Merge remote-tracking branch 'fork/develop' into develop

# Conflicts:
#	components-core/src/main/java/org/dllearner/reasoning/ClosedWorldReasoner.java
#	components-core/src/main/java/org/dllearner/utilities/Helper.java

Author: LorenzBuehmann

components-core/pom.xml

@@ -441,7 +441,7 @@
 		<dependency>
 			<groupId>com.thoughtworks.xstream</groupId>
 			<artifactId>xstream</artifactId>
-			<version>1.4.3</version>
+			<version>1.4.11.1</version>
 		</dependency>
 		<!--
                 <dependency>
@@ -577,5 +577,18 @@
 			<artifactId>commons-collections4</artifactId>
 		</dependency>
 
+
+
+			<dependency>
+				<groupId>org.apache.logging.log4j</groupId>
+				<artifactId>log4j-api</artifactId>
+				<version>2.12.1</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.logging.log4j</groupId>
+				<artifactId>log4j-core</artifactId>
+				<version>2.12.1</version>
+			</dependency>
+
     </dependencies>
 </project>

components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java

@@ -121,7 +121,7 @@ public class CELOE extends AbstractCELA implements Cloneable{
 
 	// statistical variables
 	private int expressionTests = 0;
-	private int minHorizExp = 0;
+	private int minHorizExp = 1;
 	private int maxHorizExp = 0;
 	private long totalRuntimeNs = 0;
 
@@ -349,7 +349,7 @@ public void start() {
 
 				// we ignore all refinements with lower length and too high depth
 				// (this also avoids duplicate node children)
-				if(length > horizExp && OWLClassExpressionUtils.getDepth(refinement) <= maxDepth) {
+				if(length >= horizExp && OWLClassExpressionUtils.getDepth(refinement) <= maxDepth) {
 					// add node to search tree
 					addNode(refinement, nextNode);
 				}
@@ -497,7 +497,7 @@ private TreeSet<OWLClassExpression> refineNode(OENode node) {
 		// otherwise you may see rarely occurring but critical false ordering in the nodes set)
 		searchTree.updatePrepare(node);
 		int horizExp = node.getHorizontalExpansion();
-		TreeSet<OWLClassExpression> refinements = (TreeSet<OWLClassExpression>) operator.refine(node.getDescription(), horizExp+1);
+		TreeSet<OWLClassExpression> refinements = (TreeSet<OWLClassExpression>) operator.refine(node.getDescription(), horizExp);
 //		System.out.println("refinements: " + refinements);
 		node.incHorizontalExpansion();
 		node.setRefinementCount(refinements.size());

components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java

@@ -71,7 +71,7 @@ public double getNodeScore(OENode node) {
 		}
 
 		// penalty for horizontal expansion
-		score -= node.getHorizontalExpansion() * expansionPenaltyFactor;
+		score -= (node.getHorizontalExpansion() - 1) * expansionPenaltyFactor;
 
 		// penalty for having many child nodes (stuck prevention)
 		score -= node.getRefinementCount() * nodeRefinementPenalty;

components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java

@@ -18,15 +18,15 @@
  */
 package org.dllearner.algorithms.celoe;
 
-import java.text.DecimalFormat;
-import java.util.Map;
-
 import org.dllearner.core.AbstractSearchTreeNode;
 import org.dllearner.utilities.datastructures.SearchTreeNode;
 import org.dllearner.utilities.owl.OWLAPIRenderers;
 import org.dllearner.utilities.owl.OWLClassExpressionUtils;
 import org.semanticweb.owlapi.model.OWLClassExpression;
 
+import java.text.DecimalFormat;
+import java.util.Map;
+
 /**
  * A node in the search tree of the ontology engineering algorithm.
  * 
@@ -60,7 +60,7 @@ public class OENode extends AbstractSearchTreeNode<OENode> implements SearchTree
 	public OENode(OWLClassExpression description, double accuracy) {
 		this.description = description;
 		this.accuracy = accuracy;
-		this.horizontalExpansion = OWLClassExpressionUtils.getLength(description) - 1;
+		this.horizontalExpansion = OWLClassExpressionUtils.getLength(description);
 	}
 
 //	public OENode(OENode parentNode, OWLClassExpression description, double accuracy) {

components-core/src/main/java/org/dllearner/algorithms/el/DisjunctiveHeuristic.java

@@ -46,4 +46,8 @@ public int compare(SearchTreeNode tree1, SearchTreeNode tree2) {
 	public void init() throws ComponentInitException {
 	}
 
+	@Override
+	public double getNodeScore(SearchTreeNode node) {
+		return node.getScore().getAccuracy();
+	}
 }

components-core/src/main/java/org/dllearner/algorithms/el/ELDescriptionNode.java

@@ -389,10 +389,7 @@ public OWLClassExpression transformToDescription() {
 			}
 		// return an intersection of labels and edges
 		} else {
-			Set<OWLClassExpression> operands = new TreeSet<>();
-			for(OWLClass nc : label) {
-				operands.add(nc);
-			}
+			Set<OWLClassExpression> operands = new TreeSet<OWLClassExpression>(label);
 
 			for(ELDescriptionEdge edge : edges) {
 				if(edge.isObjectProperty()){
@@ -405,8 +402,7 @@ public OWLClassExpression transformToDescription() {
 					operands.add(dsr);
 				}
 			}
-			OWLClassExpression is = df.getOWLObjectIntersectionOf(operands);
-			return is;
+			return df.getOWLObjectIntersectionOf(operands);
 		}
 	}
 

components-core/src/main/java/org/dllearner/algorithms/el/ELDescriptionTree.java

@@ -44,7 +44,7 @@
 import org.semanticweb.owlapi.model.OWLProperty;
 
 /**
- * Represents an EL OWLClassExpression tree. Unlike {@link ELDescriptionNode}, this is
+ * Represents an EL description tree. Unlike {@link ELDescriptionNode}, this is
  * a tree-wide structure, i.e. it does not implement the tree structure itself,
  * but is used to store information about the tree.
  * 

components-core/src/main/java/org/dllearner/algorithms/el/ELHeuristic.java

@@ -18,8 +18,6 @@
  */
 package org.dllearner.algorithms.el;
 
-import java.util.Comparator;
-
 import org.dllearner.core.Heuristic;
 
 /**
@@ -31,6 +29,6 @@
  * @author Jens Lehmann
  *
  */
-public interface ELHeuristic extends Comparator<SearchTreeNode>, Heuristic {
+public interface ELHeuristic extends Heuristic<SearchTreeNode> {
 
 }

components-core/src/main/java/org/dllearner/algorithms/el/StableHeuristic.java

@@ -50,4 +50,9 @@ public int compare(SearchTreeNode o1, SearchTreeNode o2) {
 	 */
 	@Override
 	public void init() throws ComponentInitException {}
+
+	@Override
+	public double getNodeScore(SearchTreeNode node) {
+		return node.getScore().getAccuracy();
+	}
 }

components-core/src/main/java/org/dllearner/algorithms/ocel/ExampleBasedHeuristic.java

@@ -18,8 +18,6 @@
  */
 package org.dllearner.algorithms.ocel;
 
-import java.util.Comparator;
-
 import org.dllearner.core.Heuristic;
 
 /**
@@ -31,6 +29,6 @@
  * @author Jens Lehmann
  *
  */
-public interface ExampleBasedHeuristic extends Comparator<ExampleBasedNode>, Heuristic{
+public interface ExampleBasedHeuristic extends Heuristic<ExampleBasedNode>{
 
 }