,136.0,315.0,0.0,0.0,125.0,1.0,1.8,2.0,0.0,6.0,2
+52.0,1.0,2.0,128.0,205.0,1.0,0.0,184.0,0.0,0.0,1.0,0.0,3.0,1
+65.0,0.0,3.0,140.0,417.0,1.0,2.0,157.0,0.0,0.8,1.0,1.0,3.0,1
+63.0,0.0,2.0,140.0,195.0,0.0,0.0,179.0,0.0,0.0,1.0,2.0,3.0,1
+45.0,0.0,2.0,130.0,234.0,0.0,2.0,175.0,0.0,0.6,2.0,0.0,3.0,1
+41.0,0.0,2.0,105.0,198.0,0.0,0.0,168.0,0.0,0.0,1.0,1.0,3.0,1
+61.0,1.0,4.0,138.0,166.0,0.0,2.0,125.0,1.0,3.6,2.0,1.0,3.0,2
+60.0,0.0,3.0,120.0,178.0,1.0,0.0,96.0,0.0,0.0,1.0,0.0,3.0,1
+59.0,0.0,4.0,174.0,249.0,0.0,0.0,143.0,1.0,0.0,2.0,0.0,3.0,2
+62.0,1.0,2.0,120.0,281.0,0.0,2.0,103.0,0.0,1.4,2.0,1.0,7.0,2
+57.0,1.0,3.0,150.0,126.0,1.0,0.0,173.0,0.0,0.2,1.0,1.0,7.0,1
+51.0,0.0,4.0,130.0,305.0,0.0,0.0,142.0,1.0,1.2,2.0,0.0,7.0,2
+44.0,1.0,3.0,120.0,226.0,0.0,0.0,169.0,0.0,0.0,1.0,0.0,3.0,1
+60.0,0.0,1.0,150.0,240.0,0.0,0.0,171.0,0.0,0.9,1.0,0.0,3.0,1
+63.0,1.0,1.0,145.0,233.0,1.0,2.0,150.0,0.0,2.3,3.0,0.0,6.0,1
+57.0,1.0,4.0,150.0,276.0,0.0,2.0,112.0,1.0,0.6,2.0,1.0,6.0,2
+51.0,1.0,4.0,140.0,261.0,0.0,2.0,186.0,1.0,0.0,1.0,0.0,3.0,1
+58.0,0.0,2.0,136.0,319.0,1.0,2.0,152.0,0.0,0.0,1.0,2.0,3.0,2
+44.0,0.0,3.0,118.0,242.0,0.0,0.0,149.0,0.0,0.3,2.0,1.0,3.0,1
+47.0,1.0,3.0,108.0,243.0,0.0,0.0,152.0,0.0,0.0,1.0,0.0,3.0,2
+61.0,1.0,4.0,120.0,260.0,0.0,0.0,140.0,1.0,3.6,2.0,1.0,7.0,2
+57.0,0.0,4.0,120.0,354.0,0.0,0.0,163.0,1.0,0.6,1.0,0.0,3.0,1
+70.0,1.0,2.0,156.0,245.0,0.0,2.0,143.0,0.0,0.0,1.0,0.0,3.0,1
+76.0,0.0,3.0,140.0,197.0,0.0,1.0,116.0,0.0,1.1,2.0,0.0,3.0,1
+67.0,0.0,4.0,106.0,223.0,0.0,0.0,142.0,0.0,0.3,1.0,2.0,3.0,1
+45.0,1.0,4.0,142.0,309.0,0.0,2.0,147.0,1.0,0.0,2.0,3.0,7.0,2
+45.0,1.0,4.0,104.0,208.0,0.0,2.0,148.0,1.0,3.0,2.0,0.0,3.0,1
+39.0,0.0,3.0,94.0,199.0,0.0,0.0,179.0,0.0,0.0,1.0,0.0,3.0,1
+42.0,0.0,3.0,120.0,209.0,0.0,0.0,173.0,0.0,0.0,2.0,0.0,3.0,1
+56.0,1.0,2.0,120.0,236.0,0.0,0.0,178.0,0.0,0.8,1.0,0.0,3.0,1
+58.0,1.0,4.0,146.0,218.0,0.0,0.0,105.0,0.0,2.0,2.0,1.0,7.0,2
+35.0,1.0,4.0,120.0,198.0,0.0,0.0,130.0,1.0,1.6,2.0,0.0,7.0,2
+58.0,1.0,4.0,150.0,270.0,0.0,2.0,111.0,1.0,0.8,1.0,0.0,7.0,2
+41.0,1.0,3.0,130.0,214.0,0.0,2.0,168.0,0.0,2.0,2.0,0.0,3.0,1
+57.0,1.0,4.0,110.0,201.0,0.0,0.0,126.0,1.0,1.5,2.0,0.0,6.0,1
+42.0,1.0,1.0,148.0,244.0,0.0,2.0,178.0,0.0,0.8,1.0,2.0,3.0,1
+62.0,1.0,2.0,128.0,208.0,1.0,2.0,140.0,0.0,0.0,1.0,0.0,3.0,1
+59.0,1.0,1.0,178.0,270.0,0.0,2.0,145.0,0.0,4.2,3.0,0.0,7.0,1
+41.0,0.0,2.0,126.0,306.0,0.0,0.0,163.0,0.0,0.0,1.0,0.0,3.0,1
+50.0,1.0,4.0,150.0,243.0,0.0,2.0,128.0,0.0,2.6,2.0,0.0,7.0,2
+59.0,1.0,2.0,140.0,221.0,0.0,0.0,164.0,1.0,0.0,1.0,0.0,3.0,1
+61.0,0.0,4.0,130.0,330.0,0.0,2.0,169.0,0.0,0.0,1.0,0.0,3.0,2
+54.0,1.0,4.0,124.0,266.0,0.0,2.0,109.0,1.0,2.2,2.0,1.0,7.0,2
+54.0,1.0,4.0,110.0,206.0,0.0,2.0,108.0,1.0,0.0,2.0,1.0,3.0,2
+52.0,1.0,4.0,125.0,212.0,0.0,0.0,168.0,0.0,1.0,1.0,2.0,7.0,2
+47.0,1.0,4.0,110.0,275.0,0.0,2.0,118.0,1.0,1.0,2.0,1.0,3.0,2
+66.0,1.0,4.0,120.0,302.0,0.0,2.0,151.0,0.0,0.4,2.0,0.0,3.0,1
+58.0,1.0,4.0,100.0,234.0,0.0,0.0,156.0,0.0,0.1,1.0,1.0,7.0,2
+64.0,0.0,3.0,140.0,313.0,0.0,0.0,133.0,0.0,0.2,1.0,0.0,7.0,1
+50.0,0.0,2.0,120.0,244.0,0.0,0.0,162.0,0.0,1.1,1.0,0.0,3.0,1
+44.0,0.0,3.0,108.0,141.0,0.0,0.0,175.0,0.0,0.6,2.0,0.0,3.0,1
+67.0,1.0,4.0,120.0,237.0,0.0,0.0,71.0,0.0,1.0,2.0,0.0,3.0,2
+49.0,0.0,4.0,130.0,269.0,0.0,0.0,163.0,0.0,0.0,1.0,0.0,3.0,1
+57.0,1.0,4.0,165.0,289.0,1.0,2.0,124.0,0.0,1.0,2.0,3.0,7.0,2
+63.0,1.0,4.0,130.0,254.0,0.0,2.0,147.0,0.0,1.4,2.0,1.0,7.0,2
+48.0,1.0,4.0,124.0,274.0,0.0,2.0,166.0,0.0,0.5,2.0,0.0,7.0,2
+51.0,1.0,3.0,100.0,222.0,0.0,0.0,143.0,1.0,1.2,2.0,0.0,3.0,1
+60.0,0.0,4.0,150.0,258.0,0.0,2.0,157.0,0.0,2.6,2.0,2.0,7.0,2
+59.0,1.0,4.0,140.0,177.0,0.0,0.0,162.0,1.0,0.0,1.0,1.0,7.0,2
+45.0,0.0,2.0,112.0,160.0,0.0,0.0,138.0,0.0,0.0,2.0,0.0,3.0,1
+55.0,0.0,4.0,180.0,327.0,0.0,1.0,117.0,1.0,3.4,2.0,0.0,3.0,2
+41.0,1.0,2.0,110.0,235.0,0.0,0.0,153.0,0.0,0.0,1.0,0.0,3.0,1
+60.0,0.0,4.0,158.0,305.0,0.0,2.0,161.0,0.0,0.0,1.0,0.0,3.0,2
+54.0,0.0,3.0,135.0,304.0,1.0,0.0,170.0,0.0,0.0,1.0,0.0,3.0,1
+42.0,1.0,2.0,120.0,295.0,0.0,0.0,162.0,0.0,0.0,1.0,0.0,3.0,1
+49.0,0.0,2.0,134.0,271.0,0.0,0.0,162.0,0.0,0.0,2.0,0.0,3.0,1
+46.0,1.0,4.0,120.0,249.0,0.0,2.0,144.0,0.0,0.8,1.0,0.0,7.0,2
+56.0,0.0,4.0,200.0,288.0,1.0,2.0,133.0,1.0,4.0,3.0,2.0,7.0,2
+66.0,0.0,1.0,150.0,226.0,0.0,0.0,114.0,0.0,2.6,3.0,0.0,3.0,1
+56.0,1.0,4.0,130.0,283.0,1.0,2.0,103.0,1.0,1.6,3.0,0.0,7.0,2
+49.0,1.0,3.0,120.0,188.0,0.0,0.0,139.0,0.0,2.0,2.0,3.0,7.0,2
+54.0,1.0,4.0,122.0,286.0,0.0,2.0,116.0,1.0,3.2,2.0,2.0,3.0,2
+57.0,1.0,4.0,152.0,274.0,0.0,0.0,88.0,1.0,1.2,2.0,1.0,7.0,2
+65.0,0.0,3.0,160.0,360.0,0.0,2.0,151.0,0.0,0.8,1.0,0.0,3.0,1
+54.0,1.0,3.0,125.0,273.0,0.0,2.0,152.0,0.0,0.5,3.0,1.0,3.0,1
+54.0,0.0,3.0,160.0,201.0,0.0,0.0,163.0,0.0,0.0,1.0,1.0,3.0,1
+62.0,1.0,4.0,120.0,267.0,0.0,0.0,99.0,1.0,1.8,2.0,2.0,7.0,2
+52.0,0.0,3.0,136.0,196.0,0.0,2.0,169.0,0.0,0.1,2.0,0.0,3.0,1
+52.0,1.0,2.0,134.0,201.0,0.0,0.0,158.0,0.0,0.8,1.0,1.0,3.0,1
+60.0,1.0,4.0,117.0,230.0,1.0,0.0,160.0,1.0,1.4,1.0,2.0,7.0,2
+63.0,0.0,4.0,108.0,269.0,0.0,0.0,169.0,1.0,1.8,2.0,2.0,3.0,2
+66.0,1.0,4.0,112.0,212.0,0.0,2.0,132.0,1.0,0.1,1.0,1.0,3.0,2
+42.0,1.0,4.0,140.0,226.0,0.0,0.0,178.0,0.0,0.0,1.0,0.0,3.0,1
+64.0,1.0,4.0,120.0,246.0,0.0,2.0,96.0,1.0,2.2,3.0,1.0,3.0,2
+54.0,1.0,3.0,150.0,232.0,0.0,2.0,165.0,0.0,1.6,1.0,0.0,7.0,1
+46.0,0.0,3.0,142.0,177.0,0.0,2.0,160.0,1.0,1.4,3.0,0.0,3.0,1
+67.0,0.0,3.0,152.0,277.0,0.0,0.0,172.0,0.0,0.0,1.0,1.0,3.0,1
+56.0,1.0,4.0,125.0,249.0,1.0,2.0,144.0,1.0,1.2,2.0,1.0,3.0,2
+34.0,0.0,2.0,118.0,210.0,0.0,0.0,192.0,0.0,0.7,1.0,0.0,3.0,1
+57.0,1.0,4.0,132.0,207.0,0.0,0.0,168.0,1.0,0.0,1.0,0.0,7.0,1
+64.0,1.0,4.0,145.0,212.0,0.0,2.0,132.0,0.0,2.0,2.0,2.0,6.0,2
+59.0,1.0,4.0,138.0,271.0,0.0,2.0,182.0,0.0,0.0,1.0,0.0,3.0,1
+50.0,1.0,3.0,140.0,233.0,0.0,0.0,163.0,0.0,0.6,2.0,1.0,7.0,2
+51.0,1.0,1.0,125.0,213.0,0.0,2.0,125.0,1.0,1.4,1.0,1.0,3.0,1
+54.0,1.0,2.0,192.0,283.0,0.0,2.0,195.0,0.0,0.0,1.0,1.0,7.0,2
+53.0,1.0,4.0,123.0,282.0,0.0,0.0,95.0,1.0,2.0,2.0,2.0,7.0,2
+52.0,1.0,4.0,112.0,230.0,0.0,0.0,160.0,0.0,0.0,1.0,1.0,3.0,2
+40.0,1.0,4.0,110.0,167.0,0.0,2.0,114.0,1.0,2.0,2.0,0.0,7.0,2
+58.0,1.0,3.0,132.0,224.0,0.0,2.0,173.0,0.0,3.2,1.0,2.0,7.0,2
+41.0,0.0,3.0,112.0,268.0,0.0,2.0,172.0,1.0,0.0,1.0,0.0,3.0,1
+41.0,1.0,3.0,112.0,250.0,0.0,0.0,179.0,0.0,0.0,1.0,0.0,3.0,1
+50.0,0.0,3.0,120.0,219.0,0.0,0.0,158.0,0.0,1.6,2.0,0.0,3.0,1
+54.0,0.0,3.0,108.0,267.0,0.0,2.0,167.0,0.0,0.0,1.0,0.0,3.0,1
+64.0,0.0,4.0,130.0,303.0,0.0,0.0,122.0,0.0,2.0,2.0,2.0,3.0,1
+51.0,0.0,3.0,130.0,256.0,0.0,2.0,149.0,0.0,0.5,1.0,0.0,3.0,1
+46.0,0.0,2.0,105.0,204.0,0.0,0.0,172.0,0.0,0.0,1.0,0.0,3.0,1
+55.0,1.0,4.0,140.0,217.0,0.0,0.0,111.0,1.0,5.6,3.0,0.0,7.0,2
+45.0,1.0,2.0,128.0,308.0,0.0,2.0,170.0,0.0,0.0,1.0,0.0,3.0,1
+56.0,1.0,1.0,120.0,193.0,0.0,2.0,162.0,0.0,1.9,2.0,0.0,7.0,1
+66.0,0.0,4.0,178.0,228.0,1.0,0.0,165.0,1.0,1.0,2.0,2.0,7.0,2
+38.0,1.0,1.0,120.0,231.0,0.0,0.0,182.0,1.0,3.8,2.0,0.0,7.0,2
+62.0,0.0,4.0,150.0,244.0,0.0,0.0,154.0,1.0,1.4,2.0,0.0,3.0,2
+55.0,1.0,2.0,130.0,262.0,0.0,0.0,155.0,0.0,0.0,1.0,0.0,3.0,1
+58.0,1.0,4.0,128.0,259.0,0.0,2.0,130.0,1.0,3.0,2.0,2.0,7.0,2
+43.0,1.0,4.0,110.0,211.0,0.0,0.0,161.0,0.0,0.0,1.0,0.0,7.0,1
+64.0,0.0,4.0,180.0,325.0,0.0,0.0,154.0,1.0,0.0,1.0,0.0,3.0,1
+50.0,0.0,4.0,110.0,254.0,0.0,2.0,159.0,0.0,0.0,1.0,0.0,3.0,1
+53.0,1.0,3.0,130.0,197.0,1.0,2.0,152.0,0.0,1.2,3.0,0.0,3.0,1
+45.0,0.0,4.0,138.0,236.0,0.0,2.0,152.0,1.0,0.2,2.0,0.0,3.0,1
+65.0,1.0,1.0,138.0,282.0,1.0,2.0,174.0,0.0,1.4,2.0,1.0,3.0,2
+69.0,1.0,1.0,160.0,234.0,1.0,2.0,131.0,0.0,0.1,2.0,1.0,3.0,1
+69.0,1.0,3.0,140.0,254.0,0.0,2.0,146.0,0.0,2.0,2.0,3.0,7.0,2
+67.0,1.0,4.0,100.0,299.0,0.0,2.0,125.0,1.0,0.9,2.0,2.0,3.0,2
+68.0,0.0,3.0,120.0,211.0,0.0,2.0,115.0,0.0,1.5,2.0,0.0,3.0,1
+34.0,1.0,1.0,118.0,182.0,0.0,2.0,174.0,0.0,0.0,1.0,0.0,3.0,1
+62.0,0.0,4.0,138.0,294.0,1.0,0.0,106.0,0.0,1.9,2.0,3.0,3.0,2
+51.0,1.0,4.0,140.0,298.0,0.0,0.0,122.0,1.0,4.2,2.0,3.0,7.0,2
+46.0,1.0,3.0,150.0,231.0,0.0,0.0,147.0,0.0,3.6,2.0,0.0,3.0,2
+67.0,1.0,4.0,125.0,254.0,1.0,0.0,163.0,0.0,0.2,2.0,2.0,7.0,2
+50.0,1.0,3.0,129.0,196.0,0.0,0.0,163.0,0.0,0.0,1.0,0.0,3.0,1
+42.0,1.0,3.0,120.0,240.0,1.0,0.0,194.0,0.0,0.8,3.0,0.0,7.0,1
+56.0,0.0,4.0,134.0,409.0,0.0,2.0,150.0,1.0,1.9,2.0,2.0,7.0,2
+41.0,1.0,4.0,110.0,172.0,0.0,2.0,158.0,0.0,0.0,1.0,0.0,7.0,2
+42.0,0.0,4.0,102.0,265.0,0.0,2.0,122.0,0.0,0.6,2.0,0.0,3.0,1
+53.0,1.0,3.0,130.0,246.0,1.0,2.0,173.0,0.0,0.0,1.0,3.0,3.0,1
+43.0,1.0,3.0,130.0,315.0,0.0,0.0,162.0,0.0,1.9,1.0,1.0,3.0,1
+56.0,1.0,4.0,132.0,184.0,0.0,2.0,105.0,1.0,2.1,2.0,1.0,6.0,2
+52.0,1.0,4.0,108.0,233.0,1.0,0.0,147.0,0.0,0.1,1.0,3.0,7.0,1
+62.0,0.0,4.0,140.0,394.0,0.0,2.0,157.0,0.0,1.2,2.0,0.0,3.0,1
+70.0,1.0,3.0,160.0,269.0,0.0,0.0,112.0,1.0,2.9,2.0,1.0,7.0,2
+54.0,1.0,4.0,140.0,239.0,0.0,0.0,160.0,0.0,1.2,1.0,0.0,3.0,1
+70.0,1.0,4.0,145.0,174.0,0.0,0.0,125.0,1.0,2.6,3.0,0.0,7.0,2
+54.0,1.0,2.0,108.0,309.0,0.0,0.0,156.0,0.0,0.0,1.0,0.0,7.0,1
+35.0,1.0,4.0,126.0,282.0,0.0,2.0,156.0,1.0,0.0,1.0,0.0,7.0,2
+48.0,1.0,3.0,124.0,255.0,1.0,0.0,175.0,0.0,0.0,1.0,2.0,3.0,1
+55.0,0.0,2.0,135.0,250.0,0.0,2.0,161.0,0.0,1.4,2.0,0.0,3.0,1
+58.0,0.0,4.0,100.0,248.0,0.0,2.0,122.0,0.0,1.0,2.0,0.0,3.0,1
+54.0,0.0,3.0,110.0,214.0,0.0,0.0,158.0,0.0,1.6,2.0,0.0,3.0,1
+69.0,0.0,1.0,140.0,239.0,0.0,0.0,151.0,0.0,1.8,1.0,2.0,3.0,1
+77.0,1.0,4.0,125.0,304.0,0.0,2.0,162.0,1.0,0.0,1.0,3.0,3.0,2
+68.0,1.0,3.0,118.0,277.0,0.0,0.0,151.0,0.0,1.0,1.0,1.0,7.0,1
+58.0,1.0,4.0,125.0,300.0,0.0,2.0,171.0,0.0,0.0,1.0,2.0,7.0,2
+60.0,1.0,4.0,125.0,258.0,0.0,2.0,141.0,1.0,2.8,2.0,1.0,7.0,2
+51.0,1.0,4.0,140.0,299.0,0.0,0.0,173.0,1.0,1.6,1.0,0.0,7.0,2
+55.0,1.0,4.0,160.0,289.0,0.0,2.0,145.0,1.0,0.8,2.0,1.0,7.0,2
+52.0,1.0,1.0,152.0,298.0,1.0,0.0,178.0,0.0,1.2,2.0,0.0,7.0,1
+60.0,0.0,3.0,102.0,318.0,0.0,0.0,160.0,0.0,0.0,1.0,1.0,3.0,1
+58.0,1.0,3.0,105.0,240.0,0.0,2.0,154.0,1.0,0.6,2.0,0.0,7.0,1
+64.0,1.0,3.0,125.0,309.0,0.0,0.0,131.0,1.0,1.8,2.0,0.0,7.0,2
+37.0,1.0,3.0,130.0,250.0,0.0,0.0,187.0,0.0,3.5,3.0,0.0,3.0,1
+59.0,1.0,1.0,170.0,288.0,0.0,2.0,159.0,0.0,0.2,2.0,0.0,7.0,2
+51.0,1.0,3.0,125.0,245.0,1.0,2.0,166.0,0.0,2.4,2.0,0.0,3.0,1
+43.0,0.0,3.0,122.0,213.0,0.0,0.0,165.0,0.0,0.2,2.0,0.0,3.0,1
+58.0,1.0,4.0,128.0,216.0,0.0,2.0,131.0,1.0,2.2,2.0,3.0,7.0,2
+29.0,1.0,2.0,130.0,204.0,0.0,2.0,202.0,0.0,0.0,1.0,0.0,3.0,1
+41.0,0.0,2.0,130.0,204.0,0.0,2.0,172.0,0.0,1.4,1.0,0.0,3.0,1
+63.0,0.0,3.0,135.0,252.0,0.0,2.0,172.0,0.0,0.0,1.0,0.0,3.0,1
+51.0,1.0,3.0,94.0,227.0,0.0,0.0,154.0,1.0,0.0,1.0,1.0,7.0,1
+54.0,1.0,3.0,120.0,258.0,0.0,2.0,147.0,0.0,0.4,2.0,0.0,7.0,1
+44.0,1.0,2.0,120.0,220.0,0.0,0.0,170.0,0.0,0.0,1.0,0.0,3.0,1
+54.0,1.0,4.0,110.0,239.0,0.0,0.0,126.0,1.0,2.8,2.0,1.0,7.0,2
+65.0,1.0,4.0,135.0,254.0,0.0,2.0,127.0,0.0,2.8,2.0,1.0,7.0,2
+57.0,1.0,3.0,150.0,168.0,0.0,0.0,174.0,0.0,1.6,1.0,0.0,3.0,1
+63.0,1.0,4.0,130.0,330.0,1.0,2.0,132.0,1.0,1.8,1.0,3.0,7.0,2
+35.0,0.0,4.0,138.0,183.0,0.0,0.0,182.0,0.0,1.4,1.0,0.0,3.0,1
+41.0,1.0,2.0,135.0,203.0,0.0,0.0,132.0,0.0,0.0,2.0,0.0,6.0,1
+62.0,0.0,3.0,130.0,263.0,0.0,0.0,97.0,0.0,1.2,2.0,1.0,7.0,2
+43.0,0.0,4.0,132.0,341.0,1.0,2.0,136.0,1.0,3.0,2.0,0.0,7.0,2
+58.0,0.0,1.0,150.0,283.0,1.0,2.0,162.0,0.0,1.0,1.0,0.0,3.0,1
+52.0,1.0,1.0,118.0,186.0,0.0,2.0,190.0,0.0,0.0,2.0,0.0,6.0,1
+61.0,0.0,4.0,145.0,307.0,0.0,2.0,146.0,1.0,1.0,2.0,0.0,7.0,2
+39.0,1.0,4.0,118.0,219.0,0.0,0.0,140.0,0.0,1.2,2.0,0.0,7.0,2
+45.0,1.0,4.0,115.0,260.0,0.0,2.0,185.0,0.0,0.0,1.0,0.0,3.0,1
+52.0,1.0,4.0,128.0,255.0,0.0,0.0,161.0,1.0,0.0,1.0,1.0,7.0,2
+62.0,1.0,3.0,130.0,231.0,0.0,0.0,146.0,0.0,1.8,2.0,3.0,7.0,1
+62.0,0.0,4.0,160.0,164.0,0.0,2.0,145.0,0.0,6.2,3.0,3.0,7.0,2
+53.0,0.0,4.0,138.0,234.0,0.0,2.0,160.0,0.0,0.0,1.0,0.0,3.0,1
+43.0,1.0,4.0,120.0,177.0,0.0,2.0,120.0,1.0,2.5,2.0,0.0,7.0,2
+47.0,1.0,3.0,138.0,257.0,0.0,2.0,156.0,0.0,0.0,1.0,0.0,3.0,1
+52.0,1.0,2.0,120.0,325.0,0.0,0.0,172.0,0.0,0.2,1.0,0.0,3.0,1
+68.0,1.0,3.0,180.0,274.0,1.0,2.0,150.0,1.0,1.6,2.0,0.0,7.0,2
+39.0,1.0,3.0,140.0,321.0,0.0,2.0,182.0,0.0,0.0,1.0,0.0,3.0,1
+53.0,0.0,4.0,130.0,264.0,0.0,2.0,143.0,0.0,0.4,2.0,0.0,3.0,1
+62.0,0.0,4.0,140.0,268.0,0.0,2.0,160.0,0.0,3.6,3.0,2.0,3.0,2
+51.0,0.0,3.0,140.0,308.0,0.0,2.0,142.0,0.0,1.5,1.0,1.0,3.0,1
+60.0,1.0,4.0,130.0,253.0,0.0,0.0,144.0,1.0,1.4,1.0,1.0,7.0,2
+65.0,1.0,4.0,110.0,248.0,0.0,2.0,158.0,0.0,0.6,1.0,2.0,6.0,2
+65.0,0.0,3.0,155.0,269.0,0.0,0.0,148.0,0.0,0.8,1.0,0.0,3.0,1
+60.0,1.0,3.0,140.0,185.0,0.0,2.0,155.0,0.0,3.0,2.0,0.0,3.0,2
+60.0,1.0,4.0,145.0,282.0,0.0,2.0,142.0,1.0,2.8,2.0,2.0,7.0,2
+54.0,1.0,4.0,120.0,188.0,0.0,0.0,113.0,0.0,1.4,2.0,1.0,7.0,2
+44.0,1.0,2.0,130.0,219.0,0.0,2.0,188.0,0.0,0.0,1.0,0.0,3.0,1
+44.0,1.0,4.0,112.0,290.0,0.0,2.0,153.0,0.0,0.0,1.0,1.0,3.0,2
+51.0,1.0,3.0,110.0,175.0,0.0,0.0,123.0,0.0,0.6,1.0,0.0,3.0,1
+59.0,1.0,3.0,150.0,212.0,1.0,0.0,157.0,0.0,1.6,1.0,0.0,3.0,1
+71.0,0.0,2.0,160.0,302.0,0.0,0.0,162.0,0.0,0.4,1.0,2.0,3.0,1
+61.0,1.0,3.0,150.0,243.0,1.0,0.0,137.0,1.0,1.0,2.0,0.0,3.0,1
+55.0,1.0,4.0,132.0,353.0,0.0,0.0,132.0,1.0,1.2,2.0,1.0,7.0,2
+64.0,1.0,3.0,140.0,335.0,0.0,0.0,158.0,0.0,0.0,1.0,0.0,3.0,2
+43.0,1.0,4.0,150.0,247.0,0.0,0.0,171.0,0.0,1.5,1.0,0.0,3.0,1
+58.0,0.0,3.0,120.0,340.0,0.0,0.0,172.0,0.0,0.0,1.0,0.0,3.0,1
+60.0,1.0,4.0,130.0,206.0,0.0,2.0,132.0,1.0,2.4,2.0,2.0,7.0,2
+58.0,1.0,2.0,120.0,284.0,0.0,2.0,160.0,0.0,1.8,2.0,0.0,3.0,2
+49.0,1.0,2.0,130.0,266.0,0.0,0.0,171.0,0.0,0.6,1.0,0.0,3.0,1
+48.0,1.0,2.0,110.0,229.0,0.0,0.0,168.0,0.0,1.0,3.0,0.0,7.0,2
+52.0,1.0,3.0,172.0,199.0,1.0,0.0,162.0,0.0,0.5,1.0,0.0,7.0,1
+44.0,1.0,2.0,120.0,263.0,0.0,0.0,173.0,0.0,0.0,1.0,0.0,7.0,1
+56.0,0.0,2.0,140.0,294.0,0.0,2.0,153.0,0.0,1.3,2.0,0.0,3.0,1
+57.0,1.0,4.0,140.0,192.0,0.0,0.0,148.0,0.0,0.4,2.0,0.0,6.0,1
+67.0,1.0,4.0,160.0,286.0,0.0,2.0,108.0,1.0,1.5,2.0,3.0,3.0,2
\ No newline at end of file

Added: trunk/test/qtl/heart/heart.owl
===================================================================
--- trunk/test/qtl/heart/heart.owl	                        (rev 0)
+++ trunk/test/qtl/heart/heart.owl	2014-05-22 11:04:32 UTC (rev 4270)
@@ -0,0 +1,5968 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://dl-learner.org/heart#"
+     xml:base="http://dl-learner.org/heart"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:heart="http://dl-learner.org/heart#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:hasBloodSugarOver120mg="http://dl-learner.org/heart#hasBloodSugarOver120mg/">
+    <owl:Ontology rdf:about="http://dl-learner.org/heart"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/heart#hasChestPain -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/heart#hasChestPain">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://dl-learner.org/heart#Thing"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasElectrocardiographicResults -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/heart#hasElectrocardiographicResults">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://dl-learner.org/heart#Thing"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasGender -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/heart#hasGender">
+        <rdfs:range rdf:resource="http://dl-learner.org/heart#Gender"/>
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasThalValue -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/heart#hasThalValue">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://dl-learner.org/heart#Thals"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Data properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/heart#hasAge -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasAge">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasAngina -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasAngina">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasBloodPressure -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasBloodPressure">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasBloodSugarOver120mg/dl -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasBloodSugarOver120mg/dl">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasCholestoral -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasCholestoral">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasMajorVessels -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasMajorVessels">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasMaximumHeartRate -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasMaximumHeartRate">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasOldPeak -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasOldPeak">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/heart#hasStSegment -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/heart#hasStSegment">
+        <rdfs:domain rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/heart#Gender -->
+
+    <owl:Class rdf:about="http://dl-learner.org/heart#Gender"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient -->
+
+    <owl:Class rdf:about="http://dl-learner.org/heart#Patient"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#Thals -->
+
+    <owl:Class rdf:about="http://dl-learner.org/heart#Thals"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#Thing -->
+
+    <owl:Class rdf:about="http://dl-learner.org/heart#Thing"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#fixed-defect -->
+
+    <owl:Class rdf:about="http://dl-learner.org/heart#fixed-defect">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/heart#Thals"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/heart#normal -->
+
+    <owl:Class rdf:about="http://dl-learner.org/heart#normal">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/heart#Thals"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/heart#reversable-defect -->
+
+    <owl:Class rdf:about="http://dl-learner.org/heart#reversable-defect">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/heart#Thals"/>
+    </owl:Class>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/heart#0.0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#0.0"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#1.0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#1.0"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#2.0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#2.0"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#3.0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#3.0"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#4.0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#4.0"/>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient0">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">109.0</hasMaximumHeartRate>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">130.0</hasBloodPressure>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.4</hasOldPeak>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">3.0</hasMajorVessels>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">322.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">70.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient1">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.6</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">115.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">160.0</hasMaximumHeartRate>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">564.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">67.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#3.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient10 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient10">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.5</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">135.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">161.0</hasMaximumHeartRate>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">234.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">59.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient100 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient100">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.6</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">108.0</hasBloodPressure>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">141.0</hasCholestoral>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">175.0</hasMaximumHeartRate>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">44.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#3.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient101 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient101">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">120.0</hasBloodPressure>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">237.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">67.0</hasAge>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">71.0</hasMaximumHeartRate>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient102 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient102">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasStSegment>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">130.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">163.0</hasMaximumHeartRate>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">269.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">49.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient103 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient103">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasOldPeak>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">124.0</hasMaximumHeartRate>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">165.0</hasBloodPressure>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">289.0</hasCholestoral>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">3.0</hasMajorVessels>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">57.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient104 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient104">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.4</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">130.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">147.0</hasMaximumHeartRate>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">254.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">63.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient105 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient105">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.5</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">124.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">166.0</hasMaximumHeartRate>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">274.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">48.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient106 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient106">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.2</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">100.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">143.0</hasMaximumHeartRate>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">222.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">51.0</hasAge>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasAngina>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#3.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient107 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient107">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">150.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">157.0</hasMaximumHeartRate>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasMajorVessels>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.6</hasOldPeak>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">258.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">60.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient108 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient108">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasMajorVessels>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasStSegment>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">140.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">162.0</hasMaximumHeartRate>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">177.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">59.0</hasAge>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasAngina>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient109 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient109">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">112.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">138.0</hasMaximumHeartRate>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">160.0</hasCholestoral>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">45.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient11 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient11">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasStSegment>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">111.0</hasMaximumHeartRate>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">142.0</hasBloodPressure>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">226.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">53.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient110 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient110">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">117.0</hasMaximumHeartRate>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">180.0</hasBloodPressure>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">3.4</hasOldPeak>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">327.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">55.0</hasAge>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasAngina>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#1.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient111 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient111">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasStSegment>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">110.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">153.0</hasMaximumHeartRate>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">235.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">41.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient112 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient112">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasStSegment>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">158.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">161.0</hasMaximumHeartRate>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">305.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">60.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient113 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient113">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasStSegment>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">135.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">170.0</hasMaximumHeartRate>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">304.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">54.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#3.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient114 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient114">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasStSegment>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">120.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">162.0</hasMaximumHeartRate>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">295.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">42.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient115 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient115">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasOldPeak>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">134.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">162.0</hasMaximumHeartRate>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasStSegment>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">271.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">49.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient116 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient116">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.8</hasOldPeak>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</hasStSegment>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">120.0</hasBloodPressure>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">144.0</hasMaximumHeartRate>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">249.0</hasCholestoral>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">46.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#female"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient117 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient117">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">133.0</hasMaximumHeartRate>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</hasMajorVessels>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">200.0</hasBloodPressure>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">288.0</hasCholestoral>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">3.0</hasStSegment>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasOldPeak>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">56.0</hasAge>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasAngina>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#reversable-defect"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient118 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient118">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">114.0</hasMaximumHeartRate>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">150.0</hasBloodPressure>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.6</hasOldPeak>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">226.0</hasCholestoral>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">3.0</hasStSegment>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">66.0</hasAge>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</hasAngina>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#0.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#1.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart#male"/>
+        <hasThalValue rdf:resource="http://dl-learner.org/heart#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/heart#Patient119 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/heart#Patient119">
+        <rdf:type rdf:resource="http://dl-learner.org/heart#Patient"/>
+        <hasMajorVessels rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</hasMajorVessels>
+        <hasOldPeak rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.6</hasOldPeak>
+        <hasMaximumHeartRate rdf:datatype="http://www.w3.org/2001/XMLSchema#double">103.0</hasMaximumHeartRate>
+        <hasBloodPressure rdf:datatype="http://www.w3.org/2001/XMLSchema#double">130.0</hasBloodPressure>
+        <hasCholestoral rdf:datatype="http://www.w3.org/2001/XMLSchema#double">283.0</hasCholestoral>
+        <hasStSegment rdf:datatype="http://www.w3.org/2001/XMLSchema#double">3.0</hasStSegment>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">56.0</hasAge>
+        <hasBloodSugarOver120mg:dl rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasBloodSugarOver120mg:dl>
+        <hasAngina rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</hasAngina>
+        <hasElectrocardiographicResults rdf:resource="http://dl-learner.org/heart#2.0"/>
+        <hasChestPain rdf:resource="http://dl-learner.org/heart#4.0"/>
+        <hasGender rdf:resource="http://dl-learner.org/heart...
 
[truncated message content]

[DL-Learner SVN] SF.net SVN: dl-learner:[4269] trunk

[<lor...@us...>]

Revision: 4269
          http://sourceforge.net/p/dl-learner/code/4269
Author:   lorenz_b
Date:     2014-05-22 02:22:16 +0000 (Thu, 22 May 2014)
Log Message:
-----------
Updated Maven libs.

Modified Paths:
--------------
    trunk/components-core/pom.xml
    trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMaxValue.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinValue.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLDataRangeConverter.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/LGGTest.java
    trunk/examples/mutagenesis/train1.conf
    trunk/pom.xml
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
    trunk/test/qtl/alzheimer/train1.conf

Added Paths:
-----------
    trunk/dllearner-parent.iml

Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/pom.xml	2014-05-22 02:22:16 UTC (rev 4269)
@@ -115,12 +115,15 @@
 			<artifactId>log4j</artifactId>
 		</dependency>
 
-		<!-- Latest JENA ARQ - we have to exclude XercesImpl and use an older version here because use version bei JENA leads to some errors  -->
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-arq</artifactId>
-           
         </dependency>
+        
+         <dependency>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>jena-core</artifactId>
+        </dependency>
 
 		<!--JSON is in Central -->
 		<dependency>

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -118,7 +118,6 @@
 	public ELLearningAlgorithm(AbstractLearningProblem problem, AbstractReasonerComponent reasoner) {
 		super(problem, reasoner);
 //		configurator = new ELLearningAlgorithmConfigurator(this);
-		
 		timeMonitor = MonitorFactory.getTimeMonitor("time");
 	}
 	

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -8,7 +8,6 @@
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.PriorityQueue;
@@ -17,11 +16,12 @@
 import java.util.SortedSet;
 import java.util.TreeSet;
 
-import org.apache.commons.collections.ListUtils;
 import org.apache.log4j.Logger;
 import org.dllearner.algorithms.qtl.cache.QueryTreeCache;
 import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
 import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.LiteralNodeConversionStrategy;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.LiteralNodeSubsumptionStrategy;
 import org.dllearner.algorithms.qtl.operations.lgg.EvaluatedQueryTree;
 import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
 import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
@@ -31,9 +31,7 @@
 import org.dllearner.core.ComponentInitException;
 import org.dllearner.core.EvaluatedDescription;
 import org.dllearner.core.KnowledgeSource;
-import org.dllearner.core.LearningProblem;
 import org.dllearner.core.LearningProblemUnsupportedException;
-import org.dllearner.core.Score;
 import org.dllearner.core.config.ConfigOption;
 import org.dllearner.core.owl.Description;
 import org.dllearner.core.owl.Individual;
@@ -43,7 +41,6 @@
 import org.dllearner.learningproblems.Heuristics;
 import org.dllearner.learningproblems.PosNegLP;
 import org.dllearner.learningproblems.QueryTreeScore;
-import org.dllearner.learningproblems.ScoreTwoValued;
 import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
 import org.dllearner.utilities.owl.OWLAPIConverter;
 import org.semanticweb.owlapi.io.ToStringRenderer;
@@ -141,6 +138,11 @@
 		super(qtl.getLearningProblem(), qtl.getReasoner());
 		this.model = ModelFactory.createDefaultModel();
 		this.model.add(qtl.model);
+		this.beta = qtl.beta;
+		this.maxExecutionTimeInSeconds = qtl.maxExecutionTimeInSeconds;
+		this.maxTreeComputationTimeInSeconds = qtl.maxTreeComputationTimeInSeconds;
+		this.tryFullCoverage = qtl.tryFullCoverage;
+		this.stopOnFirstDefinition = qtl.stopOnFirstDefinition;
 	}
 	
 	public EvaluatedQueryTree<String> getBestSolution(){
@@ -160,10 +162,10 @@
 		
 		lggGenerator = new LGGGeneratorImpl<String>();
 		
-//		if(heuristic == null){
+		if(heuristic == null){
 			heuristic = new QueryTreeHeuristic();
 			heuristic.setPosExamplesWeight(beta);
-//		}
+		}
 		
 		logger.info("Initializing...");
 		treeCache = new QueryTreeCache(model);
@@ -218,12 +220,7 @@
 	 */
 	@Override
 	public void start() {
-		String setup = "Setup:";
-		setup += "\n#Pos. examples:" + currentPosExamples.size();
-		setup += "\n#Neg. examples:" + currentNegExamples.size();
-		setup += "Heuristic:" + heuristic.getHeuristicType().name();
-		setup += "\nbeta=" + beta;
-		logger.info(setup);
+		showSetup();
 		logger.info("Running...");
 		startTime = System.currentTimeMillis();
 		
@@ -235,12 +232,9 @@
 			logger.info("#Remaining pos. examples:" + currentPosExampleTrees.size());
 			logger.info("#Remaining neg. examples:" + currentNegExampleTrees.size());
 			
-			//compute a (partial) solution
-			computeBestPartialSolution();
+			//compute best (partial) solution computed so far
+			EvaluatedQueryTree<String> bestPartialSolution = computeBestPartialSolution();
 			
-			//pick best (partial) solution computed so far
-			EvaluatedQueryTree<String> bestPartialSolution = currentPartialSolutions.first();
-			
 			//add if some criteria are satisfied
 			if(bestPartialSolution.getScore() >= minimumTreeScore){
 				
@@ -284,12 +278,13 @@
 		
 	}
 	
-	private void computeBestPartialSolution(){
+	private EvaluatedQueryTree<String> computeBestPartialSolution(){
 		logger.info("Computing best partial solution...");
 		bestCurrentScore = Double.NEGATIVE_INFINITY;
 		partialSolutionStartTime = System.currentTimeMillis();
 		initTodoList(currentPosExampleTrees, currentNegExampleTrees);
 		
+		EvaluatedQueryTree<String> bestPartialSolutionTree = null;
 		EvaluatedQueryTree<String> currentElement;
 		QueryTree<String> currentTree;
 		while(!partialSolutionTerminationCriteriaSatisfied()){
@@ -307,30 +302,34 @@
 				lggMon.stop();
 				
 				//evaluate the LGG
-				EvaluatedQueryTree<String> solution = evaluate(lgg, true);
-				double score = solution.getScore();
-				double mas = heuristic.getMaximumAchievableScore(solution);
-				
-				if(score >= bestCurrentScore){
-					//add to todo list, if not already contained in todo list or solution list
-					todo(solution);
-					if(score > bestCurrentScore){
-						logger.info("\tGot better solution:" + solution.getTreeScore());
+				Set<EvaluatedQueryTree<String>> solutions = evaluate(lgg, true);
+				for (EvaluatedQueryTree<String> solution : solutions) {
+					double score = solution.getScore();
+					double mas = heuristic.getMaximumAchievableScore(solution);
+					
+					if(score >= bestCurrentScore){
+						//add to todo list, if not already contained in todo list or solution list
+						todo(solution);
+						if(score > bestCurrentScore){
+							logger.info("\tGot better solution:" + solution.getTreeScore());
+							bestCurrentScore = score;
+							bestPartialSolutionTree = solution;
+						}
+						
+					} else if(mas >= bestCurrentScore){
+						todo(solution);
+					} else {
+//						System.out.println("Too general");
+//						System.out.println("MAS=" + mas + "\nBest=" + bestCurrentScore);
 					}
-					bestCurrentScore = solution.getScore();
-				} else if(mas < bestCurrentScore){
-					todo(solution);
-				} else {
-					System.out.println("Too general");
+					currentPartialSolutions.add(currentElement);
 				}
-				currentPartialSolutions.add(currentElement);
-				
 			}
 			currentPartialSolutions.add(currentElement);
 		}
 		long endTime = System.currentTimeMillis();
 		logger.info("...finished in " + (endTime-partialSolutionStartTime) + "ms.");
-		EvaluatedDescription bestPartialSolution = currentPartialSolutions.first().asEvaluatedDescription();
+		EvaluatedDescription bestPartialSolution = bestPartialSolutionTree.asEvaluatedDescription(LiteralNodeConversionStrategy.SOME_VALUES_FROM);
 		
 		logger.info("Best partial solution: " + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()).toString().replace("\n", "") + "\n(" + bestPartialSolution.getScore() + ")");
 		
@@ -340,9 +339,11 @@
 		logger.trace("Subsumption test time: " + subMon.getTotal() + "ms");
 		logger.trace("Avg. subsumption test time: " + subMon.getAvg() + "ms");
 		logger.trace("#Subsumption tests: " + subMon.getHits());
+		
+		return bestPartialSolutionTree;
 	}
 	
-	private EvaluatedQueryTree<String> evaluate(QueryTree<String> tree, boolean useSpecifity){
+	private EvaluatedQueryTree<String> evaluateSimple(QueryTree<String> tree, boolean useSpecifity){
 		//1. get a score for the coverage = recall oriented
 		//compute positive examples which are not covered by LGG
 		List<QueryTree<String>> uncoveredPositiveExampleTrees = getUncoveredTrees(tree, currentPosExampleTrees);
@@ -399,45 +400,191 @@
 		return evaluatedTree;
 	}
 	
-	private EvaluatedDescription buildCombinedSolution(){
-		if(partialSolutions.size() == 1){
-			EvaluatedDescription combinedSolution = partialSolutions.get(0).asEvaluatedDescription();
-			return combinedSolution;
+	/**
+	 * Returns a set of evaluated query trees. A set is returned because there are several ways how to convert literal nodes.
+	 * @param tree
+	 * @param useSpecifity
+	 * @return
+	 */
+	private Set<EvaluatedQueryTree<String>> evaluate(QueryTree<String> tree, boolean useSpecifity){
+		Set<EvaluatedQueryTree<String>> evaluatedTrees = new TreeSet<EvaluatedQueryTree<String>>();
+		
+		LiteralNodeSubsumptionStrategy[] strategies = LiteralNodeSubsumptionStrategy.values();
+		strategies = new LiteralNodeSubsumptionStrategy[]{LiteralNodeSubsumptionStrategy.DATATYPE, LiteralNodeSubsumptionStrategy.INTERVAL};
+		for (LiteralNodeSubsumptionStrategy strategy : strategies) {
+			//1. get a score for the coverage = recall oriented
+			List<QueryTree<String>> uncoveredPositiveExampleTrees = new ArrayList<QueryTree<String>>();
+			List<QueryTree<String>> coveredNegativeExampleTrees = new ArrayList<QueryTree<String>>();
+			
+			//compute positive examples which are not covered by LGG
+			for (QueryTree<String> posTree : currentPosExampleTrees) {
+				if(!posTree.isSubsumedBy(tree, strategy)){
+					uncoveredPositiveExampleTrees.add(posTree);
+				}
+			}
+			//compute negative examples which are covered by LGG
+			for (QueryTree<String> negTree : currentNegExampleTrees) {
+				if(negTree.isSubsumedBy(tree, strategy)){
+					coveredNegativeExampleTrees.add(negTree);
+				}
+			}
+			//convert to individuals
+			Set<Individual> uncoveredPosExamples = asIndividuals(uncoveredPositiveExampleTrees);
+			Set<Individual> coveredNegExamples = asIndividuals(coveredNegativeExampleTrees);
+			
+			//compute score
+			int coveredPositiveExamples = currentPosExampleTrees.size() - uncoveredPositiveExampleTrees.size();
+			double recall = coveredPositiveExamples / (double)currentPosExampleTrees.size();
+			double precision = (coveredNegativeExampleTrees.size() + coveredPositiveExamples == 0) 
+							? 0 
+							: coveredPositiveExamples / (double)(coveredPositiveExamples + coveredNegativeExampleTrees.size());
+			
+			double coverageScore = Heuristics.getFScore(recall, precision, beta);
+			
+			//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
+			int nrOfSpecificNodes = 0;
+			for (QueryTree<String> childNode : tree.getChildrenClosure()) {
+				if(!childNode.getUserObject().equals("?")){
+					nrOfSpecificNodes++;
+				}
+			}
+			double specifityScore = 0d;
+			if(useSpecifity){
+				specifityScore = Math.log(nrOfSpecificNodes);
+			}
+			
+			//3.compute the total score
+			double score = coverageWeight * coverageScore + specifityWeight * specifityScore;
+			
+			QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
+					new TreeSet<Individual>(Sets.difference(currentPosExamples, uncoveredPosExamples)), uncoveredPosExamples,
+					coveredNegExamples, new TreeSet<Individual>(Sets.difference(currentNegExamples, coveredNegExamples)),
+					specifityScore, nrOfSpecificNodes);
+			
+			EvaluatedQueryTree<String> evaluatedTree = new EvaluatedQueryTree<String>(tree, uncoveredPositiveExampleTrees, coveredNegativeExampleTrees, queryTreeScore);
+			
+			//TODO use only the heuristic to compute the score
+			score = heuristic.getScore(evaluatedTree);
+			queryTreeScore.setScore(score);
+			queryTreeScore.setAccuracy(score);
+			
+			evaluatedTrees.add(evaluatedTree);
 		}
-		List<Description> disjuncts = new ArrayList<Description>();
 		
-		Set<Individual> posCovered = new HashSet<Individual>();
-		Set<Individual> negCovered = new HashSet<Individual>();
+		return evaluatedTrees;
+	}
+	
+	/**
+	 * Returns a set of evaluated query trees. A set is returned because there are several ways how to convert literal nodes.
+	 * @param tree
+	 * @param useSpecifity
+	 * @return
+	 */
+	private Set<EvaluatedDescription> evaluate2(QueryTree<String> tree, boolean useSpecifity){
+		Set<EvaluatedDescription> evaluatedDescriptions = new TreeSet<EvaluatedDescription>();
 		
-		//build the union of all class expressions
-		Description partialDescription;
-		for (EvaluatedQueryTree<String> partialSolution : partialSolutions) {
-			partialDescription = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
-					partialSolution.getTree().asOWLClassExpression(LiteralNodeConversionStrategy.FACET_RESTRICTION));
-			disjuncts.add(partialDescription);
-			posCovered.addAll(partialSolution.getTreeScore().getCoveredPositives());
-			negCovered.addAll(partialSolution.getTreeScore().getCoveredNegatives());
+		LiteralNodeConversionStrategy[] strategies = LiteralNodeConversionStrategy.values();
+		strategies = new LiteralNodeConversionStrategy[]{LiteralNodeConversionStrategy.SOME_VALUES_FROM, LiteralNodeConversionStrategy.FACET_RESTRICTION};
+		for (LiteralNodeConversionStrategy strategy : strategies) {
+			Description d = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(tree.asOWLClassExpression(strategy));
+			//convert to individuals
+			SortedSet<Individual> coveredExamples = reasoner.getIndividuals(d);
+			Set<Individual> coveredPosExamples = new TreeSet<Individual>(Sets.intersection(currentPosExamples, coveredExamples));
+			Set<Individual> uncoveredPosExamples = new TreeSet<Individual>(Sets.difference(currentPosExamples, coveredExamples));
+			Set<Individual> coveredNegExamples = new TreeSet<Individual>(Sets.intersection(currentNegExamples, coveredExamples));
+			
+			//compute score
+			double recall = coveredPosExamples.size() / (double)currentPosExamples.size();
+			double precision = (coveredNegExamples.size() + coveredPosExamples.size() == 0) 
+							? 0 
+							: coveredPosExamples.size() / (double)(coveredPosExamples.size() + coveredNegExamples.size());
+			
+			double coverageScore = Heuristics.getFScore(recall, precision, beta);
+			
+			//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
+			int nrOfSpecificNodes = 0;
+			for (QueryTree<String> childNode : tree.getChildrenClosure()) {
+				if(!childNode.getUserObject().equals("?")){
+					nrOfSpecificNodes++;
+				}
+			}
+			double specifityScore = 0d;
+			if(useSpecifity){
+				specifityScore = Math.log(nrOfSpecificNodes);
+			}
+			
+			//3.compute the total score
+			double score = coverageWeight * coverageScore + specifityWeight * specifityScore;
+			
+			QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
+					new TreeSet<Individual>(Sets.difference(currentPosExamples, uncoveredPosExamples)), uncoveredPosExamples,
+					coveredNegExamples, new TreeSet<Individual>(Sets.difference(currentNegExamples, coveredNegExamples)),
+					specifityScore, nrOfSpecificNodes);
+			
+			//TODO use only the heuristic to compute the score
+//			score = heuristic.getScore(evaluatedTree);
+//			queryTreeScore.setScore(score);
+//			queryTreeScore.setAccuracy(score);
+//			
+//			EvaluatedDescription evaluatedDescription = new EvaluatedDescription(d, queryTreeScore);
+//			
+//			evaluatedDescriptions.add(evaluatedDescription);
 		}
-		Description unionDescription = new Union(disjuncts);
 		
-		Set<Individual> posNotCovered = Sets.difference(lp.getPositiveExamples(), posCovered);
-		Set<Individual> negNotCovered = Sets.difference(lp.getNegativeExamples(), negCovered);
-		
-		//compute the coverage
-		double recall = posCovered.size() / (double)lp.getPositiveExamples().size();
-		double precision = (posCovered.size() + negCovered.size() == 0) 
-						? 0 
-						: posCovered.size() / (double)(posCovered.size() + negCovered.size());
-		
-		double coverageScore = Heuristics.getFScore(recall, precision, beta);
-		
-//		ScoreTwoValued score = new ScoreTwoValued(posCovered, posNotCovered, negCovered, negNotCovered);
-//		score.setAccuracy(coverageScore);
-		QueryTreeScore score = new QueryTreeScore(coverageScore, coverageScore, posCovered, posNotCovered, negCovered, negNotCovered, -1, -1);
-		
-		return new EvaluatedDescription(unionDescription, score);
+		return evaluatedDescriptions;
 	}
 	
+	private EvaluatedDescription buildCombinedSolution(){
+		EvaluatedDescription bestCombinedSolution = null;
+		double bestScore = Double.NEGATIVE_INFINITY;
+		LiteralNodeConversionStrategy[] strategies = LiteralNodeConversionStrategy.values();
+		strategies = new LiteralNodeConversionStrategy[]{LiteralNodeConversionStrategy.SOME_VALUES_FROM};
+		for (LiteralNodeConversionStrategy strategy : strategies) {
+			EvaluatedDescription combinedSolution;
+			if(partialSolutions.size() == 1){
+				combinedSolution = partialSolutions.get(0).asEvaluatedDescription(strategy);
+			} else {
+				List<Description> disjuncts = new ArrayList<Description>();
+				
+				Set<Individual> posCovered = new HashSet<Individual>();
+				Set<Individual> negCovered = new HashSet<Individual>();
+				
+				//build the union of all class expressions
+				Description partialDescription;
+				for (EvaluatedQueryTree<String> partialSolution : partialSolutions) {
+					partialDescription = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
+							partialSolution.getTree().asOWLClassExpression(strategy));
+					disjuncts.add(partialDescription);
+					posCovered.addAll(partialSolution.getTreeScore().getCoveredPositives());
+					negCovered.addAll(partialSolution.getTreeScore().getCoveredNegatives());
+				}
+				Description unionDescription = new Union(disjuncts);
+				
+				Set<Individual> posNotCovered = Sets.difference(lp.getPositiveExamples(), posCovered);
+				Set<Individual> negNotCovered = Sets.difference(lp.getNegativeExamples(), negCovered);
+				
+				//compute the coverage
+				double recall = posCovered.size() / (double)lp.getPositiveExamples().size();
+				double precision = (posCovered.size() + negCovered.size() == 0) 
+								? 0 
+								: posCovered.size() / (double)(posCovered.size() + negCovered.size());
+				
+				double coverageScore = Heuristics.getFScore(recall, precision, beta);
+				
+//				ScoreTwoValued score = new ScoreTwoValued(posCovered, posNotCovered, negCovered, negNotCovered);
+//				score.setAccuracy(coverageScore);
+				QueryTreeScore score = new QueryTreeScore(coverageScore, coverageScore, posCovered, posNotCovered, negCovered, negNotCovered, -1, -1);
+				
+				combinedSolution = new EvaluatedDescription(unionDescription, score);
+			}
+			if(combinedSolution.getAccuracy() > bestScore){
+				bestCombinedSolution = combinedSolution;
+				bestCurrentScore = combinedSolution.getAccuracy();
+			}
+		}
+		return bestCombinedSolution;
+	}
+	
 	private void reset(){
 		currentBestSolution = null;
 		partialSolutions = new ArrayList<EvaluatedQueryTree<String>>();
@@ -524,7 +671,20 @@
 		return treeCache;
 	}
 
+	private Set<Individual> asIndividuals(Collection<QueryTree<String>> trees){
+		Set<Individual> individuals = new HashSet<Individual>(trees.size());
+		for (QueryTree<String> queryTree : trees) {
+			individuals.add(tree2Individual.get(queryTree));
+		}
+		return individuals;
+	}
 	
+	private void asTree(Description d){
+		QueryTree<String> tree = new QueryTreeImpl<String>("");
+		for (Description child : d.getChildren()) {
+			
+		}
+	}
 
 	/**
 	 * Return all trees from the given list {@code allTrees} which are not already subsumed by {@code tree}.
@@ -587,7 +747,7 @@
 			}
 		}
 		for (QueryTree<String> queryTree : distinctTrees) {//System.out.println(queryTree.getStringRepresentation());
-			EvaluatedQueryTree<String> evaluatedQueryTree = evaluate(queryTree, false);
+			EvaluatedQueryTree<String> evaluatedQueryTree = evaluateSimple(queryTree, false);
 			todoList.add(evaluatedQueryTree);
 		}
 	}
@@ -656,6 +816,18 @@
 	}
 	
 	/**
+	 * Shows the current setup of the algorithm.
+	 */
+	private void showSetup(){
+		String setup = "Setup:";
+		setup += "\n#Pos. examples:" + currentPosExamples.size();
+		setup += "\n#Neg. examples:" + currentNegExamples.size();
+		setup += "\nHeuristic:" + heuristic.getHeuristicType().name();
+		setup += "\nbeta=" + beta;
+		logger.info(setup);
+	}
+	
+	/**
 	 * @param noisePercentage the noisePercentage to set
 	 */
 	public void setNoisePercentage(double noisePercentage) {
@@ -684,6 +856,20 @@
 		this.maxTreeComputationTimeInSeconds = maxTreeComputationTimeInSeconds;
 	}
 	
+	/**
+	 * @return the heuristic
+	 */
+	public QueryTreeHeuristic getHeuristic() {
+		return heuristic;
+	}
+	
+	/**
+	 * @param heuristic the heuristic to set
+	 */
+	public void setHeuristic(QueryTreeHeuristic heuristic) {
+		this.heuristic = heuristic;
+	}
+	
 	/* (non-Javadoc)
 	 * @see java.lang.Object#clone()
 	 */

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -106,15 +106,19 @@
 		double mas = 0d;
 		switch (heuristicType) {
 		case FMEASURE:
+			mas = Double.POSITIVE_INFINITY;
 			break;
 		case PRED_ACC:
 			mas = (posExamplesWeight * tp + tn - fp) / (posExamplesWeight * (tp + fn) + tn + fp);
 			break;
 		case ENTROPY:
+			mas = Double.POSITIVE_INFINITY;
 			break;
 		case MATTHEWS_CORRELATION:
+			mas = Double.POSITIVE_INFINITY;
 			break;
 		case YOUDEN_INDEX:
+			mas = Double.POSITIVE_INFINITY;
 			break;
 		default:
 			break;

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -87,6 +87,8 @@
     
     void addChild(QueryTreeImpl<N> child, Object edge);
     
+    void addChild(QueryTree<N> child, Object edge);
+    
     void addChild(QueryTreeImpl<N> child, Object edge, int position);
     
     int removeChild(QueryTreeImpl<N> child);
@@ -150,6 +152,8 @@
     RDFDatatype getDatatype();
     
     Set<Literal> getLiterals();
+    
+    void setParent(QueryTree<N> parent);
 
 	/**
 	 * @param edge

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -53,6 +53,9 @@
 import org.jgrapht.ext.GraphMLExporter;
 import org.jgrapht.ext.VertexNameProvider;
 import org.jgrapht.graph.DefaultDirectedGraph;
+import org.json.JSONArray;
+import org.json.JSONException;
+import org.json.JSONObject;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLClassExpression;
 import org.semanticweb.owlapi.model.OWLDataFactory;
@@ -101,6 +104,8 @@
 	public enum LiteralNodeSubsumptionStrategy {
 		DATATYPE,
 		INTERVAL,
+		MIN,
+		MAX,
 		ENUMERATION,
 		OFF
 	}
@@ -117,7 +122,11 @@
 		/**
 		 * Literals as datatype, e.g. xsd:integer
 		 */
-		SOME_VALUES_FROM
+		SOME_VALUES_FROM,
+		
+		MIN,
+		
+		MAX,
 	}
 	
 	private N userObject;
@@ -169,7 +178,12 @@
     }
     
     public QueryTreeImpl(N userObject, NodeType nodeType) {
+        this(userObject, nodeType, 0);
+    }
+    
+    public QueryTreeImpl(N userObject, NodeType nodeType, int id) {
         this.userObject = userObject;
+        this.id = id;
         children = new ArrayList<QueryTreeImpl<N>>();
         child2EdgeMap = new HashMap<QueryTree<N>, Object>();
         edge2ChildrenMap = new HashMap<String, List<QueryTree<N>>>();
@@ -305,13 +319,33 @@
         this.parent = parent;
         this.parent.children.add(this);
     }
+    
+    /* (non-Javadoc)
+	 * @see org.dllearner.algorithms.qtl.datastructures.QueryTree#setParent(org.dllearner.algorithms.qtl.datastructures.QueryTree)
+	 */
+	@Override
+	public void setParent(QueryTree<N> parent) {
+		setParent((QueryTreeImpl<N>)parent);
+	}
 
-
     public void addChild(QueryTreeImpl<N> child) {
         children.add(child);
         child.parent = this;
     }
     
+    public void addChild(QueryTree<N> child) {
+        children.add((QueryTreeImpl<N>) child);
+        child.setParent(this);
+    }
+    
+    /* (non-Javadoc)
+	 * @see org.dllearner.algorithms.qtl.datastructures.QueryTree#addChild(org.dllearner.algorithms.qtl.datastructures.QueryTree, java.lang.Object)
+	 */
+	@Override
+	public void addChild(QueryTree<N> child, Object edge) {
+		addChild((QueryTreeImpl<N>)child, edge);
+	}
+    
     @Override
     public void addChild(QueryTreeImpl<N> child, int position) {
     	children.add(position, child);
@@ -516,10 +550,13 @@
     
     private boolean subsumes(Set<Literal> subsumer, Set<Literal> subsumee, LiteralNodeSubsumptionStrategy strategy){
     	if(strategy == LiteralNodeSubsumptionStrategy.DATATYPE){
-			
+    		//check if both datatypes are the same
+			RDFDatatype subsumerDatatype = getDatatype(subsumer);
+			RDFDatatype subsumeeDatatype = getDatatype(subsumee);
+			return subsumerDatatype.equals(subsumeeDatatype);
 		} else if(strategy == LiteralNodeSubsumptionStrategy.ENUMERATION){
 			return subsumer.containsAll(subsumee);
-		} else if(strategy == LiteralNodeSubsumptionStrategy.INTERVAL){
+		} else { 
 			//check if both datatypes are the same
 			RDFDatatype subsumerDatatype = getDatatype(subsumer);
 			RDFDatatype subsumeeDatatype = getDatatype(subsumee);
@@ -532,19 +569,35 @@
 				return true;
 			}
 			
-			//check if subsumee interval is contained in subsumer interval
-			Literal subsumerMin = getMin(subsumer);
-			Literal subsumerMax = getMax(subsumer);
+			if(strategy == LiteralNodeSubsumptionStrategy.INTERVAL){
+				//check if subsumee interval is contained in subsumer interval
+				Literal subsumerMin = getMin(subsumer);
+				Literal subsumerMax = getMax(subsumer);
+				
+				Literal subsumeeMin = getMin(subsumee);
+				Literal subsumeeMax = getMax(subsumee);
+				
+				boolean leftMoreGeneral = isLessOrEqual(subsumerMin, subsumeeMin);
+				boolean rightMoreGeneral = isGreaterOrEqual(subsumerMax, subsumeeMax);
+				
+				if(!(leftMoreGeneral && rightMoreGeneral)){
+	//				System.out.println("[" + subsumeeMin + "," + subsumeeMax + "] not in interval " + "[" + subsumerMin + "," + subsumerMax + "]");
+					return false;
+				}
+			} else if(strategy == LiteralNodeSubsumptionStrategy.MIN){
 			
-			Literal subsumeeMin = getMin(subsumee);
-			Literal subsumeeMax = getMax(subsumee);
+				//check if subsumee min is greater than subsumer min
+				Literal subsumerMin = getMin(subsumer);
+				Literal subsumeeMin = getMin(subsumee);
+				
+				return isGreaterOrEqual(subsumeeMin, subsumerMin);
+			} else if(strategy == LiteralNodeSubsumptionStrategy.MAX){
 			
-			boolean leftMoreGeneral = isLessOrEqual(subsumerMin, subsumeeMin);
-			boolean rightMoreGeneral = isGreaterOrEqual(subsumerMax, subsumeeMax);
-			
-			if(!(leftMoreGeneral && rightMoreGeneral)){
-//				System.out.println("[" + subsumeeMin + "," + subsumeeMax + "] not in interval " + "[" + subsumerMin + "," + subsumerMax + "]");
-				return false;
+				//check if subsumee min is greater than subsumer min
+				Literal subsumerMax = getMax(subsumer);
+				Literal subsumeeMax = getMax(subsumee);
+				
+				return isGreaterOrEqual(subsumerMax, subsumeeMax);
 			}
 		}
     	return true;
@@ -1417,6 +1470,10 @@
     							dataRange = asDataOneOf(df, literals);
     						} else if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.FACET_RESTRICTION){
     							dataRange = asFacet(df, literals);
+    						} else if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.MIN){
+    							dataRange = asMinFacet(df, literals);
+    						} else if(literalNodeConversionStrategy == LiteralNodeConversionStrategy.MAX){
+    							dataRange = asMaxFacet(df, literals);
     						}
     					}
             			classExpressions.add(df.getOWLDataSomeValuesFrom(p, dataRange));
@@ -1462,6 +1519,30 @@
     	return df.getOWLDatatypeRestriction(getOWLDatatype(df, literals), minRestriction, maxRestriction);
     }
     
+    private OWLDataRange asMinFacet(OWLDataFactory df, Set<Literal> literals){
+    	//return Boolean datatype because it doesn't make sense to return a facet of Boolean values
+    	if(getOWLDatatype(df, literals).equals(df.getBooleanOWLDatatype())){
+    		return df.getBooleanOWLDatatype();
+    	}
+    	Literal min = getMin(literals);
+    	
+    	OWLFacetRestriction minRestriction = df.getOWLFacetRestriction(OWLFacet.MIN_INCLUSIVE, asOWLLiteral(df, min));
+    	
+    	return df.getOWLDatatypeRestriction(getOWLDatatype(df, literals), minRestriction);
+    }
+    
+    private OWLDataRange asMaxFacet(OWLDataFactory df, Set<Literal> literals){
+    	//return Boolean datatype because it doesn't make sense to return a facet of Boolean values
+    	if(getOWLDatatype(df, literals).equals(df.getBooleanOWLDatatype())){
+    		return df.getBooleanOWLDatatype();
+    	}
+    	Literal max = getMax(literals);
+    	
+    	OWLFacetRestriction maxRestriction = df.getOWLFacetRestriction(OWLFacet.MAX_INCLUSIVE, asOWLLiteral(df, max));
+    	
+    	return df.getOWLDatatypeRestriction(getOWLDatatype(df, literals), maxRestriction);
+    }
+    
     private OWLDataRange asDataOneOf(OWLDataFactory df, Set<Literal> literals){
     	//return Boolean datatype because it doesn't make sense to return a enumeration of Boolean values
     	if(getOWLDatatype(df, literals).equals(df.getBooleanOWLDatatype())){
@@ -1506,6 +1587,45 @@
 		}
     }
     
+    public String asJSON(){
+    	
+    	PrefixCCMap prefixes = PrefixCCMap.getInstance();
+    	JSONObject json = null;
+		try {
+			json = buildJSON(this, prefixes);
+			JSONArray array = new JSONArray();
+			buildJSON2(array, this, prefixes);
+			System.out.println(array);
+		} catch (JSONException e) {
+			e.printStackTrace();
+		}
+		
+		
+    	return json.toString();
+    }
+    
+    private JSONObject buildJSON(QueryTree<N> tree, PrefixCCMap prefixes) throws JSONException{
+    	JSONObject json = new JSONObject();
+    	json.put("name", prefixed(prefixes, tree.getUserObject().toString()));
+    	JSONArray children = new JSONArray();
+    	for (QueryTree<N> child : tree.getChildren()) {
+			children.put(buildJSON(child, prefixes));
+		}
+    	json.put("children", children);
+    	return json;
+    }
+    
+    private void buildJSON2(JSONArray array, QueryTree<N> tree, PrefixCCMap prefixes) throws JSONException{
+    	for (QueryTree<N> child : tree.getChildren()) {
+    		JSONObject json = new JSONObject();
+    		json.put("source", tree.getId());
+    		json.put("target", child.getId());
+    		json.put("type", prefixed(prefixes, tree.getEdge(child).toString()));
+    		array.put(json);
+    		buildJSON2(array, child, prefixes);
+		}
+    }
+    
     private String prefixed(Map<String, String> prefixes, String uri){
     	if(uri.startsWith("http://")){
     		for (Entry<String, String> entry : prefixes.entrySet()) {
@@ -1561,5 +1681,9 @@
 			e.printStackTrace();
 		}
 	}
+
 	
+
+	
+	
 }

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -8,6 +8,9 @@
 import org.dllearner.learningproblems.QueryTreeScore;
 import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
 
+import com.google.common.collect.ComparisonChain;
+import com.google.common.collect.Ordering;
+
 public class EvaluatedQueryTree<N> implements Comparable<EvaluatedQueryTree<N>>{
 	
 	private QueryTree<N> tree;
@@ -57,14 +60,17 @@
 
 	@Override
 	public int compareTo(EvaluatedQueryTree<N> other) {
-		double diff = getScore() - other.getScore();
-		if(diff == 0){
-			return -1;
-		} else if(diff > 0){
-			return -1;
-		} else {
-			return 1;
-		}
+		return ComparisonChain.start()
+		         .compare(this.getScore(), other.getScore())
+		         .result();
+//		double diff = getScore() - other.getScore();
+//		if(diff == 0){
+//			return -1;
+//		} else if(diff > 0){
+//			return -1;
+//		} else {
+//			return 1;
+//		}
 	}
 	
 	public EvaluatedDescription asEvaluatedDescription(){
@@ -72,6 +78,11 @@
 				getTree().asOWLClassExpression(LiteralNodeConversionStrategy.FACET_RESTRICTION)), score);
 	}
 	
+	public EvaluatedDescription asEvaluatedDescription(LiteralNodeConversionStrategy strategy){
+		return new EvaluatedDescription(DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
+				getTree().asOWLClassExpression(strategy)), score);
+	}
+	
 	/* (non-Javadoc)
 	 * @see java.lang.Object#toString()
 	 */

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -4,16 +4,65 @@
 package org.dllearner.algorithms.qtl.util;
 
 import java.util.Collection;
+import java.util.Stack;
 
 import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.NodeType;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLClassExpressionVisitor;
+import org.semanticweb.owlapi.model.OWLDataAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLDataComplementOf;
+import org.semanticweb.owlapi.model.OWLDataExactCardinality;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataHasValue;
+import org.semanticweb.owlapi.model.OWLDataIntersectionOf;
+import org.semanticweb.owlapi.model.OWLDataMaxCardinality;
+import org.semanticweb.owlapi.model.OWLDataMinCardinality;
+import org.semanticweb.owlapi.model.OWLDataOneOf;
+import org.semanticweb.owlapi.model.OWLDataRangeVisitor;
+import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLDataUnionOf;
+import org.semanticweb.owlapi.model.OWLDatatype;
+import org.semanticweb.owlapi.model.OWLDatatypeRestriction;
+import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectComplementOf;
+import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
+import org.semanticweb.owlapi.model.OWLObjectHasSelf;
+import org.semanticweb.owlapi.model.OWLObjectHasValue;
+import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
+import org.semanticweb.owlapi.model.OWLObjectMaxCardinality;
+import org.semanticweb.owlapi.model.OWLObjectMinCardinality;
+import org.semanticweb.owlapi.model.OWLObjectOneOf;
+import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectUnionOf;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.PrefixManager;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.semanticweb.owlapi.util.DefaultPrefixManager;
 
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.hp.hpl.jena.vocabulary.RDF;
+
 /**
  * Converts query trees into OWL class expressions and vice versa.
  * @author Lorenz Buehmann
  *
  */
-public class QueryTreeConverter {
+public class QueryTreeConverter implements OWLClassExpressionVisitor, OWLDataRangeVisitor{
 	
+	Stack<QueryTree<String>> stack = new Stack<QueryTree<String>>();
+	int id = 0;
+	
 	/**
 	 * Returns a OWL class expression of the union of the given query trees.
 	 * @param queryTrees
@@ -23,5 +72,246 @@
 		//check for common paths
 		
 	}
+	
+	public QueryTree<String> asQueryTree(OWLClassExpression expression){
+//		stack.push(new QueryTreeImpl<String>("?"));
+		reset();
+		expression.accept(this);
+		return stack.pop();
+	}
+	
+	private void reset(){
+		id = 0;
+		stack.clear();
+	}
 
+	private void fireUnsupportedFeatureException(OWLClassExpression expression) {
+		throw new IllegalArgumentException("Conversion of " + expression.getClass().getSimpleName() + " is not supported.");
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLClass)
+	 */
+	@Override
+	public void visit(OWLClass cls) {
+		stack.peek().addChild(new QueryTreeImpl<String>(cls.toStringID(), NodeType.RESOURCE, id++), RDF.type.getURI());
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectIntersectionOf)
+	 */
+	@Override
+	public void visit(OWLObjectIntersectionOf expr) {
+		boolean root = stack.isEmpty();
+		stack.push(new QueryTreeImpl<String>("?", NodeType.VARIABLE, id++));
+		for (OWLClassExpression op : expr.getOperandsAsList()) {
+			op.accept(this);
+		}
+//		if(!root)
+//			stack.pop();
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectUnionOf)
+	 */
+	@Override
+	public void visit(OWLObjectUnionOf expr) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectComplementOf)
+	 */
+	@Override
+	public void visit(OWLObjectComplementOf expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom)
+	 */
+	@Override
+	public void visit(OWLObjectSomeValuesFrom expr) {
+		QueryTree<String> parent = stack.peek();
+		QueryTree<String> child;
+		OWLClassExpression filler = expr.getFiller();
+		if(filler.isAnonymous()){
+			if(!(filler instanceof OWLObjectIntersectionOf)){
+				stack.push(new QueryTreeImpl<String>("?", NodeType.VARIABLE, id++));
+			}
+			expr.getFiller().accept(this);
+			child = stack.pop();
+		} else {
+			child = new QueryTreeImpl<String>(filler.asOWLClass().toStringID(), NodeType.RESOURCE, id++);
+		}
+		parent.addChild(child, expr.getProperty().asOWLObjectProperty().toStringID());
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectAllValuesFrom)
+	 */
+	@Override
+	public void visit(OWLObjectAllValuesFrom expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectHasValue)
+	 */
+	@Override
+	public void visit(OWLObjectHasValue expr) {
+		QueryTree<String> tree = stack.peek();
+		tree.addChild(new QueryTreeImpl<String>(expr.getValue().asOWLNamedIndividual().toStringID(), NodeType.RESOURCE, id++), expr.getProperty().asOWLObjectProperty().toStringID());
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectMinCardinality)
+	 */
+	@Override
+	public void visit(OWLObjectMinCardinality expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectExactCardinality)
+	 */
+	@Override
+	public void visit(OWLObjectExactCardinality expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectMaxCardinality)
+	 */
+	@Override
+	public void visit(OWLObjectMaxCardinality expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectHasSelf)
+	 */
+	@Override
+	public void visit(OWLObjectHasSelf expr) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLObjectOneOf)
+	 */
+	@Override
+	public void visit(OWLObjectOneOf expr) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataSomeValuesFrom)
+	 */
+	@Override
+	public void visit(OWLDataSomeValuesFrom expr) {
+		QueryTree<String> tree = stack.peek();
+		expr.getFiller().accept(this);
+		QueryTree<String> child = stack.pop();
+		tree.addChild(child, expr.getProperty().asOWLDataProperty().toStringID());
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataAllValuesFrom)
+	 */
+	@Override
+	public void visit(OWLDataAllValuesFrom expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataHasValue)
+	 */
+	@Override
+	public void visit(OWLDataHasValue expr) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataMinCardinality)
+	 */
+	@Override
+	public void visit(OWLDataMinCardinality expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataExactCardinality)
+	 */
+	@Override
+	public void visit(OWLDataExactCardinality expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb.owlapi.model.OWLDataMaxCardinality)
+	 */
+	@Override
+	public void visit(OWLDataMaxCardinality expr) {
+		fireUnsupportedFeatureException(expr);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitor#visit(org.semanticweb.owlapi.model.OWLDatatype)
+	 */
+	@Override
+	public void visit(OWLDatatype arg0) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitor#visit(org.semanticweb.owlapi.model.OWLDataOneOf)
+	 */
+	@Override
+	public void visit(OWLDataOneOf arg0) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitor#visit(org.semanticweb.owlapi.model.OWLDataComplementOf)
+	 */
+	@Override
+	public void visit(OWLDataComplementOf arg0) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitor#visit(org.semanticweb.owlapi.model.OWLDataIntersectionOf)
+	 */
+	@Override
+	public void visit(OWLDataIntersectionOf arg0) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitor#visit(org.semanticweb.owlapi.model.OWLDataUnionOf)
+	 */
+	@Override
+	public void visit(OWLDataUnionOf arg0) {
+	}
+
+	/* (non-Javadoc)
+	 * @see org.semanticweb.owlapi.model.OWLDataRangeVisitor#visit(org.semanticweb.owlapi.model.OWLDatatypeRestriction)
+	 */
+	@Override
+	public void visit(OWLDatatypeRestriction arg0) {
+	}
+	
+	public static void main(String[] args) throws Exception {
+		ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
+		OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+		OWLDataFactory df = man.getOWLDataFactory();
+		PrefixManager pm = new DefaultPrefixManager("http://example.org/");
+		OWLClassExpression ce = df.getOWLObjectIntersectionOf(
+				df.getOWLClass("A", pm),
+				df.getOWLObjectSomeValuesFrom(
+						df.getOWLObjectProperty("p", pm),
+						df.getOWLObjectSomeValuesFrom(
+								df.getOWLObjectProperty("r", pm),
+								df.getOWLObjectIntersectionOf(
+										df.getOWLClass("A", pm),
+										df.getOWLClass("B", pm))))
+				);
+		System.out.println(ce);
+		QueryTreeConverter converter = new QueryTreeConverter();
+		QueryTree<String> tree = converter.asQueryTree(ce);
+		tree.dump();
+	}
+
 }

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMaxValue.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMaxValue.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMaxValue.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -58,11 +58,11 @@
 	 * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
 	 */
 	public String toString(String baseURI, Map<String, String> prefixes) {
-		return " <= " + value;
+		return " double[<= " + value + "]";
 	}
 	
 	public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " <= " + value;
+		return " double[<= " + value + "]";
 	}
 	
 	public void accept(KBElementVisitor visitor) {
@@ -74,7 +74,7 @@
 	 */
 	@Override
 	public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " <= " + value;
+		return " double[<= " + value + "]";
 	}
 
 	/* (non-Javadoc)

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinValue.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinValue.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinValue.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -58,11 +58,11 @@
 	 * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
 	 */
 	public String toString(String baseURI, Map<String, String> prefixes) {
-		return " >= " + value;
+		return " double[>= " + value + "]";
 	}	
 	
 	public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " >= " + value;
+		return " double[>= " + value + "]";
 	}	
 	
 	public void accept(KBElementVisitor visitor) {
@@ -74,7 +74,7 @@
 	 */
 	@Override
 	public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " >= " + value;
+		return " double[>= " + value + "]";
 	}
 
 	/* (non-Javadoc)

Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLDataRangeConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLDataRangeConverter.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLDataRangeConverter.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -97,13 +97,16 @@
 				max = OWLAPIConverter.convertConstant(value);
 			}
 		}
-		double minValue = Double.parseDouble(min.getLiteral());
-		double maxValue = Double.parseDouble(max.getLiteral());
+		
 		if(min != null && max != null){
+			double minValue = Double.parseDouble(min.getLiteral());
+			double maxValue = Double.parseDouble(max.getLiteral());
 			dataRange = new DoubleMinMaxRange(minValue, maxValue);
 		} else if(min != null && max == null){
+			double minValue = Double.parseDouble(min.getLiteral());
 			dataRange = new DoubleMinValue(minValue);
 		} else if(max != null && min == null){
+			double maxValue = Double.parseDouble(max.getLiteral());
 			dataRange = new DoubleMaxValue(maxValue);
 		} else {
 			

Modified: trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/LGGTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/LGGTest.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/LGGTest.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -67,7 +67,7 @@
 			tree.dump();
 			System.out.println("-----------------------------");
 			cnt++;
-			System.out.println(((QueryTreeImpl<String>)tree).toQuery());
+//			System.out.println(((QueryTreeImpl<String>)tree).toQuery());
 		}
 		
 		
@@ -76,6 +76,7 @@
 		
 		System.out.println("LGG");
 		lgg.dump();
+		System.out.println(((QueryTreeImpl<String>)lgg).asJSON());
 		
 		QueryTreeImpl<String> tree = factory.getQueryTree("?");
 		QueryTreeImpl<String> subTree1 = new QueryTreeImpl<String>("?");

Added: trunk/dllearner-parent.iml
===================================================================
--- trunk/dllearner-parent.iml	                        (rev 0)
+++ trunk/dllearner-parent.iml	2014-05-22 02:22:16 UTC (rev 4269)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="false">
+    <output url="file://$MODULE_DIR$/target/classes" />
+    <output-test url="file://$MODULE_DIR$/target/test-classes" />
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
+

Modified: trunk/examples/mutagenesis/train1.conf
===================================================================
--- trunk/examples/mutagenesis/train1.conf	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/examples/mutagenesis/train1.conf	2014-05-22 02:22:16 UTC (rev 4269)
@@ -246,10 +246,11 @@
 "kb:f6"
 }
 
-alg.type = "ocel"
+alg.type = "celoe"
 alg.noisePercentage = 30
 alg.writeSearchTree = false
 alg.startClass = "kb:Compound"
+alg.maxExecutionTimeInSeconds = 60
 alg.searchTreeFile = "log/mutagenesis/searchTree.log"
 
 

Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/pom.xml	2014-05-22 02:22:16 UTC (rev 4269)
@@ -195,7 +195,7 @@
 			<dependency>
 				<groupId>org.apache.jena</groupId>
 				<artifactId>jena-core</artifactId>
-				<version>2.7.2</version>
+				 <version>2.11.1</version>
 			</dependency>
 			<!--SwingX is in central -->
 			<dependency>

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -63,12 +63,12 @@
 	
 	
 	private static final Logger logger = Logger.getLogger(EProcurementUseCase.class.getName());
-	static final int maxNrOfPositiveExamples = 100;
-	static final int maxNrOfNegativeExamples = 200;
+	static final int maxNrOfPositiveExamples = 10000;
+	static final int maxNrOfNegativeExamples = 10000;
 	static boolean posOnly = false;
-	static int maxCBDDepth = 2;
+	static int maxCBDDepth = 3;
 	static int maxNrOfResults = 100;
-	static int maxExecutionTimeInSeconds = 200;
+	static int maxExecutionTimeInSeconds = 500;
 	static double noiseInPercentage = 50;
 	static boolean useNegation = false;
 	static boolean useAllConstructor = false;
@@ -117,10 +117,10 @@
 //		schema.read(new URL("http://opendata.cz/pco/public-contracts.ttl").openStream(), null, "TURTLE");
 		model.add(schema);
 		// get positive examples
-		SortedSet<Individual> positiveExamples = getExamples(model, posClass);
+		SortedSet<Individual> positiveExamples = getExamples(model, posClass, maxNrOfPositiveExamples);
 		// get negative examples
 //		SortedSet<Individual> negativeExamples = getNegativeExamples(model, cls, positiveExamples);
-		SortedSet<Individual> negativeExamples = getExamples(model, negClass);
+		SortedSet<Individual> negativeExamples = getExamples(model, negClass, maxNrOfNegativeExamples);
 		//get the lgg of the pos. examples
 //		showLGG(model, positiveExamples);
 		// build a sample of the kb
@@ -205,14 +205,14 @@
 		((QueryTreeImpl<String>) lgg).asGraph();
 	}
 	
-	private static SortedSet<Individual> getExamples(Model model, NamedClass cls){
+	private static SortedSet<Individual> getExamples(Model model, NamedClass cls, int limit){
 		logger.info("Generating examples...");
-		SortedSet<Individual> individuals = new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model)).getIndividuals(cls, 1000);
+		SortedSet<Individual> individuals = new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model)).getIndividuals(cls, limit);
 		List<Individual> individualsList = new ArrayList<>(individuals);
 //		Collections.shuffle(individualsList, new Random(1234));
 		individuals.clear();
 		individuals.addAll(individualsList.subList(0, Math.min(maxNrOfPositiveExamples, individualsList.size())));
-		logger.info("Done. Got " + individuals.size() + ": " + individuals);
+		logger.info("Done. Got " + individuals.size());
 		return individuals;
 	}
 	

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-12 09:53:57 UTC (rev 4268)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-22 02:22:16 UTC (rev 4269)
@@ -8,37 +8,30 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Collections;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Random;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
 
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
+import org.apache.log4j.Layout;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
 import org.dllearner.algorithms.qtl.QTL2Disjunctive;
 import org.dllearner.algorithms.qtl.QueryTreeFactory;
-import org.dllearner.algorithms.qtl.datastructures.QueryTree;
-import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.QueryTreeHeuristic;
 import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
 import org.dllearner.cli.CLI;
 import org.dllearner.cli.CrossValidation;
-import org.dllearner.core.AbstractLearningProblem;
+import org.dllearner.core.AbstractReasonerComponent;
 import org.dllearner.core.ComponentInitException;
 import org.dllearner.core.LearningProblemUnsupportedException;
-import org.dllearner.core.owl.Individual;
-import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.learningproblems.Heuristics.HeuristicType;
 import org.dllearner.learningproblems.PosNegLP;
-import org.dllearner.learningproblems.PosNegLPStandard;
-import org.dllearner.reasoning.FastInstanceChecker;
-import org.dllearner.scripts.NestedCrossValidation;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 
 import com.google.common.collect.Lists;
-import com.google.common.collect.Sets;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 
@@ -48,11 +41,17 @@
  */
 public class QTLEvaluation {
 	
-	int nrOfFolds = 3;
+	int nrOfFolds = 10;
 	private int nrOfPosExamples = 300;
 	private int nrOfNegExamples = 300;
 	
-	CLI cli = new CLI(new File("../test/qtl/carcinogenesis/train.conf"));
+	CLI carcinogenesis = new CLI(new File("../test/qtl/carcinogenesis/train.conf"));
+	CLI mammographic = new CLI(new File("../test/qtl/mammographic/train.conf"));
+	CLI suramin = new CLI(new File("../test/qtl/suramin/train.conf"));
+	CLI heart = new CLI(new File("../test/qtl/heart/train.conf"));
+	CLI breasttissue = new CLI(new File("../test/qtl/breasttissue/train1.conf"));
+	CLI parkinsons = new CLI(new File("../test/qtl/parkinsons/train.conf"));
+	CLI mutagenesis = new CLI(new File("../test/qtl/mutagenesis/train1.conf"));
 	
 	private Model model;
 	private OWLOntology ontology;
@@ -65,7 +64,7 @@
 		queryTreeFactory = new QueryTreeFactoryImpl();
 		queryTreeFactory.setMaxDepth(3);
 		
-		loadDataset();
+//		loadDataset();
 		
 		loadExamples();
 	}
@@ -89,46 +88,100 @@
 	
 	private void loadExamples() throws ComponentInitException, IOException{
 		
-		cli.init();
-		lp = (PosNegLP) cli.getLearningProblem();
+//		cli.init();
+//		lp = (PosNegLP) cli.getLearningProblem();
 		
 		// get examples and shuffle them
-		List<Individual> posExamples = new LinkedList<Individual>(((PosNegLP)lp).getPositiveExamples());
-		Collections.shuffle(posExamples, new Random(1));			
-		List<Individual> negExamples = new LinkedList<Individual>(((PosNegLP)lp).getNegativeExamples());
-		Collections.shuffle(negExamples, new Random(2));
-		posExamples = posExamples.subList(0, Math.min(posExamples.size(), nrOfPosExamples));
-		neg...
 
[truncated message content]

[DL-Learner SVN] SF.net SVN: dl-learner:[4268] trunk/test/qtl

[<lor...@us...>]

Revision: 4268
          http://sourceforge.net/p/dl-learner/code/4268
Author:   lorenz_b
Date:     2014-05-12 09:53:57 +0000 (Mon, 12 May 2014)
Log Message:
-----------
Added QTL example.

Added Paths:
-----------
    trunk/test/qtl/mammographic/
    trunk/test/qtl/mammographic/files/
    trunk/test/qtl/mammographic/files/mammographic_masses.data
    trunk/test/qtl/mammographic/mammographic.owl
    trunk/test/qtl/mammographic/train.conf

Added: trunk/test/qtl/mammographic/files/mammographic_masses.data
===================================================================
--- trunk/test/qtl/mammographic/files/mammographic_masses.data	                        (rev 0)
+++ trunk/test/qtl/mammographic/files/mammographic_masses.data	2014-05-12 09:53:57 UTC (rev 4268)
@@ -0,0 +1,961 @@
+5,67,3,5,3,1
+4,43,1,1,0,1
+5,58,4,5,3,1
+4,28,1,1,3,0
+5,74,1,5,0,1
+4,65,1,0,3,0
+4,70,0,0,3,0
+5,42,1,0,3,0
+5,57,1,5,3,1
+5,60,0,5,1,1
+5,76,1,4,3,1
+3,42,2,1,3,1
+4,64,1,0,3,0
+4,36,3,1,2,0
+4,60,2,1,2,0
+4,54,1,1,3,0
+3,52,3,4,3,0
+4,59,2,1,3,1
+4,54,1,1,3,1
+4,40,1,0,0,0
+0,66,0,0,1,1
+5,56,4,3,1,1
+4,43,1,0,0,0
+5,42,4,4,3,1
+4,59,2,4,3,1
+5,75,4,5,3,1
+2,66,1,1,0,0
+5,63,3,0,3,0
+5,45,4,5,3,1
+5,55,4,4,3,0
+4,46,1,5,2,0
+5,54,4,4,3,1
+5,57,4,4,3,1
+4,39,1,1,2,0
+4,81,1,1,3,0
+4,77,3,0,0,0
+4,60,2,1,3,0
+5,67,3,4,2,1
+4,48,4,5,0,1
+4,55,3,4,2,0
+4,59,2,1,0,0
+4,78,1,1,1,0
+4,50,1,1,3,0
+4,61,2,1,0,0
+5,62,3,5,2,1
+5,44,2,4,0,1
+5,64,4,5,3,1
+4,23,1,1,0,0
+2,42,0,0,4,0
+5,67,4,5,3,1
+4,74,2,1,2,0
+5,80,3,5,3,1
+4,23,1,1,0,0
+4,63,2,1,0,0
+4,53,0,5,3,1
+4,43,3,4,0,0
+4,49,2,1,1,0
+5,51,2,4,0,0
+4,45,2,1,0,0
+5,59,2,0,0,1
+5,52,4,3,3,1
+5,60,4,3,3,1
+4,57,2,5,3,0
+3,57,2,1,0,0
+5,74,4,4,3,1
+4,25,2,1,0,0
+4,49,1,1,3,0
+5,72,4,3,0,1
+4,45,2,1,3,0
+4,64,2,1,3,0
+4,73,2,1,2,0
+5,68,4,3,3,1
+5,52,4,5,3,0
+5,66,4,4,3,1
+5,70,0,4,0,1
+4,25,1,1,3,0
+5,74,1,1,2,1
+4,64,1,1,3,0
+5,60,4,3,2,1
+5,67,2,4,1,0
+4,67,4,5,3,0
+5,44,4,4,2,1
+3,68,1,1,3,1
+4,57,0,4,1,0
+5,51,4,0,0,1
+4,33,1,0,0,0
+5,58,4,4,3,1
+5,36,1,0,0,0
+4,63,1,1,0,0
+5,62,1,5,3,1
+4,73,3,4,3,1
+4,80,4,4,3,1
+4,67,1,1,0,0
+5,59,2,1,3,1
+5,60,1,0,3,0
+5,54,4,4,3,1
+4,40,1,1,0,0
+4,47,2,1,0,0
+5,62,4,4,3,0
+4,33,2,1,3,0
+5,59,2,0,0,0
+4,65,2,0,0,0
+4,58,4,4,0,0
+4,29,2,0,0,0
+4,58,1,1,0,0
+4,54,1,1,0,0
+4,44,1,1,0,1
+3,34,2,1,0,0
+4,57,1,1,3,0
+5,33,4,4,0,1
+4,45,4,4,3,0
+5,71,4,4,3,1
+5,59,4,4,2,0
+4,56,2,1,0,0
+4,40,3,4,0,0
+4,56,1,1,3,0
+4,45,2,1,0,0
+4,57,2,1,2,0
+5,55,3,4,3,1
+5,84,4,5,3,0
+5,51,4,4,3,1
+4,43,1,1,0,0
+4,24,2,1,2,0
+4,66,1,1,3,0
+5,33,4,4,3,0
+4,59,4,3,2,0
+4,76,2,3,0,0
+4,40,1,1,0,0
+4,52,0,4,0,0
+5,40,4,5,3,1
+5,67,4,4,3,1
+5,75,4,3,3,1
+5,86,4,4,3,0
+4,60,2,0,0,0
+5,66,4,4,3,1
+5,46,4,5,3,1
+4,59,4,4,3,1
+5,65,4,4,3,1
+4,53,1,1,3,0
+5,67,3,5,3,1
+5,80,4,5,3,1
+4,55,2,1,3,0
+4,48,1,1,0,0
+4,47,1,1,2,0
+4,50,2,1,0,0
+5,62,4,5,3,1
+5,63,4,4,3,1
+4,63,4,0,3,1
+4,71,4,4,3,1
+4,41,1,1,3,0
+5,57,4,4,4,1
+5,71,4,4,4,1
+4,66,1,1,3,0
+4,47,2,4,2,0
+3,34,4,4,3,0
+4,59,3,4,3,0
+5,55,2,0,0,1
+4,51,0,0,3,0
+4,62,2,1,0,0
+4,58,4,0,3,1
+5,67,4,4,3,1
+4,41,2,1,3,0
+4,23,3,1,3,0
+4,53,0,4,3,0
+4,42,2,1,3,0
+5,87,4,5,3,1
+4,68,1,1,3,1
+4,64,1,1,3,0
+5,54,3,5,3,1
+5,86,4,5,3,1
+4,21,2,1,3,0
+4,39,1,1,0,0
+4,53,4,4,3,0
+4,44,4,4,3,0
+4,54,1,1,3,0
+5,63,4,5,3,1
+4,62,2,1,0,0
+4,45,2,1,2,0
+5,71,4,5,3,0
+5,49,4,4,3,1
+4,49,4,4,3,0
+5,66,4,4,4,0
+4,19,1,1,3,0
+4,35,1,1,2,0
+4,71,3,3,0,1
+5,74,4,5,3,1
+5,37,4,4,3,1
+4,67,1,0,3,0
+5,81,3,4,3,1
+5,59,4,4,3,1
+4,34,1,1,3,0
+5,79,4,3,3,1
+5,60,3,1,3,0
+4,41,1,1,3,1
+4,50,1,1,3,0
+5,85,4,4,3,1
+4,46,1,1,3,0
+5,66,4,4,3,1
+4,73,3,1,2,0
+4,55,1,1,3,0
+4,49,2,1,3,0
+3,49,4,4,3,0
+4,51,4,5,3,1
+2,48,4,4,3,0
+4,58,4,5,3,0
+5,72,4,5,3,1
+4,46,2,3,3,0
+4,43,4,3,3,1
+0,52,4,4,3,0
+4,66,2,1,0,0
+4,46,1,1,1,0
+4,69,3,1,3,0
+2,59,1,1,0,1
+5,43,2,1,3,1
+5,76,4,5,3,1
+4,46,1,1,3,0
+4,59,2,4,3,0
+4,57,1,1,3,0
+5,43,4,5,0,0
+3,45,2,1,3,0
+3,43,2,1,3,0
+4,45,2,1,3,0
+5,57,4,5,3,1
+5,79,4,4,3,1
+5,54,2,1,3,1
+4,40,3,4,3,0
+5,63,4,4,3,1
+2,55,1,0,1,0
+4,52,2,1,3,0
+4,38,1,1,3,0
+3,72,4,3,3,0
+5,80,4,3,3,1
+5,76,4,3,3,1
+4,62,3,1,3,0
+5,64,4,5,3,1
+5,42,4,5,3,0
+3,60,0,3,1,0
+4,64,4,5,3,0
+4,63,4,4,3,1
+4,24,2,1,2,0
+5,72,4,4,3,1
+4,63,2,1,3,0
+4,46,1,1,3,0
+3,33,1,1,3,0
+5,76,4,4,3,1
+4,36,2,3,3,0
+4,40,2,1,3,0
+5,58,1,5,3,1
+4,43,2,1,3,0
+3,42,1,1,3,0
+4,32,1,1,3,0
+5,57,4,4,2,1
+4,37,1,1,3,0
+4,70,4,4,3,1
+5,56,4,2,3,1
+3,76,0,3,2,0
+5,73,4,4,3,1
+5,77,4,5,3,1
+5,67,4,4,1,1
+5,71,4,3,3,1
+5,65,4,4,3,1
+4,43,1,1,3,0
+4,40,2,1,0,0
+4,49,2,1,3,0
+5,76,4,2,3,1
+4,55,4,4,3,0
+5,72,4,5,3,1
+3,53,4,3,3,0
+5,75,4,4,3,1
+5,61,4,5,3,1
+5,67,4,4,3,1
+5,55,4,2,3,1
+5,66,4,4,3,1
+2,76,1,1,2,0
+4,57,4,4,3,1
+5,71,3,1,3,0
+5,70,4,5,3,1
+4,35,4,2,0,0
+5,79,1,0,3,1
+4,63,2,1,3,0
+5,40,1,4,3,1
+4,41,1,1,3,0
+4,47,2,1,2,0
+4,68,1,1,3,1
+4,64,4,3,3,1
+4,65,4,4,0,1
+4,73,4,3,3,0
+4,39,4,3,3,0
+5,55,4,5,4,1
+5,53,3,4,4,0
+5,66,4,4,3,1
+4,43,3,1,2,0
+5,44,4,5,3,1
+4,77,4,4,3,1
+4,62,2,4,3,0
+5,80,4,4,3,1
+4,33,4,4,3,0
+4,50,4,5,3,1
+4,71,1,0,3,0
+5,46,4,4,3,1
+5,49,4,5,3,1
+4,53,1,1,3,0
+3,46,2,1,2,0
+4,57,1,1,3,0
+4,54,3,1,3,0
+4,54,1,0,0,0
+2,49,2,1,2,0
+4,47,3,1,3,0
+4,40,1,1,3,0
+4,45,1,1,3,0
+4,50,4,5,3,1
+5,54,4,4,3,1
+4,67,4,1,3,1
+4,77,4,4,3,1
+4,66,4,3,3,0
+4,71,2,0,3,1
+4,36,2,3,3,0
+4,69,4,4,3,0
+4,48,1,1,3,0
+4,64,4,4,3,1
+4,71,4,2,3,1
+5,60,4,3,3,1
+4,24,1,1,3,0
+5,34,4,5,2,1
+4,79,1,1,2,0
+4,45,1,1,3,0
+4,37,2,1,2,0
+4,42,1,1,2,0
+4,72,4,4,3,1
+5,60,4,5,3,1
+5,85,3,5,3,1
+4,51,1,1,3,0
+5,54,4,5,3,1
+5,55,4,3,3,1
+4,64,4,4,3,0
+5,67,4,5,3,1
+5,75,4,3,3,1
+5,87,4,4,3,1
+4,46,4,4,3,1
+4,59,2,1,0,0
+55,46,4,3,3,1
+5,61,1,1,3,1
+4,44,1,4,3,0
+4,32,1,1,3,0
+4,62,1,1,3,0
+5,59,4,5,3,1
+4,61,4,1,3,0
+5,78,4,4,3,1
+5,42,4,5,3,0
+4,45,1,2,3,0
+5,34,2,1,3,1
+5,39,4,3,0,1
+4,27,3,1,3,0
+4,43,1,1,3,0
+5,83,4,4,3,1
+4,36,2,1,3,0
+4,37,2,1,3,0
+4,56,3,1,3,1
+5,55,4,4,3,1
+5,46,3,0,3,0
+4,88,4,4,3,1
+5,71,4,4,3,1
+4,41,2,1,3,0
+5,49,4,4,3,1
+3,51,1,1,4,0
+4,39,1,3,3,0
+4,46,2,1,3,0
+5,52,4,4,3,1
+5,58,4,4,3,1
+4,67,4,5,3,1
+5,80,4,4,3,1
+3,46,1,0,0,0
+3,43,1,0,0,0
+4,45,1,1,3,0
+5,68,4,4,3,1
+4,54,4,4,0,1
+4,44,2,3,3,0
+5,74,4,3,3,1
+5,55,4,5,3,0
+4,49,4,4,3,1
+4,49,1,1,3,0
+5,50,4,3,3,1
+5,52,3,5,3,1
+4,45,1,1,3,0
+4,66,1,1,3,0
+4,68,4,4,3,1
+4,72,2,1,3,0
+5,64,0,0,3,0
+2,49,0,3,3,0
+3,44,0,4,3,0
+5,74,4,4,3,1
+5,58,4,4,3,1
+4,77,2,3,3,0
+4,49,3,1,3,0
+4,34,0,0,4,0
+5,60,4,3,3,1
+5,69,4,3,3,1
+4,53,2,1,3,0
+3,46,3,4,3,0
+5,74,4,4,3,1
+4,58,1,1,3,0
+5,68,4,4,3,1
+5,46,4,3,3,0
+5,61,2,4,3,1
+5,70,4,3,3,1
+5,37,4,4,3,1
+3,65,4,5,3,1
+4,67,4,4,3,0
+5,69,3,4,3,0
+5,76,4,4,3,1
+4,65,4,3,3,0
+5,72,4,2,3,1
+4,62,4,2,3,0
+5,42,4,4,3,1
+5,66,4,3,3,1
+5,48,4,4,3,1
+4,35,1,1,3,0
+5,60,4,4,3,1
+5,67,4,2,3,1
+5,78,4,4,3,1
+4,66,1,1,3,1
+4,26,1,1,0,0
+4,48,1,1,3,0
+4,31,1,1,3,0
+5,43,4,3,3,1
+5,72,2,4,3,0
+5,66,1,1,3,1
+4,56,4,4,3,0
+5,58,4,5,3,1
+5,33,2,4,3,1
+4,37,1,1,3,0
+5,36,4,3,3,1
+4,39,2,3,3,0
+4,39,4,4,3,1
+5,83,4,4,3,1
+4,68,4,5,3,1
+5,63,3,4,3,1
+5,78,4,4,3,1
+4,38,2,3,3,0
+5,46,4,3,3,1
+5,60,4,4,3,1
+5,56,2,3,3,1
+4,33,1,1,3,0
+4,0,4,5,3,1
+4,69,1,5,3,1
+5,66,1,4,3,1
+4,72,1,3,3,0
+4,29,1,1,3,0
+5,54,4,5,3,1
+5,80,4,4,3,1
+5,68,4,3,3,1
+4,35,2,1,3,0
+4,57,3,0,3,0
+5,0,4,4,3,1
+4,50,1,1,3,0
+4,32,4,3,3,0
+0,69,4,5,3,1
+4,71,4,5,3,1
+5,87,4,5,3,1
+3,40,2,0,3,0
+4,31,1,1,0,0
+4,64,1,1,3,0
+5,55,4,5,3,1
+4,18,1,1,3,0
+3,50,2,1,0,0
+4,53,1,1,3,0
+5,84,4,5,3,1
+5,80,4,3,3,1
+4,32,1,1,3,0
+5,77,3,4,3,1
+4,38,1,1,3,0
+5,54,4,5,3,1
+4,63,1,1,3,0
+4,61,1,1,3,0
+4,52,1,1,3,0
+4,36,1,1,3,0
+4,41,0,0,3,0
+4,59,1,1,3,0
+5,51,4,4,2,1
+4,36,1,1,3,0
+5,40,4,3,3,1
+4,49,1,1,3,0
+4,37,2,3,3,0
+4,46,1,1,3,0
+4,63,1,1,3,0
+4,28,2,1,3,0
+4,47,2,1,3,0
+4,42,2,1,3,1
+5,44,4,5,3,1
+4,49,4,4,3,0
+5,47,4,5,3,1
+5,52,4,5,3,1
+4,53,1,1,3,1
+5,83,3,3,3,1
+4,50,4,4,0,1
+5,63,4,4,3,1
+4,82,0,5,3,1
+4,54,1,1,3,0
+4,50,4,4,3,0
+5,80,4,5,3,1
+5,45,2,4,3,0
+5,59,4,4,0,1
+4,28,2,1,3,0
+4,31,1,1,3,0
+4,41,2,1,3,0
+4,21,3,1,3,0
+5,44,3,4,3,1
+5,49,4,4,3,1
+5,71,4,5,3,1
+5,75,4,5,3,1
+4,38,2,1,3,0
+4,60,1,3,3,0
+5,87,4,5,3,1
+4,70,4,4,3,1
+5,55,4,5,3,1
+3,21,1,1,3,0
+4,50,1,1,3,0
+5,76,4,5,3,1
+4,23,1,1,3,0
+3,68,0,0,3,0
+4,62,4,0,3,1
+5,65,1,0,3,1
+5,73,4,5,3,1
+4,38,2,3,3,0
+2,57,1,1,3,0
+5,65,4,5,3,1
+5,67,2,4,3,1
+5,61,2,4,3,1
+5,56,4,4,3,0
+5,71,2,4,3,1
+4,49,2,2,3,0
+4,55,0,0,3,0
+4,44,2,1,3,0
+0,58,4,4,3,0
+4,27,2,1,3,0
+5,73,4,5,3,1
+4,34,2,1,3,0
+5,63,0,4,3,1
+4,50,2,1,3,1
+4,62,2,1,3,0
+3,21,3,1,3,0
+4,49,2,0,3,0
+4,36,3,1,3,0
+4,45,2,1,3,1
+5,67,4,5,3,1
+4,21,1,1,3,0
+4,57,2,1,3,0
+5,66,4,5,3,1
+4,71,4,4,3,1
+5,69,3,4,3,1
+6,80,4,5,3,1
+3,27,2,1,3,0
+4,38,2,1,3,0
+4,23,2,1,3,0
+5,70,0,5,3,1
+4,46,4,3,3,0
+4,61,2,3,3,0
+5,65,4,5,3,1
+4,60,4,3,3,0
+5,83,4,5,3,1
+5,40,4,4,3,1
+2,59,0,4,3,0
+4,53,3,4,3,0
+4,76,4,4,3,0
+5,79,1,4,3,1
+5,38,2,4,3,1
+4,61,3,4,3,0
+4,56,2,1,3,0
+4,44,2,1,3,0
+4,64,3,4,0,1
+4,66,3,3,3,0
+4,50,3,3,3,0
+4,46,1,1,3,0
+4,39,1,1,3,0
+4,60,3,0,0,0
+5,55,4,5,3,1
+4,40,2,1,3,0
+4,26,1,1,3,0
+5,84,3,2,3,1
+4,41,2,2,3,0
+4,63,1,1,3,0
+2,65,0,1,2,0
+4,49,1,1,3,0
+4,56,2,2,3,1
+5,65,4,4,3,0
+4,54,1,1,3,0
+4,36,1,1,3,0
+5,49,4,4,3,0
+4,59,4,4,3,1
+5,75,4,4,3,1
+5,59,4,2,3,0
+5,59,4,4,3,1
+4,28,4,4,3,1
+5,53,4,5,3,0
+5,57,4,4,3,0
+5,77,4,3,4,0
+5,85,4,3,3,1
+4,59,4,4,3,0
+5,59,1,5,3,1
+4,65,3,3,3,1
+4,54,2,1,3,0
+5,46,4,5,3,1
+4,63,4,4,3,1
+4,53,1,1,3,1
+4,56,1,1,3,0
+5,66,4,4,3,1
+5,66,4,5,3,1
+4,55,1,1,3,0
+4,44,1,1,3,0
+5,86,3,4,3,1
+5,47,4,5,3,1
+5,59,4,5,3,1
+5,66,4,5,3,0
+5,61,4,3,3,1
+3,46,0,5,0,1
+4,69,1,1,3,0
+5,93,1,5,3,1
+4,39,1,3,3,0
+5,44,4,5,3,1
+4,45,2,2,3,0
+4,51,3,4,3,0
+4,56,2,4,3,0
+4,66,4,4,3,0
+5,61,4,5,3,1
+4,64,3,3,3,1
+5,57,2,4,3,0
+5,79,4,4,3,1
+4,57,2,1,0,0
+4,44,4,1,1,0
+4,31,2,1,3,0
+4,63,4,4,3,0
+4,64,1,1,3,0
+5,47,4,5,3,0
+5,68,4,5,3,1
+4,30,1,1,3,0
+5,43,4,5,3,1
+4,56,1,1,3,0
+4,46,2,1,3,0
+4,67,2,1,3,0
+5,52,4,5,3,1
+4,67,4,4,3,1
+4,47,2,1,3,0
+5,58,4,5,3,1
+4,28,2,1,3,0
+4,43,1,1,3,0
+4,57,2,4,3,0
+5,68,4,5,3,1
+4,64,2,4,3,0
+4,64,2,4,3,0
+5,62,4,4,3,1
+4,38,4,1,3,0
+5,68,4,4,3,1
+4,41,2,1,3,0
+4,35,2,1,3,1
+4,68,2,1,3,0
+5,55,4,4,3,1
+5,67,4,4,3,1
+4,51,4,3,3,0
+2,40,1,1,3,0
+5,73,4,4,3,1
+4,58,0,4,3,1
+4,51,0,4,3,0
+3,50,0,0,3,1
+5,59,4,3,3,1
+6,60,3,5,3,1
+4,27,2,1,0,0
+5,54,4,3,3,0
+4,56,1,1,3,0
+5,53,4,5,3,1
+4,54,2,4,3,0
+5,79,1,4,3,1
+5,67,4,3,3,1
+5,64,3,3,3,1
+4,70,1,2,3,1
+5,55,4,3,3,1
+5,65,3,3,3,1
+5,45,4,2,3,1
+4,57,4,4,0,1
+5,49,1,1,3,1
+4,24,2,1,3,0
+4,52,1,1,3,0
+4,50,2,1,3,0
+4,35,1,1,3,0
+5,0,3,3,3,1
+5,64,4,3,3,1
+5,40,4,1,1,1
+5,66,4,4,3,1
+4,64,4,4,3,1
+5,52,4,3,3,1
+5,43,1,4,3,1
+4,56,4,4,3,0
+4,72,3,0,3,0
+6,51,4,4,3,1
+4,79,4,4,3,1
+4,22,2,1,3,0
+4,73,2,1,3,0
+4,53,3,4,3,0
+4,59,2,1,3,1
+4,46,4,4,2,0
+5,66,4,4,3,1
+4,50,4,3,3,1
+4,58,1,1,3,1
+4,55,1,1,3,0
+4,62,2,4,3,1
+4,60,1,1,3,0
+5,57,4,3,3,1
+4,57,1,1,3,0
+6,41,2,1,3,0
+4,71,2,1,3,1
+4,32,2,1,3,0
+4,57,2,1,3,0
+4,19,1,1,3,0
+4,62,2,4,3,1
+5,67,4,5,3,1
+4,50,4,5,3,0
+4,65,2,3,2,0
+4,40,2,4,2,0
+6,71,4,4,3,1
+6,68,4,3,3,1
+4,68,1,1,3,0
+4,29,1,1,3,0
+4,53,2,1,3,0
+5,66,4,4,3,1
+4,60,3,0,4,0
+5,76,4,4,3,1
+4,58,2,1,2,0
+5,96,3,4,3,1
+5,70,4,4,3,1
+4,34,2,1,3,0
+4,59,2,1,3,0
+4,45,3,1,3,1
+5,65,4,4,3,1
+4,59,1,1,3,0
+4,21,2,1,3,0
+3,43,2,1,3,0
+4,53,1,1,3,0
+4,65,2,1,3,0
+4,64,2,4,3,1
+4,53,4,4,3,0
+4,51,1,1,3,0
+4,59,2,4,3,0
+4,56,2,1,3,0
+4,60,2,1,3,0
+4,22,1,1,3,0
+4,25,2,1,3,0
+6,76,3,0,3,0
+5,69,4,4,3,1
+4,58,2,1,3,0
+5,62,4,3,3,1
+4,56,4,4,3,0
+4,64,1,1,3,0
+4,32,2,1,3,0
+5,48,0,4,0,1
+5,59,4,4,2,1
+4,52,1,1,3,0
+4,63,4,4,3,0
+5,67,4,4,3,1
+5,61,4,4,3,1
+5,59,4,5,3,1
+5,52,4,3,3,1
+4,35,4,4,3,0
+5,77,3,3,3,1
+5,71,4,3,3,1
+5,63,4,3,3,1
+4,38,2,1,2,0
+5,72,4,3,3,1
+4,76,4,3,3,1
+4,53,3,3,3,0
+4,67,4,5,3,0
+5,69,2,4,3,1
+4,54,1,1,3,0
+2,35,2,1,2,0
+5,68,4,3,3,1
+4,68,4,4,3,0
+4,67,2,4,3,1
+3,39,1,1,3,0
+4,44,2,1,3,0
+4,33,1,1,3,0
+4,60,0,4,3,0
+4,58,1,1,3,0
+4,31,1,1,3,0
+3,23,1,1,3,0
+5,56,4,5,3,1
+4,69,2,1,3,1
+6,63,1,1,3,0
+4,65,1,1,3,1
+4,44,2,1,2,0
+4,62,3,3,3,1
+4,67,4,4,3,1
+4,56,2,1,3,0
+4,52,3,4,3,0
+4,43,1,1,3,1
+4,41,4,3,2,1
+4,42,3,4,2,0
+3,46,1,1,3,0
+5,55,4,4,3,1
+5,58,4,4,2,1
+5,87,4,4,3,1
+4,66,2,1,3,0
+0,72,4,3,3,1
+5,60,4,3,3,1
+5,83,4,4,2,1
+4,31,2,1,3,0
+4,53,2,1,3,0
+4,64,2,3,3,0
+5,31,4,4,2,1
+5,62,4,4,2,1
+4,56,2,1,3,0
+5,58,4,4,3,1
+4,67,1,4,3,0
+5,75,4,5,3,1
+5,65,3,4,3,1
+5,74,3,2,3,1
+4,59,2,1,3,0
+4,57,4,4,4,1
+4,76,3,2,3,0
+4,63,1,4,3,0
+4,44,1,1,3,0
+4,42,3,1,2,0
+4,35,3,0,2,0
+5,65,4,3,3,1
+4,70,2,1,3,0
+4,48,1,1,3,0
+4,74,1,1,1,1
+6,40,0,3,4,1
+4,63,1,1,3,0
+5,60,4,4,3,1
+5,86,4,3,3,1
+4,27,1,1,3,0
+4,71,4,5,2,1
+5,85,4,4,3,1
+4,51,3,3,3,0
+6,72,4,3,3,1
+5,52,4,4,3,1
+4,66,2,1,3,0
+5,71,4,5,3,1
+4,42,2,1,3,0
+4,64,4,4,2,1
+4,41,2,2,3,0
+4,50,2,1,3,0
+4,30,1,1,3,0
+4,67,1,1,3,0
+5,62,4,4,3,1
+4,46,2,1,2,0
+4,35,1,1,3,0
+4,53,1,1,2,0
+4,59,2,1,3,0
+4,19,3,1,3,0
+5,86,2,1,3,1
+4,72,2,1,3,0
+4,37,2,1,2,0
+4,46,3,1,3,1
+4,45,1,1,3,0
+4,48,4,5,3,0
+4,58,4,4,3,1
+4,42,1,1,3,0
+4,56,2,4,3,1
+4,47,2,1,3,0
+4,49,4,4,3,1
+5,76,2,5,3,1
+5,62,4,5,3,1
+5,64,4,4,3,1
+5,53,4,3,3,1
+4,70,4,2,2,1
+5,55,4,4,3,1
+4,34,4,4,3,0
+5,76,4,4,3,1
+4,39,1,1,3,0
+2,23,1,1,3,0
+4,19,1,1,3,0
+5,65,4,5,3,1
+4,57,2,1,3,0
+5,41,4,4,3,1
+4,36,4,5,3,1
+4,62,3,3,3,0
+4,69,2,1,3,0
+4,41,3,1,3,0
+3,51,2,4,3,0
+5,50,3,2,3,1
+4,47,4,4,3,0
+4,54,4,5,3,1
+5,52,4,4,3,1
+4,30,1,1,3,0
+3,48,4,4,3,1
+5,0,4,4,3,1
+4,65,2,4,3,1
+4,50,1,1,3,0
+5,65,4,5,3,1
+5,66,4,3,3,1
+6,41,3,3,2,1
+5,72,3,2,3,1
+4,42,1,1,1,1
+4,80,4,4,3,1
+0,45,2,4,3,0
+4,41,1,1,3,0
+4,72,3,3,3,1
+4,60,4,5,3,0
+5,67,4,3,3,1
+4,55,2,1,3,0
+4,61,3,4,3,1
+4,55,3,4,3,1
+4,52,4,4,3,1
+4,42,1,1,3,0
+5,63,4,4,3,1
+4,62,4,5,3,1
+4,46,1,1,3,0
+4,65,2,1,3,0
+4,57,3,3,3,1
+4,66,4,5,3,1
+4,45,1,1,3,0
+4,77,4,5,3,1
+4,35,1,1,3,0
+4,50,4,5,3,1
+4,57,4,4,3,0
+4,74,3,1,3,1
+4,59,4,5,3,0
+4,51,1,1,3,0
+4,42,3,4,3,1
+4,35,2,4,3,0
+4,42,1,1,3,0
+4,43,2,1,3,0
+4,62,4,4,3,1
+4,27,2,1,3,0
+5,0,4,3,3,1
+4,57,4,4,3,1
+4,59,2,1,3,0
+5,40,3,2,3,1
+4,20,1,1,3,0
+5,74,4,3,3,1
+4,22,1,1,3,0
+4,57,4,3,3,0
+4,57,4,3,3,1
+4,55,2,1,2,0
+4,62,2,1,3,0
+4,54,1,1,3,0
+4,71,1,1,3,1
+4,65,3,3,3,0
+4,68,4,4,3,0
+4,64,1,1,3,0
+4,54,2,4,3,0
+4,48,4,4,3,1
+4,58,4,3,3,0
+5,58,3,4,3,1
+4,70,1,1,1,0
+5,70,1,4,3,1
+4,59,2,1,3,0
+4,57,2,4,3,0
+4,53,4,5,3,0
+4,54,4,4,3,1
+4,53,2,1,3,0
+0,71,4,4,3,1
+5,67,4,5,3,1
+4,68,4,4,3,1
+4,56,2,4,3,0
+4,35,2,1,3,0
+4,52,4,4,3,1
+4,47,2,1,3,0
+4,56,4,5,3,1
+4,64,4,5,3,0
+5,66,4,5,3,1
+4,62,3,3,3,0
\ No newline at end of file

Added: trunk/test/qtl/mammographic/mammographic.owl
===================================================================
--- trunk/test/qtl/mammographic/mammographic.owl	                        (rev 0)
+++ trunk/test/qtl/mammographic/mammographic.owl	2014-05-12 09:53:57 UTC (rev 4268)
@@ -0,0 +1,12873 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://dl-learner.org/mammographic#"
+     xml:base="http://dl-learner.org/mammographic"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:mammographic="http://dl-learner.org/mammographic#">
+    <owl:Ontology rdf:about="http://dl-learner.org/mammographic"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/mammographic#hasDensity -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/mammographic#hasDensity">
+        <rdfs:range rdf:resource="http://dl-learner.org/mammographic#Density"/>
+        <rdfs:domain rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#hasMargin -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/mammographic#hasMargin">
+        <rdfs:range rdf:resource="http://dl-learner.org/mammographic#Margin"/>
+        <rdfs:domain rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#hasShape -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/mammographic#hasShape">
+        <rdfs:domain rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <rdfs:range rdf:resource="http://dl-learner.org/mammographic#Shape"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Data properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/mammographic#hasAge -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/mammographic#hasAge">
+        <rdfs:domain rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#hasBiRads -->
+
+    <owl:DatatypeProperty rdf:about="http://dl-learner.org/mammographic#hasBiRads">
+        <rdfs:domain rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
+    </owl:DatatypeProperty>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Density -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#Density">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Measure"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Margin -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#Margin">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Measure"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Measure -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#Measure"/>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#Patient"/>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Shape -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#Shape">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Measure"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#circumscribed -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#circumscribed">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Margin"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#fat-containing -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#fat-containing">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Density"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#high -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#high">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Density"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#ill-defined -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#ill-defined">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Margin"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#irregular -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#irregular">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Shape"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#iso -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#iso">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Density"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#lobular -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#lobular">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Shape"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#low -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#low">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Density"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#microlobulated -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#microlobulated">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Margin"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#obscured -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#obscured">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Margin"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#oval -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#oval">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Shape"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#round -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#round">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Shape"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#spiculated -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#spiculated">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Margin"/>
+    </owl:Class>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#unknown -->
+
+    <owl:Class rdf:about="http://dl-learner.org/mammographic#unknown">
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Density"/>
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Margin"/>
+        <rdfs:subClassOf rdf:resource="http://dl-learner.org/mammographic#Shape"/>
+    </owl:Class>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient0">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">67.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#lobular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#spiculated"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient1">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">43.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient10 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient10">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">76.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient100 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient100">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">59.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient101 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient101">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">65.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient102 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient102">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">58.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient103 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient103">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">29.0</hasAge>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient104 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient104">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">58.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient105 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient105">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">54.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient106 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient106">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">44.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient107 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient107">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">3.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">34.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient108 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient108">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">57.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient109 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient109">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">33.0</hasAge>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient11 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient11">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">3.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">42.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient110 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient110">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">45.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient111 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient111">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">71.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient112 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient112">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">59.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#iso"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient113 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient113">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">56.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient114 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient114">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">40.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#lobular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient115 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient115">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">56.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient116 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient116">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">45.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient117 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient117">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">57.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#iso"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient118 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient118">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">55.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#lobular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient119 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient119">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">84.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#spiculated"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient12 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient12">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">64.0</hasAge>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient120 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient120">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">51.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient121 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient121">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">43.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient122 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient122">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">24.0</hasAge>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#iso"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient123 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient123">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">66.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient124 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient124">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">33.0</hasAge>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient125 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient125">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">59.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#iso"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#obscured"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient126 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient126">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">76.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#obscured"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient127 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient127">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">40.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient128 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient128">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">52.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient129 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient129">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">40.0</hasAge>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#spiculated"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient13 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient13">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">36.0</hasAge>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#iso"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#lobular"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient130 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient130">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">67.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient131 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient131">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">75.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#obscured"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient132 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient132">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">86.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient133 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient133">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">60.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient134 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient134">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">66.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient135 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient135">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">46.0</hasAge>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#spiculated"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient136 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient136">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">59.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient137 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient137">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">65.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient138 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient138">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">53.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient139 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient139">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">67.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#lobular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#spiculated"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient14 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient14">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">60.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#iso"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient140 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient140">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">80.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#spiculated"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient141 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient141">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">55.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient142 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient142">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">48.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient143 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient143">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">47.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#iso"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#round"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient144 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient144">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">50.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#circumscribed"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#oval"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient145 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient145">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">62.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#spiculated"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient146 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient146">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">5.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">63.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient147 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient147">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">63.0</hasAge>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#unknown"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient148 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/mammographic#Patient148">
+        <rdf:type rdf:resource="http://dl-learner.org/mammographic#Patient"/>
+        <hasBiRads rdf:datatype="http://www.w3.org/2001/XMLSchema#double">4.0</hasBiRads>
+        <hasAge rdf:datatype="http://www.w3.org/2001/XMLSchema#double">71.0</hasAge>
+        <hasMargin rdf:resource="http://dl-learner.org/mammographic#ill-defined"/>
+        <hasShape rdf:resource="http://dl-learner.org/mammographic#irregular"/>
+        <hasDensity rdf:resource="http://dl-learner.org/mammographic#low"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/mammographic#Patient149 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learne...
 
[truncated message content]

[DL-Learner SVN] SF.net SVN: dl-learner:[4267] trunk

[<lor...@us...>]

Revision: 4267
          http://sourceforge.net/p/dl-learner/code/4267
Author:   lorenz_b
Date:     2014-05-09 18:13:04 +0000 (Fri, 09 May 2014)
Log Message:
-----------
Modified CV script.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java
    trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
    trunk/test/qtl/breasttissue/train1.conf
    trunk/test/qtl/carcinogenesis/train.conf
    trunk/test/qtl/mutagenesis/train1.conf
    trunk/test/qtl/parkinsons/train.conf
    trunk/test/qtl/suramin/train.conf

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-09 18:13:04 UTC (rev 4267)
@@ -102,19 +102,18 @@
 	@ConfigOption(name = "noisePercentage", defaultValue="0.0", description="the (approximated) percentage of noise within the examples")
 	private double noisePercentage = 0.0;
 	@ConfigOption(defaultValue = "10", name = "maxExecutionTimeInSeconds", description = "maximum execution of the algorithm in seconds")
-	private int maxExecutionTimeInSeconds = -1;
+	private int maxExecutionTimeInSeconds = 60;
 	
 	private double coverageWeight = 0.8;
 	private double specifityWeight = 0.1;
-	private double coverageBeta = 0.5;
 	
 	private double minCoveredPosExamplesFraction = 0.2;
 	// maximum execution time to compute a part of the solution
 	private double maxTreeComputationTimeInSeconds = 10;
 	// how important not to cover negatives
-	private double posWeight = 2;
+	private double beta = 1;
 	// minimum score a query tree must have to be part of the solution
-	private double minimumTreeScore = 0.2;
+	private double minimumTreeScore = 0.3;
 	//If yes, then the algorithm tries to cover all positive examples. Note that while this improves accuracy on the testing set, 
 	//it may lead to overfitting
 	private boolean tryFullCoverage;
@@ -161,10 +160,10 @@
 		
 		lggGenerator = new LGGGeneratorImpl<String>();
 		
-		if(heuristic == null){
+//		if(heuristic == null){
 			heuristic = new QueryTreeHeuristic();
-			heuristic.setPosExamplesWeight(posWeight);
-		}
+			heuristic.setPosExamplesWeight(beta);
+//		}
 		
 		logger.info("Initializing...");
 		treeCache = new QueryTreeCache(model);
@@ -222,7 +221,8 @@
 		String setup = "Setup:";
 		setup += "\n#Pos. examples:" + currentPosExamples.size();
 		setup += "\n#Neg. examples:" + currentNegExamples.size();
-		setup += "\nPos. weight(beta):" + posWeight;
+		setup += "Heuristic:" + heuristic.getHeuristicType().name();
+		setup += "\nbeta=" + beta;
 		logger.info(setup);
 		logger.info("Running...");
 		startTime = System.currentTimeMillis();
@@ -236,7 +236,7 @@
 			logger.info("#Remaining neg. examples:" + currentNegExampleTrees.size());
 			
 			//compute a (partial) solution
-			computeNextPartialSolution();
+			computeBestPartialSolution();
 			
 			//pick best (partial) solution computed so far
 			EvaluatedQueryTree<String> bestPartialSolution = currentPartialSolutions.first();
@@ -279,29 +279,31 @@
 		long endTime = System.currentTimeMillis();
 		logger.info("Finished in " + (endTime-startTime) + "ms.");
 		
-		logger.info("Combined solution:\n" + OWLAPIConverter.getOWLAPIDescription(currentBestSolution.getDescription()));
+		logger.info("Combined solution:" + OWLAPIConverter.getOWLAPIDescription(currentBestSolution.getDescription()).toString().replace("\n", ""));
 		logger.info(currentBestSolution.getScore());
 		
 	}
 	
-	private void computeNextPartialSolution(){
+	private void computeBestPartialSolution(){
 		logger.info("Computing best partial solution...");
 		bestCurrentScore = Double.NEGATIVE_INFINITY;
 		partialSolutionStartTime = System.currentTimeMillis();
 		initTodoList(currentPosExampleTrees, currentNegExampleTrees);
 		
 		EvaluatedQueryTree<String> currentElement;
+		QueryTree<String> currentTree;
 		while(!partialSolutionTerminationCriteriaSatisfied()){
 			logger.trace("TODO list size: " + todoList.size());
 			//pick best element from todo list
 			currentElement = todoList.poll();
+			currentTree = currentElement.getTree();
 			//generate the LGG between the chosen tree and each uncovered positive example
-			for (QueryTree<String> example : currentElement.getFalseNegatives()) {
-				QueryTree<String> tree = currentElement.getTree();
-
+			Iterator<QueryTree<String>> it = currentElement.getFalseNegatives().iterator();
+			while (it.hasNext() && !isPartialSolutionTimeExpired() && !isTimeExpired()) {
+				QueryTree<String> uncoveredTree = it.next();
 				//compute the LGG
 				lggMon.start();
-				QueryTree<String> lgg = lggGenerator.getLGG(tree, example);
+				QueryTree<String> lgg = lggGenerator.getLGG(currentTree, uncoveredTree);
 				lggMon.stop();
 				
 				//evaluate the LGG
@@ -312,8 +314,8 @@
 				if(score >= bestCurrentScore){
 					//add to todo list, if not already contained in todo list or solution list
 					todo(solution);
-					if(solution.getScore() > bestCurrentScore){
-						logger.info("Got better solution:" + solution.getTreeScore());
+					if(score > bestCurrentScore){
+						logger.info("\tGot better solution:" + solution.getTreeScore());
 					}
 					bestCurrentScore = solution.getScore();
 				} else if(mas < bestCurrentScore){
@@ -330,7 +332,7 @@
 		logger.info("...finished in " + (endTime-partialSolutionStartTime) + "ms.");
 		EvaluatedDescription bestPartialSolution = currentPartialSolutions.first().asEvaluatedDescription();
 		
-		logger.info("Best partial solution:\n" + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()) + "\n(" + bestPartialSolution.getScore() + ")");
+		logger.info("Best partial solution: " + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()).toString().replace("\n", "") + "\n(" + bestPartialSolution.getScore() + ")");
 		
 		logger.trace("LGG time: " + lggMon.getTotal() + "ms");
 		logger.trace("Avg. LGG time: " + lggMon.getAvg() + "ms");
@@ -361,7 +363,7 @@
 						? 0 
 						: coveredPositiveExamples / (double)(coveredPositiveExamples + coveredNegativeExampleTrees.size());
 		
-		double coverageScore = Heuristics.getFScore(recall, precision, coverageBeta);
+		double coverageScore = Heuristics.getFScore(recall, precision, beta);
 		
 		//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
 		int nrOfSpecificNodes = 0;
@@ -400,8 +402,6 @@
 	private EvaluatedDescription buildCombinedSolution(){
 		if(partialSolutions.size() == 1){
 			EvaluatedDescription combinedSolution = partialSolutions.get(0).asEvaluatedDescription();
-			double accuracy = lp.getAccuracy(combinedSolution.getDescription());
-			System.out.println(accuracy);
 			return combinedSolution;
 		}
 		List<Description> disjuncts = new ArrayList<Description>();
@@ -423,16 +423,13 @@
 		Set<Individual> posNotCovered = Sets.difference(lp.getPositiveExamples(), posCovered);
 		Set<Individual> negNotCovered = Sets.difference(lp.getNegativeExamples(), negCovered);
 		
-		double accuracy = lp.getAccuracy(unionDescription);
-		System.out.println(accuracy);
-		
 		//compute the coverage
 		double recall = posCovered.size() / (double)lp.getPositiveExamples().size();
 		double precision = (posCovered.size() + negCovered.size() == 0) 
 						? 0 
 						: posCovered.size() / (double)(posCovered.size() + negCovered.size());
 		
-		double coverageScore = Heuristics.getFScore(recall, precision, coverageBeta);
+		double coverageScore = Heuristics.getFScore(recall, precision, beta);
 		
 //		ScoreTwoValued score = new ScoreTwoValued(posCovered, posNotCovered, negCovered, negNotCovered);
 //		score.setAccuracy(coverageScore);
@@ -442,6 +439,7 @@
 	}
 	
 	private void reset(){
+		currentBestSolution = null;
 		partialSolutions = new ArrayList<EvaluatedQueryTree<String>>();
 		
 		stop = false;
@@ -672,17 +670,18 @@
 	}
 	
 	/**
-	 * @param coverageBeta the coverageBeta to set
+	 * Default value is 1. Lower values force importance of covering positive examples.
+	 * @param beta the beta to set
 	 */
-	public void setCoverageBeta(double coverageBeta) {
-		this.coverageBeta = coverageBeta;
+	public void setBeta(double beta) {
+		this.beta = beta;
 	}
 	
 	/**
-	 * @param posWeight the posWeight to set
+	 * @param maxTreeComputationTimeInSeconds the maxTreeComputationTimeInSeconds to set
 	 */
-	public void setPosWeight(double posWeight) {
-		this.posWeight = posWeight;
+	public void setMaxTreeComputationTimeInSeconds(double maxTreeComputationTimeInSeconds) {
+		this.maxTreeComputationTimeInSeconds = maxTreeComputationTimeInSeconds;
 	}
 	
 	/* (non-Javadoc)

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-09 18:13:04 UTC (rev 4267)
@@ -26,13 +26,6 @@
 	
 	private HeuristicType heuristicType = HeuristicType.PRED_ACC;
 	
-	// F score beta value
-	private double coverageBeta = 1;
-	
-	private double coverageWeight = 0.8;
-	
-	private double specifityWeight = 0.1;
-	
 	private double posExamplesWeight = 1;
 	
 	// syntactic comparison as final comparison criterion
@@ -63,7 +56,7 @@
 			case FMEASURE : 
 				score = Heuristics.getFScore(tp/(tp+fn), tp/(tp+fp), posExamplesWeight);break;
 			case PRED_ACC : 
-				score = (tp + posExamplesWeight * tn) / ((tp + fn) + posExamplesWeight * (tn + fp));break;
+				score = (1/posExamplesWeight * tp + tn) / (1/posExamplesWeight * (tp + fn) + (tn + fp));break;
 			case ENTROPY  :{
 				double total = tp + fn;
 				double pp = tp / total;
@@ -154,6 +147,13 @@
 	}
 	
 	/**
+	 * @return the heuristicType
+	 */
+	public HeuristicType getHeuristicType() {
+		return heuristicType;
+	}
+	
+	/**
 	 * @param posExamplesWeight the posExamplesWeight to set
 	 */
 	public void setPosExamplesWeight(double posExamplesWeight) {

Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java	2014-05-09 18:13:04 UTC (rev 4267)
@@ -65,11 +65,11 @@
 	 * @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
 	 */
 	public String toString(String baseURI, Map<String, String> prefixes) {
-		return " [>= " + minValue + " <= " + maxValue + "]";
+		return " double[>= " + minValue + " <= " + maxValue + "]";
 	}
 	
 	public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " [>= " + minValue + " <= " + maxValue + "]";
+		return " double[>= " + minValue + " <= " + maxValue + "]";
 	}
 	
 	public void accept(KBElementVisitor visitor) {
@@ -81,7 +81,7 @@
 	 */
 	@Override
 	public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
-		return " [>= " + minValue + " <= " + maxValue + "]";
+		return " double[>= " + minValue + " <= " + maxValue + "]";
 	}
 
 	/* (non-Javadoc)

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java	2014-05-09 18:13:04 UTC (rev 4267)
@@ -22,7 +22,6 @@
 import static java.util.Arrays.asList;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
 import java.text.DecimalFormat;
@@ -43,15 +42,17 @@
 import org.apache.commons.beanutils.PropertyUtils;
 import org.apache.log4j.ConsoleAppender;
 import org.apache.log4j.FileAppender;
+import org.apache.log4j.Layout;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
+import org.apache.log4j.Priority;
 import org.apache.log4j.SimpleLayout;
 import org.dllearner.cli.CLI;
 import org.dllearner.core.AbstractCELA;
 import org.dllearner.core.AbstractLearningProblem;
 import org.dllearner.core.AbstractReasonerComponent;
 import org.dllearner.core.ComponentInitException;
-import org.dllearner.core.ComponentManager;
 import org.dllearner.core.owl.Description;
 import org.dllearner.core.owl.Individual;
 import org.dllearner.learningproblems.PosNegLP;
@@ -101,7 +102,10 @@
  */
 public class NestedCrossValidation {
 	
-	private File outputFile = new File("log/nested-cv.log");
+	
+	private static final Logger logger = Logger.getLogger(NestedCrossValidation.class.getName());
+	
+	private static File logFile = new File("log/nested-cv.log");
 	DecimalFormat df = new DecimalFormat();	
 	
 	// overall statistics
@@ -126,7 +130,7 @@
 
 		OptionParser parser = new OptionParser();
 		parser.acceptsAll(asList("h", "?", "help"), "Show help.");
-		parser.acceptsAll(asList("c", "conf"), "The comma separated list of conffiles to be used.").withRequiredArg().describedAs("file1, file2, ...");
+		parser.acceptsAll(asList("c", "conf"), "The comma separated list of config files to be used.").withRequiredArg().describedAs("file1, file2, ...");
 		parser.acceptsAll(asList( "v", "verbose"), "Be more verbose.");
 		parser.acceptsAll(asList( "o", "outerfolds"), "Number of outer folds.").withRequiredArg().ofType(Integer.class).describedAs("#folds");
 		parser.acceptsAll(asList( "i", "innerfolds"), "Number of inner folds.").withRequiredArg().ofType(Integer.class).describedAs("#folds");
@@ -167,13 +171,18 @@
 			
 			// create logger (a simple logger which outputs
 			// its messages to the console)
-			SimpleLayout layout = new SimpleLayout();
+			Layout layout = new PatternLayout("%m%n");
 			ConsoleAppender consoleAppender = new ConsoleAppender(layout);
 			Logger logger = Logger.getRootLogger();
 			logger.removeAllAppenders();
 			logger.addAppender(consoleAppender);
-			logger.setLevel(Level.WARN);
+			logger.setLevel(Level.ERROR);
 			Logger.getLogger("org.dllearner.algorithms").setLevel(Level.INFO);
+			Logger.getLogger("org.dllearner.scripts").setLevel(Level.INFO);
+			
+			FileAppender fileAppender = new FileAppender(layout, logFile.getPath(), false);
+			logger.addAppender(fileAppender);
+			fileAppender.setThreshold(Level.INFO);
 //			logger.addAppender(new FileAppender(layout, "nested-cv.log", false));
 			// disable OWL API info output
 			java.util.logging.Logger.getLogger("").setLevel(java.util.logging.Level.WARNING);
@@ -188,15 +197,6 @@
 		}
 
 	}
-
-	private void print(String s){
-		try {
-			Files.append(s + "\n", outputFile , Charsets.UTF_8);
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-		System.out.println(s);
-	}
 	
 	public NestedCrossValidation(File confFile, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws ComponentInitException, ParseException, org.dllearner.confparser.ParseException, IOException {
 		this(Lists.newArrayList(confFile), outerFolds, innerFolds, parameter, startValue, endValue, stepsize, verbose);
@@ -205,37 +205,38 @@
 	public NestedCrossValidation(List<File> confFiles, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws ComponentInitException, ParseException, org.dllearner.confparser.ParseException, IOException {
 		
 		for (File confFile : confFiles) {
-			print(confFile.getPath());
+			logger.info("++++++++++++++++++++++++++++++++++++++++++++++");
+			logger.info(confFile.getPath());
+			logger.info("++++++++++++++++++++++++++++++++++++++++++++++");
 			validate(confFile, outerFolds, innerFolds, parameter, startValue, endValue, stepsize, verbose);		
 		}
 		
-		print("********************************************");
-		print("********************************************");
-		print("********************************************");
+		logger.info("############################################");
+		logger.info("############################################");
 		
 		// decide for the best parameter
-		print("    Summary over parameter values:");
+		logger.info("   Overall summary over parameter values:");
 		double bestPara = startValue;
 		double bestValue = Double.NEGATIVE_INFINITY;
 		for (Entry<Double, Stat> entry : globalParaStats.entrySet()) {
 			double para = entry.getKey();
 			Stat stat = entry.getValue();
-			print("      value " + para + ": " + stat.prettyPrint("%"));
+			logger.info("      value " + para + ": " + stat.prettyPrint("%"));
 			if (stat.getMean() > bestValue) {
 				bestPara = para;
 				bestValue = stat.getMean();
 			}
 		}
-		print("      selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
+		logger.info("      selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
 		
 		// overall statistics
-		print("*******************");
-		print("* Overall Results *");
-		print("*******************");
-		print("accuracy: " + globalAcc.prettyPrint("%"));
-		print("F measure: " + globalF.prettyPrint("%"));
-		print("precision: " + globalPrecision.prettyPrint("%"));
-		print("recall: " + globalRecall.prettyPrint("%"));
+		logger.info("*******************");
+		logger.info("* Overall Results *");
+		logger.info("*******************");
+		logger.info("accuracy: " + globalAcc.prettyPrint("%"));
+		logger.info("F measure: " + globalF.prettyPrint("%"));
+		logger.info("precision: " + globalPrecision.prettyPrint("%"));
+		logger.info("recall: " + globalRecall.prettyPrint("%"));
 		
 	}
 	
@@ -255,6 +256,7 @@
 		Collections.shuffle(negExamples, new Random(2));	
 		
 		AbstractReasonerComponent rc = start.getReasonerComponent();
+		rc.init();
 		String baseURI = rc.getBaseURI();
 		
 		List<TrainTestList> posLists = getFolds(posExamples, outerFolds);
@@ -268,7 +270,7 @@
 		
 		for(int currOuterFold=0; currOuterFold<outerFolds; currOuterFold++) {
 			
-			print("Outer fold " + currOuterFold);
+			logger.info("Outer fold " + currOuterFold);
 			TrainTestList posList = posLists.get(currOuterFold);
 			TrainTestList negList = negLists.get(currOuterFold);
 			
@@ -277,7 +279,7 @@
 			
 			for(double currParaValue=startValue; currParaValue<=endValue; currParaValue+=stepsize) {
 				
-				print("  Parameter value " + currParaValue + ":");
+				logger.info("  Parameter value " + currParaValue + ":");
 				// split train folds again (computation of inner folds for each parameter
 				// value is redundant, but not a big problem)
 				List<Individual> trainPosList = posList.getTrainList();
@@ -291,7 +293,7 @@
 				
 				for(int currInnerFold=0; currInnerFold<innerFolds; currInnerFold++) {
 					
-					print("    Inner fold " + currInnerFold + ":");
+					logger.info("    Inner fold " + currInnerFold + ":");
 					// get positive & negative examples for training run
 					Set<Individual> posEx = new TreeSet<Individual>(innerPosLists.get(currInnerFold).getTrainList());
 					Set<Individual> negEx = new TreeSet<Individual>(innerNegLists.get(currInnerFold).getTrainList());
@@ -320,13 +322,12 @@
 					TreeSet<Individual> posTest = new TreeSet<Individual>(innerPosLists.get(currInnerFold).getTestList());
 					TreeSet<Individual> negTest = new TreeSet<Individual>(innerNegLists.get(currInnerFold).getTestList());
 					
-					AbstractReasonerComponent rs = start.getReasonerComponent();
 					// true positive
-					Set<Individual> posCorrect = rs.hasType(concept, posTest);
+					Set<Individual> posCorrect = rc.hasType(concept, posTest);
 					// false negative
 					Set<Individual> posError = Helper.difference(posTest, posCorrect);
 					// false positive
-					Set<Individual> negError = rs.hasType(concept, negTest);
+					Set<Individual> negError = rc.hasType(concept, negTest);
 					// true negative
 					Set<Individual> negCorrect = Helper.difference(negTest, negError);
 	
@@ -340,19 +341,16 @@
 					
 					paraCriterionStat.addNumber(accuracy);
 					
-					print("      hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
-					print("      accuracy: " + df.format(accuracy) + "%");
-					print("      precision: " + df.format(precision) + "%");
-					print("      recall: " + df.format(recall) + "%");
-					print("      F measure: " + df.format(fmeasure) + "%");
+					logger.info("      hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
+					logger.info("      accuracy: " + df.format(accuracy) + "%");
+					logger.info("      precision: " + df.format(precision) + "%");
+					logger.info("      recall: " + df.format(recall) + "%");
+					logger.info("      F measure: " + df.format(fmeasure) + "%");
 					
 					if(verbose) {
-						print("      false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
-						print("      false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
+						logger.info("      false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
+						logger.info("      false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
 					}
-					
-					// free memory
-					rs.releaseKB();
 				}
 				
 				paraStats.put(currParaValue, paraCriterionStat);
@@ -365,20 +363,20 @@
 			}
 			
 			// decide for the best parameter
-			print("    Summary over parameter values:");
+			logger.info("    Summary over parameter values:");
 			double bestPara = startValue;
 			double bestValue = Double.NEGATIVE_INFINITY;
 			for(Entry<Double,Stat> entry : paraStats.entrySet()) {
 				double para = entry.getKey();
 				Stat stat = entry.getValue();
-				print("      value " + para + ": " + stat.prettyPrint("%"));
+				logger.info("      value " + para + ": " + stat.prettyPrint("%"));
 				if(stat.getMean() > bestValue) {
 					bestPara = para;
 					bestValue = stat.getMean();
 				}
 			}
-			print("      selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
-			print("    Learn on Outer fold:");
+			logger.info("      selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
+			logger.info("    Learn on Outer fold:");
 			
 			// start a learning process with this parameter and evaluate it on the outer fold
 			start = new CLI(confFile);
@@ -418,15 +416,15 @@
 			double recall = 100 * (double) posCorrect.size() / (posCorrect.size() + posError.size());
 			double fmeasure = 2 * (precision * recall) / (precision + recall);
 	
-			print("      hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
-			print("      accuracy: " + df.format(accuracy) + "%");
-			print("      precision: " + df.format(precision) + "%");
-			print("      recall: " + df.format(recall) + "%");
-			print("      F measure: " + df.format(fmeasure) + "%");
+			logger.info("      hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
+			logger.info("      accuracy: " + df.format(accuracy) + "%");
+			logger.info("      precision: " + df.format(precision) + "%");
+			logger.info("      recall: " + df.format(recall) + "%");
+			logger.info("      F measure: " + df.format(fmeasure) + "%");
 			
 			if(verbose) {
-				print("      false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
-				print("      false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
+				logger.info("      false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
+				logger.info("      false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
 			}			
 			
 			// update overall statistics
@@ -445,13 +443,13 @@
 		globalRecall.add(recallOverall);
 		
 		// overall statistics
-		print("*******************");
-		print("* Overall Results *");
-		print("*******************");
-		print("accuracy: " + accOverall.prettyPrint("%"));
-		print("F measure: " + fOverall.prettyPrint("%"));
-		print("precision: " + precisionOverall.prettyPrint("%"));
-		print("recall: " + recallOverall.prettyPrint("%"));
+		logger.info("*******************");
+		logger.info("* Overall Results *");
+		logger.info("*******************");
+		logger.info("accuracy: " + accOverall.prettyPrint("%"));
+		logger.info("F measure: " + fOverall.prettyPrint("%"));
+		logger.info("precision: " + precisionOverall.prettyPrint("%"));
+		logger.info("recall: " + recallOverall.prettyPrint("%"));
 	}
 	
 	// convenience methods, which takes a list of examples and divides them in

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-09 18:13:04 UTC (rev 4267)
@@ -6,43 +6,39 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Random;
+import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
 
-import org.dllearner.algorithms.qtl.QTL2;
 import org.dllearner.algorithms.qtl.QTL2Disjunctive;
 import org.dllearner.algorithms.qtl.QueryTreeFactory;
 import org.dllearner.algorithms.qtl.datastructures.QueryTree;
 import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
 import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+import org.dllearner.cli.CLI;
 import org.dllearner.cli.CrossValidation;
-import org.dllearner.cli.SPARQLCrossValidation;
+import org.dllearner.core.AbstractLearningProblem;
 import org.dllearner.core.ComponentInitException;
 import org.dllearner.core.LearningProblemUnsupportedException;
 import org.dllearner.core.owl.Individual;
-import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
 import org.dllearner.kb.OWLAPIOntology;
 import org.dllearner.learningproblems.PosNegLP;
 import org.dllearner.learningproblems.PosNegLPStandard;
 import org.dllearner.reasoning.FastInstanceChecker;
-import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.scripts.NestedCrossValidation;
 import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLDataFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyChange;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.reasoner.OWLReasoner;
-import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 
-import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
 import com.google.common.collect.Lists;
+import com.google.common.collect.Sets;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 
@@ -52,363 +48,20 @@
  */
 public class QTLEvaluation {
 	
-	int nrOfFolds = 10;
+	int nrOfFolds = 3;
 	private int nrOfPosExamples = 300;
 	private int nrOfNegExamples = 300;
 	
-	List<String> posExamples = Lists.newArrayList(
-			"http://dl-learner.org/carcinogenesis#d1",
-			"http://dl-learner.org/carcinogenesis#d10",
-			"http://dl-learner.org/carcinogenesis#d101",
-			"http://dl-learner.org/carcinogenesis#d102",
-			"http://dl-learner.org/carcinogenesis#d103",
-			"http://dl-learner.org/carcinogenesis#d106",
-			"http://dl-learner.org/carcinogenesis#d107",
-			"http://dl-learner.org/carcinogenesis#d108",
-			"http://dl-learner.org/carcinogenesis#d11",
-			"http://dl-learner.org/carcinogenesis#d12",
-			"http://dl-learner.org/carcinogenesis#d13",
-			"http://dl-learner.org/carcinogenesis#d134",
-			"http://dl-learner.org/carcinogenesis#d135",
-			"http://dl-learner.org/carcinogenesis#d136",
-			"http://dl-learner.org/carcinogenesis#d138",
-			"http://dl-learner.org/carcinogenesis#d140",
-			"http://dl-learner.org/carcinogenesis#d141",
-			"http://dl-learner.org/carcinogenesis#d144",
-			"http://dl-learner.org/carcinogenesis#d145",
-			"http://dl-learner.org/carcinogenesis#d146",
-			"http://dl-learner.org/carcinogenesis#d147",
-			"http://dl-learner.org/carcinogenesis#d15",
-			"http://dl-learner.org/carcinogenesis#d17",
-			"http://dl-learner.org/carcinogenesis#d19",
-			"http://dl-learner.org/carcinogenesis#d192",
-			"http://dl-learner.org/carcinogenesis#d193",
-			"http://dl-learner.org/carcinogenesis#d195",
-			"http://dl-learner.org/carcinogenesis#d196",
-			"http://dl-learner.org/carcinogenesis#d197",
-			"http://dl-learner.org/carcinogenesis#d198",
-			"http://dl-learner.org/carcinogenesis#d199",
-			"http://dl-learner.org/carcinogenesis#d2",
-			"http://dl-learner.org/carcinogenesis#d20",
-			"http://dl-learner.org/carcinogenesis#d200",
-			"http://dl-learner.org/carcinogenesis#d201",
-			"http://dl-learner.org/carcinogenesis#d202",
-			"http://dl-learner.org/carcinogenesis#d203",
-			"http://dl-learner.org/carcinogenesis#d204",
-			"http://dl-learner.org/carcinogenesis#d205",
-			"http://dl-learner.org/carcinogenesis#d21",
-			"http://dl-learner.org/carcinogenesis#d22",
-			"http://dl-learner.org/carcinogenesis#d226",
-			"http://dl-learner.org/carcinogenesis#d227",
-			"http://dl-learner.org/carcinogenesis#d228",
-			"http://dl-learner.org/carcinogenesis#d229",
-			"http://dl-learner.org/carcinogenesis#d231",
-			"http://dl-learner.org/carcinogenesis#d232",
-			"http://dl-learner.org/carcinogenesis#d234",
-			"http://dl-learner.org/carcinogenesis#d236",
-			"http://dl-learner.org/carcinogenesis#d239",
-			"http://dl-learner.org/carcinogenesis#d23_2",
-			"http://dl-learner.org/carcinogenesis#d242",
-			"http://dl-learner.org/carcinogenesis#d245",
-			"http://dl-learner.org/carcinogenesis#d247",
-			"http://dl-learner.org/carcinogenesis#d249",
-			"http://dl-learner.org/carcinogenesis#d25",
-			"http://dl-learner.org/carcinogenesis#d252",
-			"http://dl-learner.org/carcinogenesis#d253",
-			"http://dl-learner.org/carcinogenesis#d254",
-			"http://dl-learner.org/carcinogenesis#d255",
-			"http://dl-learner.org/carcinogenesis#d26",
-			"http://dl-learner.org/carcinogenesis#d272",
-			"http://dl-learner.org/carcinogenesis#d275",
-			"http://dl-learner.org/carcinogenesis#d277",
-			"http://dl-learner.org/carcinogenesis#d279",
-			"http://dl-learner.org/carcinogenesis#d28",
-			"http://dl-learner.org/carcinogenesis#d281",
-			"http://dl-learner.org/carcinogenesis#d283",
-			"http://dl-learner.org/carcinogenesis#d284",
-			"http://dl-learner.org/carcinogenesis#d288",
-			"http://dl-learner.org/carcinogenesis#d29",
-			"http://dl-learner.org/carcinogenesis#d290",
-			"http://dl-learner.org/carcinogenesis#d291",
-			"http://dl-learner.org/carcinogenesis#d292",
-			"http://dl-learner.org/carcinogenesis#d30",
-			"http://dl-learner.org/carcinogenesis#d31",
-			"http://dl-learner.org/carcinogenesis#d32",
-			"http://dl-learner.org/carcinogenesis#d33",
-			"http://dl-learner.org/carcinogenesis#d34",
-			"http://dl-learner.org/carcinogenesis#d35",
-			"http://dl-learner.org/carcinogenesis#d36",
-			"http://dl-learner.org/carcinogenesis#d37",
-			"http://dl-learner.org/carcinogenesis#d38",
-			"http://dl-learner.org/carcinogenesis#d42",
-			"http://dl-learner.org/carcinogenesis#d43",
-			"http://dl-learner.org/carcinogenesis#d44",
-			"http://dl-learner.org/carcinogenesis#d45",
-			"http://dl-learner.org/carcinogenesis#d46",
-			"http://dl-learner.org/carcinogenesis#d47",
-			"http://dl-learner.org/carcinogenesis#d48",
-			"http://dl-learner.org/carcinogenesis#d49",
-			"http://dl-learner.org/carcinogenesis#d5",
-			"http://dl-learner.org/carcinogenesis#d51",
-			"http://dl-learner.org/carcinogenesis#d52",
-			"http://dl-learner.org/carcinogenesis#d53",
-			"http://dl-learner.org/carcinogenesis#d55",
-			"http://dl-learner.org/carcinogenesis#d58",
-			"http://dl-learner.org/carcinogenesis#d6",
-			"http://dl-learner.org/carcinogenesis#d7",
-			"http://dl-learner.org/carcinogenesis#d84",
-			"http://dl-learner.org/carcinogenesis#d85_2",
-			"http://dl-learner.org/carcinogenesis#d86",
-			"http://dl-learner.org/carcinogenesis#d87",
-			"http://dl-learner.org/carcinogenesis#d88",
-			"http://dl-learner.org/carcinogenesis#d89",
-			"http://dl-learner.org/carcinogenesis#d9",
-			"http://dl-learner.org/carcinogenesis#d91",
-			"http://dl-learner.org/carcinogenesis#d92",
-			"http://dl-learner.org/carcinogenesis#d93",
-			"http://dl-learner.org/carcinogenesis#d95",
-			"http://dl-learner.org/carcinogenesis#d96",
-			"http://dl-learner.org/carcinogenesis#d98",
-			"http://dl-learner.org/carcinogenesis#d99",
-			"http://dl-learner.org/carcinogenesis#d100",
-			"http://dl-learner.org/carcinogenesis#d104",
-			"http://dl-learner.org/carcinogenesis#d105",
-			"http://dl-learner.org/carcinogenesis#d109",
-			"http://dl-learner.org/carcinogenesis#d137",
-			"http://dl-learner.org/carcinogenesis#d139",
-			"http://dl-learner.org/carcinogenesis#d14",
-			"http://dl-learner.org/carcinogenesis#d142",
-			"http://dl-learner.org/carcinogenesis#d143",
-			"http://dl-learner.org/carcinogenesis#d148",
-			"http://dl-learner.org/carcinogenesis#d16",
-			"http://dl-learner.org/carcinogenesis#d18",
-			"http://dl-learner.org/carcinogenesis#d191",
-			"http://dl-learner.org/carcinogenesis#d206",
-			"http://dl-learner.org/carcinogenesis#d230",
-			"http://dl-learner.org/carcinogenesis#d233",
-			"http://dl-learner.org/carcinogenesis#d235",
-			"http://dl-learner.org/carcinogenesis#d237",
-			"http://dl-learner.org/carcinogenesis#d238",
-			"http://dl-learner.org/carcinogenesis#d23_1",
-			"http://dl-learner.org/carcinogenesis#d24",
-			"http://dl-learner.org/carcinogenesis#d240",
-			"http://dl-learner.org/carcinogenesis#d241",
-			"http://dl-learner.org/carcinogenesis#d243",
-			"http://dl-learner.org/carcinogenesis#d244",
-			"http://dl-learner.org/carcinogenesis#d246",
-			"http://dl-learner.org/carcinogenesis#d248",
-			"http://dl-learner.org/carcinogenesis#d250",
-			"http://dl-learner.org/carcinogenesis#d251",
-			"http://dl-learner.org/carcinogenesis#d27",
-			"http://dl-learner.org/carcinogenesis#d273",
-			"http://dl-learner.org/carcinogenesis#d274",
-			"http://dl-learner.org/carcinogenesis#d278",
-			"http://dl-learner.org/carcinogenesis#d286",
-			"http://dl-learner.org/carcinogenesis#d289",
-			"http://dl-learner.org/carcinogenesis#d3",
-			"http://dl-learner.org/carcinogenesis#d39",
-			"http://dl-learner.org/carcinogenesis#d4",
-			"http://dl-learner.org/carcinogenesis#d40",
-			"http://dl-learner.org/carcinogenesis#d41",
-			"http://dl-learner.org/carcinogenesis#d50",
-			"http://dl-learner.org/carcinogenesis#d54",
-			"http://dl-learner.org/carcinogenesis#d56",
-			"http://dl-learner.org/carcinogenesis#d57",
-			"http://dl-learner.org/carcinogenesis#d8",
-			"http://dl-learner.org/carcinogenesis#d85_1",
-			"http://dl-learner.org/carcinogenesis#d90",
-			"http://dl-learner.org/carcinogenesis#d94",
-			"http://dl-learner.org/carcinogenesis#d97",
-			"http://dl-learner.org/carcinogenesis#d296",
-			"http://dl-learner.org/carcinogenesis#d305",
-			"http://dl-learner.org/carcinogenesis#d306",
-			"http://dl-learner.org/carcinogenesis#d307",
-			"http://dl-learner.org/carcinogenesis#d308",
-			"http://dl-learner.org/carcinogenesis#d311",
-			"http://dl-learner.org/carcinogenesis#d314",
-			"http://dl-learner.org/carcinogenesis#d315",
-			"http://dl-learner.org/carcinogenesis#d316",
-			"http://dl-learner.org/carcinogenesis#d320",
-			"http://dl-learner.org/carcinogenesis#d322",
-			"http://dl-learner.org/carcinogenesis#d323",
-			"http://dl-learner.org/carcinogenesis#d325",
-			"http://dl-learner.org/carcinogenesis#d329",
-			"http://dl-learner.org/carcinogenesis#d330",
-			"http://dl-learner.org/carcinogenesis#d331",
-			"http://dl-learner.org/carcinogenesis#d332",
-			"http://dl-learner.org/carcinogenesis#d333",
-			"http://dl-learner.org/carcinogenesis#d336",
-			"http://dl-learner.org/carcinogenesis#d337"
-			);
+	CLI cli = new CLI(new File("../test/qtl/carcinogenesis/train.conf"));
 	
-	List<String> negExamples = Lists.newArrayList(
-			"http://dl-learner.org/carcinogenesis#d110",
-			"http://dl-learner.org/carcinogenesis#d111",
-			"http://dl-learner.org/carcinogenesis#d114",
-			"http://dl-learner.org/carcinogenesis#d116",
-			"http://dl-learner.org/carcinogenesis#d117",
-			"http://dl-learner.org/carcinogenesis#d119",
-			"http://dl-learner.org/carcinogenesis#d121",
-			"http://dl-learner.org/carcinogenesis#d123",
-			"http://dl-learner.org/carcinogenesis#d124",
-			"http://dl-learner.org/carcinogenesis#d125",
-			"http://dl-learner.org/carcinogenesis#d127",
-			"http://dl-learner.org/carcinogenesis#d128",
-			"http://dl-learner.org/carcinogenesis#d130",
-			"http://dl-learner.org/carcinogenesis#d133",
-			"http://dl-learner.org/carcinogenesis#d150",
-			"http://dl-learner.org/carcinogenesis#d151",
-			"http://dl-learner.org/carcinogenesis#d154",
-			"http://dl-learner.org/carcinogenesis#d155",
-			"http://dl-learner.org/carcinogenesis#d156",
-			"http://dl-learner.org/carcinogenesis#d159",
-			"http://dl-learner.org/carcinogenesis#d160",
-			"http://dl-learner.org/carcinogenesis#d161",
-			"http://dl-learner.org/carcinogenesis#d162",
-			"http://dl-learner.org/carcinogenesis#d163",
-			"http://dl-learner.org/carcinogenesis#d164",
-			"http://dl-learner.org/carcinogenesis#d165",
-			"http://dl-learner.org/carcinogenesis#d166",
-			"http://dl-learner.org/carcinogenesis#d169",
-			"http://dl-learner.org/carcinogenesis#d170",
-			"http://dl-learner.org/carcinogenesis#d171",
-			"http://dl-learner.org/carcinogenesis#d172",
-			"http://dl-learner.org/carcinogenesis#d173",
-			"http://dl-learner.org/carcinogenesis#d174",
-			"http://dl-learner.org/carcinogenesis#d178",
-			"http://dl-learner.org/carcinogenesis#d179",
-			"http://dl-learner.org/carcinogenesis#d180",
-			"http://dl-learner.org/carcinogenesis#d181",
-			"http://dl-learner.org/carcinogenesis#d183",
-			"http://dl-learner.org/carcinogenesis#d184",
-			"http://dl-learner.org/carcinogenesis#d185",
-			"http://dl-learner.org/carcinogenesis#d186",
-			"http://dl-learner.org/carcinogenesis#d188",
-			"http://dl-learner.org/carcinogenesis#d190",
-			"http://dl-learner.org/carcinogenesis#d194",
-			"http://dl-learner.org/carcinogenesis#d207",
-			"http://dl-learner.org/carcinogenesis#d208_1",
-			"http://dl-learner.org/carcinogenesis#d209",
-			"http://dl-learner.org/carcinogenesis#d210",
-			"http://dl-learner.org/carcinogenesis#d211",
-			"http://dl-learner.org/carcinogenesis#d212",
-			"http://dl-learner.org/carcinogenesis#d213",
-			"http://dl-learner.org/carcinogenesis#d214",
-			"http://dl-learner.org/carcinogenesis#d215",
-			"http://dl-learner.org/carcinogenesis#d217",
-			"http://dl-learner.org/carcinogenesis#d218",
-			"http://dl-learner.org/carcinogenesis#d219",
-			"http://dl-learner.org/carcinogenesis#d220",
-			"http://dl-learner.org/carcinogenesis#d224",
-			"http://dl-learner.org/carcinogenesis#d256",
-			"http://dl-learner.org/carcinogenesis#d257",
-			"http://dl-learner.org/carcinogenesis#d258",
-			"http://dl-learner.org/carcinogenesis#d261",
-			"http://dl-learner.org/carcinogenesis#d262",
-			"http://dl-learner.org/carcinogenesis#d263",
-			"http://dl-learner.org/carcinogenesis#d264",
-			"http://dl-learner.org/carcinogenesis#d265",
-			"http://dl-learner.org/carcinogenesis#d266",
-			"http://dl-learner.org/carcinogenesis#d267",
-			"http://dl-learner.org/carcinogenesis#d269",
-			"http://dl-learner.org/carcinogenesis#d271",
-			"http://dl-learner.org/carcinogenesis#d276",
-			"http://dl-learner.org/carcinogenesis#d280",
-			"http://dl-learner.org/carcinogenesis#d285",
-			"http://dl-learner.org/carcinogenesis#d287",
-			"http://dl-learner.org/carcinogenesis#d293",
-			"http://dl-learner.org/carcinogenesis#d294",
-			"http://dl-learner.org/carcinogenesis#d59",
-			"http://dl-learner.org/carcinogenesis#d60",
-			"http://dl-learner.org/carcinogenesis#d61",
-			"http://dl-learner.org/carcinogenesis#d63",
-			"http://dl-learner.org/carcinogenesis#d64",
-			"http://dl-learner.org/carcinogenesis#d65",
-			"http://dl-learner.org/carcinogenesis#d69",
-			"http://dl-learner.org/carcinogenesis#d70",
-			"http://dl-learner.org/carcinogenesis#d71",
-			"http://dl-learner.org/carcinogenesis#d72",
-			"http://dl-learner.org/carcinogenesis#d73",
-			"http://dl-learner.org/carcinogenesis#d74",
-			"http://dl-learner.org/carcinogenesis#d75",
-			"http://dl-learner.org/carcinogenesis#d76",
-			"http://dl-learner.org/carcinogenesis#d77",
-			"http://dl-learner.org/carcinogenesis#d78",
-			"http://dl-learner.org/carcinogenesis#d79",
-			"http://dl-learner.org/carcinogenesis#d80",
-			"http://dl-learner.org/carcinogenesis#d81",
-			"http://dl-learner.org/carcinogenesis#d82",
-			"http://dl-learner.org/carcinogenesis#d112",
-			"http://dl-learner.org/carcinogenesis#d113",
-			"http://dl-learner.org/carcinogenesis#d115",
-			"http://dl-learner.org/carcinogenesis#d118",
-			"http://dl-learner.org/carcinogenesis#d120",
-			"http://dl-learner.org/carcinogenesis#d122",
-			"http://dl-learner.org/carcinogenesis#d126",
-			"http://dl-learner.org/carcinogenesis#d129",
-			"http://dl-learner.org/carcinogenesis#d131",
-			"http://dl-learner.org/carcinogenesis#d132",
-			"http://dl-learner.org/carcinogenesis#d149",
-			"http://dl-learner.org/carcinogenesis#d152",
-			"http://dl-learner.org/carcinogenesis#d153",
-			"http://dl-learner.org/carcinogenesis#d157",
-			"http://dl-learner.org/carcinogenesis#d158",
-			"http://dl-learner.org/carcinogenesis#d167",
-			"http://dl-learner.org/carcinogenesis#d168",
-			"http://dl-learner.org/carcinogenesis#d175",
-			"http://dl-learner.org/carcinogenesis#d176",
-			"http://dl-learner.org/carcinogenesis#d177",
-			"http://dl-learner.org/carcinogenesis#d182",
-			"http://dl-learner.org/carcinogenesis#d187",
-			"http://dl-learner.org/carcinogenesis#d189",
-			"http://dl-learner.org/carcinogenesis#d208_2",
-			"http://dl-learner.org/carcinogenesis#d216",
-			"http://dl-learner.org/carcinogenesis#d221",
-			"http://dl-learner.org/carcinogenesis#d222",
-			"http://dl-learner.org/carcinogenesis#d223",
-			"http://dl-learner.org/carcinogenesis#d225",
-			"http://dl-learner.org/carcinogenesis#d259",
-			"http://dl-learner.org/carcinogenesis#d260",
-			"http://dl-learner.org/carcinogenesis#d268",
-			"http://dl-learner.org/carcinogenesis#d270",
-			"http://dl-learner.org/carcinogenesis#d282",
-			"http://dl-learner.org/carcinogenesis#d295",
-			"http://dl-learner.org/carcinogenesis#d62",
-			"http://dl-learner.org/carcinogenesis#d66",
-			"http://dl-learner.org/carcinogenesis#d67",
-			"http://dl-learner.org/carcinogenesis#d68",
-			"http://dl-learner.org/carcinogenesis#d83",
-			"http://dl-learner.org/carcinogenesis#d297",
-			"http://dl-learner.org/carcinogenesis#d298",
-			"http://dl-learner.org/carcinogenesis#d299",
-			"http://dl-learner.org/carcinogenesis#d300",
-			"http://dl-learner.org/carcinogenesis#d302",
-			"http://dl-learner.org/carcinogenesis#d303",
-			"http://dl-learner.org/carcinogenesis#d304",
-			"http://dl-learner.org/carcinogenesis#d309",
-			"http://dl-learner.org/carcinogenesis#d312",
-			"http://dl-learner.org/carcinogenesis#d313",
-			"http://dl-learner.org/carcinogenesis#d317",
-			"http://dl-learner.org/carcinogenesis#d318",
-			"http://dl-learner.org/carcinogenesis#d319",
-			"http://dl-learner.org/carcinogenesis#d324",
-			"http://dl-learner.org/carcinogenesis#d326",
-			"http://dl-learner.org/carcinogenesis#d327",
-			"http://dl-learner.org/carcinogenesis#d328",
-			"http://dl-learner.org/carcinogenesis#d334",
-			"http://dl-learner.org/carcinogenesis#d335"
-			);
-	
 	private Model model;
 	private OWLOntology ontology;
 	private QueryTreeFactory<String> queryTreeFactory;
-	private List<QueryTree<String>> posExampleTrees;
-	private List<QueryTree<String>> negExampleTrees;
 	private PosNegLP lp;
 
 	
 	
-	public QTLEvaluation() throws ComponentInitException {
+	public QTLEvaluation() throws ComponentInitException, IOException {
 		queryTreeFactory = new QueryTreeFactoryImpl();
 		queryTreeFactory.setMaxDepth(3);
 		
@@ -434,59 +87,29 @@
 		}
 	}
 	
-	private void loadExamples() throws ComponentInitException{
+	private void loadExamples() throws ComponentInitException, IOException{
 		
-		Collections.shuffle(posExamples, new Random(1));
-		Collections.shuffle(negExamples, new Random(2));	
+		cli.init();
+		lp = (PosNegLP) cli.getLearningProblem();
+		
+		// get examples and shuffle them
+		List<Individual> posExamples = new LinkedList<Individual>(((PosNegLP)lp).getPositiveExamples());
+		Collections.shuffle(posExamples, new Random(1));			
+		List<Individual> negExamples = new LinkedList<Individual>(((PosNegLP)lp).getNegativeExamples());
+		Collections.shuffle(negExamples, new Random(2));
 		posExamples = posExamples.subList(0, Math.min(posExamples.size(), nrOfPosExamples));
 		negExamples = negExamples.subList(0, Math.min(negExamples.size(), nrOfNegExamples));
 		
-//		posExamples.clear();
-//		String string = "http://dl-learner.org/carcinogenesis#d101, http://dl-learner.org/carcinogenesis#d103, http://dl-learner.org/carcinogenesis#d107, http://dl-learner.org/carcinogenesis#d108, http://dl-learner.org/carcinogenesis#d135, http://dl-learner.org/carcinogenesis#d139, http://dl-learner.org/carcinogenesis#d14, http://dl-learner.org/carcinogenesis#d141, http://dl-learner.org/carcinogenesis#d143, http://dl-learner.org/carcinogenesis#d147, http://dl-learner.org/carcinogenesis#d17, http://dl-learner.org/carcinogenesis#d19, http://dl-learner.org/carcinogenesis#d193, http://dl-learner.org/carcinogenesis#d198, http://dl-learner.org/carcinogenesis#d228, http://dl-learner.org/carcinogenesis#d236, http://dl-learner.org/carcinogenesis#d242, http://dl-learner.org/carcinogenesis#d244, http://dl-learner.org/carcinogenesis#d273, http://dl-learner.org/carcinogenesis#d275, http://dl-learner.org/carcinogenesis#d28, http://dl-learner.org/carcinogenesis#d283, http://dl-learner.org/carcinogenesis#d286, http://dl-learner.org/carcinogenesis#d291, http://dl-learner.org/carcinogenesis#d292, http://dl-learner.org/carcinogenesis#d307, http://dl-learner.org/carcinogenesis#d31, http://dl-learner.org/carcinogenesis#d325, http://dl-learner.org/carcinogenesis#d33, http://dl-learner.org/carcinogenesis#d333, http://dl-learner.org/carcinogenesis#d34, http://dl-learner.org/carcinogenesis#d36, http://dl-learner.org/carcinogenesis#d38, http://dl-learner.org/carcinogenesis#d4, http://dl-learner.org/carcinogenesis#d40, http://dl-learner.org/carcinogenesis#d44, http://dl-learner.org/carcinogenesis#d51, http://dl-learner.org/carcinogenesis#d85_2, http://dl-learner.org/carcinogenesis#d98, http://dl-learner.org/carcinogenesis#d99";
-//		String[] split = string.split(",");
-//		for (String s : split) {
-//			posExamples.add(s.trim());
-//		}
-//		negExamples.clear();
-//		string = "http://dl-learner.org/carcinogenesis#d112, http://dl-learner.org/carcinogenesis#d116, http://dl-learner.org/carcinogenesis#d117, http://dl-learner.org/carcinogenesis#d119, http://dl-learner.org/carcinogenesis#d157, http://dl-learner.org/carcinogenesis#d160, http://dl-learner.org/carcinogenesis#d161, http://dl-learner.org/carcinogenesis#d162, http://dl-learner.org/carcinogenesis#d163, http://dl-learner.org/carcinogenesis#d167, http://dl-learner.org/carcinogenesis#d169, http://dl-learner.org/carcinogenesis#d175, http://dl-learner.org/carcinogenesis#d177, http://dl-learner.org/carcinogenesis#d184, http://dl-learner.org/carcinogenesis#d194, http://dl-learner.org/carcinogenesis#d208_2, http://dl-learner.org/carcinogenesis#d209, http://dl-learner.org/carcinogenesis#d217, http://dl-learner.org/carcinogenesis#d256, http://dl-learner.org/carcinogenesis#d257, http://dl-learner.org/carcinogenesis#d260, http://dl-learner.org/carcinogenesis#d271, http://dl-learner.org/carcinogenesis#d276, http://dl-learner.org/carcinogenesis#d282, http://dl-learner.org/carcinogenesis#d287, http://dl-learner.org/carcinogenesis#d294, http://dl-learner.org/carcinogenesis#d298, http://dl-learner.org/carcinogenesis#d300, http://dl-learner.org/carcinogenesis#d309, http://dl-learner.org/carcinogenesis#d319, http://dl-learner.org/carcinogenesis#d326, http://dl-learner.org/carcinogenesis#d328, http://dl-learner.org/carcinogenesis#d334, http://dl-learner.org/carcinogenesis#d60, http://dl-learner.org/carcinogenesis#d61, http://dl-learner.org/carcinogenesis#d66, http://dl-learner.org/carcinogenesis#d75, http://dl-learner.org/carcinogenesis#d79, http://dl-learner.org/carcinogenesis#d80, http://dl-learner.org/carcinogenesis#d83";
-//		split = string.split(",");
-//		for (String s : split) {
-//			negExamples.add(s.trim());
-//		}
+		Set<Individual> posSet = new TreeSet<Individual>(
+				NestedCrossValidation.getFolds(NestedCrossValidation.getFolds(posExamples, 3).get(0).getTrainList(), 3).get(0).getTrainList());
+		Set<Individual> negSet = new TreeSet<Individual>(
+				NestedCrossValidation.getFolds(NestedCrossValidation.getFolds(negExamples, 3).get(0).getTrainList(), 3).get(0).getTrainList());
 		
-		posExampleTrees = new ArrayList<QueryTree<String>>();
-		for (String ex : posExamples) {
-			QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model);
-			posExampleTrees.add(tree);
-		}
 		
-		negExampleTrees = new ArrayList<QueryTree<String>>();
-		for (String ex : negExamples) {
-			QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model);
-			negExampleTrees.add(tree);
-		}
 		
-		int cnt = 1;
-		for(QueryTree<String> tree : posExampleTrees){
-//			System.out.println("TREE " + cnt);
-//			tree.dump();
-//			
-//			System.out.println("-----------------------------");
-			cnt++;
-//			System.out.println(((QueryTreeImpl<String>)tree).toQuery());
-		}
-		
-		SortedSet<Individual> pos = new TreeSet<Individual>();
-		for (String ex : posExamples) {
-			pos.add(new Individual(ex));
-		}
-		SortedSet<Individual> neg = new TreeSet<Individual>();
-		for (String ex : negExamples) {
-			neg.add(new Individual(ex));
-		}
-		lp = new PosNegLPStandard();
-		lp.setPositiveExamples(pos);
-		lp.setNegativeExamples(neg);
+		this.lp = new PosNegLPStandard();
+		this.lp.setPositiveExamples(posSet);
+		this.lp.setNegativeExamples(negSet);
 	}
 	
 	public void run(boolean multiThreaded) throws ComponentInitException, LearningProblemUnsupportedException{
@@ -496,13 +119,14 @@
 		lp.setReasoner(reasoner);
 		lp.init();
 		QTL2Disjunctive la = new QTL2Disjunctive(lp, reasoner);
-//		la.init();
-//		la.start();
+		la.setBeta(0.5);
+		la.init();
+		la.start();
 		
 		CrossValidation.outputFile = new File("log/qtl-cv.log");
 		CrossValidation.writeToFile = true;
 		CrossValidation.multiThreaded = multiThreaded;
-		CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
+//		CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
 		long endTime = System.currentTimeMillis();
 		System.err.println((endTime - startTime) + "ms");
 	}

Modified: trunk/test/qtl/breasttissue/train1.conf
===================================================================
--- trunk/test/qtl/breasttissue/train1.conf	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/breasttissue/train1.conf	2014-05-09 18:13:04 UTC (rev 4267)
@@ -8,6 +8,8 @@
 
 // QTL configuration
 alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
 
 // learning problem
 lp.type = "posNegStandard"

Modified: trunk/test/qtl/carcinogenesis/train.conf
===================================================================
--- trunk/test/qtl/carcinogenesis/train.conf	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/carcinogenesis/train.conf	2014-05-09 18:13:04 UTC (rev 4267)
@@ -8,6 +8,11 @@
 reasoner.type = "fast instance checker"
 reasoner.sources = { ks }
 
+// QTL configuration
+alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
+
 // learning problem
 lp.type = "posNegStandard"
 lp.positiveExamples = {
@@ -352,5 +357,3 @@
 "kb:d335"
 }
 
-// QTL configuration
-alg.type = "qtl2dis"

Modified: trunk/test/qtl/mutagenesis/train1.conf
===================================================================
--- trunk/test/qtl/mutagenesis/train1.conf	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/mutagenesis/train1.conf	2014-05-09 18:13:04 UTC (rev 4267)
@@ -11,6 +11,8 @@
 
 // QTL configuration
 alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
 
 // learning problem
 lp.type = "posNegStandard"

Modified: trunk/test/qtl/parkinsons/train.conf
===================================================================
--- trunk/test/qtl/parkinsons/train.conf	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/parkinsons/train.conf	2014-05-09 18:13:04 UTC (rev 4267)
@@ -7,6 +7,8 @@
 
 // QTL configuration
 alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
 
 // learning problem
 lp.type = "posNegStandard"

Modified: trunk/test/qtl/suramin/train.conf
===================================================================
--- trunk/test/qtl/suramin/train.conf	2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/suramin/train.conf	2014-05-09 18:13:04 UTC (rev 4267)
@@ -30,4 +30,6 @@
 }
 
 // QTL configuration
-alg.type = "qtl2dis"
\ No newline at end of file
+alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
\ No newline at end of file

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4266] trunk

[<lor...@us...>]

Revision: 4266
          http://sourceforge.net/p/dl-learner/code/4266
Author:   lorenz_b
Date:     2014-05-08 18:19:32 +0000 (Thu, 08 May 2014)
Log Message:
-----------
Extended CV script.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
    trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-08 14:40:15 UTC (rev 4265)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-08 18:19:32 UTC (rev 4266)
@@ -110,7 +110,7 @@
 	
 	private double minCoveredPosExamplesFraction = 0.2;
 	// maximum execution time to compute a part of the solution
-	private double maxTreeComputationTimeInSeconds = 60;
+	private double maxTreeComputationTimeInSeconds = 10;
 	// how important not to cover negatives
 	private double posWeight = 2;
 	// minimum score a query tree must have to be part of the solution

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java	2014-05-08 14:40:15 UTC (rev 4265)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java	2014-05-08 18:19:32 UTC (rev 4266)
@@ -334,9 +334,9 @@
 //					double negErrorRate = 100*(negError.size()/posTest.size());
 					
 					double accuracy = 100*((double)(posCorrect.size()+negCorrect.size())/(posTest.size()+negTest.size()));
-					double precision = 100 * (double) posCorrect.size() / (posCorrect.size() + negError.size());
-					double recall = 100 * (double) posCorrect.size() / (posCorrect.size() + posError.size());
-					double fmeasure = 2 * (precision * recall) / (precision + recall);
+					double precision = 100 * (double) posCorrect.size() / (posCorrect.size() + negError.size()) == 0 ? 0 : (posCorrect.size() + negError.size());
+					double recall = 100 * (double) posCorrect.size() / (posCorrect.size() + posError.size()) == 0 ? 0 : (posCorrect.size() + posError.size());
+					double fmeasure = 2 * (precision * recall) / (precision + recall) == 0 ? 0 : (precision + recall);
 					
 					paraCriterionStat.addNumber(accuracy);
 					

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4265] trunk

[<lor...@us...>]

Revision: 4265
          http://sourceforge.net/p/dl-learner/code/4265
Author:   lorenz_b
Date:     2014-05-08 14:40:15 +0000 (Thu, 08 May 2014)
Log Message:
-----------
Extended CV script.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
    trunk/components-core/src/main/java/org/dllearner/utilities/statistics/Stat.java
    trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-08 14:39:43 UTC (rev 4264)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-08 14:40:15 UTC (rev 4265)
@@ -17,6 +17,7 @@
 import java.util.SortedSet;
 import java.util.TreeSet;
 
+import org.apache.commons.collections.ListUtils;
 import org.apache.log4j.Logger;
 import org.dllearner.algorithms.qtl.cache.QueryTreeCache;
 import org.dllearner.algorithms.qtl.datastructures.QueryTree;
@@ -69,7 +70,7 @@
 	private Queue<EvaluatedQueryTree<String>> todoList;
 	private SortedSet<EvaluatedQueryTree<String>> currentPartialSolutions;
 	
-	private double currentlyBestScore = 0d;
+	private double bestCurrentScore = 0d;
 
 	private List<QueryTree<String>> currentPosExampleTrees;
 	private List<QueryTree<String>> currentNegExampleTrees;
@@ -114,11 +115,17 @@
 	private double posWeight = 2;
 	// minimum score a query tree must have to be part of the solution
 	private double minimumTreeScore = 0.2;
+	//If yes, then the algorithm tries to cover all positive examples. Note that while this improves accuracy on the testing set, 
+	//it may lead to overfitting
+	private boolean tryFullCoverage;
+	//algorithm will terminate immediately when a correct definition is found
+	private boolean stopOnFirstDefinition;
 	
 	private long startTime;
-
 	private long partialSolutionStartTime;
 	
+	private double startPosExamplesSize;
+	
 	public QTL2Disjunctive() {}
 	
 	public QTL2Disjunctive(PosNegLP learningProblem, AbstractReasonerComponent reasoner) throws LearningProblemUnsupportedException{
@@ -156,7 +163,7 @@
 		
 		if(heuristic == null){
 			heuristic = new QueryTreeHeuristic();
-			heuristic.setPosExamplesWeight(2);
+			heuristic.setPosExamplesWeight(posWeight);
 		}
 		
 		logger.info("Initializing...");
@@ -168,6 +175,8 @@
 		currentPosExamples = new TreeSet<Individual>(lp.getPositiveExamples());
 		currentNegExamples =  new TreeSet<Individual>(lp.getNegativeExamples());
 		
+		startPosExamplesSize = currentPosExamples.size();
+		
 		//get the query trees
 		generateTrees();
 		
@@ -178,6 +187,15 @@
 		//console rendering of class expressions
 		ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
 		ToStringRenderer.getInstance().setShortFormProvider(new SimpleShortFormProvider());
+		
+		//compute the LGG for all examples
+		//this allows us to prune all other trees because we can omit paths in trees which are contained in all positive
+		//as well as negative examples
+//		List<QueryTree<String>> allExamplesTrees = new ArrayList<QueryTree<String>>();
+//		allExamplesTrees.addAll(currentPosExampleTrees);
+//		allExamplesTrees.addAll(currentNegExampleTrees);
+//		QueryTree<String> lgg = lggGenerator.getLGG(allExamplesTrees);
+//		lgg.dump();
 	}
 	
 	private void generateTrees(){
@@ -204,7 +222,7 @@
 		String setup = "Setup:";
 		setup += "\n#Pos. examples:" + currentPosExamples.size();
 		setup += "\n#Neg. examples:" + currentNegExamples.size();
-		setup += "\nCoverage beta:" + coverageBeta;
+		setup += "\nPos. weight(beta):" + posWeight;
 		logger.info(setup);
 		logger.info("Running...");
 		startTime = System.currentTimeMillis();
@@ -268,7 +286,7 @@
 	
 	private void computeNextPartialSolution(){
 		logger.info("Computing best partial solution...");
-		currentlyBestScore = 0d;
+		bestCurrentScore = Double.NEGATIVE_INFINITY;
 		partialSolutionStartTime = System.currentTimeMillis();
 		initTodoList(currentPosExampleTrees, currentNegExampleTrees);
 		
@@ -291,14 +309,14 @@
 				double score = solution.getScore();
 				double mas = heuristic.getMaximumAchievableScore(solution);
 				
-				if(score >= currentlyBestScore){
+				if(score >= bestCurrentScore){
 					//add to todo list, if not already contained in todo list or solution list
 					todo(solution);
-					if(solution.getScore() > currentlyBestScore){
+					if(solution.getScore() > bestCurrentScore){
 						logger.info("Got better solution:" + solution.getTreeScore());
 					}
-					currentlyBestScore = solution.getScore();
-				} else if(mas < currentlyBestScore){
+					bestCurrentScore = solution.getScore();
+				} else if(mas < bestCurrentScore){
 					todo(solution);
 				} else {
 					System.out.println("Too general");
@@ -431,6 +449,8 @@
 		
 		subMon.reset();
 		lggMon.reset();
+		
+		bestCurrentScore = minimumTreeScore;
 	}
 	
 	
@@ -578,8 +598,31 @@
 		return tree1.isSubsumedBy(tree2) && tree2.isSubsumedBy(tree1);
 	}
 	
-	private boolean terminationCriteriaSatisfied(){
-		return stop || isTimeExpired() || currentPosExampleTrees.isEmpty();
+	private boolean terminationCriteriaSatisfied() {
+		//stop was called or time expired
+		if(stop || isTimeExpired()){
+			return true;
+		}
+		
+		// stop if there are no more positive examples to cover
+		if (stopOnFirstDefinition && currentPosExamples.isEmpty()) {
+			return true;
+		}
+
+		// we stop when the score of the last tree added is too low
+		// (indicating that the algorithm could not find anything appropriate
+		// in the timeframe set)
+		if (bestCurrentScore < minimumTreeScore) {
+			return true;
+		}
+
+		// stop when almost all positive examples have been covered
+		if (tryFullCoverage) {
+			return false;
+		} else {
+			int maxPosRemaining = (int) Math.ceil(startPosExamplesSize * 0.05d);
+			return (currentPosExamples.size() <= maxPosRemaining);
+		}
 	}
 	
 	private boolean partialSolutionTerminationCriteriaSatisfied(){
@@ -635,6 +678,13 @@
 		this.coverageBeta = coverageBeta;
 	}
 	
+	/**
+	 * @param posWeight the posWeight to set
+	 */
+	public void setPosWeight(double posWeight) {
+		this.posWeight = posWeight;
+	}
+	
 	/* (non-Javadoc)
 	 * @see java.lang.Object#clone()
 	 */

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-08 14:39:43 UTC (rev 4264)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-08 14:40:15 UTC (rev 4265)
@@ -63,7 +63,7 @@
 			case FMEASURE : 
 				score = Heuristics.getFScore(tp/(tp+fn), tp/(tp+fp), posExamplesWeight);break;
 			case PRED_ACC : 
-				score = (posExamplesWeight * tp + tn) / (posExamplesWeight * (tp + fn) + tn + fp);break;
+				score = (tp + posExamplesWeight * tn) / ((tp + fn) + posExamplesWeight * (tn + fp));break;
 			case ENTROPY  :{
 				double total = tp + fn;
 				double pp = tp / total;

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-05-08 14:39:43 UTC (rev 4264)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-05-08 14:40:15 UTC (rev 4265)
@@ -161,7 +161,7 @@
             			label += "Values: " + object.getLiterals();
             		}
             	}
-            	label += object.isResourceNode() + "," + object.isLiteralNode();
+//            	label += object.isResourceNode() + "," + object.isLiteralNode();
                 return label;
             }
         };
@@ -801,13 +801,16 @@
         writer.println(ren);
         for (QueryTree<N> child : getChildren()) {
             Object edge = getEdge(child);
-            if (edge != null) {
+            boolean meaningful = !edge.equals(RDF.type.getURI()) || meaningful(child);
+            if (edge != null && meaningful) {
                 writer.print(sb.toString());
                 writer.print("--- ");
                 writer.print(edge);
                 writer.print(" ---\n");
             }
-            child.dump(writer, indent);
+            if(meaningful){
+            	child.dump(writer, indent);
+            }
         }
         writer.flush();
 //    	int depth = getPathToRoot().size();
@@ -832,6 +835,23 @@
 //        writer.flush();
     }
 
+    private boolean meaningful(QueryTree<N> tree){
+    	if(tree.isResourceNode() || tree.isLiteralNode()){
+    		return true;
+    	} else {
+    		for (QueryTree<N> child : tree.getChildren()) {
+    			Object edge = tree.getEdge(child);
+    			if(!edge.equals(RDFS.subClassOf.getURI())){
+    				return true;
+    			} else if(child.isResourceNode()){
+    				return true;
+    			} else if(meaningful(child)){
+    				return true;
+    			}
+    		}
+    	}
+    	return false;
+    }
 
     public List<N> fillDepthFirst() {
         List<N> results = new ArrayList<N>();

Modified: trunk/components-core/src/main/java/org/dllearner/utilities/statistics/Stat.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/statistics/Stat.java	2014-05-08 14:39:43 UTC (rev 4264)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/statistics/Stat.java	2014-05-08 14:40:15 UTC (rev 4265)
@@ -75,6 +75,14 @@
     	}
     }
     
+    public void add(Stat stat){
+    	count += stat.count;
+		sum += stat.sum;
+    	squareSum += stat.squareSum;
+    	min = Math.min(min, stat.min);
+    	max = Math.max(max, stat.max);
+    }
+    
     /**
      * Add a number to this object.
      * 

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java	2014-05-08 14:39:43 UTC (rev 4264)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java	2014-05-08 14:40:15 UTC (rev 4265)
@@ -26,6 +26,7 @@
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
 import java.text.DecimalFormat;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedList;
@@ -60,6 +61,7 @@
 import org.dllearner.utilities.statistics.Stat;
 
 import com.google.common.base.Charsets;
+import com.google.common.collect.Lists;
 import com.google.common.io.Files;
 
 /**
@@ -100,6 +102,15 @@
 public class NestedCrossValidation {
 	
 	private File outputFile = new File("log/nested-cv.log");
+	DecimalFormat df = new DecimalFormat();	
+	
+	// overall statistics
+	Stat globalAcc = new Stat();
+	Stat globalF = new Stat();
+	Stat globalRecall = new Stat();
+	Stat globalPrecision = new Stat();
+	
+	Map<Double,Stat> globalParaStats = new HashMap<Double,Stat>();
 
 	/**
 	 * Entry method, which uses JOptSimple to parse parameters.
@@ -115,8 +126,7 @@
 
 		OptionParser parser = new OptionParser();
 		parser.acceptsAll(asList("h", "?", "help"), "Show help.");
-		parser.acceptsAll(asList("c", "conf"), "Conf file to use.").withRequiredArg().ofType(
-				File.class);
+		parser.acceptsAll(asList("c", "conf"), "The comma separated list of conffiles to be used.").withRequiredArg().describedAs("file1, file2, ...");
 		parser.acceptsAll(asList( "v", "verbose"), "Be more verbose.");
 		parser.acceptsAll(asList( "o", "outerfolds"), "Number of outer folds.").withRequiredArg().ofType(Integer.class).describedAs("#folds");
 		parser.acceptsAll(asList( "i", "innerfolds"), "Number of inner folds.").withRequiredArg().ofType(Integer.class).describedAs("#folds");
@@ -139,7 +149,12 @@
 		// all options present => start nested cross validation
 		} else if(options.has("c") && options.has("o") && options.has("i") && options.has("p") && options.has("r")) {
 			// read all options in variables and parse option values
-			File confFile = (File) options.valueOf("c");
+			String confFilesString = (String) options.valueOf("c");
+			List<File> confFiles = new ArrayList<File>();
+			for (String fileString : confFilesString.split(",")) {
+				confFiles.add(new File(fileString.trim()));
+			}
+			
 			int outerFolds = (Integer) options.valueOf("o");
 			int innerFolds = (Integer) options.valueOf("i");
 			String parameter = (String) options.valueOf("p");
@@ -164,7 +179,7 @@
 			java.util.logging.Logger.getLogger("").setLevel(java.util.logging.Level.WARNING);
 			
 			System.out.println("Warning: The script is not well tested yet. (No known bugs, but needs more testing.)");
-			new NestedCrossValidation(confFile, outerFolds, innerFolds, parameter, rangeStart, rangeEnd, stepsize, verbose);
+			new NestedCrossValidation(confFiles, outerFolds, innerFolds, parameter, rangeStart, rangeEnd, stepsize, verbose);
 			
 		// an option is missing => print help screen and message
 		} else {
@@ -182,16 +197,52 @@
 		}
 		System.out.println(s);
 	}
+	
+	public NestedCrossValidation(File confFile, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws ComponentInitException, ParseException, org.dllearner.confparser.ParseException, IOException {
+		this(Lists.newArrayList(confFile), outerFolds, innerFolds, parameter, startValue, endValue, stepsize, verbose);
+	}
 
-	public NestedCrossValidation(File confFile, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws ComponentInitException, ParseException, org.dllearner.confparser.ParseException, IOException {
+	public NestedCrossValidation(List<File> confFiles, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws ComponentInitException, ParseException, org.dllearner.confparser.ParseException, IOException {
 		
-		DecimalFormat df = new DecimalFormat();	
-		ComponentManager cm = ComponentManager.getInstance();
+		for (File confFile : confFiles) {
+			print(confFile.getPath());
+			validate(confFile, outerFolds, innerFolds, parameter, startValue, endValue, stepsize, verbose);		
+		}
 		
+		print("********************************************");
+		print("********************************************");
+		print("********************************************");
+		
+		// decide for the best parameter
+		print("    Summary over parameter values:");
+		double bestPara = startValue;
+		double bestValue = Double.NEGATIVE_INFINITY;
+		for (Entry<Double, Stat> entry : globalParaStats.entrySet()) {
+			double para = entry.getKey();
+			Stat stat = entry.getValue();
+			print("      value " + para + ": " + stat.prettyPrint("%"));
+			if (stat.getMean() > bestValue) {
+				bestPara = para;
+				bestValue = stat.getMean();
+			}
+		}
+		print("      selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
+		
+		// overall statistics
+		print("*******************");
+		print("* Overall Results *");
+		print("*******************");
+		print("accuracy: " + globalAcc.prettyPrint("%"));
+		print("F measure: " + globalF.prettyPrint("%"));
+		print("precision: " + globalPrecision.prettyPrint("%"));
+		print("recall: " + globalRecall.prettyPrint("%"));
+		
+	}
+	
+	private void validate(File confFile, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws IOException, ComponentInitException{
 		CLI start = new CLI(confFile);
 		start.init();
 		AbstractLearningProblem lp = start.getLearningProblem();
-		System.out.println(lp);
 		if(!(lp instanceof PosNegLP)) {
 			System.out.println("Positive only learning not supported yet.");
 			System.exit(0);
@@ -213,7 +264,7 @@
 		Stat accOverall = new Stat();
 		Stat fOverall = new Stat();
 		Stat recallOverall = new Stat();
-		Stat precisionOverall = new Stat();		
+		Stat precisionOverall = new Stat();
 		
 		for(int currOuterFold=0; currOuterFold<outerFolds; currOuterFold++) {
 			
@@ -302,11 +353,15 @@
 					
 					// free memory
 					rs.releaseKB();
-					cm.freeAllComponents();
 				}
 				
 				paraStats.put(currParaValue, paraCriterionStat);
-				
+				Stat globalParaStat = globalParaStats.get(currParaValue);
+				if(globalParaStat == null){
+					globalParaStat = new Stat();
+					globalParaStats.put(currParaValue, globalParaStat);
+				}
+				globalParaStat.add(paraCriterionStat);
 			}
 			
 			// decide for the best parameter
@@ -382,9 +437,13 @@
 			
 			// free memory
 			rs.releaseKB();
-			cm.freeAllComponents();			
 		}
 		
+		globalAcc.add(accOverall);
+		globalF.add(fOverall);
+		globalPrecision.add(precisionOverall);
+		globalRecall.add(recallOverall);
+		
 		// overall statistics
 		print("*******************");
 		print("* Overall Results *");
@@ -393,7 +452,6 @@
 		print("F measure: " + fOverall.prettyPrint("%"));
 		print("precision: " + precisionOverall.prettyPrint("%"));
 		print("recall: " + recallOverall.prettyPrint("%"));
-		
 	}
 	
 	// convenience methods, which takes a list of examples and divides them in

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-08 14:39:43 UTC (rev 4264)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-08 14:40:15 UTC (rev 4265)
@@ -496,13 +496,13 @@
 		lp.setReasoner(reasoner);
 		lp.init();
 		QTL2Disjunctive la = new QTL2Disjunctive(lp, reasoner);
-		la.init();
-		la.start();
+//		la.init();
+//		la.start();
 		
 		CrossValidation.outputFile = new File("log/qtl-cv.log");
 		CrossValidation.writeToFile = true;
 		CrossValidation.multiThreaded = multiThreaded;
-//		CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
+		CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
 		long endTime = System.currentTimeMillis();
 		System.err.println((endTime - startTime) + "ms");
 	}

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4264] trunk/test/qtl

[<lor...@us...>]

Revision: 4264
          http://sourceforge.net/p/dl-learner/code/4264
Author:   lorenz_b
Date:     2014-05-08 14:39:43 +0000 (Thu, 08 May 2014)
Log Message:
-----------
Added QTL examples.

Modified Paths:
--------------
    trunk/test/qtl/mutagenesis/train1.conf

Added Paths:
-----------
    trunk/test/qtl/alzheimer/
    trunk/test/qtl/alzheimer/alzheimer.owl
    trunk/test/qtl/alzheimer/prolog/
    trunk/test/qtl/alzheimer/prolog/amine_uptake/
    trunk/test/qtl/alzheimer/prolog/amine_uptake/d_alz_ne.b
    trunk/test/qtl/alzheimer/prolog/amine_uptake/ne.f
    trunk/test/qtl/alzheimer/prolog/amine_uptake/ne.n
    trunk/test/qtl/alzheimer/prolog/choline/
    trunk/test/qtl/alzheimer/prolog/choline/d_alz_inh.b
    trunk/test/qtl/alzheimer/prolog/choline/inh.f
    trunk/test/qtl/alzheimer/prolog/choline/inh.n
    trunk/test/qtl/alzheimer/prolog/d_alz.b
    trunk/test/qtl/alzheimer/prolog/nd_alz.b
    trunk/test/qtl/alzheimer/prolog/scopolamine/
    trunk/test/qtl/alzheimer/prolog/scopolamine/d_alz_rsd.b
    trunk/test/qtl/alzheimer/prolog/scopolamine/rsd.f
    trunk/test/qtl/alzheimer/prolog/scopolamine/rsd.n
    trunk/test/qtl/alzheimer/prolog/toxic/
    trunk/test/qtl/alzheimer/prolog/toxic/d_alz_toxic.b
    trunk/test/qtl/alzheimer/prolog/toxic/toxic.f
    trunk/test/qtl/alzheimer/prolog/toxic/toxic.n
    trunk/test/qtl/alzheimer/train1.conf
    trunk/test/qtl/alzheimer/train2.conf
    trunk/test/qtl/alzheimer/train3.conf
    trunk/test/qtl/alzheimer/train4.conf
    trunk/test/qtl/breasttissue/
    trunk/test/qtl/breasttissue/breasttissue.owl
    trunk/test/qtl/breasttissue/files/
    trunk/test/qtl/breasttissue/files/breasttissue.txt
    trunk/test/qtl/breasttissue/train1.conf
    trunk/test/qtl/breasttissue/train2.conf
    trunk/test/qtl/breasttissue/train3.conf
    trunk/test/qtl/breasttissue/train4.conf
    trunk/test/qtl/breasttissue/train5.conf
    trunk/test/qtl/breasttissue/train6.conf
    trunk/test/qtl/breasttissue/train7.conf
    trunk/test/qtl/cardiotocography/
    trunk/test/qtl/cardiotocography/cardiotocography.zip
    trunk/test/qtl/cardiotocography/files/
    trunk/test/qtl/cardiotocography/files/cardiotocography.txt
    trunk/test/qtl/cardiotocography/train1.conf
    trunk/test/qtl/cardiotocography/train10.conf
    trunk/test/qtl/cardiotocography/train11.conf
    trunk/test/qtl/cardiotocography/train12.conf
    trunk/test/qtl/cardiotocography/train13.conf
    trunk/test/qtl/cardiotocography/train2.conf
    trunk/test/qtl/cardiotocography/train3.conf
    trunk/test/qtl/cardiotocography/train4.conf
    trunk/test/qtl/cardiotocography/train5.conf
    trunk/test/qtl/cardiotocography/train6.conf
    trunk/test/qtl/cardiotocography/train7.conf
    trunk/test/qtl/cardiotocography/train8.conf
    trunk/test/qtl/cardiotocography/train9.conf
    trunk/test/qtl/parkinsons/
    trunk/test/qtl/parkinsons/files/
    trunk/test/qtl/parkinsons/parkinsons.data
    trunk/test/qtl/parkinsons/parkinsons.owl
    trunk/test/qtl/parkinsons/train.conf
    trunk/test/qtl/suramin/
    trunk/test/qtl/suramin/catalog.xml
    trunk/test/qtl/suramin/prolog/
    trunk/test/qtl/suramin/prolog/suramin.pl
    trunk/test/qtl/suramin/suramin.owl
    trunk/test/qtl/suramin/train.conf

Added: trunk/test/qtl/alzheimer/alzheimer.owl
===================================================================
--- trunk/test/qtl/alzheimer/alzheimer.owl	                        (rev 0)
+++ trunk/test/qtl/alzheimer/alzheimer.owl	2014-05-08 14:39:43 UTC (rev 4264)
@@ -0,0 +1,2285 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://dl-learner.org/alzheimer#"
+     xml:base="http://dl-learner.org/alzheimer"
+     xmlns:alzheimer="http://dl-learner.org/alzheimer#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:CH2="http://dl-learner.org/alzheimer#CH2&#8211;"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+    <owl:Ontology rdf:about="http://dl-learner.org/alzheimer"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsNrOfReplacementsInMiddleRing -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsNrOfReplacementsInMiddleRing"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsReplacedAtPosition -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsReplacedAtPosition"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsReplacedBy -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsReplacedBy"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsReplacedByFirst -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsReplacedByFirst"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsReplacedBySecond -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsReplacedBySecond"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsReplacedByThird -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsReplacedByThird"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsReplacedWith -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsReplacedWith"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsRingReplacedAtPosition -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsRingReplacedAtPosition"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#getsRingReplacementAt -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#getsRingReplacementAt"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#hasFlex -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#hasFlex"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#hasNrOfAlkylSubstitutions -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#hasNrOfAlkylSubstitutions"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#hasPolatisation -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#hasPolatisation"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#hasRingStructure -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#hasRingStructure"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#hasSigma -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#hasSigma"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#hasSize -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#hasSize"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreater -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreater"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreaterFlex -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreaterFlex"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreaterHAcceptor -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreaterHAcceptor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreaterHDonor -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreaterHDonor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreaterPiAcceptor -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreaterPiAcceptor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreaterPiDonor -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreaterPiDonor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreaterPolar -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreaterPolar"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreaterSigma -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreaterSigma"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isGreaterSize -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isGreaterSize"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isHAcceptor -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isHAcceptor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isHDoner -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isHDoner"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isPiAcceptor -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isPiAcceptor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isPiDoner -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isPiDoner"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#isPolarisable -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#isPolarisable"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#nrOfSubstitutionsInRing -->
+
+    <owl:ObjectProperty rdf:about="http://dl-learner.org/alzheimer#nrOfSubstitutionsInRing"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#Drug -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#Drug"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#Flex -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#Flex"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#HAcceptor -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#HAcceptor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#HDonor -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#HDonor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#PiAcceptor -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#PiAcceptor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#PiDonor -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#PiDonor"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#Polar -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#Polar"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#Sigma -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#Sigma"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#Size -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#Size"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#Substituent -->
+
+    <owl:Class rdf:about="http://dl-learner.org/alzheimer#Substituent"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#(Aromatic-Ring)2 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#(Aromatic-Ring)2"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#(CH3)2 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#(CH3)2"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#(CH3)3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#(CH3)3"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#0"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#1">
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#0"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#2 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#2">
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#1"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#3">
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#2"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#4 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#4">
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <isGreater rdf:resource="http://dl-learner.org/alzheimer#3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#5 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#5"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#6 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#6"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#7 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#7"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#Aromatic-Ring -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#CH2&#8211;CH3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#CH2&#8211;CH3"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#CH3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#CH3"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#N(CH3)2 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#N(CH3)2">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Substituent"/>
+        <hasFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isHDoner rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isPiAcceptor rdf:resource="http://dl-learner.org/alzheimer#pi_acc0"/>
+        <isPiDoner rdf:resource="http://dl-learner.org/alzheimer#pi_don2"/>
+        <hasPolatisation rdf:resource="http://dl-learner.org/alzheimer#polar1"/>
+        <isPolarisable rdf:resource="http://dl-learner.org/alzheimer#polari1"/>
+        <hasSigma rdf:resource="http://dl-learner.org/alzheimer#sigma1"/>
+        <hasSize rdf:resource="http://dl-learner.org/alzheimer#size2"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#a1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#a1">
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#h"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#h"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#aa1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#aa1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Drug"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#4"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedWith rdf:resource="http://dl-learner.org/alzheimer#ch3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#ch3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#b1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#b1">
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#7"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cl"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#h"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#h"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#bb1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#bb1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Drug"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#4"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#ch3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#c1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#c1">
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cl"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#h"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#h"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#cc1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#cc1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Drug"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedWith rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#cf3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#cf3">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Substituent"/>
+        <hasFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isHDoner rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isPiAcceptor rdf:resource="http://dl-learner.org/alzheimer#pi_acc0"/>
+        <isPiDoner rdf:resource="http://dl-learner.org/alzheimer#pi_don0"/>
+        <hasPolatisation rdf:resource="http://dl-learner.org/alzheimer#polar3"/>
+        <isPolarisable rdf:resource="http://dl-learner.org/alzheimer#polari0"/>
+        <hasSigma rdf:resource="http://dl-learner.org/alzheimer#sigma3"/>
+        <hasSize rdf:resource="http://dl-learner.org/alzheimer#size1"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#ch3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#ch3">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Substituent"/>
+        <hasFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isHDoner rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isPiAcceptor rdf:resource="http://dl-learner.org/alzheimer#pi_acc0"/>
+        <isPiDoner rdf:resource="http://dl-learner.org/alzheimer#pi_don0"/>
+        <hasPolatisation rdf:resource="http://dl-learner.org/alzheimer#polar0"/>
+        <isPolarisable rdf:resource="http://dl-learner.org/alzheimer#polari1"/>
+        <hasSigma rdf:resource="http://dl-learner.org/alzheimer#sigma0"/>
+        <hasSize rdf:resource="http://dl-learner.org/alzheimer#size1"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#cl -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#cl">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Substituent"/>
+        <hasFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isHDoner rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isPiAcceptor rdf:resource="http://dl-learner.org/alzheimer#pi_acc0"/>
+        <isPiDoner rdf:resource="http://dl-learner.org/alzheimer#pi_don0"/>
+        <hasPolatisation rdf:resource="http://dl-learner.org/alzheimer#polar3"/>
+        <isPolarisable rdf:resource="http://dl-learner.org/alzheimer#polari1"/>
+        <hasSigma rdf:resource="http://dl-learner.org/alzheimer#sigma3"/>
+        <hasSize rdf:resource="http://dl-learner.org/alzheimer#size1"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#d1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#d1">
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#h"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#h"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#och3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#dd1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#dd1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Drug"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+        <getsReplacedWith rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#e1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#e1">
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#h"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#h"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#ee1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#ee1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Drug"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#4"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#4"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+        <getsReplacedWith rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#f -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#f">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Substituent"/>
+        <hasFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isHDoner rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isPiAcceptor rdf:resource="http://dl-learner.org/alzheimer#pi_acc0"/>
+        <isPiDoner rdf:resource="http://dl-learner.org/alzheimer#pi_don0"/>
+        <hasPolatisation rdf:resource="http://dl-learner.org/alzheimer#polar5"/>
+        <isPolarisable rdf:resource="http://dl-learner.org/alzheimer#polari0"/>
+        <hasSigma rdf:resource="http://dl-learner.org/alzheimer#sigma5"/>
+        <hasSize rdf:resource="http://dl-learner.org/alzheimer#size1"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#f1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#f1">
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#f"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#h"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#h"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#ff1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#ff1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Drug"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#4"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#4"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#5"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#5"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#5"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#f"/>
+        <getsReplacedWith rdf:resource="http://dl-learner.org/alzheimer#f"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex0">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex2 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex2">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex1"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex3">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex1"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex2"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex4 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex4">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex1"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex2"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex5 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex5">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex1"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex2"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex3"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex4"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex6 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex6">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex1"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex2"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex3"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex4"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex5"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex7 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex7">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex1"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex2"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex3"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex4"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex5"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex6"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex8 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex8">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex1"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex2"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex3"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex4"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex5"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex6"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex7"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#flex9 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#flex9">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Flex"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex0"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex1"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex2"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex3"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex4"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex5"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex6"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex7"/>
+        <isGreaterFlex rdf:resource="http://dl-learner.org/alzheimer#flex8"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#g1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#g1">
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#h"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#h"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h"/>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h1">
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc0">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc2 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc2">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc3">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc2"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc4 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc4">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc2"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc5 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc5">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc2"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc3"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc4"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc6 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc6">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc2"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc3"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc4"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc5"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc7 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc7">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc2"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc3"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc4"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc5"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc6"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc8 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc8">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc2"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc3"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc4"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc5"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc6"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc7"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_acc9 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_acc9">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HAcceptor"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc0"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc1"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc2"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc3"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc4"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc5"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc6"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc7"/>
+        <isGreaterHAcceptor rdf:resource="http://dl-learner.org/alzheimer#h_acc8"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don0 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don0">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don2 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don2">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don1"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don3 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don3">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don1"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don2"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don4 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don4">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don1"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don2"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don5 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don5">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don1"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don2"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don3"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don4"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don6 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don6">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don1"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don2"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don3"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don4"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don5"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don7 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don7">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don1"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don2"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don3"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don4"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don5"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don6"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don8 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don8">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don1"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don2"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don3"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don4"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don5"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don6"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don7"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#h_don9 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#h_don9">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#HDonor"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don0"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don1"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don2"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don3"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don4"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don5"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don6"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don7"/>
+        <isGreaterHDonor rdf:resource="http://dl-learner.org/alzheimer#h_don8"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#hh1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#hh1">
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cl"/>
+        <hasRingStructure rdf:resource="http://dl-learner.org/alzheimer#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#i1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#i1">
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#(CH3)3"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#(CH3)3"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#3"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#ii1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#ii1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Drug"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#4"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#4"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cl"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#f"/>
+        <getsReplacedWith rdf:resource="http://dl-learner.org/alzheimer#f"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#j1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#j1">
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#(CH3)2"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#(CH3)2"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#N(CH3)2"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#N(CH3)2"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#jj1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#jj1">
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#f"/>
+        <hasRingStructure rdf:resource="http://dl-learner.org/alzheimer#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#k1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#k1">
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#(CH3)2"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#(CH3)2"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <hasRingStructure rdf:resource="http://dl-learner.org/alzheimer#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#kk1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#kk1">
+        <rdf:type rdf:resource="http://dl-learner.org/alzheimer#Drug"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacementAt rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsRingReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedWith rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#f"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#l1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#l1">
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#(CH3)3"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#(CH3)3"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <getsReplacedByThird rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <hasRingStructure rdf:resource="http://dl-learner.org/alzheimer#normal"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#o"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#o"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#ll1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#ll1">
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsReplacedAtPosition rdf:resource="http://dl-learner.org/alzheimer#6"/>
+        <getsReplacedBySecond rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#Aromatic-Ring"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#CH3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#cf3"/>
+        <hasRingStructure rdf:resource="http://dl-learner.org/alzheimer#normal"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://dl-learner.org/alzheimer#m1 -->
+
+    <owl:NamedIndividual rdf:about="http://dl-learner.org/alzheimer#m1">
+        <getsReplacedByThird rdf:resource="http://dl-learner.org/alzheimer#(Aromatic-Ring)2"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#(Aromatic-Ring)2"/>
+        <getsReplacedByFirst rdf:resource="http://dl-learner.org/alzheimer#(CH3)3"/>
+        <getsReplacedBy rdf:resource="http://dl-learner.org/alzheimer#(CH3)3"/>
+        <nrOfSubstitutionsInRing rdf:resource="http://dl-learner.org/alzheimer#0"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#1"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#2"/>
+        <getsNrOfReplacementsInMiddleRing rdf:resource="http://dl-learner.org/alzheimer#3"/>
+        <hasNrOfAlkylSubstitutions rdf:resource="http://dl-learner.org/alzheimer#4"...
 
[truncated message content]

[DL-Learner SVN] SF.net SVN: dl-learner:[4263] trunk

[<lor...@us...>]

Revision: 4263
          http://sourceforge.net/p/dl-learner/code/4263
Author:   lorenz_b
Date:     2014-05-08 11:45:45 +0000 (Thu, 08 May 2014)
Log Message:
-----------
Added more termination criteria for QTL algorithm. Added heuristics for tree score.

Modified Paths:
--------------
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
    trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java
    trunk/components-core/src/main/java/org/dllearner/learningproblems/QueryTreeScore.java
    trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-07 13:43:54 UTC (rev 4262)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-08 11:45:45 UTC (rev 4263)
@@ -2,6 +2,7 @@
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
+import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -61,6 +62,7 @@
 	
 	
 	private static final Logger logger = Logger.getLogger(QTL2Disjunctive.class.getName());
+	private final DecimalFormat df = new DecimalFormat("0.00"); 
 	
 	private LGGGenerator<String> lggGenerator;
 	
@@ -92,21 +94,31 @@
 	
 	private EvaluatedDescription currentBestSolution;
 	
+	private QueryTreeHeuristic heuristic;
 	
 	
 	//Parameters
 	@ConfigOption(name = "noisePercentage", defaultValue="0.0", description="the (approximated) percentage of noise within the examples")
 	private double noisePercentage = 0.0;
 	@ConfigOption(defaultValue = "10", name = "maxExecutionTimeInSeconds", description = "maximum execution of the algorithm in seconds")
-	private int maxExecutionTimeInSeconds = 10;
-	private double minimumTreeScore = 0.2;
+	private int maxExecutionTimeInSeconds = -1;
+	
 	private double coverageWeight = 0.8;
 	private double specifityWeight = 0.1;
-	private double noise = 0.3;
-	private double coverageBeta = 0.7;
+	private double coverageBeta = 0.5;
 	
-	private double posExampleWeight = 1;
+	private double minCoveredPosExamplesFraction = 0.2;
+	// maximum execution time to compute a part of the solution
+	private double maxTreeComputationTimeInSeconds = 60;
+	// how important not to cover negatives
+	private double posWeight = 2;
+	// minimum score a query tree must have to be part of the solution
+	private double minimumTreeScore = 0.2;
 	
+	private long startTime;
+
+	private long partialSolutionStartTime;
+	
 	public QTL2Disjunctive() {}
 	
 	public QTL2Disjunctive(PosNegLP learningProblem, AbstractReasonerComponent reasoner) throws LearningProblemUnsupportedException{
@@ -142,6 +154,11 @@
 		
 		lggGenerator = new LGGGeneratorImpl<String>();
 		
+		if(heuristic == null){
+			heuristic = new QueryTreeHeuristic();
+			heuristic.setPosExamplesWeight(2);
+		}
+		
 		logger.info("Initializing...");
 		treeCache = new QueryTreeCache(model);
 		tree2Individual = new HashMap<QueryTree<String>, Individual>(lp.getPositiveExamples().size()+lp.getNegativeExamples().size());
@@ -164,6 +181,7 @@
 	}
 	
 	private void generateTrees(){
+		logger.info("Generating trees...");
 		QueryTree<String> queryTree;
 		for (Individual ind : lp.getPositiveExamples()) {
 			queryTree = treeCache.getQueryTree(ind.getName());
@@ -175,6 +193,7 @@
 			tree2Individual.put(queryTree, ind);
 			currentNegExampleTrees.add(queryTree);
 		}
+		logger.info("...done.");
 	}
 	
 	/* (non-Javadoc)
@@ -183,46 +202,59 @@
 	@Override
 	public void start() {
 		String setup = "Setup:";
-		setup += "#Pos. examples:" + currentPosExamples.size();
-		setup += "#Neg. examples:" + currentNegExamples.size();
-		setup += "Coverage beta:" + coverageBeta;
+		setup += "\n#Pos. examples:" + currentPosExamples.size();
+		setup += "\n#Neg. examples:" + currentNegExamples.size();
+		setup += "\nCoverage beta:" + coverageBeta;
 		logger.info(setup);
 		logger.info("Running...");
-		long startTime = System.currentTimeMillis();
+		startTime = System.currentTimeMillis();
 		
 		reset();
 		
 		int i = 1;
-		do {
+		while(!terminationCriteriaSatisfied()){
 			logger.info(i++ + ". iteration...");
 			logger.info("#Remaining pos. examples:" + currentPosExampleTrees.size());
 			logger.info("#Remaining neg. examples:" + currentNegExampleTrees.size());
 			
-			//compute LGG
-			computeLGG();
+			//compute a (partial) solution
+			computeNextPartialSolution();
 			
 			//pick best (partial) solution computed so far
 			EvaluatedQueryTree<String> bestPartialSolution = currentPartialSolutions.first();
-			partialSolutions.add(bestPartialSolution);
 			
-			//remove all covered examples
-			QueryTree<String> tree;
-			for (Iterator<QueryTree<String>> iterator = currentPosExampleTrees.iterator(); iterator.hasNext();) {
-				tree = iterator.next();
-				if(tree.isSubsumedBy(bestPartialSolution.getTree())){
-					iterator.remove();
-					currentPosExamples.remove(tree2Individual.get(tree));
+			//add if some criteria are satisfied
+			if(bestPartialSolution.getScore() >= minimumTreeScore){
+				
+				partialSolutions.add(bestPartialSolution);
+				
+				//remove all covered examples
+				QueryTree<String> tree;
+				for (Iterator<QueryTree<String>> iterator = currentPosExampleTrees.iterator(); iterator.hasNext();) {
+					tree = iterator.next();
+					if(tree.isSubsumedBy(bestPartialSolution.getTree())){
+						iterator.remove();
+						currentPosExamples.remove(tree2Individual.get(tree));
+					}
 				}
-			}
-			for (Iterator<QueryTree<String>> iterator = currentNegExampleTrees.iterator(); iterator.hasNext();) {
-				tree = iterator.next();
-				if(tree.isSubsumedBy(bestPartialSolution.getTree())){
-					iterator.remove();
-					currentNegExamples.remove(tree2Individual.get(tree));
+				for (Iterator<QueryTree<String>> iterator = currentNegExampleTrees.iterator(); iterator.hasNext();) {
+					tree = iterator.next();
+					if(tree.isSubsumedBy(bestPartialSolution.getTree())){
+						iterator.remove();
+						currentNegExamples.remove(tree2Individual.get(tree));
+					}
 				}
+				//build the current combined solution
+				currentBestSolution = buildCombinedSolution();
+				
+				logger.info("combined accuracy: " + df.format(currentBestSolution.getAccuracy()));
+			} else {
+				logger.info("no tree found, which satisfies the minimum criteria - the best was: "
+						+ currentBestSolution.getDescription().toManchesterSyntaxString(baseURI, prefixes)
+						+ " with score " + currentBestSolution.getScore());
 			}
-			currentBestSolution = buildCombinedSolution();
-		} while (!(stop || currentPosExampleTrees.isEmpty()));
+			
+		};
 		
 		isRunning = false;
 		
@@ -234,6 +266,119 @@
 		
 	}
 	
+	private void computeNextPartialSolution(){
+		logger.info("Computing best partial solution...");
+		currentlyBestScore = 0d;
+		partialSolutionStartTime = System.currentTimeMillis();
+		initTodoList(currentPosExampleTrees, currentNegExampleTrees);
+		
+		EvaluatedQueryTree<String> currentElement;
+		while(!partialSolutionTerminationCriteriaSatisfied()){
+			logger.trace("TODO list size: " + todoList.size());
+			//pick best element from todo list
+			currentElement = todoList.poll();
+			//generate the LGG between the chosen tree and each uncovered positive example
+			for (QueryTree<String> example : currentElement.getFalseNegatives()) {
+				QueryTree<String> tree = currentElement.getTree();
+
+				//compute the LGG
+				lggMon.start();
+				QueryTree<String> lgg = lggGenerator.getLGG(tree, example);
+				lggMon.stop();
+				
+				//evaluate the LGG
+				EvaluatedQueryTree<String> solution = evaluate(lgg, true);
+				double score = solution.getScore();
+				double mas = heuristic.getMaximumAchievableScore(solution);
+				
+				if(score >= currentlyBestScore){
+					//add to todo list, if not already contained in todo list or solution list
+					todo(solution);
+					if(solution.getScore() > currentlyBestScore){
+						logger.info("Got better solution:" + solution.getTreeScore());
+					}
+					currentlyBestScore = solution.getScore();
+				} else if(mas < currentlyBestScore){
+					todo(solution);
+				} else {
+					System.out.println("Too general");
+				}
+				currentPartialSolutions.add(currentElement);
+				
+			}
+			currentPartialSolutions.add(currentElement);
+		}
+		long endTime = System.currentTimeMillis();
+		logger.info("...finished in " + (endTime-partialSolutionStartTime) + "ms.");
+		EvaluatedDescription bestPartialSolution = currentPartialSolutions.first().asEvaluatedDescription();
+		
+		logger.info("Best partial solution:\n" + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()) + "\n(" + bestPartialSolution.getScore() + ")");
+		
+		logger.trace("LGG time: " + lggMon.getTotal() + "ms");
+		logger.trace("Avg. LGG time: " + lggMon.getAvg() + "ms");
+		logger.info("#LGG computations: " + lggMon.getHits());
+		logger.trace("Subsumption test time: " + subMon.getTotal() + "ms");
+		logger.trace("Avg. subsumption test time: " + subMon.getAvg() + "ms");
+		logger.trace("#Subsumption tests: " + subMon.getHits());
+	}
+	
+	private EvaluatedQueryTree<String> evaluate(QueryTree<String> tree, boolean useSpecifity){
+		//1. get a score for the coverage = recall oriented
+		//compute positive examples which are not covered by LGG
+		List<QueryTree<String>> uncoveredPositiveExampleTrees = getUncoveredTrees(tree, currentPosExampleTrees);
+		Set<Individual> uncoveredPosExamples = new TreeSet<Individual>();
+		for (QueryTree<String> queryTree : uncoveredPositiveExampleTrees) {
+			uncoveredPosExamples.add(tree2Individual.get(queryTree));
+		}
+		//compute negative examples which are covered by LGG
+		Collection<QueryTree<String>> coveredNegativeExampleTrees = getCoveredTrees(tree, currentNegExampleTrees);
+		Set<Individual> coveredNegExamples = new TreeSet<Individual>();
+		for (QueryTree<String> queryTree : coveredNegativeExampleTrees) {
+			coveredNegExamples.add(tree2Individual.get(queryTree));
+		}
+		//compute score
+		int coveredPositiveExamples = currentPosExampleTrees.size() - uncoveredPositiveExampleTrees.size();
+		double recall = coveredPositiveExamples / (double)currentPosExampleTrees.size();
+		double precision = (coveredNegativeExampleTrees.size() + coveredPositiveExamples == 0) 
+						? 0 
+						: coveredPositiveExamples / (double)(coveredPositiveExamples + coveredNegativeExampleTrees.size());
+		
+		double coverageScore = Heuristics.getFScore(recall, precision, coverageBeta);
+		
+		//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
+		int nrOfSpecificNodes = 0;
+		for (QueryTree<String> childNode : tree.getChildrenClosure()) {
+			if(!childNode.getUserObject().equals("?")){
+				nrOfSpecificNodes++;
+			}
+		}
+		double specifityScore = 0d;
+		if(useSpecifity){
+			specifityScore = Math.log(nrOfSpecificNodes);
+		}
+		
+		//3.compute the total score
+		double score = coverageWeight * coverageScore + specifityWeight * specifityScore;
+		
+		QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
+				new TreeSet<Individual>(Sets.difference(currentPosExamples, uncoveredPosExamples)), uncoveredPosExamples,
+				coveredNegExamples, new TreeSet<Individual>(Sets.difference(currentNegExamples, coveredNegExamples)),
+				specifityScore, nrOfSpecificNodes);
+		
+//		QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
+//				null,null,null,null,
+//				specifityScore, nrOfSpecificNodes);
+		
+		EvaluatedQueryTree<String> evaluatedTree = new EvaluatedQueryTree<String>(tree, uncoveredPositiveExampleTrees, coveredNegativeExampleTrees, queryTreeScore);
+		
+		//TODO use only the heuristic to compute the score
+		score = heuristic.getScore(evaluatedTree);
+		queryTreeScore.setScore(score);
+		queryTreeScore.setAccuracy(score);
+		
+		return evaluatedTree;
+	}
+	
 	private EvaluatedDescription buildCombinedSolution(){
 		if(partialSolutions.size() == 1){
 			EvaluatedDescription combinedSolution = partialSolutions.get(0).asEvaluatedDescription();
@@ -288,58 +433,8 @@
 		lggMon.reset();
 	}
 	
-	private void computeLGG(){
-		logger.info("Computing best partial solution...");
-		currentlyBestScore = 0d;
-		
-		initTodoList(currentPosExampleTrees, currentNegExampleTrees);
-		
-		long startTime = System.currentTimeMillis();
-		EvaluatedQueryTree<String> currentElement;
-		do{
-			logger.trace("TODO list size: " + todoList.size());
-			//pick best element from todo list
-			currentElement = todoList.poll();
-			//generate the LGG between the chosen tree and each uncovered positive example
-			for (QueryTree<String> example : currentElement.getFalseNegatives()) {
-				QueryTree<String> tree = currentElement.getTree();
-
-				//compute the LGG
-				lggMon.start();
-				QueryTree<String> lgg = lggGenerator.getLGG(tree, example);
-				lggMon.stop();
-				
-				//evaluate the LGG
-				EvaluatedQueryTree<String> solution = evaluate(lgg, true);
-				
-				if(solution.getScore() >= currentlyBestScore){
-					//add to todo list, if not already contained in todo list or solution list
-					todo(solution);
-					if(solution.getScore() > currentlyBestScore){
-						logger.info("Got better solution:" + solution.getTreeScore());
-					}
-					currentlyBestScore = solution.getScore();
-				}
-				currentPartialSolutions.add(currentElement);
-				
-			}
-			currentPartialSolutions.add(currentElement);
-//			todoList.remove(currentElement);
-		} while(!terminationCriteriaSatisfied());
-		long endTime = System.currentTimeMillis();
-		logger.info("...finished in " + (endTime-startTime) + "ms.");
-		EvaluatedDescription bestPartialSolution = currentPartialSolutions.first().asEvaluatedDescription();
-		
-		logger.info("Best partial solution:\n" + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()) + "\n(" + bestPartialSolution.getScore() + ")");
-		
-		logger.trace("LGG time: " + lggMon.getTotal() + "ms");
-		logger.trace("Avg. LGG time: " + lggMon.getAvg() + "ms");
-		logger.trace("#LGG computations: " + lggMon.getHits());
-		logger.trace("Subsumption test time: " + subMon.getTotal() + "ms");
-		logger.trace("Avg. subsumption test time: " + subMon.getAvg() + "ms");
-		logger.trace("#Subsumption tests: " + subMon.getHits());
-	}
 	
+	
 	/* (non-Javadoc)
 	 * @see org.dllearner.core.StoppableLearningAlgorithm#stop()
 	 */
@@ -411,58 +506,7 @@
 		return treeCache;
 	}
 
-	private EvaluatedQueryTree<String> evaluate(QueryTree<String> tree, boolean useSpecifity){
-		//1. get a score for the coverage = recall oriented
-		//compute positive examples which are not covered by LGG
-		List<QueryTree<String>> uncoveredPositiveExampleTrees = getUncoveredTrees(tree, currentPosExampleTrees);
-		Set<Individual> uncoveredPosExamples = new TreeSet<Individual>();
-		for (QueryTree<String> queryTree : uncoveredPositiveExampleTrees) {
-			uncoveredPosExamples.add(tree2Individual.get(queryTree));
-		}
-		//compute negative examples which are covered by LGG
-		Collection<QueryTree<String>> coveredNegativeExampleTrees = getCoveredTrees(tree, currentNegExampleTrees);
-		Set<Individual> coveredNegExamples = new TreeSet<Individual>();
-		for (QueryTree<String> queryTree : coveredNegativeExampleTrees) {
-			coveredNegExamples.add(tree2Individual.get(queryTree));
-		}
-		//compute score
-		int coveredPositiveExamples = currentPosExampleTrees.size() - uncoveredPositiveExampleTrees.size();
-		double recall = coveredPositiveExamples / (double)currentPosExampleTrees.size();
-		double precision = (coveredNegativeExampleTrees.size() + coveredPositiveExamples == 0) 
-						? 0 
-						: coveredPositiveExamples / (double)(coveredPositiveExamples + coveredNegativeExampleTrees.size());
-		
-		double beta = 0.5;
-		double coverageScore = Heuristics.getFScore(recall, precision, beta);
-		
-		//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
-		int nrOfSpecificNodes = 0;
-		for (QueryTree<String> childNode : tree.getChildrenClosure()) {
-			if(!childNode.getUserObject().equals("?")){
-				nrOfSpecificNodes++;
-			}
-		}
-		double specifityScore = 0d;
-		if(useSpecifity){
-			specifityScore = Math.log(nrOfSpecificNodes);
-		}
-		
-		//3.compute the total score
-		double score = coverageWeight * coverageScore + specifityWeight * specifityScore;
-		
-		QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
-				new TreeSet<Individual>(Sets.difference(currentPosExamples, uncoveredPosExamples)), uncoveredPosExamples,
-				coveredNegExamples, new TreeSet<Individual>(Sets.difference(currentNegExamples, coveredNegExamples)),
-				specifityScore, nrOfSpecificNodes);
-		
-//		QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
-//				null,null,null,null,
-//				specifityScore, nrOfSpecificNodes);
-		
-		EvaluatedQueryTree<String> evaluatedTree = new EvaluatedQueryTree<String>(tree, uncoveredPositiveExampleTrees, coveredNegativeExampleTrees, queryTreeScore);
-		
-		return evaluatedTree;
-	}
+	
 
 	/**
 	 * Return all trees from the given list {@code allTrees} which are not already subsumed by {@code tree}.
@@ -535,9 +579,21 @@
 	}
 	
 	private boolean terminationCriteriaSatisfied(){
-		return stop || todoList.isEmpty() || currentPosExampleTrees.isEmpty();
+		return stop || isTimeExpired() || currentPosExampleTrees.isEmpty();
 	}
 	
+	private boolean partialSolutionTerminationCriteriaSatisfied(){
+		return stop || todoList.isEmpty() || currentPosExampleTrees.isEmpty() || isPartialSolutionTimeExpired() || isTimeExpired();
+	}
+	
+	private boolean isTimeExpired(){
+		return maxExecutionTimeInSeconds <= 0 ? false : (System.currentTimeMillis() - startTime)/1000d >= maxExecutionTimeInSeconds;
+	}
+	
+	private boolean isPartialSolutionTimeExpired(){
+		return maxTreeComputationTimeInSeconds <= 0 ? false : (System.currentTimeMillis() - partialSolutionStartTime)/1000d >= maxTreeComputationTimeInSeconds;
+	}
+	
 	/**
 	 * Add tree to todo list if not already contained in that list or the solutions.
 	 * @param solution

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-07 13:43:54 UTC (rev 4262)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-08 11:45:45 UTC (rev 4263)
@@ -13,6 +13,7 @@
 import org.dllearner.core.Heuristic;
 import org.dllearner.core.owl.Individual;
 import org.dllearner.learningproblems.Heuristics;
+import org.dllearner.learningproblems.Heuristics.HeuristicType;
 import org.dllearner.learningproblems.QueryTreeScore;
 import org.dllearner.utilities.owl.ConceptComparator;
 
@@ -23,6 +24,8 @@
 @ComponentAnn(name = "QueryTreeHeuristic", shortName = "qtree_heuristic", version = 0.1)
 public class QueryTreeHeuristic extends AbstractComponent implements Heuristic, Comparator<EvaluatedQueryTree<String>>{
 	
+	private HeuristicType heuristicType = HeuristicType.PRED_ACC;
+	
 	// F score beta value
 	private double coverageBeta = 1;
 	
@@ -30,6 +33,8 @@
 	
 	private double specifityWeight = 0.1;
 	
+	private double posExamplesWeight = 1;
+	
 	// syntactic comparison as final comparison criterion
 	private ConceptComparator conceptComparator = new ConceptComparator();
 
@@ -43,23 +48,88 @@
 	public double getScore(EvaluatedQueryTree<String> tree){
 		QueryTreeScore treeScore = tree.getTreeScore();
 		
-		//TODO
-		double score = treeScore.getScore();
+		Set<Individual> truePositives = treeScore.getCoveredPositives();
+		Set<Individual> trueNegatives = treeScore.getNotCoveredNegatives();
+		Set<Individual> falsePositives = treeScore.getNotCoveredPositives();
+		Set<Individual> falseNegatives = treeScore.getCoveredNegatives();
 		
+		double tp = truePositives.size();
+		double tn = trueNegatives.size();
+		double fp = falsePositives.size();
+		double fn = falseNegatives.size();
+		
+		double score = 0;
+		switch(heuristicType){
+			case FMEASURE : 
+				score = Heuristics.getFScore(tp/(tp+fn), tp/(tp+fp), posExamplesWeight);break;
+			case PRED_ACC : 
+				score = (posExamplesWeight * tp + tn) / (posExamplesWeight * (tp + fn) + tn + fp);break;
+			case ENTROPY  :{
+				double total = tp + fn;
+				double pp = tp / total;
+				double pn = fn / total;
+				score = pp * Math.log(pp) + pn * Math.log(pn);
+				break;}
+			case MATTHEWS_CORRELATION  :
+				score = (tp * tn - fp * fn) / Math.sqrt((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn));break;
+			case YOUDEN_INDEX : score = tp / (tp + fn) + tn / (fp + tn) - 1;break;
+		default:
+			break;
+			
+		}
+		
 		return score;
 	}
 	
-	private double getPredictedAccuracy(EvaluatedQueryTree<String> tree){
+	/**
+	 * Returns the maximum achievable score according to the used score function.
+	 * @return
+	 */
+	public double getMaximumAchievableScore(EvaluatedQueryTree<String> tree) {
 		QueryTreeScore treeScore = tree.getTreeScore();
 		
 		Set<Individual> truePositives = treeScore.getCoveredPositives();
 		Set<Individual> trueNegatives = treeScore.getNotCoveredNegatives();
 		Set<Individual> falsePositives = treeScore.getNotCoveredPositives();
 		Set<Individual> falseNegatives = treeScore.getCoveredNegatives();
-		return 0;
 		
+		double tp = truePositives.size();
+		double tn = trueNegatives.size();
+		double fp = falsePositives.size();
+		double fn = falseNegatives.size();
+		
+		return getMaximumAchievableScore(tp, tn, fp, fn);
 	}
+	
+	/**
+	 * Returns the maximum achievable score according to the used score function.
+	 * @param tp
+	 * @param tn
+	 * @param fp
+	 * @param fn
+	 * @return
+	 */
+	private double getMaximumAchievableScore(double tp, double tn, double fp, double fn) {
+		double mas = 0d;
+		switch (heuristicType) {
+		case FMEASURE:
+			break;
+		case PRED_ACC:
+			mas = (posExamplesWeight * tp + tn - fp) / (posExamplesWeight * (tp + fn) + tn + fp);
+			break;
+		case ENTROPY:
+			break;
+		case MATTHEWS_CORRELATION:
+			break;
+		case YOUDEN_INDEX:
+			break;
+		default:
+			break;
 
+		}
+		return mas;
+	}
+	
 	/* (non-Javadoc)
 	 * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
 	 */
@@ -75,5 +145,19 @@
 			return conceptComparator.compare(tree1.asEvaluatedDescription().getDescription(), tree2.asEvaluatedDescription().getDescription());
 		}
 	}
+	
+	/**
+	 * @param heuristicType the heuristicType to set
+	 */
+	public void setHeuristicType(HeuristicType heuristicType) {
+		this.heuristicType = heuristicType;
+	}
+	
+	/**
+	 * @param posExamplesWeight the posExamplesWeight to set
+	 */
+	public void setPosExamplesWeight(double posExamplesWeight) {
+		this.posExamplesWeight = posExamplesWeight;
+	}
 
 }

Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java	2014-05-07 13:43:54 UTC (rev 4262)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java	2014-05-08 11:45:45 UTC (rev 4263)
@@ -29,7 +29,7 @@
  */
 public class Heuristics {
 
-	public static enum HeuristicType { PRED_ACC, AMEASURE, JACCARD, FMEASURE, GEN_FMEASURE };	
+	public static enum HeuristicType { PRED_ACC, AMEASURE, JACCARD, FMEASURE, GEN_FMEASURE, ENTROPY, MATTHEWS_CORRELATION, YOUDEN_INDEX };	
 	
 	/**
 	 * Computes F1-Score.

Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/QueryTreeScore.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/QueryTreeScore.java	2014-05-07 13:43:54 UTC (rev 4262)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/QueryTreeScore.java	2014-05-08 11:45:45 UTC (rev 4263)
@@ -16,7 +16,7 @@
 	
 	private double score;
 	
-	private double coverageScore;
+	private double accuracy;
 	
 	private double specifityScore;
 	private int nrOfSpecificNodes;
@@ -26,12 +26,12 @@
     private Set<Individual> negAsPos;
     private Set<Individual> negAsNeg;    
 
-	public QueryTreeScore(double score, double coverageScore, 
+	public QueryTreeScore(double score, double accuracy, 
 			Set<Individual> posAsPos, Set<Individual> posAsNeg, Set<Individual> negAsPos, Set<Individual> negAsNeg,
 			double specifityScore, int nrOfSpecificNodes) {
 		super();
 		this.score = score;
-		this.coverageScore = coverageScore;
+		this.accuracy = accuracy;
 		this.posAsPos = posAsPos;
 		this.posAsNeg = posAsNeg;
 		this.negAsPos = negAsPos;
@@ -46,15 +46,29 @@
 	public double getScore() {
 		return score;
 	}
+	
+	/**
+	 * @param score the score to set
+	 */
+	public void setScore(double score) {
+		this.score = score;
+	}
 
 	/* (non-Javadoc)
 	 * @see org.dllearner.core.Score#getAccuracy()
 	 */
 	@Override
 	public double getAccuracy() {
-		return score;
+		return accuracy;
 	}
 	
+	/**
+	 * @param accuracy the accuracy to set
+	 */
+	public void setAccuracy(double accuracy) {
+		this.accuracy = accuracy;
+	}
+	
 	public Set<Individual> getCoveredNegatives() {
 		return negAsPos;
 	}
@@ -77,7 +91,7 @@
 	@Override
 	public String toString() {
 		return score
-				 + "(coverage=" + coverageScore 
+				 + "(accuracy=" + accuracy 
 				 + "(+" + posAsPos.size() + "/" + (posAsPos.size() + posAsNeg.size())
 				 + "|-" + negAsPos.size() + "/" + (negAsPos.size() + negAsNeg.size()) + ")|"
 				 + "specifity=" + specifityScore + "(" + nrOfSpecificNodes + "))";   

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java	2014-05-07 13:43:54 UTC (rev 4262)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java	2014-05-08 11:45:45 UTC (rev 4263)
@@ -19,44 +19,49 @@
  */
 package org.dllearner.scripts;
 
+import static java.util.Arrays.asList;
+
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
 import java.text.DecimalFormat;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Random;
 import java.util.Set;
 import java.util.TreeSet;
-import java.util.Map.Entry;
 
+import joptsimple.OptionParser;
+import joptsimple.OptionSet;
+
+import org.apache.commons.beanutils.PropertyUtils;
 import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
-import org.dllearner.cli.Start;
-import org.dllearner.core.ComponentInitException;
-import org.dllearner.core.ComponentManager;
+import org.dllearner.cli.CLI;
 import org.dllearner.core.AbstractCELA;
 import org.dllearner.core.AbstractLearningProblem;
 import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
 import org.dllearner.core.owl.Description;
 import org.dllearner.core.owl.Individual;
 import org.dllearner.learningproblems.PosNegLP;
 import org.dllearner.parser.ParseException;
 import org.dllearner.utilities.Helper;
-import org.dllearner.utilities.datastructures.Datastructures;
 import org.dllearner.utilities.datastructures.TrainTestList;
 import org.dllearner.utilities.statistics.Stat;
 
-import joptsimple.OptionParser;
-import joptsimple.OptionSet;
+import com.google.common.base.Charsets;
+import com.google.common.io.Files;
 
-import static java.util.Arrays.*;
-
 /**
  * Performs nested cross validation for the given problem. A k fold outer and l
  * fold inner cross validation is used. Parameters:
@@ -93,6 +98,8 @@
  * 
  */
 public class NestedCrossValidation {
+	
+	private File outputFile = new File("log/nested-cv.log");
 
 	/**
 	 * Entry method, which uses JOptSimple to parse parameters.
@@ -115,6 +122,7 @@
 		parser.acceptsAll(asList( "i", "innerfolds"), "Number of inner folds.").withRequiredArg().ofType(Integer.class).describedAs("#folds");
 		parser.acceptsAll(asList( "p", "parameter"), "Parameter to vary.").withRequiredArg();
 		parser.acceptsAll(asList( "r", "pvalues", "range"), "Values of parameter. $x-$y can be used for integer ranges.").withRequiredArg();
+		parser.acceptsAll(asList( "s", "stepsize", "steps"), "Step size of range.").withOptionalArg().ofType(Double.class).defaultsTo(1d);
 
 		// parse options and display a message for the user in case of problems
 		OptionSet options = null;
@@ -137,8 +145,9 @@
 			String parameter = (String) options.valueOf("p");
 			String range = (String) options.valueOf("r");
 			String[] rangeSplit = range.split("-");
-			int rangeStart = new Integer(rangeSplit[0]);
-			int rangeEnd = new Integer(rangeSplit[1]);
+			double rangeStart = Double.valueOf(rangeSplit[0]);
+			double rangeEnd = Double.valueOf(rangeSplit[1]);
+			double stepsize = (Double) options.valueOf("s");
 			boolean verbose = options.has("v");
 			
 			// create logger (a simple logger which outputs
@@ -149,11 +158,13 @@
 			logger.removeAllAppenders();
 			logger.addAppender(consoleAppender);
 			logger.setLevel(Level.WARN);
+			Logger.getLogger("org.dllearner.algorithms").setLevel(Level.INFO);
+//			logger.addAppender(new FileAppender(layout, "nested-cv.log", false));
 			// disable OWL API info output
 			java.util.logging.Logger.getLogger("").setLevel(java.util.logging.Level.WARNING);
 			
 			System.out.println("Warning: The script is not well tested yet. (No known bugs, but needs more testing.)");
-			new NestedCrossValidation(confFile, outerFolds, innerFolds, parameter, rangeStart, rangeEnd, verbose);
+			new NestedCrossValidation(confFile, outerFolds, innerFolds, parameter, rangeStart, rangeEnd, stepsize, verbose);
 			
 		// an option is missing => print help screen and message
 		} else {
@@ -163,14 +174,24 @@
 
 	}
 
-	public NestedCrossValidation(File confFile, int outerFolds, int innerFolds, String parameter, int startValue, int endValue, boolean verbose) throws FileNotFoundException, ComponentInitException, ParseException, org.dllearner.confparser.ParseException {
+	private void print(String s){
+		try {
+			Files.append(s + "\n", outputFile , Charsets.UTF_8);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		System.out.println(s);
+	}
+
+	public NestedCrossValidation(File confFile, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws ComponentInitException, ParseException, org.dllearner.confparser.ParseException, IOException {
 		
 		DecimalFormat df = new DecimalFormat();	
 		ComponentManager cm = ComponentManager.getInstance();
 		
-		Start start = new Start(confFile);
+		CLI start = new CLI(confFile);
+		start.init();
 		AbstractLearningProblem lp = start.getLearningProblem();
-		
+		System.out.println(lp);
 		if(!(lp instanceof PosNegLP)) {
 			System.out.println("Positive only learning not supported yet.");
 			System.exit(0);
@@ -196,16 +217,16 @@
 		
 		for(int currOuterFold=0; currOuterFold<outerFolds; currOuterFold++) {
 			
-			System.out.println("Outer fold " + currOuterFold);
+			print("Outer fold " + currOuterFold);
 			TrainTestList posList = posLists.get(currOuterFold);
 			TrainTestList negList = negLists.get(currOuterFold);
 			
 			// measure relevant criterion (accuracy, F-measure) over different parameter values
-			Map<Integer,Stat> paraStats = new HashMap<Integer,Stat>();
+			Map<Double,Stat> paraStats = new HashMap<Double,Stat>();
 			
-			for(int currParaValue=startValue; currParaValue<=endValue; currParaValue++) {
+			for(double currParaValue=startValue; currParaValue<=endValue; currParaValue+=stepsize) {
 				
-				System.out.println("  Parameter value " + currParaValue + ":");
+				print("  Parameter value " + currParaValue + ":");
 				// split train folds again (computation of inner folds for each parameter
 				// value is redundant, but not a big problem)
 				List<Individual> trainPosList = posList.getTrainList();
@@ -219,19 +240,24 @@
 				
 				for(int currInnerFold=0; currInnerFold<innerFolds; currInnerFold++) {
 					
-					System.out.println("    Inner fold " + currInnerFold + ":");
+					print("    Inner fold " + currInnerFold + ":");
 					// get positive & negative examples for training run
 					Set<Individual> posEx = new TreeSet<Individual>(innerPosLists.get(currInnerFold).getTrainList());
 					Set<Individual> negEx = new TreeSet<Individual>(innerNegLists.get(currInnerFold).getTrainList());
 					
 					// read conf file and exchange options for pos/neg examples 
 					// and parameter to optimise
-					start = new Start(confFile);
+					start = new CLI(confFile);
+					start.init();
 					AbstractLearningProblem lpIn = start.getLearningProblem();
-					cm.applyConfigEntry(lpIn, "positiveExamples", Datastructures.individualSetToStringSet(posEx));
-					cm.applyConfigEntry(lpIn, "negativeExamples", Datastructures.individualSetToStringSet(negEx));
+					((PosNegLP)lpIn).setPositiveExamples(posEx);
+					((PosNegLP)lpIn).setNegativeExamples(negEx);
 					AbstractCELA laIn = start.getLearningAlgorithm();
-					cm.applyConfigEntry(laIn, parameter, (double)currParaValue);
+					try {
+						PropertyUtils.setSimpleProperty(laIn, parameter, currParaValue);
+					} catch (IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
+						e.printStackTrace();
+					}
 					
 					lpIn.init();
 					laIn.init();
@@ -263,15 +289,15 @@
 					
 					paraCriterionStat.addNumber(accuracy);
 					
-					System.out.println("      hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
-					System.out.println("      accuracy: " + df.format(accuracy) + "%");
-					System.out.println("      precision: " + df.format(precision) + "%");
-					System.out.println("      recall: " + df.format(recall) + "%");
-					System.out.println("      F measure: " + df.format(fmeasure) + "%");
+					print("      hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
+					print("      accuracy: " + df.format(accuracy) + "%");
+					print("      precision: " + df.format(precision) + "%");
+					print("      recall: " + df.format(recall) + "%");
+					print("      F measure: " + df.format(fmeasure) + "%");
 					
 					if(verbose) {
-						System.out.println("      false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
-						System.out.println("      false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
+						print("      false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
+						print("      false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
 					}
 					
 					// free memory
@@ -284,28 +310,33 @@
 			}
 			
 			// decide for the best parameter
-			System.out.println("    Summary over parameter values:");
-			int bestPara = startValue;
+			print("    Summary over parameter values:");
+			double bestPara = startValue;
 			double bestValue = Double.NEGATIVE_INFINITY;
-			for(Entry<Integer,Stat> entry : paraStats.entrySet()) {
-				int para = entry.getKey();
+			for(Entry<Double,Stat> entry : paraStats.entrySet()) {
+				double para = entry.getKey();
 				Stat stat = entry.getValue();
-				System.out.println("      value " + para + ": " + stat.prettyPrint("%"));
+				print("      value " + para + ": " + stat.prettyPrint("%"));
 				if(stat.getMean() > bestValue) {
 					bestPara = para;
 					bestValue = stat.getMean();
 				}
 			}
-			System.out.println("      selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
-			System.out.println("    Learn on Outer fold:");
+			print("      selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
+			print("    Learn on Outer fold:");
 			
 			// start a learning process with this parameter and evaluate it on the outer fold
-			start = new Start(confFile);
+			start = new CLI(confFile);
+			start.init();
 			AbstractLearningProblem lpOut = start.getLearningProblem();
-			cm.applyConfigEntry(lpOut, "positiveExamples", Datastructures.individualListToStringSet(posLists.get(currOuterFold).getTrainList()));
-			cm.applyConfigEntry(lpOut, "negativeExamples", Datastructures.individualListToStringSet(negLists.get(currOuterFold).getTrainList()));
+			((PosNegLP)lpOut).setPositiveExamples(new TreeSet<Individual>(posLists.get(currOuterFold).getTrainList()));
+			((PosNegLP)lpOut).setNegativeExamples(new TreeSet<Individual>(negLists.get(currOuterFold).getTrainList()));
 			AbstractCELA laOut = start.getLearningAlgorithm();
-			cm.applyConfigEntry(laOut, parameter, (double)bestPara);
+			try {
+				PropertyUtils.setSimpleProperty(laOut, parameter, bestPara);
+			} catch (IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
+				e.printStackTrace();
+			}
 			
 			lpOut.init();
 			laOut.init();
@@ -332,15 +363,15 @@
 			double recall = 100 * (double) posCorrect.size() / (posCorrect.size() + posError.size());
 			double fmeasure = 2 * (precision * recall) / (precision + recall);
 	
-			System.out.println("      hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
-			System.out.println("      accuracy: " + df.format(accuracy) + "%");
-			System.out.println("      precision: " + df.format(precision) + "%");
-			System.out.println("      recall: " + df.format(recall) + "%");
-			System.out.println("      F measure: " + df.format(fmeasure) + "%");
+			print("      hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
+			print("      accuracy: " + df.format(accuracy) + "%");
+			print("      precision: " + df.format(precision) + "%");
+			print("      recall: " + df.format(recall) + "%");
+			print("      F measure: " + df.format(fmeasure) + "%");
 			
 			if(verbose) {
-				System.out.println("      false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
-				System.out.println("      false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
+				print("      false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
+				print("      false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
 			}			
 			
 			// update overall statistics
@@ -355,14 +386,13 @@
 		}
 		
 		// overall statistics
-		System.out.println();
-		System.out.println("*******************");
-		System.out.println("* Overall Results *");
-		System.out.println("*******************");
-		System.out.println("accuracy: " + accOverall.prettyPrint("%"));
-		System.out.println("F measure: " + fOverall.prettyPrint("%"));
-		System.out.println("precision: " + precisionOverall.prettyPrint("%"));
-		System.out.println("recall: " + recallOverall.prettyPrint("%"));
+		print("*******************");
+		print("* Overall Results *");
+		print("*******************");
+		print("accuracy: " + accOverall.prettyPrint("%"));
+		print("F measure: " + fOverall.prettyPrint("%"));
+		print("precision: " + precisionOverall.prettyPrint("%"));
+		print("recall: " + recallOverall.prettyPrint("%"));
 		
 	}
 	

Modified: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-07 13:43:54 UTC (rev 4262)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-08 11:45:45 UTC (rev 4263)
@@ -53,8 +53,8 @@
 public class QTLEvaluation {
 	
 	int nrOfFolds = 10;
-	private int nrOfPosExamples = 100;
-	private int nrOfNegExamples = 100;
+	private int nrOfPosExamples = 300;
+	private int nrOfNegExamples = 300;
 	
 	List<String> posExamples = Lists.newArrayList(
 			"http://dl-learner.org/carcinogenesis#d1",
@@ -496,13 +496,13 @@
 		lp.setReasoner(reasoner);
 		lp.init();
 		QTL2Disjunctive la = new QTL2Disjunctive(lp, reasoner);
-//		la.init();
-//		la.start();
+		la.init();
+		la.start();
 		
 		CrossValidation.outputFile = new File("log/qtl-cv.log");
 		CrossValidation.writeToFile = true;
 		CrossValidation.multiThreaded = multiThreaded;
-		CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
+//		CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
 		long endTime = System.currentTimeMillis();
 		System.err.println((endTime - startTime) + "ms");
 	}

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[DL-Learner SVN] SF.net SVN: dl-learner:[4262] trunk

[<lor...@us...>]

Revision: 4262
          http://sourceforge.net/p/dl-learner/code/4262
Author:   lorenz_b
Date:     2014-05-07 13:43:54 +0000 (Wed, 07 May 2014)
Log Message:
-----------
Updated libs.

Modified Paths:
--------------
    trunk/components-core/pom.xml
    trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/SearchTreeNode.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/AbstractRelevanceMetric.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/RelevanceMetric.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/QueryTreeFactoryImpl.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java
    trunk/components-core/src/main/java/org/dllearner/core/AbstractCELA.java
    trunk/components-core/src/main/java/org/dllearner/core/AbstractReasonerComponent.java
    trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
    trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java
    trunk/components-core/src/main/java/org/dllearner/kb/aquisitors/SparqlTupleAquisitorImproved.java
    trunk/components-core/src/main/java/org/dllearner/learningproblems/PosNegLPStandard.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
    trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
    trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
    trunk/components-core/src/main/resources/log4j.properties
    trunk/components-core/src/test/java/org/dllearner/algorithms/isle/DBpediaExperiment.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/LGGTest.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/QALDExperiment.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/QTLTest.java
    trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/TreeSubsumptionTest.java
    trunk/examples/family-benchmark/Brother.conf
    trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
    trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java
    trunk/interfaces/src/main/java/org/dllearner/cli/SPARQLCrossValidation.java
    trunk/pom.xml
    trunk/protege/src/main/resources/META-INF/MANIFEST.MF
    trunk/scripts/pom.xml
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java

Added Paths:
-----------
    trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/DefaultRelevanceWeightings.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/RelevanceWeightedStableHeuristic.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/RelevanceWeightings.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/syntactic/EntityFrequencyCache.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2DisjunctiveMT.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
    trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/QueryTreeConverter.java

Removed Paths:
-------------
    trunk/test/fuzzydll/fuzzyOWL2fuzzyDLparserOutput.fuzzyDL.txt

Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml	2014-05-07 11:25:54 UTC (rev 4261)
+++ trunk/components-core/pom.xml	2014-05-07 13:43:54 UTC (rev 4262)
@@ -232,10 +232,10 @@
         	<artifactId>commons-pool</artifactId>
         </dependency>
         <dependency>
-        	<groupId>org.semanticweb.elk</groupId>
-        	<artifactId>elk-owlapi</artifactId>
-        	<version>0.3.0</version>
-        </dependency>
+	<groupId>org.semanticweb.elk</groupId>
+	<artifactId>elk-owlapi</artifactId>
+	<version>0.4.1</version>
+</dependency>
            <dependency>
         	<groupId>de.tudresden.inf.lat.cel</groupId>
         	<artifactId>reasoner</artifactId>
@@ -281,7 +281,7 @@
 			<dependency>
       <groupId>org.aksw.jena-sparql-api</groupId>
       <artifactId>jena-sparql-api-core</artifactId>
-      <version>2.10.0-5-SNAPSHOT</version>
+      <version>2.10.0-8</version>
     </dependency>
     <dependency>
 			<groupId>org.apache.commons</groupId>

Added: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/DefaultRelevanceWeightings.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/DefaultRelevanceWeightings.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/DefaultRelevanceWeightings.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -0,0 +1,31 @@
+/**
+ * 
+ */
+package org.dllearner.algorithms.elcopy;
+
+import org.dllearner.algorithms.isle.metrics.ChiSquareRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.DiceRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.JaccardRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.LLRRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.PMIRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.SCIRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.SignificantPMIRelevanceMetric;
+import org.dllearner.algorithms.isle.metrics.TTestRelevanceMetric;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class DefaultRelevanceWeightings extends RelevanceWeightings{
+	
+	public DefaultRelevanceWeightings() {
+		put(PMIRelevanceMetric.class, 1.0);
+		put(SignificantPMIRelevanceMetric.class, 1.0);
+		put(ChiSquareRelevanceMetric.class, 1.0);
+		put(TTestRelevanceMetric.class, 1.0);
+		put(JaccardRelevanceMetric.class, 1.0);
+		put(DiceRelevanceMetric.class, 1.0);
+		put(SCIRelevanceMetric.class, 1.0);
+		put(LLRRelevanceMetric.class, 1.0);
+	}
+}

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java	2014-05-07 11:25:54 UTC (rev 4261)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/ELLearningAlgorithm.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -45,6 +45,7 @@
 import org.dllearner.learningproblems.EvaluatedDescriptionPosNeg;
 import org.dllearner.learningproblems.PosNegLP;
 import org.dllearner.learningproblems.ScorePosNeg;
+import org.dllearner.learningproblems.ScoreTwoValued;
 import org.dllearner.refinementoperators.ELDown3;
 import org.dllearner.utilities.Helper;
 import org.dllearner.utilities.owl.EvaluatedDescriptionSet;
@@ -148,7 +149,10 @@
 	@Override
 	public void init() throws ComponentInitException {
 		// currently we use the stable heuristic
-		heuristic = new StableHeuristic();
+		if(heuristic == null){
+			heuristic = new StableHeuristic();
+		}
+		
 		candidates = new TreeSet<SearchTreeNode>(heuristic);
 		
 		if(ignoredConcepts != null) {
@@ -167,6 +171,13 @@
 		bestEvaluatedDescriptions = new EvaluatedDescriptionSet(maxNrOfResults);
 	}	
 	
+	/**
+	 * @param heuristic the heuristic to set
+	 */
+	public void setHeuristic(ELHeuristic heuristic) {
+		this.heuristic = heuristic;
+	}
+	
 	@Override
 	public void start() {
 		stop = false;
@@ -237,7 +248,13 @@
 			} else {
 				node.setCoveredNegatives(negCovers);
 			}
-			node.setScore(accuracy);
+			node.setAccuracy(accuracy);
+			if(heuristic instanceof RelevanceWeightedStableHeuristic){
+				node.setScore(((RelevanceWeightedStableHeuristic)heuristic).getNodeScore(node));
+			} else {
+				node.setScore(accuracy);
+			}
+			
 //			System.out.println(description + ":" + accuracy);
 			// link to parent (unless start node)
 			if(parentNode == null) {
@@ -259,6 +276,7 @@
 				// for fully computing the evaluated description
 				if(bestEvaluatedDescriptions.size() == 0 || ((EvaluatedDescriptionPosNeg)bestEvaluatedDescriptions.getWorst()).getCoveredNegatives().size() >= node.getCoveredNegatives()) {
 					ScorePosNeg score = (ScorePosNeg) learningProblem.computeScore(description);
+					((ScoreTwoValued)score).setAccuracy(node.getScore());
 					EvaluatedDescriptionPosNeg ed = new EvaluatedDescriptionPosNeg(description, score);
 					bestEvaluatedDescriptions.add(ed);
 				}
@@ -329,7 +347,9 @@
 			
 			//non of the equivalent classes must occur on the first level
 			TreeSet<Description> toTest = new TreeSet<Description>(descriptionComparator);
-			toTest.add(classToDescribe);
+			if(classToDescribe != null){
+				toTest.add(classToDescribe);
+			}
 			while(!toTest.isEmpty()) {
 				Description d = toTest.pollFirst();
 				if(occursOnFirstLevel(description, d)) {
@@ -341,7 +361,9 @@
 			// none of the superclasses of the class to learn must appear on the
 			// outermost property level
 			TreeSet<Description> toTest = new TreeSet<Description>(descriptionComparator);
-			toTest.add(classToDescribe);
+			if(classToDescribe != null){
+				toTest.add(classToDescribe);
+			}
 			while(!toTest.isEmpty()) {
 				Description d = toTest.pollFirst();
 				if(occursOnFirstLevel(description, d)) {

Added: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/RelevanceWeightedStableHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/RelevanceWeightedStableHeuristic.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/RelevanceWeightedStableHeuristic.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -0,0 +1,124 @@
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.dllearner.algorithms.elcopy;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.dllearner.algorithms.isle.metrics.RelevanceMetric;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Entity;
+import org.dllearner.core.owl.NamedClass;
+
+
+/**
+ * A stable comparator for search tree nodes. Stable means that the order
+ * of nodes will not change during the run of the learning algorithm. In
+ * this implementation, this is ensured by using only covered examples
+ * and tree size as criteria.
+ * 
+ * @author Jens Lehmann
+ *
+ */
+public class RelevanceWeightedStableHeuristic implements ELHeuristic {
+
+	private ELDescriptionTreeComparator cmp = new ELDescriptionTreeComparator();
+	private RelevanceWeightings weightings;
+	private List<RelevanceMetric> relevanceMetrics;
+	private NamedClass classToDescribe;
+	
+	
+	public RelevanceWeightedStableHeuristic(NamedClass classToDescribe, RelevanceWeightings weightings, RelevanceMetric... relevanceMetrics) {
+		this.classToDescribe = classToDescribe;
+		this.weightings = weightings;
+		this.relevanceMetrics = Arrays.asList(relevanceMetrics);
+	}
+	
+	public RelevanceWeightedStableHeuristic(NamedClass classToDescribe, RelevanceWeightings weightings, List<RelevanceMetric> relevanceMetrics) {
+		this.classToDescribe = classToDescribe;
+		this.weightings = weightings;
+		this.relevanceMetrics = relevanceMetrics;
+	}
+	
+	public RelevanceWeightedStableHeuristic(NamedClass classToDescribe, RelevanceMetric... relevanceMetrics) {
+		this(classToDescribe, new DefaultRelevanceWeightings(), relevanceMetrics);
+	}
+	
+	public RelevanceWeightedStableHeuristic(NamedClass classToDescribe, List<RelevanceMetric> relevanceMetrics) {
+		this(classToDescribe, new DefaultRelevanceWeightings(), relevanceMetrics);
+	}
+	
+	/**
+	 * @param weightings the weightings to set
+	 */
+	public void setWeightings(RelevanceWeightings weightings) {
+		this.weightings = weightings;
+	}
+	
+	/**
+	 * @param relevanceMetrics the relevanceMetrics to set
+	 */
+	public void setRelevanceMetrics(List<RelevanceMetric> relevanceMetrics) {
+		this.relevanceMetrics = relevanceMetrics;
+	}
+	
+	/**
+	 * @param classToDescribe the classToDescribe to set
+	 */
+	public void setClassToDescribe(NamedClass classToDescribe) {
+		this.classToDescribe = classToDescribe;
+	}
+	
+	public double getNodeScore(SearchTreeNode node){
+		double score = node.getAccuracy();
+		Description d = node.getDescriptionTree().transformToDescription();
+		for (RelevanceMetric metric : relevanceMetrics) {
+			score += weightings.getWeight(metric.getClass()) * metric.getRelevance(classToDescribe, d);
+		}
+		return score;
+	}
+	
+	@Override
+	public int compare(SearchTreeNode o1, SearchTreeNode o2) {
+	
+//		int diff = o2.getCoveredNegatives() - o1.getCoveredNegatives();
+		double score1 = o1.getScore();
+		double score2 = o2.getScore();
+		int diff = Double.compare(score1, score2);
+		if(diff>0) {		
+			return 1;
+		} else if(diff<0) {
+			return -1;
+		} else {
+			
+			double sizeDiff = o2.getDescriptionTree().size - o1.getDescriptionTree().size;
+			
+			if(sizeDiff == 0) {
+				return cmp.compare(o1.getDescriptionTree(), o2.getDescriptionTree());
+			} else if(sizeDiff>0) {
+				return 1;
+			} else {
+				return -1;
+			}
+			
+		}		
+	}
+
+}

Added: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/RelevanceWeightings.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/RelevanceWeightings.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/RelevanceWeightings.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -0,0 +1,24 @@
+/**
+ * 
+ */
+package org.dllearner.algorithms.elcopy;
+
+import java.util.HashMap;
+
+import org.dllearner.algorithms.isle.metrics.RelevanceMetric;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class RelevanceWeightings extends HashMap<Class<? extends RelevanceMetric>, Double>{
+	
+	public double getWeight(RelevanceMetric metric){
+		return get(metric.getClass());
+	}
+	
+	public double getWeight(Class<? extends RelevanceMetric> metricClass){
+		return get(metricClass);
+	}
+
+}

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/SearchTreeNode.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/SearchTreeNode.java	2014-05-07 11:25:54 UTC (rev 4261)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/elcopy/SearchTreeNode.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -38,6 +38,7 @@
 	private boolean tooWeak = false;
 	
 	private double score;
+	protected double accuracy;
 	
 	public SearchTreeNode(ELDescriptionTree descriptionTree) {
 		this.descriptionTree = descriptionTree;
@@ -127,4 +128,18 @@
 		this.score = score;
 	}	
 	
+	/**
+	 * @return the accuracy
+	 */
+	public double getAccuracy() {
+		return accuracy;
+	}
+	
+	/**
+	 * @param accuracy the accuracy to set
+	 */
+	public void setAccuracy(double accuracy) {
+		this.accuracy = accuracy;
+	}
+	
 }

Added: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/syntactic/EntityFrequencyCache.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/syntactic/EntityFrequencyCache.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/syntactic/EntityFrequencyCache.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -0,0 +1,17 @@
+/**
+ * 
+ */
+package org.dllearner.algorithms.isle.index.syntactic;
+
+import java.util.HashMap;
+import java.util.Set;
+
+import org.dllearner.core.owl.Entity;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class EntityFrequencyCache extends HashMap<Set<Entity>, Long>{
+
+}

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/AbstractRelevanceMetric.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/AbstractRelevanceMetric.java	2014-05-07 11:25:54 UTC (rev 4261)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/AbstractRelevanceMetric.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -5,8 +5,10 @@
 
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Set;
 
 import org.dllearner.algorithms.isle.index.Index;
+import org.dllearner.core.owl.Description;
 import org.dllearner.core.owl.Entity;
 
 /**
@@ -16,9 +18,12 @@
 public abstract class AbstractRelevanceMetric implements RelevanceMetric {
 
 	protected Index index;
+	protected String name;
 
 	public AbstractRelevanceMetric(Index index) {
 		this.index = index;
+		
+		name = getClass().getSimpleName().replace("RelevanceMetric", "");
 	}
 
 	public static Map<Entity, Double> normalizeMinMax(Map<Entity, Double> hmEntity2Score) {
@@ -53,5 +58,47 @@
 		}
 		return hmEntity2Norm;
 	}
+	
+	public String getName() {
+		return name;
+	}
+	
+	public double getRelevance(Entity entity, Description desc){
+		Set<Entity> entities = desc.getSignature();
+		double score = 0;
+		for (Entity otherEntity : entities) {
+			double relevance = getRelevance(entity, otherEntity);
+			if(!Double.isInfinite(relevance)){
+				score += relevance/entities.size();
+			}
+		}
+		return score;
+	}
 
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((name == null) ? 0 : name.hashCode());
+		return result;
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		AbstractRelevanceMetric other = (AbstractRelevanceMetric) obj;
+		if (name == null) {
+			if (other.name != null)
+				return false;
+		} else if (!name.equals(other.name))
+			return false;
+		return true;
+	}
+	
+
 }

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/RelevanceMetric.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/RelevanceMetric.java	2014-05-07 11:25:54 UTC (rev 4261)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/metrics/RelevanceMetric.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -20,6 +20,7 @@
 
 package org.dllearner.algorithms.isle.metrics;
 
+import org.dllearner.core.owl.Description;
 import org.dllearner.core.owl.Entity;
 
 
@@ -38,4 +39,6 @@
 	 * @return
 	 */
 	double getNormalizedRelevance(Entity entity1, Entity entity2);
+	
+	double getRelevance(Entity entity, Description desc);
 }
\ No newline at end of file

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-07 11:25:54 UTC (rev 4261)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -1,5 +1,6 @@
 package org.dllearner.algorithms.qtl;
 
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -28,14 +29,19 @@
 import org.dllearner.core.ComponentInitException;
 import org.dllearner.core.EvaluatedDescription;
 import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningProblem;
 import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.Score;
+import org.dllearner.core.config.ConfigOption;
 import org.dllearner.core.owl.Description;
 import org.dllearner.core.owl.Individual;
 import org.dllearner.core.owl.Union;
+import org.dllearner.kb.OWLAPIOntology;
 import org.dllearner.kb.OWLFile;
 import org.dllearner.learningproblems.Heuristics;
 import org.dllearner.learningproblems.PosNegLP;
 import org.dllearner.learningproblems.QueryTreeScore;
+import org.dllearner.learningproblems.ScoreTwoValued;
 import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
 import org.dllearner.utilities.owl.OWLAPIConverter;
 import org.semanticweb.owlapi.io.ToStringRenderer;
@@ -51,12 +57,12 @@
 import com.jamonapi.MonitorFactory;
 
 @ComponentAnn(name="query tree learner with noise (disjunctive)", shortName="qtl2dis", version=0.8)
-public class QTL2Disjunctive extends AbstractCELA {
+public class QTL2Disjunctive extends AbstractCELA implements Cloneable{
 	
 	
 	private static final Logger logger = Logger.getLogger(QTL2Disjunctive.class.getName());
 	
-	private LGGGenerator<String> lggGenerator = new LGGGeneratorImpl<String>();
+	private LGGGenerator<String> lggGenerator;
 	
 	private Queue<EvaluatedQueryTree<String>> todoList;
 	private SortedSet<EvaluatedQueryTree<String>> currentPartialSolutions;
@@ -69,9 +75,6 @@
 	private Set<Individual> currentNegExamples;
 	
 	private Map<QueryTree<String>, Individual> tree2Individual;
-
-	private double coverageWeight = 0.8;
-	private double specifityWeight = 0.2;
 	
 	private QueryTreeCache treeCache;
 
@@ -79,8 +82,6 @@
 
 	private Model model;
 
-	private AbstractReasonerComponent reasoner;
-
 	private volatile boolean stop;
 	private boolean isRunning;
 
@@ -89,16 +90,39 @@
 
 	private List<EvaluatedQueryTree<String>> partialSolutions;
 	
+	private EvaluatedDescription currentBestSolution;
+	
+	
+	
+	//Parameters
+	@ConfigOption(name = "noisePercentage", defaultValue="0.0", description="the (approximated) percentage of noise within the examples")
+	private double noisePercentage = 0.0;
+	@ConfigOption(defaultValue = "10", name = "maxExecutionTimeInSeconds", description = "maximum execution of the algorithm in seconds")
+	private int maxExecutionTimeInSeconds = 10;
+	private double minimumTreeScore = 0.2;
+	private double coverageWeight = 0.8;
+	private double specifityWeight = 0.1;
+	private double noise = 0.3;
+	private double coverageBeta = 0.7;
+	
+	private double posExampleWeight = 1;
+	
 	public QTL2Disjunctive() {}
 	
 	public QTL2Disjunctive(PosNegLP learningProblem, AbstractReasonerComponent reasoner) throws LearningProblemUnsupportedException{
-		this.lp = learningProblem;
-		this.reasoner = reasoner;
+		super(learningProblem, reasoner);
+		loadModel();
 	}
 	
-	public QTL2Disjunctive(PosNegLP lp, Model model) {
-		this.lp = lp;
-		this.model = model;
+//	public QTL2Disjunctive(PosNegLP lp, Model model) {
+//		this.learningProblem = lp;
+//		this.model = model;
+//	}
+	
+	public QTL2Disjunctive(QTL2Disjunctive qtl) {
+		super(qtl.getLearningProblem(), qtl.getReasoner());
+		this.model = ModelFactory.createDefaultModel();
+		this.model.add(qtl.model);
 	}
 	
 	public EvaluatedQueryTree<String> getBestSolution(){
@@ -110,6 +134,14 @@
 	 */
 	@Override
 	public void init() throws ComponentInitException {
+		
+		if(!(learningProblem instanceof PosNegLP)){
+			throw new IllegalArgumentException("Only PosNeg learning problems are supported");
+		}
+		lp = (PosNegLP) learningProblem;
+		
+		lggGenerator = new LGGGeneratorImpl<String>();
+		
 		logger.info("Initializing...");
 		treeCache = new QueryTreeCache(model);
 		tree2Individual = new HashMap<QueryTree<String>, Individual>(lp.getPositiveExamples().size()+lp.getNegativeExamples().size());
@@ -120,6 +152,18 @@
 		currentNegExamples =  new TreeSet<Individual>(lp.getNegativeExamples());
 		
 		//get the query trees
+		generateTrees();
+		
+		//some logging
+		subMon = MonitorFactory.getTimeMonitor("subsumption-mon");
+		lggMon = MonitorFactory.getTimeMonitor("lgg-mon");
+		
+		//console rendering of class expressions
+		ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
+		ToStringRenderer.getInstance().setShortFormProvider(new SimpleShortFormProvider());
+	}
+	
+	private void generateTrees(){
 		QueryTree<String> queryTree;
 		for (Individual ind : lp.getPositiveExamples()) {
 			queryTree = treeCache.getQueryTree(ind.getName());
@@ -131,14 +175,6 @@
 			tree2Individual.put(queryTree, ind);
 			currentNegExampleTrees.add(queryTree);
 		}
-		
-		//some logging
-		subMon = MonitorFactory.getTimeMonitor("subsumption-mon");
-		lggMon = MonitorFactory.getTimeMonitor("lgg-mon");
-		
-		//console rendering of class expressions
-		ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
-		ToStringRenderer.getInstance().setShortFormProvider(new SimpleShortFormProvider());
 	}
 	
 	/* (non-Javadoc)
@@ -146,6 +182,11 @@
 	 */
 	@Override
 	public void start() {
+		String setup = "Setup:";
+		setup += "#Pos. examples:" + currentPosExamples.size();
+		setup += "#Neg. examples:" + currentNegExamples.size();
+		setup += "Coverage beta:" + coverageBeta;
+		logger.info(setup);
 		logger.info("Running...");
 		long startTime = System.currentTimeMillis();
 		
@@ -180,6 +221,7 @@
 					currentNegExamples.remove(tree2Individual.get(tree));
 				}
 			}
+			currentBestSolution = buildCombinedSolution();
 		} while (!(stop || currentPosExampleTrees.isEmpty()));
 		
 		isRunning = false;
@@ -187,22 +229,53 @@
 		long endTime = System.currentTimeMillis();
 		logger.info("Finished in " + (endTime-startTime) + "ms.");
 		
-		EvaluatedDescription combinedSolution = buildCombinedSolution();
-		System.out.println(OWLAPIConverter.getOWLAPIDescription(combinedSolution.getDescription()));
+		logger.info("Combined solution:\n" + OWLAPIConverter.getOWLAPIDescription(currentBestSolution.getDescription()));
+		logger.info(currentBestSolution.getScore());
 		
 	}
 	
 	private EvaluatedDescription buildCombinedSolution(){
+		if(partialSolutions.size() == 1){
+			EvaluatedDescription combinedSolution = partialSolutions.get(0).asEvaluatedDescription();
+			double accuracy = lp.getAccuracy(combinedSolution.getDescription());
+			System.out.println(accuracy);
+			return combinedSolution;
+		}
 		List<Description> disjuncts = new ArrayList<Description>();
+		
+		Set<Individual> posCovered = new HashSet<Individual>();
+		Set<Individual> negCovered = new HashSet<Individual>();
+		
+		//build the union of all class expressions
 		Description partialDescription;
 		for (EvaluatedQueryTree<String> partialSolution : partialSolutions) {
 			partialDescription = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
 					partialSolution.getTree().asOWLClassExpression(LiteralNodeConversionStrategy.FACET_RESTRICTION));
 			disjuncts.add(partialDescription);
+			posCovered.addAll(partialSolution.getTreeScore().getCoveredPositives());
+			negCovered.addAll(partialSolution.getTreeScore().getCoveredNegatives());
 		}
 		Description unionDescription = new Union(disjuncts);
 		
-		return new EvaluatedDescription(unionDescription, null);
+		Set<Individual> posNotCovered = Sets.difference(lp.getPositiveExamples(), posCovered);
+		Set<Individual> negNotCovered = Sets.difference(lp.getNegativeExamples(), negCovered);
+		
+		double accuracy = lp.getAccuracy(unionDescription);
+		System.out.println(accuracy);
+		
+		//compute the coverage
+		double recall = posCovered.size() / (double)lp.getPositiveExamples().size();
+		double precision = (posCovered.size() + negCovered.size() == 0) 
+						? 0 
+						: posCovered.size() / (double)(posCovered.size() + negCovered.size());
+		
+		double coverageScore = Heuristics.getFScore(recall, precision, coverageBeta);
+		
+//		ScoreTwoValued score = new ScoreTwoValued(posCovered, posNotCovered, negCovered, negNotCovered);
+//		score.setAccuracy(coverageScore);
+		QueryTreeScore score = new QueryTreeScore(coverageScore, coverageScore, posCovered, posNotCovered, negCovered, negNotCovered, -1, -1);
+		
+		return new EvaluatedDescription(unionDescription, score);
 	}
 	
 	private void reset(){
@@ -216,6 +289,7 @@
 	}
 	
 	private void computeLGG(){
+		logger.info("Computing best partial solution...");
 		currentlyBestScore = 0d;
 		
 		initTodoList(currentPosExampleTrees, currentNegExampleTrees);
@@ -246,16 +320,17 @@
 					}
 					currentlyBestScore = solution.getScore();
 				}
+				currentPartialSolutions.add(currentElement);
 				
 			}
 			currentPartialSolutions.add(currentElement);
 //			todoList.remove(currentElement);
 		} while(!terminationCriteriaSatisfied());
 		long endTime = System.currentTimeMillis();
-		logger.info("Finished in " + (endTime-startTime) + "ms.");
-		EvaluatedDescription bestSolution = getCurrentlyBestEvaluatedDescription();
+		logger.info("...finished in " + (endTime-startTime) + "ms.");
+		EvaluatedDescription bestPartialSolution = currentPartialSolutions.first().asEvaluatedDescription();
 		
-		logger.info("Best solution:\n" + OWLAPIConverter.getOWLAPIDescription(bestSolution.getDescription()) + "\n(" + bestSolution.getScore() + ")");
+		logger.info("Best partial solution:\n" + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()) + "\n(" + bestPartialSolution.getScore() + ")");
 		
 		logger.trace("LGG time: " + lggMon.getTotal() + "ms");
 		logger.trace("Avg. LGG time: " + lggMon.getAvg() + "ms");
@@ -278,7 +353,7 @@
 	 */
 	@Override
 	public Description getCurrentlyBestDescription() {
-		return getCurrentlyBestEvaluatedDescription().getDescription();
+		return currentBestSolution.getDescription();
 	}
 	
 	/* (non-Javadoc)
@@ -286,8 +361,7 @@
 	 */
 	@Override
 	public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
-		EvaluatedQueryTree<String> bestSolution = currentPartialSolutions.first();
-		return bestSolution.asEvaluatedDescription();
+		return currentBestSolution;
 	}
 	
 	/* (non-Javadoc)
@@ -298,14 +372,18 @@
 		return isRunning;
 	}
 	
+//	@Autowired
+//	public void setLearningProblem(PosNegLP learningProblem) {
+//		this.lp = learningProblem;
+//	}
+	
 	@Autowired
-	public void setLearningProblem(PosNegLP learningProblem) {
-		this.lp = learningProblem;
+	public void setReasoner(AbstractReasonerComponent reasoner){
+		super.setReasoner(reasoner);
+		loadModel();
 	}
 	
-	@Autowired
-	public void setReasoner(AbstractReasonerComponent reasoner){
-		this.reasoner = reasoner;
+	private void loadModel(){
 		model = ModelFactory.createDefaultModel();
 		for (KnowledgeSource ks : reasoner.getSources()) {
 			if(ks instanceof OWLFile){
@@ -314,6 +392,14 @@
 				} catch (IOException e) {
 					e.printStackTrace();
 				}
+			} else if(ks instanceof OWLAPIOntology){
+				ByteArrayInputStream bais = new ByteArrayInputStream(((OWLAPIOntology) ks).getConverter().convert(((OWLAPIOntology) ks).getOntology()));
+				model.read(bais, null);
+				try {
+					bais.close();
+				} catch (IOException e) {
+					e.printStackTrace();
+				}
 			}
 		}
 	}
@@ -328,14 +414,14 @@
 	private EvaluatedQueryTree<String> evaluate(QueryTree<String> tree, boolean useSpecifity){
 		//1. get a score for the coverage = recall oriented
 		//compute positive examples which are not covered by LGG
-		Set<QueryTree<String>> uncoveredPositiveExampleTrees = getUncoveredTrees(tree, currentPosExampleTrees);
-		Set<Individual> uncoveredPosExamples = new HashSet<Individual>();
+		List<QueryTree<String>> uncoveredPositiveExampleTrees = getUncoveredTrees(tree, currentPosExampleTrees);
+		Set<Individual> uncoveredPosExamples = new TreeSet<Individual>();
 		for (QueryTree<String> queryTree : uncoveredPositiveExampleTrees) {
 			uncoveredPosExamples.add(tree2Individual.get(queryTree));
 		}
 		//compute negative examples which are covered by LGG
 		Collection<QueryTree<String>> coveredNegativeExampleTrees = getCoveredTrees(tree, currentNegExampleTrees);
-		Set<Individual> coveredNegExamples = new HashSet<Individual>();
+		Set<Individual> coveredNegExamples = new TreeSet<Individual>();
 		for (QueryTree<String> queryTree : coveredNegativeExampleTrees) {
 			coveredNegExamples.add(tree2Individual.get(queryTree));
 		}
@@ -346,7 +432,8 @@
 						? 0 
 						: coveredPositiveExamples / (double)(coveredPositiveExamples + coveredNegativeExampleTrees.size());
 		
-		double coverageScore = Heuristics.getFScore(recall, precision);
+		double beta = 0.5;
+		double coverageScore = Heuristics.getFScore(recall, precision, beta);
 		
 		//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
 		int nrOfSpecificNodes = 0;
@@ -364,8 +451,8 @@
 		double score = coverageWeight * coverageScore + specifityWeight * specifityScore;
 		
 		QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
-				Sets.difference(currentPosExamples, uncoveredPosExamples), uncoveredPosExamples,
-				coveredNegExamples, Sets.difference(currentNegExamples, coveredNegExamples),
+				new TreeSet<Individual>(Sets.difference(currentPosExamples, uncoveredPosExamples)), uncoveredPosExamples,
+				coveredNegExamples, new TreeSet<Individual>(Sets.difference(currentNegExamples, coveredNegExamples)),
 				specifityScore, nrOfSpecificNodes);
 		
 //		QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
@@ -400,8 +487,8 @@
 	 * @param allTrees
 	 * @return
 	 */
-	private Set<QueryTree<String>> getUncoveredTrees(QueryTree<String> tree, List<QueryTree<String>> allTrees){
-		Set<QueryTree<String>> uncoveredTrees = new LinkedHashSet<QueryTree<String>>();
+	private List<QueryTree<String>> getUncoveredTrees(QueryTree<String> tree, List<QueryTree<String>> allTrees){
+		List<QueryTree<String>> uncoveredTrees = new ArrayList<QueryTree<String>>();
 		for (QueryTree<String> queryTree : allTrees) {
 			boolean subsumed = queryTree.isSubsumedBy(tree);
 			if(!subsumed){
@@ -470,4 +557,33 @@
 		}
 		todoList.add(solution);
 	}
+	
+	/**
+	 * @param noisePercentage the noisePercentage to set
+	 */
+	public void setNoisePercentage(double noisePercentage) {
+		this.noisePercentage = noisePercentage;
+	}
+	
+	/**
+	 * @param maxExecutionTimeInSeconds the maxExecutionTimeInSeconds to set
+	 */
+	public void setMaxExecutionTimeInSeconds(int maxExecutionTimeInSeconds) {
+		this.maxExecutionTimeInSeconds = maxExecutionTimeInSeconds;
+	}
+	
+	/**
+	 * @param coverageBeta the coverageBeta to set
+	 */
+	public void setCoverageBeta(double coverageBeta) {
+		this.coverageBeta = coverageBeta;
+	}
+	
+	/* (non-Javadoc)
+	 * @see java.lang.Object#clone()
+	 */
+	@Override
+	public Object clone() throws CloneNotSupportedException {
+		return new QTL2Disjunctive(this);
+	}
 }

Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2DisjunctiveMT.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2DisjunctiveMT.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2DisjunctiveMT.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -0,0 +1,559 @@
+package org.dllearner.algorithms.qtl;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.PriorityQueue;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+import java.util.concurrent.BlockingQueue;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.PriorityBlockingQueue;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.log4j.Logger;
+import org.dllearner.algorithms.qtl.cache.QueryTreeCache;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl.LiteralNodeConversionStrategy;
+import org.dllearner.algorithms.qtl.operations.lgg.EvaluatedQueryTree;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
+import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.EvaluatedDescription;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.kb.OWLFile;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.learningproblems.QueryTreeScore;
+import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
+import org.dllearner.utilities.owl.OWLAPIConverter;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.util.SimpleShortFormProvider;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+import com.google.common.collect.Sets;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
+
+@ComponentAnn(name="query tree learner with noise (disjunctive)", shortName="qtl2dis", version=0.8)
+public class QTL2DisjunctiveMT extends AbstractCELA {
+	
+	
+	private static final Logger logger = Logger.getLogger(QTL2DisjunctiveMT.class.getName());
+	
+	private LGGGenerator<String> lggGenerator = new LGGGeneratorImpl<String>();
+	
+	private BlockingQueue<EvaluatedQueryTree<String>> todoList;
+	private SortedSet<EvaluatedQueryTree<String>> solutions;
+	
+	private double currentlyBestScore = 0d;
+
+	private List<QueryTree<String>> currentPosExampleTrees;
+	private List<QueryTree<String>> currentNegExampleTrees;
+	
+	private Map<QueryTree<String>, Individual> tree2Indivual;
+
+	private double coverageWeight = 0.8;
+	private double specifityWeight = 0.2;
+	
+	private QueryTreeCache treeCache;
+
+	private PosNegLP lp;
+
+	private Model model;
+
+	private AbstractReasonerComponent reasoner;
+
+	private volatile boolean stop;
+	private boolean isRunning;
+
+	private Monitor subMon;
+	private Monitor lggMon;
+	
+	private final EvaluatedQueryTree<String> STOP_ELEMENT = new EvaluatedQueryTree<String>(new QueryTreeImpl<String>("STOP"), null, null, null);
+	
+	
+	public QTL2DisjunctiveMT() {}
+	
+	public QTL2DisjunctiveMT(PosNegLP learningProblem, AbstractReasonerComponent reasoner) throws LearningProblemUnsupportedException{
+		this.lp = learningProblem;
+		this.reasoner = reasoner;
+		
+	}
+	
+	public QTL2DisjunctiveMT(PosNegLP lp, Model model) {
+		this.lp = lp;
+		this.model = model;
+	}
+	
+	public EvaluatedQueryTree<String> getBestSolution(){
+		return solutions.first();
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.Component#init()
+	 */
+	@Override
+	public void init() throws ComponentInitException {
+		logger.info("Initializing...");
+		treeCache = new QueryTreeCache(model);
+		tree2Indivual = new HashMap<QueryTree<String>, Individual>(lp.getPositiveExamples().size()+lp.getNegativeExamples().size());
+		
+		currentPosExampleTrees = new ArrayList<QueryTree<String>>(lp.getPositiveExamples().size());
+		currentNegExampleTrees = new ArrayList<QueryTree<String>>(lp.getNegativeExamples().size());
+		
+		//get the query trees
+		QueryTree<String> queryTree;
+		for (Individual ind : lp.getPositiveExamples()) {
+			queryTree = treeCache.getQueryTree(ind.getName());
+			tree2Indivual.put(queryTree, ind);
+			currentPosExampleTrees.add(queryTree);
+		}
+		for (Individual ind : lp.getNegativeExamples()) {
+			queryTree = treeCache.getQueryTree(ind.getName());
+			tree2Indivual.put(queryTree, ind);
+			currentNegExampleTrees.add(treeCache.getQueryTree(ind.getName()));
+		}
+		
+		//some logging
+		subMon = MonitorFactory.getTimeMonitor("subsumption-mon");
+		lggMon = MonitorFactory.getTimeMonitor("lgg-mon");
+		
+		//console rendering of class expressions
+		ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
+		ToStringRenderer.getInstance().setShortFormProvider(new SimpleShortFormProvider());
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.LearningAlgorithm#start()
+	 */
+	@Override
+	public void start() {
+		logger.info("Running...");
+		stop = false;
+		isRunning = true;
+		long startTime = System.currentTimeMillis();
+		
+		subMon = MonitorFactory.getTimeMonitor("subsumption-mon");
+		lggMon = MonitorFactory.getTimeMonitor("lgg-mon");
+		
+		
+		//outer loop: compute LGG, pick best solution and remove all covered positive and negative examples 
+		List<EvaluatedQueryTree<String>> unionSolutions = new ArrayList<EvaluatedQueryTree<String>>();
+		do {
+			//compute LGG
+			computeLGG();
+			
+			//pick best solution computed so far
+			EvaluatedQueryTree<String> bestSolution = solutions.first();
+			unionSolutions.add(bestSolution);
+			logger.info("#Uncovered pos. examples:" + bestSolution.getFalseNegatives().size());
+			
+			//remove all covered examples
+			QueryTree<String> tree;
+			for (Iterator<QueryTree<String>> iterator = currentPosExampleTrees.iterator(); iterator.hasNext();) {
+				tree = iterator.next();
+				if(tree.isSubsumedBy(bestSolution.getTree())){
+					iterator.remove();
+				}
+			}
+			for (Iterator<QueryTree<String>> iterator = currentNegExampleTrees.iterator(); iterator.hasNext();) {
+				tree = iterator.next();
+				if(tree.isSubsumedBy(bestSolution.getTree())){
+					iterator.remove();
+				}
+			}
+		} while (!(stop || currentPosExampleTrees.isEmpty()));
+		
+		
+	}
+	
+	private void computeLGG(){
+		currentlyBestScore = 0d;
+		initTodoList(currentPosExampleTrees, currentNegExampleTrees);
+		long startTime = System.currentTimeMillis();
+		int nrOfThreads = Runtime.getRuntime().availableProcessors() - 1;
+		nrOfThreads = 2;
+		ExecutorService es = Executors.newFixedThreadPool(nrOfThreads);
+		for(int i = 0; i < nrOfThreads; i++){
+			es.submit(new QueryTreeProcessor());
+		}
+		es.shutdown();
+		try {
+			es.awaitTermination(1, TimeUnit.HOURS);
+		} catch (InterruptedException e) {
+			e.printStackTrace();
+		}
+		long endTime = System.currentTimeMillis();
+		logger.info("Finished in " + (endTime-startTime) + "ms.");
+		EvaluatedDescription bestSolution = getCurrentlyBestEvaluatedDescription();
+		ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
+		ToStringRenderer.getInstance().setShortFormProvider(new SimpleShortFormProvider());
+//		solutions.first().getTree().dump();
+		logger.info("Best solution:\n" + OWLAPIConverter.getOWLAPIDescription(bestSolution.getDescription()) + "\n(" + bestSolution.getScore() + ")");
+		
+		logger.trace("LGG time: " + lggMon.getTotal() + "ms");
+		logger.trace("Avg. LGG time: " + lggMon.getAvg() + "ms");
+		logger.trace("#LGG computations: " + lggMon.getHits());
+		logger.trace("Subsumption test time: " + subMon.getTotal() + "ms");
+		logger.trace("Avg. subsumption test time: " + subMon.getAvg() + "ms");
+		logger.trace("#Subsumption tests: " + subMon.getHits());
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.StoppableLearningAlgorithm#stop()
+	 */
+	@Override
+	public void stop() {
+		stop = true;
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.AbstractCELA#getCurrentlyBestDescription()
+	 */
+	@Override
+	public Description getCurrentlyBestDescription() {
+		return getCurrentlyBestEvaluatedDescription().getDescription();
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.AbstractCELA#getCurrentlyBestEvaluatedDescription()
+	 */
+	@Override
+	public EvaluatedDescription getCurrentlyBestEvaluatedDescription() {
+		EvaluatedQueryTree<String> bestSolution = solutions.first();
+		Description description = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(
+				bestSolution.getTree().asOWLClassExpression(LiteralNodeConversionStrategy.FACET_RESTRICTION));
+		return new EvaluatedDescription(description, bestSolution.getTreeScore());
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.StoppableLearningAlgorithm#isRunning()
+	 */
+	@Override
+	public boolean isRunning() {
+		return isRunning;
+	}
+	
+	@Autowired
+	public void setLearningProblem(PosNegLP learningProblem) {
+		this.lp = learningProblem;
+	}
+	
+	@Autowired
+	public void setReasoner(AbstractReasonerComponent reasoner){
+		this.reasoner = reasoner;
+		model = ModelFactory.createDefaultModel();
+		for (KnowledgeSource ks : reasoner.getSources()) {
+			if(ks instanceof OWLFile){
+				try {
+					model.read(((OWLFile) ks).getURL().openStream(), null);
+				} catch (IOException e) {
+					e.printStackTrace();
+				}
+			}
+		}
+	}
+	
+	/**
+	 * @return the treeCache
+	 */
+	public QueryTreeCache getTreeCache() {
+		return treeCache;
+	}
+	
+	private EvaluatedQueryTree<String> evaluate(QueryTree<String> tree, boolean useSpecifity){
+		//1. get a score for the coverage = recall oriented
+		//compute positive examples which are not covered by LGG
+		Collection<QueryTree<String>> uncoveredPositiveExampleTrees = getUncoveredTrees(tree, currentPosExampleTrees);
+		Set<Individual> uncoveredPosExamples = new HashSet<Individual>();
+		for (QueryTree<String> queryTree : uncoveredPositiveExampleTrees) {
+			uncoveredPosExamples.add(tree2Indivual.get(queryTree));
+		}
+		//compute negative examples which are covered by LGG
+		Collection<QueryTree<String>> coveredNegativeExampleTrees = getCoveredTrees(tree, currentNegExampleTrees);
+		Set<Individual> coveredNegExamples = new HashSet<Individual>();
+		for (QueryTree<String> queryTree : coveredNegativeExampleTrees) {
+			coveredNegExamples.add(tree2Indivual.get(queryTree));
+		}
+		//compute score
+		int coveredPositiveExamples = currentPosExampleTrees.size() - uncoveredPositiveExampleTrees.size();
+		double recall = coveredPositiveExamples / (double)currentPosExampleTrees.size();
+		double precision = (coveredNegativeExampleTrees.size() + coveredPositiveExamples == 0) 
+						? 0 
+						: coveredPositiveExamples / (double)(coveredPositiveExamples + coveredNegativeExampleTrees.size());
+		
+		double coverageScore = recall;//Heuristics.getFScore(recall, precision);
+		
+		//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
+		int nrOfSpecificNodes = 0;
+		for (QueryTree<String> childNode : tree.getChildrenClosure()) {
+			if(!childNode.getUserObject().equals("?")){
+				nrOfSpecificNodes++;
+			}
+		}
+		double specifityScore = Math.log(nrOfSpecificNodes);
+		
+		//3.compute the total score
+		double score = coverageWeight * coverageScore + specifityWeight * specifityScore;
+		
+		QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
+				uncoveredPosExamples, Sets.difference(lp.getPositiveExamples(), uncoveredPosExamples),
+				coveredNegExamples, Sets.difference(lp.getNegativeExamples(), coveredNegExamples),
+				specifityScore, nrOfSpecificNodes);
+		
+		EvaluatedQueryTree<String> evaluatedTree = new EvaluatedQueryTree<String>(tree, uncoveredPositiveExampleTrees, coveredNegativeExampleTrees, queryTreeScore);
+		
+		return evaluatedTree;
+	}
+
+	/**
+	 * Initializes the todo list with all distinct trees contained in the given list {@code trees}.
+	 * Firstly, distinct trees are computed and afterwards, for each tree a score is computed.
+	 * @param trees
+	 */
+	private void initTodoList(List<QueryTree<String>> posExamples, List<QueryTree<String>> negExamples){
+		todoList = new PriorityBlockingQueue<EvaluatedQueryTree<String>>();
+		solutions = new TreeSet<EvaluatedQueryTree<String>>();
+//		EvaluatedQueryTree<String> dummy = new EvaluatedQueryTree<String>(new QueryTreeImpl<String>((N)"TOP"), trees, 0d);
+//		todoList.add(dummy);
+		//compute distinct trees
+		Collection<QueryTree<String>> distinctTrees = new ArrayList<QueryTree<String>>();
+		for (QueryTree<String> queryTree : posExamples) {
+			boolean distinct = true;
+			for (QueryTree<String> otherTree : distinctTrees) {
+				if(!queryTree.equals(otherTree)){
+					if(queryTree.isSameTreeAs(otherTree)){
+						distinct = false;
+						break;
+					}
+				}
+			}
+			if(distinct){
+				distinctTrees.add(queryTree);
+			}
+		}
+		for (QueryTree<String> queryTree : distinctTrees) {//System.out.println(queryTree.getStringRepresentation());
+			EvaluatedQueryTree<String> evaluatedQueryTree = evaluate(queryTree, false);
+			todoList.add(evaluatedQueryTree);
+		}
+	}
+	
+	/**
+	 * Return all trees from the given list {@code allTrees} which are not already subsumed by {@code tree}.
+	 * @param tree
+	 * @param allTrees
+	 * @return
+	 */
+	private Collection<QueryTree<String>> getCoveredTrees(QueryTree<String> tree, List<QueryTree<String>> trees){
+		Collection<QueryTree<String>> coveredTrees = new ArrayList<QueryTree<String>>();
+		for (QueryTree<String> queryTree : trees) {
+			boolean subsumed = queryTree.isSubsumedBy(tree);
+			if(subsumed){
+				coveredTrees.add(queryTree);
+			}
+		}
+		return coveredTrees;
+	}
+
+	/**
+	 * Return all trees from the given list {@code allTrees} which are not already subsumed by {@code tree}.
+	 * @param tree
+	 * @param allTrees
+	 * @return
+	 */
+	private Collection<QueryTree<String>> getUncoveredTrees(QueryTree<String> tree, List<QueryTree<String>> allTrees){
+		Collection<QueryTree<String>> uncoveredTrees = new ArrayList<QueryTree<String>>();
+		for (QueryTree<String> queryTree : allTrees) {
+			boolean subsumed = queryTree.isSubsumedBy(tree);
+			if(!subsumed){
+				uncoveredTrees.add(queryTree);
+			}
+		}
+		return uncoveredTrees;
+	}
+
+	private boolean sameTrees(QueryTree<String> tree1, QueryTree<String> tree2){
+		return tree1.isSubsumedBy(tree2) && tree2.isSubsumedBy(tree1);
+	}
+	
+	private synchronized boolean terminationCriteriaSatisfied(){
+		return stop || todoList.isEmpty() || currentPosExampleTrees.isEmpty();
+	}
+	
+	/**
+	 * Add tree to todo list if not already contained in that list or the solutions.
+	 * @param solution
+	 */
+	private void todo(EvaluatedQueryTree<String> solution){
+		//check if not already contained in todo list
+		for (EvaluatedQueryTree<String> evTree : todoList) {
+			if(sameTrees(solution.getTree(), evTree.getTree())){
+				return;
+			}
+		}
+		//check if not already contained in solutions
+		for (EvaluatedQueryTree<String> evTree : solutions) {
+			if(sameTrees(solution.getTree(), evTree.getTree())){
+				return;
+			}
+		}
+		try {
+			todoList.put(solution);
+		} catch (InterruptedException e) {
+			e.printStackTrace();
+		}
+	}
+	
+	class QueryTreeProcessor implements Runnable {
+		
+		volatile boolean isRunning;
+		LGGGenerator<String> lggGenerator = new LGGGeneratorImpl<String>();
+		
+		/**
+		 * 
+		 */
+		public QueryTreeProcessor() {
+		}
+
+		/* (non-Javadoc)
+		 * @see java.lang.Runnable#run()
+		 */
+		@Override
+		public void run() {
+			long startTime = System.currentTimeMillis();
+			while(!terminationCriteriaSatisfied()){
+				double currentlyBestScore = 0d;
+				try {
+					long t1 = System.currentTimeMillis();
+					EvaluatedQueryTree<String> evaluatedQueryTree = todoList.take();
+					long t2 = System.currentTimeMillis();
+					System.out.println(Thread.currentThread().getId() + "\t waiting time:" + (t2-t1));
+					for (QueryTree<String> example : evaluatedQueryTree.getFalseNegatives()) {
+						//compute the LGG
+//						lggMon.start();
+						QueryTree<String> lgg = lggGenerator.getLGG(evaluatedQueryTree.getTree(), example);
+//						lggMon.stop();
+						
+						//evaluate the LGG
+						EvaluatedQueryTree<String> solution = evaluate(lgg, true);
+						
+						if(solution.getScore() >= currentlyBestScore){
+							//add to todo list, if not already contained in todo list or solution list
+							todo(solution);
+							if(solution.getScore() > currentlyBestScore){
+								logger.info("Got better solution:" + solution.getTreeScore());
+							}
+							currentlyBestScore = solution.getScore();
+						}
+					}
+					long t3 = System.currentTimeMillis();
+					System.out.println(Thread.currentThread().getId() + "\t processing time:" + (t3-t2));
+					// add currently processed tree to solutions
+					solutions.add(evaluatedQueryTree);
+				} catch (InterruptedException e) {
+					e.printStackTrace();
+				}
+			}
+			System.out.println(System.currentTimeMillis() + ":" + Thread.currentThread().getId() + " finished");
+		}
+		
+		private EvaluatedQueryTree<String> evaluate(QueryTree<String> tree, boolean useSpecifity){
+			//1. get a score for the coverage = recall oriented
+			//compute positive examples which are not covered by LGG
+			Collection<QueryTree<String>> uncoveredPositiveExampleTrees = getUncoveredTrees(tree, currentPosExampleTrees);
+			Set<Individual> uncoveredPosExamples = new HashSet<Individual>();
+			for (QueryTree<String> queryTree : uncoveredPositiveExampleTrees) {
+				uncoveredPosExamples.add(tree2Indivual.get(queryTree));
+			}
+			//compute negative examples which are covered by LGG
+			Collection<QueryTree<String>> coveredNegativeExampleTrees = getCoveredTrees(tree, currentNegExampleTrees);
+			Set<Individual> coveredNegExamples = new HashSet<Individual>();
+			for (QueryTree<String> queryTree : coveredNegativeExampleTrees) {
+				coveredNegExamples.add(tree2Indivual.get(queryTree));
+			}
+			//compute score
+			int coveredPositiveExamples = currentPosExampleTrees.size() - uncoveredPositiveExampleTrees.size();
+			double recall = coveredPositiveExamples / (double)currentPosExampleTrees.size();
+			double precision = (coveredNegativeExampleTrees.size() + coveredPositiveExamples == 0) 
+							? 0 
+							: coveredPositiveExamples / (double)(coveredPositiveExamples + coveredNegativeExampleTrees.size());
+			
+			double coverageScore = recall;//Heuristics.getFScore(recall, precision);
+			
+			//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
+			int nrOfSpecificNodes = 0;
+			for (QueryTree<String> childNode : tree.getChildrenClosure()) {
+				if(!childNode.getUserObject().equals("?")){
+					nrOfSpecificNodes++;
+				}
+			}
+			double specifityScore = Math.log(nrOfSpecificNodes);
+			
+			//3.compute the total score
+			double score = coverageWeight * coverageScore + specifityWeight * specifityScore;
+			
+			QueryTreeScore queryTreeScore = new QueryTreeScore(score, coverageScore, 
+					uncoveredPosExamples, Sets.difference(lp.getPositiveExamples(), uncoveredPosExamples),
+					coveredNegExamples, Sets.difference(lp.getNegativeExamples(), coveredNegExamples),
+					specifityScore, nrOfSpecificNodes);
+			
+			EvaluatedQueryTree<String> evaluatedTree = new EvaluatedQueryTree<String>(tree, uncoveredPositiveExampleTrees, coveredNegativeExampleTrees, queryTreeScore);
+			
+			return evaluatedTree;
+		}
+		
+		/**
+		 * Return all trees from the given list {@code allTrees} which are not already subsumed by {@code tree}.
+		 * @param tree
+		 * @param allTrees
+		 * @return
+		 */
+		private Collection<QueryTree<String>> getCoveredTrees(QueryTree<String> tree, List<QueryTree<String>> trees){
+			Collection<QueryTree<String>> coveredTrees = new ArrayList<QueryTree<String>>();
+			for (QueryTree<String> queryTree : trees) {
+				boolean subsumed = queryTree.isSubsumedBy(tree);
+				if(subsumed){
+					coveredTrees.add(queryTree);
+				}
+			}
+			return coveredTrees;
+		}
+
+		/**
+		 * Return all trees from the given list {@code allTrees} which are not already subsumed by {@code tree}.
+		 * @param tree
+		 * @param allTrees
+		 * @return
+		 */
+		private Collection<QueryTree<String>> getUncoveredTrees(QueryTree<String> tree, List<QueryTree<String>> allTrees){
+			Collection<QueryTree<String>> uncoveredTrees = new ArrayList<QueryTree<String>>();
+			for (QueryTree<String> queryTree : allTrees) {
+				boolean subsumed = queryTree.isSubsumedBy(tree);
+				if(!subsumed){
+					uncoveredTrees.add(queryTree);
+				}
+			}
+			return uncoveredTrees;
+		}
+		
+	}
+
+}

Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	                        (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -0,0 +1,79 @@
+/**
+ * 
+ */
+package org.dllearner.algorithms.qtl;
+
+import java.util.Comparator;
+import java.util.Set;
+
+import org.dllearner.algorithms.qtl.operations.lgg.EvaluatedQueryTree;
+import org.dllearner.core.AbstractComponent;
+import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.Heuristic;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.learningproblems.Heuristics;
+import org.dllearner.learningproblems.QueryTreeScore;
+import org.dllearner.utilities.owl.ConceptComparator;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+@ComponentAnn(name = "QueryTreeHeuristic", shortName = "qtree_heuristic", version = 0.1)
+public class QueryTreeHeuristic extends AbstractComponent implements Heuristic, Comparator<EvaluatedQueryTree<String>>{
+	
+	// F score beta value
+	private double coverageBeta = 1;
+	
+	private double coverageWeight = 0.8;
+	
+	private double specifityWeight = 0.1;
+	
+	// syntactic comparison as final comparison criterion
+	private ConceptComparator conceptComparator = new ConceptComparator();
+
+	/* (non-Javadoc)
+	 * @see org.dllearner.core.Component#init()
+	 */
+	@Override
+	public void init() throws ComponentInitException {
+	}
+	
+	public double getScore(EvaluatedQueryTree<String> tree){
+		QueryTreeScore treeScore = tree.getTreeScore();
+		
+		//TODO
+		double score = treeScore.getScore();
+		
+		return score;
+	}
+	
+	private double getPredictedAccuracy(EvaluatedQueryTree<String> tree){
+		QueryTreeScore treeScore = tree.getTreeScore();
+		
+		Set<Individual> truePositives = treeScore.getCoveredPositives();
+		Set<Individual> trueNegatives = treeScore.getNotCoveredNegatives();
+		Set<Individual> falsePositives = treeScore.getNotCoveredPositives();
+		Set<Individual> falseNegatives = treeScore.getCoveredNegatives();
+		return 0;
+		
+	}
+
+	/* (non-Javadoc)
+	 * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
+	 */
+	@Override
+	public int compare(EvaluatedQueryTree<String> tree1, EvaluatedQueryTree<String> tree2) {
+		double diff = getScore(tree1) - getScore(tree2);
+		
+		if (diff > 0) {
+			return 1;
+		} else if (diff < 0) {
+			return -1;
+		} else {
+			return conceptComparator.compare(tree1.asEvaluatedDescription().getDescription(), tree2.asEvaluatedDescription().getDescription());
+		}
+	}
+
+}

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-05-07 11:25:54 UTC (rev 4261)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java	2014-05-07 13:43:54 UTC (rev 4262)
@@ -1488,7 +1488,7 @@
     
     private String prefixed(Map<String, String> prefixes, String uri){
     	if(uri.startsWith("http://")){
-    		for (Entry<String, String> entry : prefixes.entrySet()) {System.out.println(entry);
+    		for (Entry<String, String> entry : prefixes.entrySet()) {
     			String prefix = entry.getKey();
     			String ns = entry.getValue();
     			if(uri.startsWith(ns)){

Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/QueryTre...
 
[truncated message content]

[DL-Learner SVN] SF.net SVN: dl-learner:[4261] trunk/scripts/src/main

[<lor...@us...>]

Revision: 4261
          http://sourceforge.net/p/dl-learner/code/4261
Author:   lorenz_b
Date:     2014-05-07 11:25:54 +0000 (Wed, 07 May 2014)
Log Message:
-----------
Added eprocurement eval script.

Added Paths:
-----------
    trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java
    trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java
    trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
    trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java
    trunk/scripts/src/main/java/org/dllearner/scripts/pattern/UserEvaluation.java
    trunk/scripts/src/main/resources/db_settings.ini

Added: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java	                        (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomsHTMLWriter.java	2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,91 @@
+package org.dllearner.scripts;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.text.DecimalFormat;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.dllearner.utilities.MapUtils;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.AxiomType;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+public class OWLAxiomsHTMLWriter {
+
+	public static void main(String[] args) throws Exception{
+		if(args.length != 2){
+			System.out.println("Usage: OWLAxiomsHTMLWriter <ontology> <targetFile>");
+		}
+		ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
+		
+		String ontologyURL = args[0];
+		OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+		OWLDataFactory dataFactory = man.getOWLDataFactory();
+		OWLOntology ontology = man.loadOntologyFromOntologyDocument(new File(ontologyURL));
+		OWLAnnotationProperty anProp = dataFactory.getOWLAnnotationProperty(IRI.create("http://www.dl-learner.org/ontologies/enrichment.owl#confidence"));
+		
+		StringBuilder sb = new StringBuilder();
+		DecimalFormat dfPercent = new DecimalFormat("0.00%");
+		sb.append("<html>\n");
+		sb.append("<table border=\"3\">\n");
+		sb.append("<thead><tr><th>Source Class</th><th>Equivalent Class Expression</th><th>Accuracy</th></tr></thead>\n");
+		sb.append("<tbody>\n");
+		
+		SortedMap<OWLClass, Map<OWLClassExpression, Double>> map = new TreeMap<OWLClass, Map<OWLClassExpression,Double>>();
+		for (OWLEquivalentClassesAxiom axiom : ontology.getAxioms(AxiomType.EQUIVALENT_CLASSES)) {
+			List<OWLClassExpression> classExpressionsAsList = axiom.getClassExpressionsAsList();
+			OWLClass left = classExpressionsAsList.get(0).asOWLClass();
+			if(!left.toStringID().startsWith("http://dbpedia.org/ontology/"))continue;//skip not DBpedia
+			OWLClassExpression right = classExpressionsAsList.get(1);
+			OWLLiteral lit = (OWLLiteral) axiom.getAnnotations(anProp).iterator().next().getValue();
+			double accuracy = lit.parseDouble();
+			Map<OWLClassExpression, Double> equivalentClasses = map.get(left);
+			if(equivalentClasses == null){
+				equivalentClasses = new HashMap<OWLClassExpression, Double>();
+				map.put(left, equivalentClasses);
+			}
+			equivalentClasses.put(right, accuracy);
+		}
+		
+		for (Entry<OWLClass, Map<OWLClassExpression, Double>> entry : map.entrySet()) {
+			OWLClass cls = entry.getKey();
+			Map<OWLClassExpression, Double> equivalentClasses = entry.getValue();
+			List<Entry<OWLClassExpression, Double>> sorted = MapUtils.sortByValues(equivalentClasses);
+			sb.append("<tr><th rowspan=\"" + (sorted.size()+1) + "\">" + cls.toString() + "</th>\n");
+			for (Entry<OWLClassExpression, Double> expr : sorted) {
+				OWLClassExpression classExpression = expr.getKey();
+				Double value = expr.getValue();
+				sb.append("<tr>"); 
+		     	sb.append("<td>" + classExpression.toString() + "</td>");
+		     	sb.append("<td>" + dfPercent.format(value.doubleValue()) + "</td>");
+		     	sb.append("</tr>\n");
+			}
+
+		}
+		
+		sb.append("</tbody>\n");
+		sb.append("</table>\n");
+		sb.append("</html>\n");
+		
+		FileOutputStream fos = new FileOutputStream(new File(args[1]));
+		fos.write(sb.toString().getBytes());
+		fos.close();
+	}
+
+}

Added: trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java	                        (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/RAChallenge.java	2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,299 @@
+/**
+ * 
+ */
+package org.dllearner.scripts;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FilenameFilter;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.algorithms.celoe.OEHeuristicRuntime;
+import org.dllearner.algorithms.elcopy.ELLearningAlgorithm;
+import org.dllearner.algorithms.qtl.QueryTreeFactory;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
+import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.dllearner.refinementoperators.RhoDRDown;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.util.SimpleShortFormProvider;
+
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDF;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class RAChallenge {
+
+	
+	private static boolean useEL = false;
+	
+	static Map<String, String> prefixes = new HashMap<>();
+
+	private static String baseURI = "http://bio2rdf.org/ra.challenge:";
+	
+	static {
+		
+//		prefixes.put("ra", "http://bio2rdf.org/ra.challenge:");
+		prefixes.put("ra-voc", "http://bio2rdf.org/ra.challenge_vocabulary:");
+		prefixes.put("dbsnp", "http://bio2rdf.org/dbsnp:");
+		prefixes.put("xsd", "http://www.w3.org/2001/XMLSchema#");
+		prefixes.put("foaf", "http://xmlns.com/foaf/0.1/");
+		prefixes.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
+		prefixes.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+		prefixes.put("drug-voc", "http://bio2rdf.org/drugbank_vocabulary:");
+		
+		
+	}
+
+	public static void main(String[] args) throws Exception{
+		//load the data
+		File dataDir = new File(args[0]);
+		File[] files = dataDir.listFiles(new FilenameFilter() {
+			@Override
+			public boolean accept(File dir, String name) {
+				return name.endsWith(".nt") || name.endsWith(".ttl") || name.endsWith(".rdf") || name.endsWith(".owl");
+			}
+		});
+		System.out.println("loading data...");
+		Model model = ModelFactory.createDefaultModel();
+		for (File file : files) {
+			model.read(new FileInputStream(file), null, "TURTLE");
+		}
+		
+		analyzeData(model);
+		
+		//get the positive and negative examples via SPARQL
+		//<http://bio2rdf.org/ra.challenge:1877000> <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> "true"^^<http://www.w3.org/2001/XMLSchema#boolean>  .
+		System.out.println("extracting pos/neg examples...");
+		SortedSet<Individual> posExamples = new TreeSet<Individual>();
+		SortedSet<Individual> negExamples = new TreeSet<Individual>();
+		String query = "SELECT ?s WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>} limit 400";
+		QueryExecution qe = QueryExecutionFactory.create(query, model);
+		ResultSet rs = qe.execSelect();
+		QuerySolution qs;
+		while(rs.hasNext()){
+			qs = rs.next();
+			posExamples.add(new Individual(qs.getResource("s").getURI()));
+		}
+		query = "SELECT ?s WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>} limit 400";
+		qe = QueryExecutionFactory.create(query, model);
+		rs = qe.execSelect();
+		while(rs.hasNext()){
+			qs = rs.next();
+			negExamples.add(new Individual(qs.getResource("s").getURI()));
+		}
+		qe.close();
+		System.out.println("#pos examples: " + posExamples.size());
+		System.out.println("#neg examples: " + negExamples.size());
+		
+		//remove triples with property non-responder
+		model.remove(model.listStatements(null, model.createProperty("http://bio2rdf.org/ra.challenge_vocabulary:non-responder"), (RDFNode)null));
+		
+		//enrich with additional data
+		enrich(model);
+		
+		//check the LGG 
+//		computeLGG(model, posExamples);
+		
+		//convert JENA model to OWL API ontology
+		ByteArrayOutputStream baos = new ByteArrayOutputStream();
+		model.write(baos , "N-TRIPLES");
+		OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+		OWLOntology ontology = man.loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray()));
+		
+		//init knowledge source
+		KnowledgeSource ks = new OWLAPIOntology(ontology);
+		
+		//init reasoner
+		System.out.println("initializing reasoner...");
+		OWLAPIReasoner baseReasoner = new OWLAPIReasoner(ks);
+//		baseReasoner.setReasonerTypeString("elk");
+		baseReasoner.init();
+		FastInstanceChecker rc = new FastInstanceChecker(ks);
+		rc.setReasonerComponent(baseReasoner);
+		rc.setBaseURI(baseURI);
+		rc.setPrefixes(prefixes);
+		rc.init();
+		
+		//init learning problem
+		System.out.println("initializing learning problem...");
+		PosNegLPStandard lp = new PosNegLPStandard(rc, posExamples, negExamples);
+		lp.setUseApproximations(true);
+		lp.init();
+		
+		//init learning algorithm
+		System.out.println("initializing learning algorithm...");
+		AbstractCELA la;
+		if(useEL){
+			la = new ELLearningAlgorithm(lp, rc);
+			((ELLearningAlgorithm) la).setNoisePercentage(30);
+			((ELLearningAlgorithm) la).setMaxNrOfResults(50);
+			((ELLearningAlgorithm) la).setTreeSearchTimeSeconds(10);
+		} else {
+			OEHeuristicRuntime heuristic = new OEHeuristicRuntime();
+			heuristic.setExpansionPenaltyFactor(0.1);
+			la = new CELOE(lp, rc);
+			((CELOE) la).setHeuristic(heuristic);
+			((CELOE) la).setMaxExecutionTimeInSeconds(100);
+			((CELOE) la).setNoisePercentage(50);
+			((CELOE) la).setMaxNrOfResults(50);
+			((CELOE) la).setWriteSearchTree(true);
+			((CELOE) la).setReplaceSearchTree(true);
+			((CELOE) la).setStartClass(new NamedClass("http://xmlns.com/foaf/0.1/Person"));
+			RhoDRDown op = new RhoDRDown();
+			op.setUseHasValueConstructor(true);
+			op.setUseObjectValueNegation(true);
+			op.setReasoner(rc);
+			op.init();
+//			((CELOE) la).setOperator(op);
+		}
+		la.init();
+		
+		la.start();
+	}
+	
+	/**
+	 * Do some statistical queries.
+	 * @param model
+	 */
+	private static void analyzeData(Model model){
+		String query = "SELECT (COUNT(DISTINCT ?s)AS ?cnt) WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o.} ";
+		QueryExecution qe = QueryExecutionFactory.create(query, model);
+		ResultSet rs = qe.execSelect();
+		System.out.println(ResultSetFormatter.asText(rs));
+		
+		query = "SELECT ?o (COUNT(?s) AS ?cnt)  WHERE {?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+//				+ "OPTIONAL{?s_res <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>.FILTER(?s=s_res)} "
+//				+ "?s_non_res <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>"
+				+ "}"
+				+ " GROUP BY ?o ORDER BY DESC(?cnt)";
+		qe = QueryExecutionFactory.create(query, model);
+		rs = qe.execSelect();
+		System.out.println(ResultSetFormatter.asText(rs));
+		
+		query = "SELECT ?o (COUNT(?s) AS ?cnt)  WHERE {"
+				+ "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+				+ "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>."
+				+ "}"
+				+ " GROUP BY ?o ORDER BY DESC(?cnt)";
+		qe = QueryExecutionFactory.create(query, model);
+		rs = qe.execSelect();
+		System.out.println(ResultSetFormatter.asText(rs));
+		
+		query = "SELECT ?o (COUNT(?s) AS ?total) (Min(?cnt_res) as ?responder) (Min(?cnt_non_res) as ?non_responder)  WHERE {"
+				+ "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+				+ "{SELECT ?o (COUNT(?s) AS ?cnt_res)  WHERE {"
+				+ "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+				+ "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>."
+				+ "} GROUP BY ?o}"
+				+ "{SELECT ?o (COUNT(?s) AS ?cnt_non_res)  WHERE {"
+				+ "?s <http://bio2rdf.org/ra.challenge_vocabulary:has-two> ?o."
+				+ "?s <http://bio2rdf.org/ra.challenge_vocabulary:non-responder> \"false\"^^<http://www.w3.org/2001/XMLSchema#boolean>."
+				+ "}"
+				+ " GROUP BY ?o}} GROUP BY ?o ORDER BY DESC(?total)";
+		qe = QueryExecutionFactory.create(query, model);
+		rs = qe.execSelect();
+		System.out.println(ResultSetFormatter.asText(rs));
+	}
+	
+	private static void computeLGG(Model model, SortedSet<Individual> posExamples){
+		QueryTreeFactory<String> queryTreeFactory = new QueryTreeFactoryImpl();
+		
+		List<QueryTree<String>> posExampleTrees = new ArrayList<QueryTree<String>>();
+		for (Individual ex : posExamples) {
+			QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex.getName(), model);
+			posExampleTrees.add(tree);
+		}
+		
+		LGGGenerator<String> lggGenerator = new LGGGeneratorImpl<String>();
+		QueryTree<String> lgg = lggGenerator.getLGG(posExampleTrees);
+		String lggString = lgg.getStringRepresentation(true);
+		lggString = lggString.replace(baseURI, "");
+		for (Entry<String, String> entry : prefixes.entrySet()) {
+			String key = entry.getKey();
+			String value = entry.getValue();
+			lggString = lggString.replace(value, key + ":");
+		}
+		System.out.println(lggString);
+		
+		OWLClassExpression classExpression = lgg.asOWLClassExpression();
+		ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
+		ToStringRenderer.getInstance().setShortFormProvider(new SimpleShortFormProvider());
+		System.out.println(classExpression);
+	}
+	
+	private static void enrich(Model model) throws MalformedURLException, FileNotFoundException{
+		System.out.println("enriching data...");
+		SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://cu.drugbank.bio2rdf.org/sparql"));
+		
+//		StmtIterator stmtIterator = model.listStatements(null, RDF.type, (RDFNode)null);
+//		Model classes = ModelFactory.createDefaultModel();
+//		while(stmtIterator.hasNext()){
+//			Statement st = stmtIterator.next();
+//			classes.add(classes.createStatement(st.getObject().asResource(), RDF.type, OWL.Class));
+//		}
+//		classes.write(new FileOutputStream("classes.nt"), "TURTLE");
+		
+		ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(endpoint, "cache/drugbank");
+		List<RDFNode> drugs = model.listObjectsOfProperty(model.getProperty("http://bio2rdf.org/ra.challenge_vocabulary:drug")).toList();
+		Model drugbankData = ModelFactory.createDefaultModel();
+		Model cbd;
+		for (RDFNode drug : drugs) {
+			 cbd = cbdGen.getConciseBoundedDescription(drug.asResource().getURI(), 0, true);
+			 drugbankData.add(cbd);
+		}
+		drugbankData.setNsPrefix("drug-voc", "http://bio2rdf.org/drugbank_vocabulary:");
+		drugbankData.setNsPrefix("drug-res", "http://bio2rdf.org/drugbank_resource:");
+		drugbankData.setNsPrefix("drug", "http://bio2rdf.org/drugbank:");
+		
+		drugbankData.write(new FileOutputStream("drugbank.ttl"), "TURTLE", null);
+		model.add(drugbankData);
+		
+		
+	}
+}

Added: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java	                        (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/EProcurementUseCase.java	2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,290 @@
+/**
+ * 
+ */
+package org.dllearner.scripts.evaluation;
+
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SIBLING;
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SUPERCLASS;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.SortedSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.algorithms.elcopy.ELLearningAlgorithm;
+import org.dllearner.algorithms.qtl.QueryTreeFactory;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
+import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.AbstractKnowledgeSource;
+import org.dllearner.core.AbstractLearningProblem;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
+import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.refinementoperators.RhoDRDown;
+import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2;
+import org.dllearner.utilities.owl.OWLEntityTypeAdder;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import com.google.common.collect.Sets;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDFS;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class EProcurementUseCase {
+	
+	
+	private static final Logger logger = Logger.getLogger(EProcurementUseCase.class.getName());
+	static final int maxNrOfPositiveExamples = 100;
+	static final int maxNrOfNegativeExamples = 200;
+	static boolean posOnly = false;
+	static int maxCBDDepth = 2;
+	static int maxNrOfResults = 100;
+	static int maxExecutionTimeInSeconds = 200;
+	static double noiseInPercentage = 50;
+	static boolean useNegation = false;
+	static boolean useAllConstructor = false;
+	static String testFolder = "logs/eprocurement";
+	
+	static boolean useEL = false;
+	private static int maxClassExpressionDepth = 2;
+	
+	static Map<String, String> prefixes = new HashMap<String, String>();;
+	static {
+		prefixes.put("pc", "http://purl.org/procurement/public-contracts#");
+		prefixes.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
+		prefixes.put("skos", "http://www.w3.org/2004/02/skos/core#");
+		prefixes.put("dcterms", "http://purl.org/dc/terms/");
+		prefixes.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+		prefixes.put("activities", "http://purl.org/procurement/public-contracts-activities#");
+		prefixes.put("gr", "http://purl.org/goodrelations/v1#");
+		prefixes.put("schema", "http://schema.org/");
+	
+		
+	}
+
+	/**
+	 * @param args
+	 */
+	public static void main(String[] args) throws Exception{
+		NamedClass posClass = new NamedClass("http://purl.org/procurement/public-contracts#SuccessfulTender");
+		NamedClass negClass = new NamedClass("http://purl.org/procurement/public-contracts#UnsuccessfulTender");
+		
+		//1. setup the knowledge base
+		Model model = ModelFactory.createDefaultModel();
+		//the data
+		model.read(new FileInputStream("../test/eprocurement/dl-learner-sample-with-classes-pco.rdf"), null);
+		//the schema
+		Model schema = ModelFactory.createDefaultModel();
+		schema.read(new FileInputStream("../test/eprocurement/pco.rdf"), null);
+		schema.add(schema.getResource("http://purl.org/procurement/public-contracts#SuccessfulTender"), 
+				OWL.disjointWith, 
+				schema.getResource("http://purl.org/procurement/public-contracts#UnsuccessfulTender"));
+		schema.add(schema.getResource("http://purl.org/procurement/public-contracts#SuccessfulTender"), 
+				RDFS.subClassOf, 
+				schema.getResource("http://purl.org/procurement/public-contracts#Tender"));
+		schema.add(schema.getResource("http://purl.org/procurement/public-contracts#UnsuccessfulTender"), 
+				RDFS.subClassOf, 
+				schema.getResource("http://purl.org/procurement/public-contracts#Tender"));
+//		schema.read(new URL("http://opendata.cz/pco/public-contracts.ttl").openStream(), null, "TURTLE");
+		model.add(schema);
+		// get positive examples
+		SortedSet<Individual> positiveExamples = getExamples(model, posClass);
+		// get negative examples
+//		SortedSet<Individual> negativeExamples = getNegativeExamples(model, cls, positiveExamples);
+		SortedSet<Individual> negativeExamples = getExamples(model, negClass);
+		//get the lgg of the pos. examples
+//		showLGG(model, positiveExamples);
+		// build a sample of the kb
+		model = getSample(model, Sets.union(positiveExamples, negativeExamples));
+		//add inferred entity types
+		OWLEntityTypeAdder.addEntityTypes(model);
+		//the ontology
+		model.add(schema);
+		//convert all into DL-Learner kb object
+		ByteArrayOutputStream baos = new ByteArrayOutputStream();
+		model.write(baos, "TURTLE");
+		OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray()));
+		AbstractKnowledgeSource ks = new OWLAPIOntology(ontology);
+		ks.init();
+		
+		
+		
+		//2. setup the reasoner
+		AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+		rc.init();
+		
+		//3. setup the learning problem
+		AbstractLearningProblem lp;
+//		lp = new ClassLearningProblem(rc);
+//		((ClassLearningProblem)lp).setClassToDescribe(cls);
+//		((ClassLearningProblem)lp).setEquivalence(true);
+		lp = new PosNegLPStandard(rc, positiveExamples, negativeExamples);
+		lp.init();
+		
+		//4. setup the learning algorithm
+		AbstractCELA la;
+		if(useEL){
+			la = new ELLearningAlgorithm(lp, rc);
+			((ELLearningAlgorithm)la).setNoisePercentage(noiseInPercentage);
+//			((ELLearningAlgorithm)la).setStartClass(startClass);
+			((ELLearningAlgorithm)la).setIgnoredConcepts(Sets.newHashSet(posClass));
+			((ELLearningAlgorithm)la).setClassToDescribe(posClass);
+			((ELLearningAlgorithm)la).setTreeSearchTimeSeconds(maxExecutionTimeInSeconds);
+			((ELLearningAlgorithm)la).setMaxNrOfResults(maxNrOfResults);
+			((ELLearningAlgorithm)la).setMaxClassExpressionDepth(maxClassExpressionDepth );
+//			la = new ELLearningAlgorithmDisjunctive(lp, reasoner);
+		} else {
+			//set up the refinement operator and the allowed OWL constructs
+			RhoDRDown rop = new RhoDRDown();
+			rop.setReasoner(rc);
+			rop.setUseNegation(useNegation);
+			rop.setUseAllConstructor(useAllConstructor);
+			rop.init();
+			//build CELOE la
+			CELOE laTmp = new CELOE(lp, rc);
+			laTmp.setMaxNrOfResults(maxNrOfResults);
+			laTmp.setOperator(rop);
+			laTmp.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+//			laTmp.setStartClass(startClass);
+			laTmp.setNoisePercentage(noiseInPercentage);
+			new File(testFolder).mkdirs();
+			laTmp.setSearchTreeFile(testFolder  + "searchTree.txt");
+			laTmp.setWriteSearchTree(true);
+//			isle.setTerminateOnNoiseReached(true);
+			laTmp.setIgnoredConcepts(Collections.singleton(posClass));
+			laTmp.setReplaceSearchTree(true);
+			laTmp.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+			laTmp.setExpandAccuracy100Nodes(true);
+			la = laTmp;
+		}
+		la.init();
+		
+		//5. run
+		la.start();
+		
+
+	}
+	
+	private static void showLGG(Model model, SortedSet<Individual> positiveExamples){
+		LGGGenerator<String> lggGen = new LGGGeneratorImpl<String>();
+		QueryTree<String> lgg = lggGen.getLGG(buildTrees(model, positiveExamples));
+		String s = lgg.getStringRepresentation();
+		for (Entry<String, String> entry : prefixes.entrySet()) {
+			s = s.replace(entry.getValue(), entry.getKey() + ":");
+		}
+		System.out.println(s);
+		((QueryTreeImpl<String>) lgg).asGraph();
+	}
+	
+	private static SortedSet<Individual> getExamples(Model model, NamedClass cls){
+		logger.info("Generating examples...");
+		SortedSet<Individual> individuals = new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model)).getIndividuals(cls, 1000);
+		List<Individual> individualsList = new ArrayList<>(individuals);
+//		Collections.shuffle(individualsList, new Random(1234));
+		individuals.clear();
+		individuals.addAll(individualsList.subList(0, Math.min(maxNrOfPositiveExamples, individualsList.size())));
+		logger.info("Done. Got " + individuals.size() + ": " + individuals);
+		return individuals;
+	}
+	
+	private static SortedSet<Individual> getPositiveExamples(Model model, NamedClass cls){
+		logger.info("Generating positive examples...");
+		SortedSet<Individual> individuals = new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model)).getIndividuals(cls, 1000);
+		List<Individual> individualsList = new ArrayList<>(individuals);
+//		Collections.shuffle(individualsList, new Random(1234));
+		individuals.clear();
+		individuals.addAll(individualsList.subList(0, Math.min(maxNrOfPositiveExamples, individualsList.size())));
+		logger.info("Done. Got " + individuals.size() + ": " + individuals);
+		return individuals;
+	}
+	
+	private static SortedSet<Individual> getNegativeExamples(Model model, NamedClass classToDescribe, Set<Individual> positiveExamples){
+		logger.info("Generating positive examples...");
+		SortedSet<Individual> individuals = new AutomaticNegativeExampleFinderSPARQL2(new SPARQLReasoner(new LocalModelBasedSparqlEndpointKS(model))).getNegativeExamples(classToDescribe, positiveExamples, Arrays.asList(SIBLING, SUPERCLASS), maxNrOfNegativeExamples);
+		logger.info("Done. Got " + individuals.size() + ": " + individuals);
+		return individuals;
+	}
+	
+	private static Model getSample(Model model, Individual individual){
+		logger.info("Generating sample...");
+		ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(model, maxCBDDepth);
+		Model sample = cbdGen.getConciseBoundedDescription(individual.getName(), maxCBDDepth, true);
+		logger.info("Done. Got " + sample.size() + " triples.");
+		return sample;
+	}
+	
+	private static Model getSample(Model model, Set<Individual> individuals){
+		logger.info("Generating sample...");
+		ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(model, maxCBDDepth);
+		Model sample = ModelFactory.createDefaultModel();
+		Model cbd;
+		for (Individual individual : individuals) {
+//			System.out.println("##########################");
+//			System.out.println(individual);
+			try {
+				cbd = cbdGen.getConciseBoundedDescription(individual.getName(), maxCBDDepth, true);
+//				showTree(individual, model);
+				sample.add(cbd);
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+		}
+		logger.info("Done. Got " + sample.size() + " triples.");
+		return sample;
+	}
+	
+	private static QueryTree<String> buildTree(Individual ind, Model model){
+		QueryTreeFactory<String> qf = new QueryTreeFactoryImpl();
+		QueryTreeImpl<String> queryTree = qf.getQueryTree(ind.getName(), model);
+		return queryTree;
+	}
+	
+	private static List<QueryTree<String>> buildTrees(Model model, Collection<Individual> individuals){
+		List<QueryTree<String>> trees = new ArrayList<QueryTree<String>>();
+		for (Individual individual : individuals) {
+			trees.add(buildTree(individual, getSample(model, individual)));
+		}
+		return trees;
+	}
+	
+	private static void showTree(Individual ind, Model model){
+		QueryTree<String> tree = buildTree(ind, model);
+		String s = tree.getStringRepresentation();
+		
+		for (Entry<String, String> entry : prefixes.entrySet()) {
+			s = s.replace(entry.getValue(), entry.getKey() + ":");
+		}
+		System.out.println(s);
+	}
+	
+
+}

Added: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	                        (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java	2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,516 @@
+/**
+ * 
+ */
+package org.dllearner.scripts.evaluation;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Random;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.qtl.QTL2;
+import org.dllearner.algorithms.qtl.QTL2Disjunctive;
+import org.dllearner.algorithms.qtl.QueryTreeFactory;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+import org.dllearner.cli.CrossValidation;
+import org.dllearner.cli.SPARQLCrossValidation;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
+import org.dllearner.kb.OWLAPIOntology;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.google.common.collect.Lists;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class QTLEvaluation {
+	
+	int nrOfFolds = 10;
+	private int nrOfPosExamples = 100;
+	private int nrOfNegExamples = 100;
+	
+	List<String> posExamples = Lists.newArrayList(
+			"http://dl-learner.org/carcinogenesis#d1",
+			"http://dl-learner.org/carcinogenesis#d10",
+			"http://dl-learner.org/carcinogenesis#d101",
+			"http://dl-learner.org/carcinogenesis#d102",
+			"http://dl-learner.org/carcinogenesis#d103",
+			"http://dl-learner.org/carcinogenesis#d106",
+			"http://dl-learner.org/carcinogenesis#d107",
+			"http://dl-learner.org/carcinogenesis#d108",
+			"http://dl-learner.org/carcinogenesis#d11",
+			"http://dl-learner.org/carcinogenesis#d12",
+			"http://dl-learner.org/carcinogenesis#d13",
+			"http://dl-learner.org/carcinogenesis#d134",
+			"http://dl-learner.org/carcinogenesis#d135",
+			"http://dl-learner.org/carcinogenesis#d136",
+			"http://dl-learner.org/carcinogenesis#d138",
+			"http://dl-learner.org/carcinogenesis#d140",
+			"http://dl-learner.org/carcinogenesis#d141",
+			"http://dl-learner.org/carcinogenesis#d144",
+			"http://dl-learner.org/carcinogenesis#d145",
+			"http://dl-learner.org/carcinogenesis#d146",
+			"http://dl-learner.org/carcinogenesis#d147",
+			"http://dl-learner.org/carcinogenesis#d15",
+			"http://dl-learner.org/carcinogenesis#d17",
+			"http://dl-learner.org/carcinogenesis#d19",
+			"http://dl-learner.org/carcinogenesis#d192",
+			"http://dl-learner.org/carcinogenesis#d193",
+			"http://dl-learner.org/carcinogenesis#d195",
+			"http://dl-learner.org/carcinogenesis#d196",
+			"http://dl-learner.org/carcinogenesis#d197",
+			"http://dl-learner.org/carcinogenesis#d198",
+			"http://dl-learner.org/carcinogenesis#d199",
+			"http://dl-learner.org/carcinogenesis#d2",
+			"http://dl-learner.org/carcinogenesis#d20",
+			"http://dl-learner.org/carcinogenesis#d200",
+			"http://dl-learner.org/carcinogenesis#d201",
+			"http://dl-learner.org/carcinogenesis#d202",
+			"http://dl-learner.org/carcinogenesis#d203",
+			"http://dl-learner.org/carcinogenesis#d204",
+			"http://dl-learner.org/carcinogenesis#d205",
+			"http://dl-learner.org/carcinogenesis#d21",
+			"http://dl-learner.org/carcinogenesis#d22",
+			"http://dl-learner.org/carcinogenesis#d226",
+			"http://dl-learner.org/carcinogenesis#d227",
+			"http://dl-learner.org/carcinogenesis#d228",
+			"http://dl-learner.org/carcinogenesis#d229",
+			"http://dl-learner.org/carcinogenesis#d231",
+			"http://dl-learner.org/carcinogenesis#d232",
+			"http://dl-learner.org/carcinogenesis#d234",
+			"http://dl-learner.org/carcinogenesis#d236",
+			"http://dl-learner.org/carcinogenesis#d239",
+			"http://dl-learner.org/carcinogenesis#d23_2",
+			"http://dl-learner.org/carcinogenesis#d242",
+			"http://dl-learner.org/carcinogenesis#d245",
+			"http://dl-learner.org/carcinogenesis#d247",
+			"http://dl-learner.org/carcinogenesis#d249",
+			"http://dl-learner.org/carcinogenesis#d25",
+			"http://dl-learner.org/carcinogenesis#d252",
+			"http://dl-learner.org/carcinogenesis#d253",
+			"http://dl-learner.org/carcinogenesis#d254",
+			"http://dl-learner.org/carcinogenesis#d255",
+			"http://dl-learner.org/carcinogenesis#d26",
+			"http://dl-learner.org/carcinogenesis#d272",
+			"http://dl-learner.org/carcinogenesis#d275",
+			"http://dl-learner.org/carcinogenesis#d277",
+			"http://dl-learner.org/carcinogenesis#d279",
+			"http://dl-learner.org/carcinogenesis#d28",
+			"http://dl-learner.org/carcinogenesis#d281",
+			"http://dl-learner.org/carcinogenesis#d283",
+			"http://dl-learner.org/carcinogenesis#d284",
+			"http://dl-learner.org/carcinogenesis#d288",
+			"http://dl-learner.org/carcinogenesis#d29",
+			"http://dl-learner.org/carcinogenesis#d290",
+			"http://dl-learner.org/carcinogenesis#d291",
+			"http://dl-learner.org/carcinogenesis#d292",
+			"http://dl-learner.org/carcinogenesis#d30",
+			"http://dl-learner.org/carcinogenesis#d31",
+			"http://dl-learner.org/carcinogenesis#d32",
+			"http://dl-learner.org/carcinogenesis#d33",
+			"http://dl-learner.org/carcinogenesis#d34",
+			"http://dl-learner.org/carcinogenesis#d35",
+			"http://dl-learner.org/carcinogenesis#d36",
+			"http://dl-learner.org/carcinogenesis#d37",
+			"http://dl-learner.org/carcinogenesis#d38",
+			"http://dl-learner.org/carcinogenesis#d42",
+			"http://dl-learner.org/carcinogenesis#d43",
+			"http://dl-learner.org/carcinogenesis#d44",
+			"http://dl-learner.org/carcinogenesis#d45",
+			"http://dl-learner.org/carcinogenesis#d46",
+			"http://dl-learner.org/carcinogenesis#d47",
+			"http://dl-learner.org/carcinogenesis#d48",
+			"http://dl-learner.org/carcinogenesis#d49",
+			"http://dl-learner.org/carcinogenesis#d5",
+			"http://dl-learner.org/carcinogenesis#d51",
+			"http://dl-learner.org/carcinogenesis#d52",
+			"http://dl-learner.org/carcinogenesis#d53",
+			"http://dl-learner.org/carcinogenesis#d55",
+			"http://dl-learner.org/carcinogenesis#d58",
+			"http://dl-learner.org/carcinogenesis#d6",
+			"http://dl-learner.org/carcinogenesis#d7",
+			"http://dl-learner.org/carcinogenesis#d84",
+			"http://dl-learner.org/carcinogenesis#d85_2",
+			"http://dl-learner.org/carcinogenesis#d86",
+			"http://dl-learner.org/carcinogenesis#d87",
+			"http://dl-learner.org/carcinogenesis#d88",
+			"http://dl-learner.org/carcinogenesis#d89",
+			"http://dl-learner.org/carcinogenesis#d9",
+			"http://dl-learner.org/carcinogenesis#d91",
+			"http://dl-learner.org/carcinogenesis#d92",
+			"http://dl-learner.org/carcinogenesis#d93",
+			"http://dl-learner.org/carcinogenesis#d95",
+			"http://dl-learner.org/carcinogenesis#d96",
+			"http://dl-learner.org/carcinogenesis#d98",
+			"http://dl-learner.org/carcinogenesis#d99",
+			"http://dl-learner.org/carcinogenesis#d100",
+			"http://dl-learner.org/carcinogenesis#d104",
+			"http://dl-learner.org/carcinogenesis#d105",
+			"http://dl-learner.org/carcinogenesis#d109",
+			"http://dl-learner.org/carcinogenesis#d137",
+			"http://dl-learner.org/carcinogenesis#d139",
+			"http://dl-learner.org/carcinogenesis#d14",
+			"http://dl-learner.org/carcinogenesis#d142",
+			"http://dl-learner.org/carcinogenesis#d143",
+			"http://dl-learner.org/carcinogenesis#d148",
+			"http://dl-learner.org/carcinogenesis#d16",
+			"http://dl-learner.org/carcinogenesis#d18",
+			"http://dl-learner.org/carcinogenesis#d191",
+			"http://dl-learner.org/carcinogenesis#d206",
+			"http://dl-learner.org/carcinogenesis#d230",
+			"http://dl-learner.org/carcinogenesis#d233",
+			"http://dl-learner.org/carcinogenesis#d235",
+			"http://dl-learner.org/carcinogenesis#d237",
+			"http://dl-learner.org/carcinogenesis#d238",
+			"http://dl-learner.org/carcinogenesis#d23_1",
+			"http://dl-learner.org/carcinogenesis#d24",
+			"http://dl-learner.org/carcinogenesis#d240",
+			"http://dl-learner.org/carcinogenesis#d241",
+			"http://dl-learner.org/carcinogenesis#d243",
+			"http://dl-learner.org/carcinogenesis#d244",
+			"http://dl-learner.org/carcinogenesis#d246",
+			"http://dl-learner.org/carcinogenesis#d248",
+			"http://dl-learner.org/carcinogenesis#d250",
+			"http://dl-learner.org/carcinogenesis#d251",
+			"http://dl-learner.org/carcinogenesis#d27",
+			"http://dl-learner.org/carcinogenesis#d273",
+			"http://dl-learner.org/carcinogenesis#d274",
+			"http://dl-learner.org/carcinogenesis#d278",
+			"http://dl-learner.org/carcinogenesis#d286",
+			"http://dl-learner.org/carcinogenesis#d289",
+			"http://dl-learner.org/carcinogenesis#d3",
+			"http://dl-learner.org/carcinogenesis#d39",
+			"http://dl-learner.org/carcinogenesis#d4",
+			"http://dl-learner.org/carcinogenesis#d40",
+			"http://dl-learner.org/carcinogenesis#d41",
+			"http://dl-learner.org/carcinogenesis#d50",
+			"http://dl-learner.org/carcinogenesis#d54",
+			"http://dl-learner.org/carcinogenesis#d56",
+			"http://dl-learner.org/carcinogenesis#d57",
+			"http://dl-learner.org/carcinogenesis#d8",
+			"http://dl-learner.org/carcinogenesis#d85_1",
+			"http://dl-learner.org/carcinogenesis#d90",
+			"http://dl-learner.org/carcinogenesis#d94",
+			"http://dl-learner.org/carcinogenesis#d97",
+			"http://dl-learner.org/carcinogenesis#d296",
+			"http://dl-learner.org/carcinogenesis#d305",
+			"http://dl-learner.org/carcinogenesis#d306",
+			"http://dl-learner.org/carcinogenesis#d307",
+			"http://dl-learner.org/carcinogenesis#d308",
+			"http://dl-learner.org/carcinogenesis#d311",
+			"http://dl-learner.org/carcinogenesis#d314",
+			"http://dl-learner.org/carcinogenesis#d315",
+			"http://dl-learner.org/carcinogenesis#d316",
+			"http://dl-learner.org/carcinogenesis#d320",
+			"http://dl-learner.org/carcinogenesis#d322",
+			"http://dl-learner.org/carcinogenesis#d323",
+			"http://dl-learner.org/carcinogenesis#d325",
+			"http://dl-learner.org/carcinogenesis#d329",
+			"http://dl-learner.org/carcinogenesis#d330",
+			"http://dl-learner.org/carcinogenesis#d331",
+			"http://dl-learner.org/carcinogenesis#d332",
+			"http://dl-learner.org/carcinogenesis#d333",
+			"http://dl-learner.org/carcinogenesis#d336",
+			"http://dl-learner.org/carcinogenesis#d337"
+			);
+	
+	List<String> negExamples = Lists.newArrayList(
+			"http://dl-learner.org/carcinogenesis#d110",
+			"http://dl-learner.org/carcinogenesis#d111",
+			"http://dl-learner.org/carcinogenesis#d114",
+			"http://dl-learner.org/carcinogenesis#d116",
+			"http://dl-learner.org/carcinogenesis#d117",
+			"http://dl-learner.org/carcinogenesis#d119",
+			"http://dl-learner.org/carcinogenesis#d121",
+			"http://dl-learner.org/carcinogenesis#d123",
+			"http://dl-learner.org/carcinogenesis#d124",
+			"http://dl-learner.org/carcinogenesis#d125",
+			"http://dl-learner.org/carcinogenesis#d127",
+			"http://dl-learner.org/carcinogenesis#d128",
+			"http://dl-learner.org/carcinogenesis#d130",
+			"http://dl-learner.org/carcinogenesis#d133",
+			"http://dl-learner.org/carcinogenesis#d150",
+			"http://dl-learner.org/carcinogenesis#d151",
+			"http://dl-learner.org/carcinogenesis#d154",
+			"http://dl-learner.org/carcinogenesis#d155",
+			"http://dl-learner.org/carcinogenesis#d156",
+			"http://dl-learner.org/carcinogenesis#d159",
+			"http://dl-learner.org/carcinogenesis#d160",
+			"http://dl-learner.org/carcinogenesis#d161",
+			"http://dl-learner.org/carcinogenesis#d162",
+			"http://dl-learner.org/carcinogenesis#d163",
+			"http://dl-learner.org/carcinogenesis#d164",
+			"http://dl-learner.org/carcinogenesis#d165",
+			"http://dl-learner.org/carcinogenesis#d166",
+			"http://dl-learner.org/carcinogenesis#d169",
+			"http://dl-learner.org/carcinogenesis#d170",
+			"http://dl-learner.org/carcinogenesis#d171",
+			"http://dl-learner.org/carcinogenesis#d172",
+			"http://dl-learner.org/carcinogenesis#d173",
+			"http://dl-learner.org/carcinogenesis#d174",
+			"http://dl-learner.org/carcinogenesis#d178",
+			"http://dl-learner.org/carcinogenesis#d179",
+			"http://dl-learner.org/carcinogenesis#d180",
+			"http://dl-learner.org/carcinogenesis#d181",
+			"http://dl-learner.org/carcinogenesis#d183",
+			"http://dl-learner.org/carcinogenesis#d184",
+			"http://dl-learner.org/carcinogenesis#d185",
+			"http://dl-learner.org/carcinogenesis#d186",
+			"http://dl-learner.org/carcinogenesis#d188",
+			"http://dl-learner.org/carcinogenesis#d190",
+			"http://dl-learner.org/carcinogenesis#d194",
+			"http://dl-learner.org/carcinogenesis#d207",
+			"http://dl-learner.org/carcinogenesis#d208_1",
+			"http://dl-learner.org/carcinogenesis#d209",
+			"http://dl-learner.org/carcinogenesis#d210",
+			"http://dl-learner.org/carcinogenesis#d211",
+			"http://dl-learner.org/carcinogenesis#d212",
+			"http://dl-learner.org/carcinogenesis#d213",
+			"http://dl-learner.org/carcinogenesis#d214",
+			"http://dl-learner.org/carcinogenesis#d215",
+			"http://dl-learner.org/carcinogenesis#d217",
+			"http://dl-learner.org/carcinogenesis#d218",
+			"http://dl-learner.org/carcinogenesis#d219",
+			"http://dl-learner.org/carcinogenesis#d220",
+			"http://dl-learner.org/carcinogenesis#d224",
+			"http://dl-learner.org/carcinogenesis#d256",
+			"http://dl-learner.org/carcinogenesis#d257",
+			"http://dl-learner.org/carcinogenesis#d258",
+			"http://dl-learner.org/carcinogenesis#d261",
+			"http://dl-learner.org/carcinogenesis#d262",
+			"http://dl-learner.org/carcinogenesis#d263",
+			"http://dl-learner.org/carcinogenesis#d264",
+			"http://dl-learner.org/carcinogenesis#d265",
+			"http://dl-learner.org/carcinogenesis#d266",
+			"http://dl-learner.org/carcinogenesis#d267",
+			"http://dl-learner.org/carcinogenesis#d269",
+			"http://dl-learner.org/carcinogenesis#d271",
+			"http://dl-learner.org/carcinogenesis#d276",
+			"http://dl-learner.org/carcinogenesis#d280",
+			"http://dl-learner.org/carcinogenesis#d285",
+			"http://dl-learner.org/carcinogenesis#d287",
+			"http://dl-learner.org/carcinogenesis#d293",
+			"http://dl-learner.org/carcinogenesis#d294",
+			"http://dl-learner.org/carcinogenesis#d59",
+			"http://dl-learner.org/carcinogenesis#d60",
+			"http://dl-learner.org/carcinogenesis#d61",
+			"http://dl-learner.org/carcinogenesis#d63",
+			"http://dl-learner.org/carcinogenesis#d64",
+			"http://dl-learner.org/carcinogenesis#d65",
+			"http://dl-learner.org/carcinogenesis#d69",
+			"http://dl-learner.org/carcinogenesis#d70",
+			"http://dl-learner.org/carcinogenesis#d71",
+			"http://dl-learner.org/carcinogenesis#d72",
+			"http://dl-learner.org/carcinogenesis#d73",
+			"http://dl-learner.org/carcinogenesis#d74",
+			"http://dl-learner.org/carcinogenesis#d75",
+			"http://dl-learner.org/carcinogenesis#d76",
+			"http://dl-learner.org/carcinogenesis#d77",
+			"http://dl-learner.org/carcinogenesis#d78",
+			"http://dl-learner.org/carcinogenesis#d79",
+			"http://dl-learner.org/carcinogenesis#d80",
+			"http://dl-learner.org/carcinogenesis#d81",
+			"http://dl-learner.org/carcinogenesis#d82",
+			"http://dl-learner.org/carcinogenesis#d112",
+			"http://dl-learner.org/carcinogenesis#d113",
+			"http://dl-learner.org/carcinogenesis#d115",
+			"http://dl-learner.org/carcinogenesis#d118",
+			"http://dl-learner.org/carcinogenesis#d120",
+			"http://dl-learner.org/carcinogenesis#d122",
+			"http://dl-learner.org/carcinogenesis#d126",
+			"http://dl-learner.org/carcinogenesis#d129",
+			"http://dl-learner.org/carcinogenesis#d131",
+			"http://dl-learner.org/carcinogenesis#d132",
+			"http://dl-learner.org/carcinogenesis#d149",
+			"http://dl-learner.org/carcinogenesis#d152",
+			"http://dl-learner.org/carcinogenesis#d153",
+			"http://dl-learner.org/carcinogenesis#d157",
+			"http://dl-learner.org/carcinogenesis#d158",
+			"http://dl-learner.org/carcinogenesis#d167",
+			"http://dl-learner.org/carcinogenesis#d168",
+			"http://dl-learner.org/carcinogenesis#d175",
+			"http://dl-learner.org/carcinogenesis#d176",
+			"http://dl-learner.org/carcinogenesis#d177",
+			"http://dl-learner.org/carcinogenesis#d182",
+			"http://dl-learner.org/carcinogenesis#d187",
+			"http://dl-learner.org/carcinogenesis#d189",
+			"http://dl-learner.org/carcinogenesis#d208_2",
+			"http://dl-learner.org/carcinogenesis#d216",
+			"http://dl-learner.org/carcinogenesis#d221",
+			"http://dl-learner.org/carcinogenesis#d222",
+			"http://dl-learner.org/carcinogenesis#d223",
+			"http://dl-learner.org/carcinogenesis#d225",
+			"http://dl-learner.org/carcinogenesis#d259",
+			"http://dl-learner.org/carcinogenesis#d260",
+			"http://dl-learner.org/carcinogenesis#d268",
+			"http://dl-learner.org/carcinogenesis#d270",
+			"http://dl-learner.org/carcinogenesis#d282",
+			"http://dl-learner.org/carcinogenesis#d295",
+			"http://dl-learner.org/carcinogenesis#d62",
+			"http://dl-learner.org/carcinogenesis#d66",
+			"http://dl-learner.org/carcinogenesis#d67",
+			"http://dl-learner.org/carcinogenesis#d68",
+			"http://dl-learner.org/carcinogenesis#d83",
+			"http://dl-learner.org/carcinogenesis#d297",
+			"http://dl-learner.org/carcinogenesis#d298",
+			"http://dl-learner.org/carcinogenesis#d299",
+			"http://dl-learner.org/carcinogenesis#d300",
+			"http://dl-learner.org/carcinogenesis#d302",
+			"http://dl-learner.org/carcinogenesis#d303",
+			"http://dl-learner.org/carcinogenesis#d304",
+			"http://dl-learner.org/carcinogenesis#d309",
+			"http://dl-learner.org/carcinogenesis#d312",
+			"http://dl-learner.org/carcinogenesis#d313",
+			"http://dl-learner.org/carcinogenesis#d317",
+			"http://dl-learner.org/carcinogenesis#d318",
+			"http://dl-learner.org/carcinogenesis#d319",
+			"http://dl-learner.org/carcinogenesis#d324",
+			"http://dl-learner.org/carcinogenesis#d326",
+			"http://dl-learner.org/carcinogenesis#d327",
+			"http://dl-learner.org/carcinogenesis#d328",
+			"http://dl-learner.org/carcinogenesis#d334",
+			"http://dl-learner.org/carcinogenesis#d335"
+			);
+	
+	private Model model;
+	private OWLOntology ontology;
+	private QueryTreeFactory<String> queryTreeFactory;
+	private List<QueryTree<String>> posExampleTrees;
+	private List<QueryTree<String>> negExampleTrees;
+	private PosNegLP lp;
+
+	
+	
+	public QTLEvaluation() throws ComponentInitException {
+		queryTreeFactory = new QueryTreeFactoryImpl();
+		queryTreeFactory.setMaxDepth(3);
+		
+		loadDataset();
+		
+		loadExamples();
+	}
+	
+	private void loadDataset(){
+		File file = new File("../examples/carcinogenesis/carcinogenesis.owl");
+		model = ModelFactory.createDefaultModel();
+		try {
+			model.read(new FileInputStream(file), null, "RDF/XML");
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+		}
+		
+		OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+		try {
+			ontology = man.loadOntologyFromOntologyDocument(file);
+		} catch (OWLOntologyCreationException e) {
+			e.printStackTrace();
+		}
+	}
+	
+	private void loadExamples() throws ComponentInitException{
+		
+		Collections.shuffle(posExamples, new Random(1));
+		Collections.shuffle(negExamples, new Random(2));	
+		posExamples = posExamples.subList(0, Math.min(posExamples.size(), nrOfPosExamples));
+		negExamples = negExamples.subList(0, Math.min(negExamples.size(), nrOfNegExamples));
+		
+//		posExamples.clear();
+//		String string = "http://dl-learner.org/carcinogenesis#d101, http://dl-learner.org/carcinogenesis#d103, http://dl-learner.org/carcinogenesis#d107, http://dl-learner.org/carcinogenesis#d108, http://dl-learner.org/carcinogenesis#d135, http://dl-learner.org/carcinogenesis#d139, http://dl-learner.org/carcinogenesis#d14, http://dl-learner.org/carcinogenesis#d141, http://dl-learner.org/carcinogenesis#d143, http://dl-learner.org/carcinogenesis#d147, http://dl-learner.org/carcinogenesis#d17, http://dl-learner.org/carcinogenesis#d19, http://dl-learner.org/carcinogenesis#d193, http://dl-learner.org/carcinogenesis#d198, http://dl-learner.org/carcinogenesis#d228, http://dl-learner.org/carcinogenesis#d236, http://dl-learner.org/carcinogenesis#d242, http://dl-learner.org/carcinogenesis#d244, http://dl-learner.org/carcinogenesis#d273, http://dl-learner.org/carcinogenesis#d275, http://dl-learner.org/carcinogenesis#d28, http://dl-learner.org/carcinogenesis#d283, http://dl-learner.org/carcinogenesis#d286, http://dl-learner.org/carcinogenesis#d291, http://dl-learner.org/carcinogenesis#d292, http://dl-learner.org/carcinogenesis#d307, http://dl-learner.org/carcinogenesis#d31, http://dl-learner.org/carcinogenesis#d325, http://dl-learner.org/carcinogenesis#d33, http://dl-learner.org/carcinogenesis#d333, http://dl-learner.org/carcinogenesis#d34, http://dl-learner.org/carcinogenesis#d36, http://dl-learner.org/carcinogenesis#d38, http://dl-learner.org/carcinogenesis#d4, http://dl-learner.org/carcinogenesis#d40, http://dl-learner.org/carcinogenesis#d44, http://dl-learner.org/carcinogenesis#d51, http://dl-learner.org/carcinogenesis#d85_2, http://dl-learner.org/carcinogenesis#d98, http://dl-learner.org/carcinogenesis#d99";
+//		String[] split = string.split(",");
+//		for (String s : split) {
+//			posExamples.add(s.trim());
+//		}
+//		negExamples.clear();
+//		string = "http://dl-learner.org/carcinogenesis#d112, http://dl-learner.org/carcinogenesis#d116, http://dl-learner.org/carcinogenesis#d117, http://dl-learner.org/carcinogenesis#d119, http://dl-learner.org/carcinogenesis#d157, http://dl-learner.org/carcinogenesis#d160, http://dl-learner.org/carcinogenesis#d161, http://dl-learner.org/carcinogenesis#d162, http://dl-learner.org/carcinogenesis#d163, http://dl-learner.org/carcinogenesis#d167, http://dl-learner.org/carcinogenesis#d169, http://dl-learner.org/carcinogenesis#d175, http://dl-learner.org/carcinogenesis#d177, http://dl-learner.org/carcinogenesis#d184, http://dl-learner.org/carcinogenesis#d194, http://dl-learner.org/carcinogenesis#d208_2, http://dl-learner.org/carcinogenesis#d209, http://dl-learner.org/carcinogenesis#d217, http://dl-learner.org/carcinogenesis#d256, http://dl-learner.org/carcinogenesis#d257, http://dl-learner.org/carcinogenesis#d260, http://dl-learner.org/carcinogenesis#d271, http://dl-learner.org/carcinogenesis#d276, http://dl-learner.org/carcinogenesis#d282, http://dl-learner.org/carcinogenesis#d287, http://dl-learner.org/carcinogenesis#d294, http://dl-learner.org/carcinogenesis#d298, http://dl-learner.org/carcinogenesis#d300, http://dl-learner.org/carcinogenesis#d309, http://dl-learner.org/carcinogenesis#d319, http://dl-learner.org/carcinogenesis#d326, http://dl-learner.org/carcinogenesis#d328, http://dl-learner.org/carcinogenesis#d334, http://dl-learner.org/carcinogenesis#d60, http://dl-learner.org/carcinogenesis#d61, http://dl-learner.org/carcinogenesis#d66, http://dl-learner.org/carcinogenesis#d75, http://dl-learner.org/carcinogenesis#d79, http://dl-learner.org/carcinogenesis#d80, http://dl-learner.org/carcinogenesis#d83";
+//		split = string.split(",");
+//		for (String s : split) {
+//			negExamples.add(s.trim());
+//		}
+		
+		posExampleTrees = new ArrayList<QueryTree<String>>();
+		for (String ex : posExamples) {
+			QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model);
+			posExampleTrees.add(tree);
+		}
+		
+		negExampleTrees = new ArrayList<QueryTree<String>>();
+		for (String ex : negExamples) {
+			QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model);
+			negExampleTrees.add(tree);
+		}
+		
+		int cnt = 1;
+		for(QueryTree<String> tree : posExampleTrees){
+//			System.out.println("TREE " + cnt);
+//			tree.dump();
+//			
+//			System.out.println("-----------------------------");
+			cnt++;
+//			System.out.println(((QueryTreeImpl<String>)tree).toQuery());
+		}
+		
+		SortedSet<Individual> pos = new TreeSet<Individual>();
+		for (String ex : posExamples) {
+			pos.add(new Individual(ex));
+		}
+		SortedSet<Individual> neg = new TreeSet<Individual>();
+		for (String ex : negExamples) {
+			neg.add(new Individual(ex));
+		}
+		lp = new PosNegLPStandard();
+		lp.setPositiveExamples(pos);
+		lp.setNegativeExamples(neg);
+	}
+	
+	public void run(boolean multiThreaded) throws ComponentInitException, LearningProblemUnsupportedException{
+		long startTime = System.currentTimeMillis();
+		FastInstanceChecker reasoner = new FastInstanceChecker(new OWLAPIOntology(ontology));
+		reasoner.init();
+		lp.setReasoner(reasoner);
+		lp.init();
+		QTL2Disjunctive la = new QTL2Disjunctive(lp, reasoner);
+		la.init();
+		la.start();
+		
+//		CrossValidation.outputFile = new File("log/qtl-cv.log");
+//		CrossValidation.writeToFile = true;
+//		CrossValidation.multiThreaded = multiThreaded;
+//		CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
+		long endTime = System.currentTimeMillis();
+		System.err.println((endTime - startTime) + "ms");
+	}
+
+	
+	public static void main(String[] args) throws Exception {
+		boolean multiThreaded = Boolean.valueOf(args[0]);
+		new QTLEvaluation().run(multiThreaded);
+	}
+
+}

Added: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java	                        (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/FixPointDetection.java	2014-05-07 11:25:54 UTC (rev 4261)
@@ -0,0 +1,281 @@
+/**
+ * 
+ */
+package org.dllearner.scripts.pattern;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Random;
+import java.util.Set;
+import java.util.TreeMap;
+import java.util.prefs.Preferences;
+
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+import com.google.common.base.Charsets;
+import com.google.common.base.Joiner;
+import com.google.common.collect.LinkedListMultimap;
+import com.google.common.collect.Multimap;
+import com.google.common.io.Files;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class FixPointDetection {
+	
+	private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
+	
+	public FixPointDetection() {
+		initDBConnection();
+		
+		File dir = new File("pattern-fixpoint");
+		dir.mkdir();
+	}
+	
+	private Connection conn;
+	private PreparedStatement ps;
+	
+	private void initDBConnection() {
+		try {
+			InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini");
+			Preferences prefs = new IniPreferences(is);
+			String dbServer = prefs.node("database").get("server", null);
+			String dbName = prefs.node("database").get("name", null);
+			String dbUser = prefs.node("database").get("user", null);
+			String dbPass = prefs.node("database").get("pass", null);
+
+			Class.forName("com.mysql.jdbc.Driver");
+			String url = "jdbc:mysql://" + dbServer + "/" + dbName;
+			conn = DriverManager.getConnection(url, dbUser, dbPass);
+		} catch (ClassNotFoundException e) {
+			e.printStackTrace();
+		} catch (SQLException e) {
+			e.printStackTrace();
+		} catch (InvalidFileFormatException e) {
+			e.printStackTrace();
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		
+		try {
+			ps = conn.prepareStatement("SELECT occurrences FROM Ontology_Pattern WHERE pattern_id=? AND ontology_id=?");
+		} catch (SQLException e) {
+			e.printStackTrace();
+		}
+	}
+
+	
+	private List<Integer> getProcessedOntologies() throws SQLException{
+		List<Integer> ids = new ArrayList<Integer>();
+		ResultSet rs = conn.createStatement().executeQuery("SELECT DISTINCT id FROM Ontology");
+		while(rs.next()){
+			int id = rs.getInt(1);
+	...
 
[truncated message content]