[DL-Learner SVN] SF.net SVN: dl-learner:[1871] trunk/src/dl-learner/org/dllearner

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

Revision: 1871
          http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1871&view=rev
Author:   lorenz_b
Date:     2009-10-01 12:05:40 +0000 (Thu, 01 Oct 2009)

Log Message:
-----------
continued auto learning mode

Modified Paths:
--------------
    trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java
    trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java
    trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/ResultTableModel.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/WizardController.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/AutoLearnPanelDescriptor.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/InconsistencyExplanationPanelDescriptor.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ManualLearnPanelDescriptor.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/AutoLearnPanel.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ClassChoosePanel.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/InconsistencyExplanationPanel.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/UnsatisfiableExplanationPanel.java

Added Paths:
-----------
    trunk/src/dl-learner/org/dllearner/tools/ore/ConcurrencyBug.java

Modified: trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/core/LearningAlgorithm.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -254,7 +254,7 @@
 				// be in the search of the learning algorith, which leads to
 				// unpredictable behaviour)
 				Description d = ed.getDescription().clone();
-				ConceptTransformation.replaceRange(d, reasoner);
+//				ConceptTransformation.replaceRange(d, reasoner);
 				ed.setDescription(d);
 				
 				returnList.add(ed);

Added: trunk/src/dl-learner/org/dllearner/tools/ore/ConcurrencyBug.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ConcurrencyBug.java	                        (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ConcurrencyBug.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -0,0 +1,95 @@
+package org.dllearner.tools.ore;
+
+import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.Timer;
+import java.util.TimerTask;
+
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.kb.OWLFile;
+import org.dllearner.learningproblems.ClassLearningProblem;
+import org.dllearner.reasoning.PelletReasoner;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.model.OWLClass;
+import org.semanticweb.owl.model.OWLDataFactory;
+import org.semanticweb.owl.model.OWLObjectAllRestriction;
+import org.semanticweb.owl.model.OWLObjectProperty;
+import org.semanticweb.owl.model.OWLObjectSomeRestriction;
+import org.semanticweb.owl.model.OWLOntologyCreationException;
+import org.semanticweb.owl.model.OWLOntologyManager;
+import org.semanticweb.owl.model.OWLSubClassAxiom;
+
+public class ConcurrencyBug {
+
+	/**
+	 * @param args
+	 * @throws MalformedURLException 
+	 * @throws ComponentInitException 
+	 * @throws URISyntaxException 
+	 * @throws OWLOntologyCreationException 
+	 * @throws LearningProblemUnsupportedException 
+	 */
+	public static void main(String[] args) throws MalformedURLException, ComponentInitException, OWLOntologyCreationException, URISyntaxException, LearningProblemUnsupportedException {
+		File file = new File("examples/swore/swore.rdf");
+		URL classToDescribe = new URL("http://ns.softwiki.de/req/CustomerRequirement");
+		
+		ComponentManager cm = ComponentManager.getInstance();
+		OWLFile ks = cm.knowledgeSource(OWLFile.class);
+		((OWLFile)ks).getConfigurator().setUrl(file.toURI().toURL());
+		ks.init();
+		
+		PelletReasoner reasoner = cm.reasoner(PelletReasoner.class, ks);
+		reasoner.init();
+		reasoner.loadOntologies();
+		reasoner.dematerialise();
+		
+		ClassLearningProblem lp = cm.learningProblem(ClassLearningProblem.class, reasoner);
+		lp.getConfigurator().setClassToDescribe(classToDescribe);
+		lp.init();
+		
+		String NS = "http://ns.softwiki.de/req/";
+		OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+		OWLDataFactory factory = manager.getOWLDataFactory();
+		OWLClass customerRequirement = factory.getOWLClass(URI.create(NS +"CustomerRequirement"));
+		OWLClass comment = factory.getOWLClass(URI.create(NS + "Comment"));
+		OWLObjectProperty idDefinedBy = factory.getOWLObjectProperty(URI.create(NS + "isDefinedBy"));
+		OWLObjectProperty defines = factory.getOWLObjectProperty(URI.create(NS + "defines"));
+		
+		OWLObjectSomeRestriction some = factory.getOWLObjectSomeRestriction(defines, comment);
+		OWLObjectAllRestriction all = factory.getOWLObjectAllRestriction(idDefinedBy, some);
+		OWLSubClassAxiom sub = factory.getOWLSubClassAxiom(customerRequirement, all);
+		
+//		System.out.println(reasoner.remainsSatisfiableImpl(sub));
+		
+		final CELOE la = cm.learningAlgorithm(CELOE.class, lp, reasoner);
+		la.getConfigurator().setMaxExecutionTimeInSeconds(8);
+		la.getConfigurator().setUseNegation(false);
+		la.getConfigurator().setNoisePercentage(0.05);
+		la.getConfigurator().setMaxNrOfResults(10);
+		la.init();
+		
+		Timer timer = new Timer();
+		timer.schedule(new TimerTask() {
+			
+			@Override
+			public void run() {
+				if(la.isRunning()){
+					System.out.println(la.getCurrentlyBestEvaluatedDescriptions(10, 0.8, true));
+				} else {
+					cancel();
+				}
+				
+			}
+		}, 1000, 1000);
+		la.start();
+		
+
+	}
+
+}

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -43,7 +43,7 @@
 	private RootFinder rootFinder;
 
 	private boolean isComputeAllExplanations = false;
-	private int maxExplantionCount = 1;
+	private int maxExplanationCount = 1;
 	private boolean allExplanationWarningChecked = false;
 	
 	private Map<Explanation, List<Map<OWLAxiom, Integer>>> orderingMap;
@@ -113,7 +113,7 @@
 		if (isComputeAllExplanations) {
 			explanations = gen.getExplanations(entailment);
 		} else {
-			explanations = gen.getExplanations(entailment, maxExplantionCount);
+			explanations = gen.getExplanations(entailment, maxExplanationCount);
 		}
 
 		return explanations;
@@ -127,9 +127,9 @@
 		if (isComputeAllExplanations) {
 			explanations = gen.getExplanations(entailment);
 		} else {
-			explanations = gen.getExplanations(entailment, maxExplantionCount);
+			explanations = gen.getExplanations(entailment, maxExplanationCount);
 		}
-
+		
 		return explanations;
 	}
 	
@@ -244,12 +244,12 @@
 	}
 	
 	public void setMaxExplantionCount(int limit){
-		maxExplantionCount = limit;
+		maxExplanationCount = limit;
 		fireExplanationLimitChanged();
 	}
 	
 	public int getMaxExplantionCount(){
-		return maxExplantionCount;
+		return maxExplanationCount;
 	}
 	
 	public void addListener(ExplanationManagerListener l){

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -69,7 +69,7 @@
 
 	@Override
 	public Set<Explanation> getExplanations(OWLAxiom entailment){		
-		return getExplanations(entailment, -1);
+		return getExplanations(entailment, Integer.MAX_VALUE);
 	}
 	
 	public int getArity(OWLAxiom axiom){

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -8,6 +8,8 @@
 import org.dllearner.tools.ore.explanation.laconic.LaconicExplanationGenerator;
 import org.mindswap.pellet.owlapi.PelletReasonerFactory;
 import org.mindswap.pellet.owlapi.Reasoner;
+import org.mindswap.pellet.utils.Timer;
+import org.mindswap.pellet.utils.Timers;
 import org.semanticweb.owl.apibinding.OWLManager;
 import org.semanticweb.owl.inference.OWLReasoner;
 import org.semanticweb.owl.inference.OWLReasonerException;
@@ -69,7 +71,7 @@
 	}
 	
 	public static void miniEconomyTest() {
-		String	file	= "file:examples/ore/miniEconomy.owl";
+		String	file	= "file:examples/ore/koala.owl";
 		
 		try {
 			
@@ -78,28 +80,43 @@
 			OWLOntology ontology = manager.loadOntologyFromPhysicalURI(URI
 					.create(file));
 			
-			PelletReasonerFactory resonerFact = new PelletReasonerFactory();
+			PelletReasonerFactory reasonerFact = new PelletReasonerFactory();
 			OWLDataFactory dataFactory = manager.getOWLDataFactory();
 		
-			Reasoner reasoner = resonerFact.createReasoner(manager);
+			Reasoner reasoner = reasonerFact.createReasoner(manager);
 			reasoner.loadOntology(ontology);
 			
 			reasoner.classify();
-			System.out.println(reasoner.getInconsistentClasses());
-		
 			
+			
 			LaconicExplanationGenerator expGen = new LaconicExplanationGenerator(
-					manager, resonerFact, Collections.singleton(ontology));
+					manager, reasonerFact, Collections.singleton(ontology));
 			
+//			org.semanticweb.owl.explanation.api.ExplanationGenerator<OWLAxiom> copy = org.semanticweb.owl.explanation.api.
+//			ExplanationManager.createLaconicExplanationGeneratorFactory(reasonerFact).createExplanationGenerator(ontology.getAxioms());
+			
+			
 			Set<OWLClass> unsatClasses = reasoner.getInconsistentClasses();
 			OWLSubClassAxiom unsatAxiom;
-
+			Timers timers = new Timers();
 			for (OWLClass unsat : unsatClasses) {
 				unsatAxiom = dataFactory.getOWLSubClassAxiom(unsat, dataFactory
 						.getOWLNothing());
+				Timer t1 = timers.createTimer("t1");
+				Timer t2 =timers.createTimer("t2");
+				t1.start();
 				Set<Explanation> explanations = expGen
 						.getExplanations(unsatAxiom);
-				System.out.println(explanations);
+				t1.stop();
+//				System.out.println(explanations);
+				t2.start();
+//				Set<org.semanticweb.owl.explanation.api.Explanation<OWLAxiom>> expl = copy.getExplanations(unsatAxiom);
+				t2.stop();
+//				System.out.println(expl);
+				
+				for(Timer timer : timers.getTimers()){
+					System.out.println(timer.getTotal());
+				}
 			}
 
 

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/ResultTableModel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/ResultTableModel.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/ResultTableModel.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -22,7 +22,7 @@
 	public ResultTableModel(){
 		super();
 		resultList = new ArrayList<EvaluatedDescriptionClass>();
-		df = new DecimalFormat("00.00%");
+		df = new DecimalFormat("00%");
 	}
 	
 	public ResultTableModel(List<EvaluatedDescriptionClass> resultList){

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/WizardController.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/WizardController.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/WizardController.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -29,6 +29,7 @@
 import org.dllearner.tools.ore.ui.wizard.descriptors.AutoLearnPanelDescriptor;
 import org.dllearner.tools.ore.ui.wizard.descriptors.ClassChoosePanelDescriptor;
 import org.dllearner.tools.ore.ui.wizard.descriptors.InconsistencyExplanationPanelDescriptor;
+import org.dllearner.tools.ore.ui.wizard.descriptors.IntroductionPanelDescriptor;
 import org.dllearner.tools.ore.ui.wizard.descriptors.KnowledgeSourcePanelDescriptor;
 import org.dllearner.tools.ore.ui.wizard.descriptors.ManualLearnPanelDescriptor;
 import org.dllearner.tools.ore.ui.wizard.descriptors.RepairPanelDescriptor;
@@ -272,25 +273,25 @@
     
     void refreshLeftPanel(Object panelDescriptor){
     	
-    	if(panelDescriptor.equals("INTRODUCTION_PANEL")){
+    	if(panelDescriptor.equals(IntroductionPanelDescriptor.IDENTIFIER)){
         	wizard.setLeftPanel(0);
-        }
-    	if(panelDescriptor.equals("KNOWLEDGESOURCE_CHOOSE_PANEL")){
+        } else
+    	if(panelDescriptor.equals(KnowledgeSourcePanelDescriptor.IDENTIFIER)){
         	wizard.setLeftPanel(1);
-        }
-    	if(panelDescriptor.equals("CLASS_CHOOSE_OWL_PANEL") || panelDescriptor.equals("CLASS_CHOOSE_SPARQL_PANEL")){
+        } else 
+    	if(panelDescriptor.equals(ClassChoosePanelDescriptor.IDENTIFIER)){
         	wizard.setLeftPanel(3);
-        }
-    	if(panelDescriptor.equals("LEARNING_PANEL")){
+        } else
+    	if(panelDescriptor.equals(ManualLearnPanelDescriptor.IDENTIFIER) || panelDescriptor.equals(AutoLearnPanelDescriptor.IDENTIFIER)){
         	wizard.setLeftPanel(4);
-        }
-    	if(panelDescriptor.equals("REPAIR_PANEL")){
+        } else 
+    	if(panelDescriptor.equals(RepairPanelDescriptor.IDENTIFIER)){
         	wizard.setLeftPanel(5);
-        }
-    	if(panelDescriptor.equals("SAVE_PANEL")){
+        } else
+    	if(panelDescriptor.equals(SavePanelDescriptor.IDENTIFIER)){
         	wizard.setLeftPanel(6);
-        }
-    	if(panelDescriptor.equals(UnsatisfiableExplanationPanelDescriptor.IDENTIFIER)){
+        } else {
+    	
         	wizard.setLeftPanel(2);
         }
     	

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/AutoLearnPanelDescriptor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/AutoLearnPanelDescriptor.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/AutoLearnPanelDescriptor.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -1,5 +1,8 @@
 package org.dllearner.tools.ore.ui.wizard.descriptors;
 
+import java.awt.Cursor;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
@@ -22,7 +25,7 @@
 import org.dllearner.tools.ore.ui.wizard.WizardPanelDescriptor;
 import org.dllearner.tools.ore.ui.wizard.panels.AutoLearnPanel;
 
-public class AutoLearnPanelDescriptor extends WizardPanelDescriptor{
+public class AutoLearnPanelDescriptor extends WizardPanelDescriptor implements ActionListener{
 	/**
 	 * Identification string for class choose panel.
 	 */
@@ -35,6 +38,12 @@
     private AutoLearnPanel autoLearnPanel;
     
     private List<NamedClass> classes;
+    
+    private EquivalentLearningTask equivalentLearningTask;
+    private SuperClassLearningTask superLearningTask;
+    
+    private int currentClassIndex = 0;
+    
    
     /**
      * Constructor creates new panel and adds listener to list.
@@ -43,6 +52,8 @@
     	autoLearnPanel = new AutoLearnPanel();
         setPanelDescriptorIdentifier(IDENTIFIER);
         setPanelComponent(autoLearnPanel);        
+    
+        autoLearnPanel.addActionListener(this);
         classes = new ArrayList<NamedClass>();
     }
     
@@ -63,19 +74,38 @@
     }
 	
 	public void fillClassesTable(){
+		TaskManager.getInstance().setTaskStarted("Retrieving atomic classes...");
 		new ClassRetrievingTask().execute();
 	}
 	
 	public void learnEquivalentClassExpressions(){
-		TaskManager.getInstance().setTaskStarted("Learning equivalent class expressions...");
-		new EquivalentLearningTask().execute();
+		TaskManager.getInstance().getStatusBar().setMessage("Learning equivalent class expressions...");
+		getWizard().getDialog().setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
+		equivalentLearningTask = new EquivalentLearningTask();
+		equivalentLearningTask.addPropertyChangeListener(TaskManager.getInstance().getStatusBar());
+		equivalentLearningTask.execute();
 	}
 	
 	public void learnSubClassExpressions(){
-		TaskManager.getInstance().setTaskStarted("Learning superclass expressions...");
-		new SuperClassLearningTask().execute();
+		TaskManager.getInstance().getStatusBar().setMessage("Learning superclass expressions...");
+		TaskManager.getInstance().getStatusBar().setProgress(0);
+		getWizard().getDialog().setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
+		superLearningTask = new SuperClassLearningTask();
+		superLearningTask.addPropertyChangeListener(TaskManager.getInstance().getStatusBar());
+		superLearningTask.execute();
 	}
 	
+	public void learnNextClass(){
+		autoLearnPanel.resetPanel();
+		OREManager.getInstance().setCurrentClass2Learn(new NamedClass("http://ns.softwiki.de/req/CustomerRequirement"));//classes.get(currentClassIndex));
+		learnEquivalentClassExpressions();
+		currentClassIndex++;
+	}
+	
+	@Override
+	public void actionPerformed(ActionEvent e) {
+		learnNextClass();		
+	}
   
     /**
      * Inner class to get all atomic classes in a background thread.
@@ -122,7 +152,7 @@
 					autoLearnPanel.fillClassesTable(result);
 					OREManager.getInstance().setCurrentClass2Learn(classes.get(0));
 					TaskManager.getInstance().setTaskFinished();
-					learnEquivalentClassExpressions();
+					learnNextClass();
 				}
 			});					
 		}
@@ -130,134 +160,118 @@
     
     class EquivalentLearningTask extends SwingWorker<Void, List<? extends EvaluatedDescription>> {
     	
+    	private Timer timer;
+    	private LearningAlgorithm la;
+    	private final int maxNrOfResults = OREManager.getInstance().getMaxNrOfResults();
+	    private final double threshold = OREManager.getInstance().getThreshold();
 
 		@Override
 		public Void doInBackground() {
 			OREManager.getInstance().setLearningType("equivalence");
 			OREManager.getInstance().setLearningProblem();
 		    OREManager.getInstance().setLearningAlgorithm();
-		    
-		    final LearningAlgorithm la = OREManager.getInstance().getLa();
-		    Timer timer = new Timer();
+		    la = OREManager.getInstance().getLa();
+		  		    
+		    timer = new Timer();
+		    setProgress(0);
+			TaskManager.getInstance().getStatusBar().setMaximumValue(OREManager.getInstance().getMaxExecutionTimeInSeconds());
 			timer.schedule(new TimerTask(){
 
+				int progress = 0;
+				List<? extends EvaluatedDescription> result;
 				@SuppressWarnings("unchecked")
 				@Override
 				public void run() {
-					if(!isCancelled() && la.isRunning()){
-						publish(la.getCurrentlyBestEvaluatedDescriptions(OREManager.getInstance().getMaxNrOfResults(), 
-								OREManager.getInstance().getThreshold(), true));
+					if(la.isRunning()){
+						progress += 1;
+						setProgress(progress);
+						result = la.getCurrentlyBestEvaluatedDescriptions(maxNrOfResults, threshold, true);
+						publish(result);
 					}
 				}
 				
-			}, 1000, 2000);
+			}, 1000, 1000);
 			la.start();
 			return null;
 		}
 
 		@Override
 		public void done() {
-			SwingUtilities.invokeLater(new Runnable() {
-				
-				@SuppressWarnings("unchecked")
-				@Override
-				public void run() {
-					
-					autoLearnPanel.fillEquivalentClassExpressionsTable((List<EvaluatedDescriptionClass>)OREManager.getInstance().getLa().
-							getCurrentlyBestEvaluatedDescriptions(OREManager.getInstance().getMaxNrOfResults(), OREManager.getInstance().getThreshold(), true));
-					learnSubClassExpressions();
-					
-				}
-			});					
+			timer.cancel();
+			List<? extends EvaluatedDescription> result = la.getCurrentlyBestEvaluatedDescriptions(maxNrOfResults, threshold, true);
+			updateList(result);
+			learnSubClassExpressions();
 		}
 		
 		@Override
-		protected void process(List<List<? extends EvaluatedDescription>> resultLists) {
-					
+		protected void process(List<List<? extends EvaluatedDescription>> resultLists) {					
 			for (List<? extends EvaluatedDescription> list : resultLists) {
 				updateList(list);
 			}
 		}
 		
-		private void updateList(final List<? extends EvaluatedDescription> result) {
-			
-			Runnable doUpdateList = new Runnable() {
-							
-				@SuppressWarnings("unchecked")
-				public void run() {
-					autoLearnPanel.fillEquivalentClassExpressionsTable((List<EvaluatedDescriptionClass>) result);
-				}
-			};
-			SwingUtilities.invokeLater(doUpdateList);
-
+		@SuppressWarnings("unchecked")
+		private void updateList(final List<? extends EvaluatedDescription> result) {		
+			autoLearnPanel.fillEquivalentClassExpressionsTable((List<EvaluatedDescriptionClass>) result);
 		}
 	}
     
     class SuperClassLearningTask extends SwingWorker<Void, List<? extends EvaluatedDescription>> {
     	
+    	private Timer timer;
+    	private LearningAlgorithm la;
+    	private final int maxNrOfResults = OREManager.getInstance().getMaxNrOfResults();
+	    private final double threshold = OREManager.getInstance().getThreshold();
 
 		@Override
 		public Void doInBackground() {
 			OREManager.getInstance().setLearningType("superClass");
 			OREManager.getInstance().setLearningProblem();
 		    OREManager.getInstance().setLearningAlgorithm();
-			
-		    final LearningAlgorithm la = OREManager.getInstance().getLa();
-		    Timer timer = new Timer();
+		    la = OREManager.getInstance().getLa();
+  		    
+		    timer = new Timer();
+		    setProgress(0);
+			TaskManager.getInstance().getStatusBar().setMaximumValue(OREManager.getInstance().getMaxExecutionTimeInSeconds());
 			timer.schedule(new TimerTask(){
 
+				int progress = 0;
+				List<? extends EvaluatedDescription> result;
 				@SuppressWarnings("unchecked")
 				@Override
 				public void run() {
-					if(!isCancelled() && la.isRunning()){
-						publish(la.getCurrentlyBestEvaluatedDescriptions(OREManager.getInstance().getMaxNrOfResults(), 
-								OREManager.getInstance().getThreshold(), true));
+					if(la.isRunning()){
+						progress += 1;
+						setProgress(progress);
+						result = la.getCurrentlyBestEvaluatedDescriptions(maxNrOfResults, threshold, true);
+						publish(result);
 					}
 				}
 				
-			}, 1000, 2000);
+			}, 1000, 1000);
 			la.start();
-		    
 			return null;
 		}
 
 		@Override
 		public void done() {
-			SwingUtilities.invokeLater(new Runnable() {
-				
-				@SuppressWarnings("unchecked")
-				@Override
-				public void run() {
-					
-					autoLearnPanel.fillSuperClassExpressionsTable((List<EvaluatedDescriptionClass>)OREManager.getInstance().getLa().
-							getCurrentlyBestEvaluatedDescriptions(OREManager.getInstance().getMaxNrOfResults(), OREManager.getInstance().getThreshold(), true));		
-					TaskManager.getInstance().setTaskFinished();
-				}
-			});					
+			timer.cancel();
+			List<? extends EvaluatedDescription> result = la.getCurrentlyBestEvaluatedDescriptions(maxNrOfResults, threshold, true);
+			updateList(result);	
+			TaskManager.getInstance().setTaskFinished();
+			setProgress(0);
 		}
 		
 		@Override
-		protected void process(List<List<? extends EvaluatedDescription>> resultLists) {
-					
+		protected void process(List<List<? extends EvaluatedDescription>> resultLists) {				
 			for (List<? extends EvaluatedDescription> list : resultLists) {
 				updateList(list);
 			}
 		}
 		
+		@SuppressWarnings("unchecked")
 		private void updateList(final List<? extends EvaluatedDescription> result) {
-			
-			Runnable doUpdateList = new Runnable() {
-							
-				@SuppressWarnings("unchecked")
-				public void run() {
-					autoLearnPanel.fillSuperClassExpressionsTable((List<EvaluatedDescriptionClass>) result);
-				}
-			};
-			SwingUtilities.invokeLater(doUpdateList);
-
+			autoLearnPanel.fillSuperClassExpressionsTable((List<EvaluatedDescriptionClass>) result);
 		}
 	}
-
-	
-	
 }

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/InconsistencyExplanationPanelDescriptor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/InconsistencyExplanationPanelDescriptor.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/InconsistencyExplanationPanelDescriptor.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -1,13 +1,22 @@
 package org.dllearner.tools.ore.ui.wizard.descriptors;
 
+import java.awt.BorderLayout;
+import java.awt.Component;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.List;
 
-import javax.swing.SwingUtilities;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSpinner;
 import javax.swing.SwingWorker;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
 
 import org.dllearner.tools.ore.ExplanationManager;
+import org.dllearner.tools.ore.ExplanationManagerListener;
 import org.dllearner.tools.ore.OREManager;
 import org.dllearner.tools.ore.RepairManager;
 import org.dllearner.tools.ore.RepairManagerListener;
@@ -18,7 +27,7 @@
 import org.mindswap.pellet.owlapi.Reasoner;
 import org.semanticweb.owl.model.OWLOntologyChange;
 
-public class InconsistencyExplanationPanelDescriptor extends WizardPanelDescriptor implements ActionListener,  RepairManagerListener{
+public class InconsistencyExplanationPanelDescriptor extends WizardPanelDescriptor implements ActionListener,ChangeListener, ExplanationManagerListener,  RepairManagerListener{
 	public static final String IDENTIFIER = "INCONSISTENCY_PANEL";
     public static final String INFORMATION = "";
 
@@ -32,14 +41,18 @@
 	}
 
 	public void init() {
-		reasoner = OREManager.getInstance().getReasoner()
-				.getReasoner();
+		reasoner = OREManager.getInstance().getReasoner().getReasoner();
+		
 		expMan = ExplanationManager.getInstance(OREManager.getInstance());
-		expMan.setComputeAllExplanationsMode(true);
+		expMan.addListener(this);
+		
 		repMan = RepairManager.getInstance(OREManager.getInstance());
 		repMan.addListener(this);
+		
 		panel = new InconsistencyExplanationPanel();
 		panel.addActionListeners(this);
+		panel.addChangeListener(this);
+		
 		setPanelComponent(panel);
 	}
     
@@ -79,28 +92,77 @@
     	showExplanations();
     }
 
-	@Override
-	public void actionPerformed(ActionEvent e) {
-		if (e.getActionCommand().equals("regular")) {
-			expMan.setLaconicMode(false);
-		} else if (e.getActionCommand().equals("laconic")) {
-			expMan.setLaconicMode(true);
-		}	
-	}
+	
+		@Override
+		public void actionPerformed(ActionEvent e) {
+			if (e.getActionCommand().equals("regular")) {
+				expMan.setLaconicMode(false);
+			} else if (e.getActionCommand().equals("laconic")) {
+				expMan.setLaconicMode(true);		
+			} else if (e.getActionCommand().equals("all")){
+				conditionalWarning("Computing all explanations might take a long time!", getWizard().getDialog());
+				expMan.setComputeAllExplanationsMode(true);
+				panel.setMaxExplanationsMode(false);
+			} else if (e.getActionCommand().equals("max")){
+				expMan.setComputeAllExplanationsMode(false);
+				panel.setMaxExplanationsMode(true);
+			} 		
+		}
+	
 
 	@Override
 	public void repairPlanChanged() {
 		// TODO Auto-generated method stub
 		
 	}
+	
+	@Override
+	public void stateChanged(ChangeEvent e) {
+		JSpinner spinner = (JSpinner)e.getSource();
+		expMan.setMaxExplantionCount(((Integer)spinner.getValue()).intValue());
+		
+	}
 
 	@Override
+	public void explanationLimitChanged() {
+		showExplanations();	
+	}
+	
+	@Override
+	public void explanationTypeChanged() {
+		showExplanations();	
+	}
+
+	@Override
 	public void repairPlanExecuted(List<OWLOntologyChange> changes) {
 		showExplanations();
 		panel.repaint();
 		setNextButtonEnabled2ConsistentOntology();
 	}
 	
+	private void conditionalWarning(final String notice, Component parent) {
+        class NotifyPanel extends JPanel {
+            /**
+			 * 
+			 */
+			private static final long serialVersionUID = -5602333953438722592L;
+
+			public NotifyPanel() {
+                final JCheckBox enough = new JCheckBox("Don't show this message again", expMan.isAllExplanationWarningChecked());
+                enough.addActionListener(new ActionListener() {
+                    public void actionPerformed(ActionEvent e) {
+                        expMan.setAllExplanationWarningChecked();
+                    }
+                });
+                setLayout(new BorderLayout());
+                add(new JLabel("<html><font size=+1>" + notice + "</font></html>"), BorderLayout.CENTER);
+                add(enough, BorderLayout.SOUTH);
+            }
+        }
+        if( ! expMan.isAllExplanationWarningChecked())
+            JOptionPane.showMessageDialog(parent, new NotifyPanel(), "Warning", JOptionPane.WARNING_MESSAGE);
+    }
+	
 	class ExplanationTask extends SwingWorker<Void, Void>{
 		
 		@Override
@@ -118,22 +180,16 @@
 		}
 		
 		private void showExplanations(){
-			
-			SwingUtilities.invokeLater(new Runnable() {
-				
-				@Override
-				public void run() {
-					panel.clearExplanationsPanel();
-					int counter = 1;
-					for (Explanation explanation : expMan
-							.getInconsistencyExplanations()) {
-						panel.addExplanation(explanation, counter);
-						counter++;
-					}
-					panel.validate();
-					
+			panel.clearExplanationsPanel();
+			int counter = 1;
+			for (Explanation explanation : expMan.getInconsistencyExplanations()) {
+				panel.addExplanation(explanation, counter);
+				counter++;
+				if(counter > expMan.getMaxExplantionCount() && !expMan.isComputeAllExplanationsMode()){
+					break;
 				}
-			});
+			}
+			panel.validate();
 			TaskManager.getInstance().setTaskFinished();
 		}
 

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ManualLearnPanelDescriptor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ManualLearnPanelDescriptor.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ManualLearnPanelDescriptor.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -26,9 +26,7 @@
 import java.util.List;
 import java.util.Timer;
 import java.util.TimerTask;
-import java.util.concurrent.ExecutionException;
 
-import javax.swing.SwingUtilities;
 import javax.swing.SwingWorker;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
@@ -212,12 +210,12 @@
 	 * @author Lorenz Buehmann
 	 *
 	 */
-	class LearningTask extends SwingWorker<List<? extends EvaluatedDescription>, List<? extends EvaluatedDescription>> {
+	class LearningTask extends SwingWorker<Void, List<? extends EvaluatedDescription>> {
 		    	
     	
 		@SuppressWarnings("unchecked")
 		@Override
-		public List<? extends EvaluatedDescription> doInBackground() {
+		public Void doInBackground() {
 			
 			OREManager.getInstance().setLearningProblem();
 		    OREManager.getInstance().setLearningAlgorithm();
@@ -233,32 +231,27 @@
 				@Override
 				public void run() {progress += 1;setProgress(progress);
 					if(!isCancelled() && la.isRunning()){
-						publish(la.getCurrentlyBestEvaluatedDescriptions(OREManager.getInstance().getMaxNrOfResults(), 
-								OREManager.getInstance().getThreshold(), true));
+						List<? extends EvaluatedDescription> result = la.getCurrentlyBestEvaluatedDescriptions(OREManager.getInstance().getMaxNrOfResults(), 
+								OREManager.getInstance().getThreshold(), true);
+						publish(result);
 					}
 				}
 				
 			}, 1000, 1000);
-			OREManager.getInstance().start();
+			la.start();
 	
-			List<? extends EvaluatedDescription> result = la.getCurrentlyBestEvaluatedDescriptions
-								(OREManager.getInstance().getMaxNrOfResults(), OREManager.getInstance().getThreshold(), true);
 			
-			return result;
+			
+			return null;
 		}
 
 		@Override
 		public void done() {
 			
 			timer.cancel();
-			List<? extends EvaluatedDescription> result = null;
-			try {
-				result = get();
-			} catch (InterruptedException e) {
-				e.printStackTrace();
-			} catch (ExecutionException e) {
-				e.printStackTrace();
-			}
+			
+			List<? extends EvaluatedDescription> result = la.getCurrentlyBestEvaluatedDescriptions(OREManager.getInstance().getMaxNrOfResults(), 
+								OREManager.getInstance().getThreshold(), true);
 			updateList(result);
 			TaskManager.getInstance().setTaskFinished();
 			setProgress(0);
@@ -269,22 +262,14 @@
 
 		@Override
 		protected void process(List<List<? extends EvaluatedDescription>> resultLists) {
-					
 			for (List<? extends EvaluatedDescription> list : resultLists) {
 				updateList(list);
 			}
 		}
 		
-		private void updateList(final List<? extends EvaluatedDescription> result) {
-			
-			Runnable doUpdateList = new Runnable() {
-							
-				@SuppressWarnings("unchecked")
-				public void run() {
-					learnPanel.getResultTable().addResults((List<EvaluatedDescriptionClass>) result);
-				}
-			};
-			SwingUtilities.invokeLater(doUpdateList);
+		@SuppressWarnings("unchecked")
+		private void updateList(final List<? extends EvaluatedDescription> result) {			
+			learnPanel.getResultTable().addResults((List<EvaluatedDescriptionClass>) result);
 		}
 	}
 

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/AutoLearnPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/AutoLearnPanel.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/AutoLearnPanel.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -1,11 +1,17 @@
 package org.dllearner.tools.ore.ui.wizard.panels;
 
 import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionListener;
 import java.util.List;
 import java.util.Set;
 
 import javax.swing.BorderFactory;
+import javax.swing.JButton;
 import javax.swing.JComponent;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JSplitPane;
@@ -36,7 +42,15 @@
 	
 	private GraphicalCoveragePanel equivalentClassCoveragePanel;
 	private GraphicalCoveragePanel superClassCoveragePanel;
-
+	
+	private JLabel equivalentInconsistencyLabel;
+	private JLabel superInconsistencyLabel;
+	
+	private JButton skipButton;
+	
+	private final static String INCONSISTENY_WARNING = "<html><font color=red>" +
+														"Warning. Selected class expressions leads to an inconsistent ontology!" +
+														"</font></html>";
 	public AutoLearnPanel(){
 		createUI();
 	}
@@ -68,29 +82,78 @@
 		equivSubSplitPane.setOneTouchExpandable(true);
 		equivSubSplitPane.setDividerLocation(0.5);
 		
+		equivSubSplitPane.setTopComponent(createEquivalentPanel());
+		equivSubSplitPane.setBottomComponent(createSuperPanel());
+		
+		addTableSelectionListeners();
+		
+		skipButton = new JButton("Skip");
+		skipButton.setActionCommand("skip");
+		
+		resultPanel.add(equivSubSplitPane, BorderLayout.CENTER);
+		resultPanel.add(skipButton, BorderLayout.SOUTH);
+		
+		return resultPanel;
+	}
+	
+	private JComponent createEquivalentPanel(){
+		GridBagConstraints c = new GridBagConstraints();
 		equivalentPanel = new JPanel();
+		equivalentPanel.setLayout(new GridBagLayout());
+		
+		c.weightx = 1.0;
+		c.weighty = 1.0;
+		c.fill = GridBagConstraints.BOTH;
+		c.gridx = 0;
+		c.gridy = 0;
 		equivalentClassResultsTable = new EquivalentClassExpressionsTable();
 		equivalentClassResultsTable.setName("equivalent");
-		equivalentPanel.add(new JScrollPane(equivalentClassResultsTable));
+		equivalentPanel.add(new JScrollPane(equivalentClassResultsTable), c);
+		
+		c.weightx = 0.0;
+		c.weighty = 0.0;
+		c.gridx = 1;
+		c.gridy = 0;
 		equivalentClassCoveragePanel = new GraphicalCoveragePanel("");
-		equivalentPanel.add(equivalentClassCoveragePanel);
+		equivalentPanel.add(equivalentClassCoveragePanel, c);
 		equivalentPanel.setBorder(BorderFactory.createTitledBorder("Equivalent class expressions"));
 		
+		c.gridx = 0;
+		c.gridy = 1;
+		equivalentInconsistencyLabel = new JLabel(" ");
+		equivalentPanel.add(equivalentInconsistencyLabel, c);
+		
+		return equivalentPanel;
+	}
+	
+	private JComponent createSuperPanel(){
+		GridBagConstraints c = new GridBagConstraints();
 		superPanel = new JPanel();
+		superPanel.setLayout(new GridBagLayout());
+		
+		c.weightx = 1.0;
+		c.weighty = 1.0;
+		c.fill = GridBagConstraints.BOTH;
+		c.gridx = 0;
+		c.gridy = 0;
 		superClassResultsTable = new EquivalentClassExpressionsTable();
 		superClassResultsTable.setName("super");
-		superPanel.add(new JScrollPane(superClassResultsTable));
+		superPanel.add(new JScrollPane(superClassResultsTable), c);
+		
+		c.weightx = 0.0;
+		c.weighty = 0.0;
+		c.gridx = 1;
+		c.gridy = 0;
 		superClassCoveragePanel = new GraphicalCoveragePanel("");
-		superPanel.add(superClassCoveragePanel);
+		superPanel.add(superClassCoveragePanel, c);
 		superPanel.setBorder(BorderFactory.createTitledBorder("Superclass expressions"));
 		
-		addTableSelectionListeners();
+		c.gridx = 0;
+		c.gridy = 1;
+		superInconsistencyLabel = new JLabel(" ");
+		superPanel.add(superInconsistencyLabel, c);
 		
-		equivSubSplitPane.setTopComponent(equivalentPanel);
-		equivSubSplitPane.setBottomComponent(superPanel);
-		
-		resultPanel.add(equivSubSplitPane);
-		return resultPanel;
+		return superPanel;
 	}
 	
 	public void fillClassesTable(Set<NamedClass> classes){
@@ -105,6 +168,17 @@
 		equivalentClassResultsTable.addResults(resultList);
 	}
 	
+	public void addActionListener(ActionListener aL){
+		skipButton.addActionListener(aL);
+	}
+	
+	public void resetPanel(){
+		equivalentClassResultsTable.clear();
+		superClassResultsTable.clear();
+		equivalentClassCoveragePanel.clear();
+		superClassCoveragePanel.clear();
+	}
+	
 	private void addTableSelectionListeners(){
 		equivalentClassResultsTable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {		
 				@Override
@@ -114,7 +188,12 @@
 						
 						EvaluatedDescriptionClass selectedClassExpression = equivalentClassResultsTable.getSelectedValue();
 						OREManager.getInstance().setNewClassDescription(selectedClassExpression);
-						equivalentClassCoveragePanel.setNewClassDescription(selectedClassExpression);					
+						equivalentClassCoveragePanel.setNewClassDescription(selectedClassExpression);
+						if(!selectedClassExpression.isConsistent()){
+							equivalentInconsistencyLabel.setText(INCONSISTENY_WARNING);
+						} else {
+							equivalentInconsistencyLabel.setText(" ");
+						}
 					}				
 				}			
 			
@@ -129,7 +208,12 @@
 					
 					EvaluatedDescriptionClass selectedClassExpression = superClassResultsTable.getSelectedValue();
 					OREManager.getInstance().setNewClassDescription(selectedClassExpression);
-					superClassCoveragePanel.setNewClassDescription(selectedClassExpression);					
+					superClassCoveragePanel.setNewClassDescription(selectedClassExpression);
+					if(!selectedClassExpression.isConsistent()){
+						superInconsistencyLabel.setText(INCONSISTENY_WARNING);
+					} else {
+						superInconsistencyLabel.setText(" ");
+					}
 				}				
 			}	
 		});
@@ -143,4 +227,14 @@
 		superClassCoveragePanel.setNewClassDescription(desc);
 	}
 	
+	public static void main(String[] args){
+		JFrame frame = new JFrame();
+		
+		
+		frame.add(new AutoLearnPanel());
+		frame.pack();
+		frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+		frame.setVisible(true);
+	}
+	
 }

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ClassChoosePanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ClassChoosePanel.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ClassChoosePanel.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -28,6 +28,7 @@
 
 import javax.swing.BorderFactory;
 import javax.swing.ButtonGroup;
+import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
@@ -72,29 +73,45 @@
 	
 	private void createUI(){
 		setLayout(new GridBagLayout());
+		GridBagConstraints c = new GridBagConstraints();
+		
 		JPanel optionsPanel = new JPanel(new GridLayout(0, 1));
+		
 		autoLearnButton = new JRadioButton("Automatic learning mode");
 		autoLearnButton.setActionCommand("auto");
+		
 		manualLearnButton = new JRadioButton("Manual learning mode");
 		manualLearnButton.setActionCommand("manual");
+		
 		ButtonGroup learningType = new ButtonGroup();
 		learningType.add(manualLearnButton);
 		learningType.add(autoLearnButton);
 		autoLearnButton.setSelected(true);
 		optionsPanel.add(autoLearnButton);
 		optionsPanel.add(manualLearnButton);
+		
 		HelpablePanel optionsHelpPanel = new HelpablePanel(optionsPanel);
 		optionsHelpPanel.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
-		add(optionsHelpPanel);
+		c.gridwidth = GridBagConstraints.REMAINDER;
+		add(optionsHelpPanel, c);
+		
 		createAutoLearnPanel();
 		createManualLearnPanel();
+		
+		Dimension size = new Dimension(500, 500);
+		autoLearnPanel.setPreferredSize(size);
+		manualLearnPanel.setPreferredSize(size);
+		
 		currentPanel = autoLearnPanel;
-		add(currentPanel);
+		add(currentPanel, c);
 		
 	}
 	
 	private void createAutoLearnPanel(){
 		JPanel panel = new JPanel(new GridBagLayout());
+		GridBagConstraints c = new GridBagConstraints();
+		
+		c.gridwidth = GridBagConstraints.REMAINDER;
 		JPanel minInstancesCountPanel = new JPanel();
 		minInstancesCountPanel.add(new JLabel("Min. instance count per class: "));
 		minInstanceCountSpinner = new JSpinner();
@@ -102,9 +119,10 @@
 	    javax.swing.SpinnerModel spinnerModel = new SpinnerNumberModel(1, 1, 500, 1);
 	    minInstanceCountSpinner.setModel(spinnerModel);
 	    minInstancesCountPanel.add(minInstanceCountSpinner);
-	    panel.add(minInstancesCountPanel);
+	    panel.add(minInstancesCountPanel, c);
+	    
 	    learningOptionsPanel = new LearningOptionsPanel();
-		panel.add(learningOptionsPanel);
+		panel.add(learningOptionsPanel, c);
 		
 		autoLearnPanel = panel;
 	}
@@ -187,8 +205,19 @@
     	OREManager.getInstance().setMaxExecutionTimeInSeconds(learningOptionsPanel.getMaxExecutionTime());
     	OREManager.getInstance().setMaxNrOfResults(learningOptionsPanel.getNrOfConcepts());
     	OREManager.getInstance().setNoisePercentage(learningOptionsPanel.getMinAccuracy());
+    	OREManager.getInstance().setThreshold(learningOptionsPanel.getThreshold());
     	OREManager.getInstance().setMinInstanceCount(((Integer)(minInstanceCountSpinner.getValue())).intValue());
     	
     }
+    
+    public static void main(String[] args){
+		JFrame frame = new JFrame();
+		
+		
+		frame.add(new ClassChoosePanel());
+		frame.pack();
+		frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+		frame.setVisible(true);
+	}
 
 }
\ No newline at end of file

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/InconsistencyExplanationPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/InconsistencyExplanationPanel.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/InconsistencyExplanationPanel.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -2,8 +2,13 @@
 
 import java.awt.BorderLayout;
 import java.awt.Color;
-import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
 import java.awt.event.ActionListener;
+import java.util.HashSet;
+import java.util.Set;
 
 import javax.swing.BorderFactory;
 import javax.swing.Box;
@@ -13,12 +18,18 @@
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
 import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
 import javax.swing.JSplitPane;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.border.EtchedBorder;
+import javax.swing.event.ChangeListener;
 
 import org.dllearner.tools.ore.explanation.Explanation;
 import org.dllearner.tools.ore.ui.ExplanationTable;
 import org.dllearner.tools.ore.ui.ExplanationTablePanel;
+import org.dllearner.tools.ore.ui.HelpablePanel;
 import org.dllearner.tools.ore.ui.RepairPlanPanel;
+import org.dllearner.tools.ore.ui.UnsatisfiableClassesTable;
 import org.semanticweb.owl.apibinding.OWLManager;
 
 public class InconsistencyExplanationPanel extends JPanel{
@@ -28,81 +39,142 @@
 	 */
 	private static final long serialVersionUID = 9206626647697013786L;
 
-	private JSplitPane statsSplitPane;
-	
 	private JScrollPane explanationsScrollPane;
 	private JComponent explanationsPanel;
+	
 	private JPanel buttonExplanationsPanel;
-	private JPanel buttonPanel;
+	
+	
 	private ButtonGroup explanationType;
 	private JRadioButton regularButton;
 	private JRadioButton laconicButton;
+	private JRadioButton computeAllExplanationsRadioButton;
+    private  JRadioButton computeMaxExplanationsRadioButton;
+	private JSpinner maxExplanationsSelector;
+	
+	
+	private Set<ExplanationTablePanel> explanationPanels;
+	private Set<ExplanationTable> explanationTables;
+	
+	
 
 	public InconsistencyExplanationPanel() {
+		createUI();
+	}
 	
+	private void createUI(){
 		setLayout(new BorderLayout());
+		add(createDebuggingPanel());		
+	}
+	
+	private JComponent createDebuggingPanel(){
+		JSplitPane debuggingSplitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
+		debuggingSplitPane.setDividerLocation(500);
+		debuggingSplitPane.setOneTouchExpandable(true);
 
-		Dimension minimumSize = new Dimension(400, 400);
-
-
+		debuggingSplitPane.setTopComponent(createExplanationPanel());
+		debuggingSplitPane.setBottomComponent(createRepairPanel());
+		
+		return debuggingSplitPane;
+	}
+	
+	private JComponent createExplanationPanel(){
 		explanationsPanel = new Box(1);
+		
+		explanationPanels = new HashSet<ExplanationTablePanel>();
+		explanationTables = new HashSet<ExplanationTable>();
 
 		JPanel pan = new JPanel(new BorderLayout());
 		pan.add(explanationsPanel, BorderLayout.NORTH);
 		explanationsScrollPane = new JScrollPane(pan);
-		explanationsScrollPane.setPreferredSize(minimumSize);
-		explanationsScrollPane.setBorder(BorderFactory
-				.createLineBorder(Color.LIGHT_GRAY));
+
+		explanationsScrollPane.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY));
 		explanationsScrollPane.getViewport().setOpaque(false);
 		explanationsScrollPane.getViewport().setBackground(null);
 		explanationsScrollPane.setOpaque(false);
+	       
+		buttonExplanationsPanel = new JPanel();
+		buttonExplanationsPanel.setLayout(new BorderLayout());
+		buttonExplanationsPanel.add(explanationsScrollPane, BorderLayout.CENTER);
+		JPanel holder = new JPanel(new BorderLayout());
+		holder.add(createExplanationHeaderPanel(), BorderLayout.WEST);
+		buttonExplanationsPanel.add(holder, BorderLayout.NORTH);
+		
+		return buttonExplanationsPanel;
 
-		regularButton = new JRadioButton("regular", true);
+	}
+	
+	private JComponent createExplanationHeaderPanel(){
+		JPanel headerPanel = new JPanel(new GridBagLayout());
+		GridBagConstraints c = new GridBagConstraints();
+		
+		
+		JPanel explanationTypePanel = new JPanel(new GridLayout(0, 1));
+		regularButton = new JRadioButton("Show regular explanations", true);
 		regularButton.setActionCommand("regular");
-
-		laconicButton = new JRadioButton("laconic");
+		regularButton.setSelected(true);
+		laconicButton = new JRadioButton("Show precise explanations");
 		laconicButton.setActionCommand("laconic");
-
 		explanationType = new ButtonGroup();
 		explanationType.add(regularButton);
 		explanationType.add(laconicButton);
-		buttonPanel = new JPanel();
-		buttonPanel.add(regularButton);
-		buttonPanel.add(laconicButton);
-
-		buttonExplanationsPanel = new JPanel();
-		buttonExplanationsPanel.setLayout(new BorderLayout());
-		buttonExplanationsPanel
-				.add(explanationsScrollPane, BorderLayout.CENTER);
-		buttonExplanationsPanel.add(buttonPanel, BorderLayout.NORTH);
-
-		statsSplitPane = new JSplitPane(0);
-		statsSplitPane.setResizeWeight(1.0D);
-		statsSplitPane.setTopComponent(buttonExplanationsPanel);
+		explanationTypePanel.add(regularButton);
+		explanationTypePanel.add(laconicButton);
+		HelpablePanel explanationTypeHelpPanel = new HelpablePanel(explanationTypePanel);
+		explanationTypeHelpPanel.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
 		
-		//repair panel
-		JPanel repairPanelHolder = new JPanel();
-		repairPanelHolder.setOpaque(false);
-		repairPanelHolder.setLayout(new BorderLayout());
-		repairPanelHolder.add(new JLabel("Repair plan"), BorderLayout.NORTH);
-		RepairPlanPanel repairPanel = new RepairPlanPanel(); 
-		repairPanelHolder.add(repairPanel);
 		
+		JPanel explanationCountPanel = new JPanel(new GridBagLayout());
 		
-		statsSplitPane.setBottomComponent(repairPanelHolder);
-		
-		statsSplitPane.setBorder(null);
-		statsSplitPane.setDividerLocation(500);
-		statsSplitPane.setOneTouchExpandable(true);
-		
-		add(statsSplitPane);
+		maxExplanationsSelector = new JSpinner();
+		maxExplanationsSelector.setEnabled(true);
+	    javax.swing.SpinnerModel spinnerModel = new SpinnerNumberModel(1, 1, 500, 1);
+	    maxExplanationsSelector.setModel(spinnerModel);
+	    maxExplanationsSelector.setBorder(BorderFactory.createEmptyBorder(0, 30, 0, 0));
+	    
+	    computeAllExplanationsRadioButton = new JRadioButton("Compute all explanations");
+	    computeAllExplanationsRadioButton.setActionCommand("all");
+	            
+	    computeMaxExplanationsRadioButton = new JRadioButton("Limit explanation count to:");
+	    computeMaxExplanationsRadioButton.setActionCommand("max");
+	    computeMaxExplanationsRadioButton.setSelected(true);
+	    
+	    ButtonGroup limitButtonGroup = new ButtonGroup();
+	    limitButtonGroup.add(computeAllExplanationsRadioButton);
+	    limitButtonGroup.add(computeMaxExplanationsRadioButton);
+	       
+	    explanationCountPanel.add(computeAllExplanationsRadioButton, new GridBagConstraints(0, 0, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 0, 0), 0, 0));
+	    explanationCountPanel.add(computeMaxExplanationsRadioButton, new GridBagConstraints(0, 1, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 0, 0), 0, 0));
+	    explanationCountPanel.add(maxExplanationsSelector, new GridBagConstraints(1, 1, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 0, 0), 0, 0));
+	    
+	    HelpablePanel explanationCountHelpPanel = new HelpablePanel(explanationCountPanel);
+	    explanationCountHelpPanel.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+	    
+	    c.fill = GridBagConstraints.VERTICAL;
+	    
+	    headerPanel.add(explanationTypeHelpPanel, c);
+	    c.anchor = GridBagConstraints.LINE_END;
+	    headerPanel.add(explanationCountHelpPanel, c);
+	    
+	    return headerPanel;
+	}
 	
+	private JComponent createRepairPanel(){
+		JPanel repairPanel = new JPanel(new BorderLayout());
+		repairPanel.add(new JLabel("Repair plan"), BorderLayout.NORTH);
+		repairPanel.add(new RepairPlanPanel(), BorderLayout.CENTER);
+		return repairPanel;
 	}
 	
-	public void clearExplanationsPanel(){
+	public void clearExplanationsPanel() {		
 		explanationsPanel.removeAll();
+		explanationsPanel.validate();
 	}
 	
+	public void setMaxExplanationsMode(boolean value){
+		maxExplanationsSelector.setEnabled(value);	
+	}
+	
 	public void addExplanation(Explanation explanation, int counter){
 		ExplanationTable expTable = new ExplanationTable(explanation, OWLManager.createOWLOntologyManager().getOWLDataFactory().getOWLThing());
 		explanationsPanel.add(new ExplanationTablePanel(expTable, counter));
@@ -113,6 +185,12 @@
 	public void addActionListeners(ActionListener aL){
 		regularButton.addActionListener(aL);
 		laconicButton.addActionListener(aL);
+		computeAllExplanationsRadioButton.addActionListener(aL);
+		computeMaxExplanationsRadioButton.addActionListener(aL);
 	}
 	
+	public void addChangeListener(ChangeListener cL){
+		maxExplanationsSelector.addChangeListener(cL);
+	}
+	
 }

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/UnsatisfiableExplanationPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/UnsatisfiableExplanationPanel.java	2009-09-30 06:19:13 UTC (rev 1870)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/UnsatisfiableExplanationPanel.java	2009-10-01 12:05:40 UTC (rev 1871)
@@ -137,56 +137,11 @@
 		JPanel pan = new JPanel(new BorderLayout());
 		pan.add(explanationsPanel, BorderLayout.NORTH);
 		explanationsScrollPane = new JScrollPane(pan);
-//		explanationsScrollPane.setPreferredSize(minimumSize);
+
 		explanationsScrollPane.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY));
 		explanationsScrollPane.getViewport().setOpaque(false);
 		explanationsScrollPane.getViewport().setBackground(null);
 		explanationsScrollPane.setOpaque(false);
-			
-//		regularButton = new JRadioButton("Show regular explanations", true);
-//		regularButton.setActionCommand("regular");
-//		regularButton.setSelected(true);
-//		laconicButton = new JRadioButton("Show precise explanations");
-//		laconicButton.setActionCommand("laconic");
-//			
-//		explanationType = new ButtonGroup();
-//		explanationType.add(regularButton);
-//		explanationType.add(laconicButton);
-//		
-//		buttonPanel = new JPanel();
-//		buttonPanel.setLayout(new GridBagLayout());
-//		buttonPanel.add(regularButton, new GridBagConstraints(0, 0, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 2, 30), 0, 0));
-//		buttonPanel.add(laconicButton, new GridBagConstraints(0, 1, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 0, 30), 0, 0));
-//		HelpablePanel explanationTypeHelpPanel = new HelpablePanel(buttonPanel);
-//		explanationTypeHelpPanel.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
-//		
-//		JPanel buttonPanelHolder = new JPanel(new BorderLayout());
-//		buttonPanelHolder.add(explanationTypeHelpPanel, "West");
-//		
-//		maxExplanationsSelector = new JSpinner();
-//		maxExplanationsSelector.setEnabled(true);
-//	    javax.swing.SpinnerModel spinnerModel = new SpinnerNumberModel(1, 1, 500, 1);
-//	    maxExplanationsSelector.setModel(spinnerModel);
-//	    maxExplanationsSelector.setBorder(BorderFactory.createEmptyBorder(0, 30, 0, 0));
-//	    
-//	    computeAllExplanationsRadioButton = new JRadioButton("Compute all explanations");
-//	    computeAllExplanationsRadioButton.setActionCommand("all");
-//	            
-//	    computeMaxExplanationsRadioButton = new JRadioButton("Limit explanation count to:");
-//	    computeMaxExplanationsRadioButton.setActionCommand("MAX");
-//	    computeMaxExplanationsRadioButton.setSelected(true);
-//	    
-//	    ButtonGroup limitButtonGroup = new ButtonGroup();
-//	    limitButtonGroup.add(computeAllExplanationsRadioButton);
-//	    limitButtonGroup.add(computeMaxExplanationsRadioButton);
-//	       
-////	    buttonPanel.add(computeAllExplanationsRadioButton, new GridBagConstraints(1, 0, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 0, 0), 0, 0));
-////	    buttonPanel.add(computeMaxExplanationsRadioButton, new GridBagConstraints(1, 1, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 0, 0), 0, 0));
-////	    buttonPanel.add(maxExplanationsSelector, new GridBagConstraints(3, 1, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 0, 0), 0, 0));
-//	  
-//	    strikeOutBox = new JCheckBox("Strike out irrelevant parts");
-//	    strikeOutBox.setActionCommand("strike");
-////	    buttonPanel.add(strikeOutBox, new GridBagConstraints(3, 0, 1, 1, 0.0D, 0.0D, 12, 2, new Insets(0, 0, 0, 0), 0, 0));
 	       
 		buttonExplanationsPanel = new JPanel();
 		buttonExplanationsPanel.setLayout(new BorderLayout());
@@ -231,7 +186,7 @@
 	    computeAllExplanationsRadioButton.setActionCommand("all");
 	            
 	    computeMaxExplanationsRadioButton = new JRadioButton("Limit explanation count to:");
-	    computeMaxExplanationsRadioButton.setActionCommand("MAX");
+	    computeMaxExplanationsRadioButton.setActionCommand("max");
 	    computeMaxExplanationsRadioButton.setSelected(true);
 	    
 	    ButtonGroup limitButtonGroup = new ButtonGroup();
@@ -283,20 +238,20 @@
 		return impactRepairPanel;
 	}
 	
-	private JComponent createRepairPanel(){
-		return new RepairPlanPanel();
-	}
+//	private JComponent createRepairPanel(){
+//		return new RepairPlanPanel();
+//	}
+//	
+//	private JComponent createImpactPanel(){
+//		ImpactTable impactTable = new ImpactTable();
+//		JScrollPane impScr = new JScrollPane(impactTable);
+//		JPanel impactPanel = new JPanel();
+//		impactPanel.setLayout(new BorderLayout());
+//		impactPanel.add(new JLabel("Impact"), BorderLayout.NORTH);
+//		impactPanel.add(impScr);
+//		return impactPanel;
+//	}
 	
-	private JComponent createImpactPanel(){
-		ImpactTable impactTable = new ImpactTable();
-		JScrollPane impScr = new JScrollPane(impactTable);
-		JPanel impactPanel = new JPanel();
-		impactPanel.setLayout(new BorderLayout());
-		impactPanel.add(new JLabel("Impact"), BorderLayout.NORTH);
-		impactPanel.add(impScr);
-		return impactPanel;
-	}
-	
 	public void fillUnsatClassesTable(List<OWLClass> unsatClasses) {
 		unsatClassesTable.addUnsatClasses(unsatClasses);
 		unsatClassesScrollPane.validate();
@@ -306,17 +261,6 @@
 		explanationsPanel.removeAll();
 		explanationsPanel.validate();
 	}
-
-	public void addExplanation(Explanation explanation, OWLClass unsat, int counter) {
-		ExplanationTable expTable = new ExplanationTable(explanation, unsat);
-		ExplanationTablePanel panel = new ExplanationTablePanel(expTable, counter);
-		explanationsPanel.add(panel);
-		explanationsPanel.add(Box.createVerticalStrut(10));
-		explanationPanels.add(panel);
-//		explanationsPanel.add(new JSeparator());
-//		explanationsPanel.add(Box.createVerticalStrut(10));
-//		this.updateUI();
-	}
 	
 	public void addExplanations(Set<Explanation> explanations, OWLClass unsat){
 		explanationTables.clear();


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