[DL-Learner SVN] SF.net SVN: dl-learner:[1962] trunk/src/dl-learner/org/dllearner

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

Revision: 1962
          http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1962&view=rev
Author:   lorenz_b
Date:     2009-12-29 18:00:50 +0000 (Tue, 29 Dec 2009)

Log Message:
-----------
Added new constructor to Stat class.
Implemented isEquivalentClass method in PelletReasoner.
Started new class StatsGenerator to generate statistics from evaluation protocol files.
Some small fixes.

Modified Paths:
--------------
    trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java
    trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationComputingScript.java
    trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationGUI.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/SelectableClassExpressionsTable.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/SelectableClassExpressionsTableModel.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/ManualLearnPanelDescriptor.java
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ManualLearnPanel.java
    trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java

Added Paths:
-----------
    trunk/src/dl-learner/org/dllearner/scripts/evaluation/StatsGenerator.java
    trunk/src/dl-learner/org/dllearner/scripts/evaluation/father.ser

Removed Paths:
-------------
    trunk/src/dl-learner/org/dllearner/scripts/evaluation/test.ser
    trunk/src/dl-learner/org/dllearner/tools/ore/ui/ReasonerProgressUI.java

Modified: trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -535,13 +535,15 @@
 	
 	@Override
 	public boolean isSuperClassOfImpl(Description superConcept, Description subConcept) {
-		
-//			System.out.println("super: " + superConcept + "; sub: " + subConcept);
-			return reasoner.isSubClassOf(OWLAPIDescriptionConvertVisitor.getOWLDescription(subConcept), OWLAPIDescriptionConvertVisitor.getOWLDescription(superConcept));			
-		
+		return reasoner.isSubClassOf(OWLAPIDescriptionConvertVisitor.getOWLDescription(subConcept), OWLAPIDescriptionConvertVisitor.getOWLDescription(superConcept));			
 	}
 	
 	@Override
+	protected boolean isEquivalentClassImpl(Description class1, Description class2) {
+		return reasoner.isEquivalentClass(OWLAPIDescriptionConvertVisitor.getOWLDescription(class1), OWLAPIDescriptionConvertVisitor.getOWLDescription(class2));			
+	}
+
+	@Override
 	protected TreeSet<Description> getSuperClassesImpl(Description concept) {
 		Set<Set<OWLClass>> classes = null;
 		

Modified: trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationComputingScript.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationComputingScript.java	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationComputingScript.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -10,6 +10,7 @@
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.text.DecimalFormat;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedList;
@@ -17,6 +18,7 @@
 import java.util.Map;
 import java.util.Set;
 import java.util.TreeSet;
+import java.util.Map.Entry;
 
 import org.dllearner.algorithms.celoe.CELOE;
 import org.dllearner.core.ComponentInitException;
@@ -25,7 +27,10 @@
 import org.dllearner.core.LearningProblemUnsupportedException;
 import org.dllearner.core.ReasonerComponent;
 import org.dllearner.core.configurators.CELOEConfigurator;
+import org.dllearner.core.owl.Axiom;
+import org.dllearner.core.owl.EquivalentClassesAxiom;
 import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.SubClassAxiom;
 import org.dllearner.core.owl.Thing;
 import org.dllearner.kb.OWLFile;
 import org.dllearner.learningproblems.ClassLearningProblem;
@@ -41,6 +46,7 @@
 import org.semanticweb.owl.model.OWLOntologyCreationException;
 import org.semanticweb.owl.model.OWLOntologyManager;
 
+
 public class EvaluationComputingScript {
 	
 	private ReasonerComponent reasoner;
@@ -109,11 +115,71 @@
 		computeWithApproximation();
 		computeSuggestions();
 		computeGenFMeasureWithoutDefaultNegation();
-		getAssertedAxioms();
+//		getAssertedAxioms();
+		evaluateInconsistencies();
 		saveResults();
 		
 	}
 	
+	
+	private void evaluateInconsistencies(){
+		List<Map<NamedClass, List<EvaluatedDescriptionClass>>> superMapList = new ArrayList<Map<NamedClass,List<EvaluatedDescriptionClass>>>();
+		List<Map<NamedClass, List<EvaluatedDescriptionClass>>> equivalenceMapList = new ArrayList<Map<NamedClass,List<EvaluatedDescriptionClass>>>();
+		
+		equivalenceMapList.add(defaultEquivalenceMap);
+		equivalenceMapList.add(owlEquivalenceFMeasureMap);
+		equivalenceMapList.add(owlEquivalenceGenFMeasureMap);
+		equivalenceMapList.add(owlEquivalenceJaccardMap);
+		equivalenceMapList.add(owlEquivalencePredaccMap);
+		equivalenceMapList.add(owlEquivalenceStandardMap);
+		equivalenceMapList.add(fastEquivalenceFMeasureMap);
+		equivalenceMapList.add(fastEquivalenceGenFMeasureMap);
+		equivalenceMapList.add(fastEquivalenceJaccardMap);
+		equivalenceMapList.add(fastEquivalencePredaccMap);
+		equivalenceMapList.add(fastEquivalenceStandardMap);
+		
+		superMapList.add(defaultSuperMap);
+		superMapList.add(owlSuperFMeasureMap);
+		superMapList.add(owlSuperGenFMeasureMap);
+		superMapList.add(owlSuperJaccardMap);
+		superMapList.add(owlSuperPredaccMap);
+		superMapList.add(owlSuperStandardMap);
+		superMapList.add(fastSuperFMeasureMap);
+		superMapList.add(fastSuperGenFMeasureMap);
+		superMapList.add(fastSuperJaccardMap);
+		superMapList.add(fastSuperPredaccMap);
+		superMapList.add(fastSuperStandardMap);
+		
+		Axiom axiom;
+		NamedClass nc;
+		for(Map<NamedClass, List<EvaluatedDescriptionClass>> map : equivalenceMapList){
+			for(Entry<NamedClass, List<EvaluatedDescriptionClass>> entry : map.entrySet()){
+				nc = entry.getKey();
+				for(EvaluatedDescriptionClass cl : entry.getValue()){
+					axiom = new EquivalentClassesAxiom(nc, cl.getDescription());
+					boolean followsFromKB = reasoner.isEquivalentClass(cl.getDescription(), nc);
+					boolean isConsistent = followsFromKB || reasoner.remainsSatisfiable(axiom);
+					cl.setConsistent(isConsistent);
+					cl.setFollowsFromKB(followsFromKB);
+				}
+				
+			}
+		}
+		for(Map<NamedClass, List<EvaluatedDescriptionClass>> map : superMapList){
+			for(Entry<NamedClass, List<EvaluatedDescriptionClass>> entry : map.entrySet()){
+				nc = entry.getKey();
+				for(EvaluatedDescriptionClass cl : entry.getValue()){
+					axiom = new SubClassAxiom(nc, cl.getDescription());
+					boolean followsFromKB = reasoner.isSuperClassOf(cl.getDescription(), nc);
+					boolean isConsistent = followsFromKB || reasoner.remainsSatisfiable(axiom);
+					cl.setConsistent(isConsistent);
+					cl.setFollowsFromKB(followsFromKB);
+				}
+				
+			}
+		}
+	}
+	
 	private void getAssertedAxioms(){
 		try {
 			OWLOntologyManager man = OWLManager.createOWLOntologyManager();
@@ -146,7 +212,13 @@
 
 	private void saveResults() {
 		OutputStream fos = null;
-		File file = new File("test2.ser");
+		File old = new File(ontologyURI);
+		int index = old.getName().lastIndexOf('.');
+		String fileName = "test.res";
+	    if (index>0&& index <= old.getName().length() - 2 ) {
+	    	  fileName = old.getName().substring(0, index) + ".res";
+	    }  
+		File file = new File(fileName);
 		try {
 			fos = new FileOutputStream(file);
 			ObjectOutputStream o = new ObjectOutputStream(fos);
@@ -233,6 +305,7 @@
 						for (int k = 0; k <= 3; k++) {
 							ClassLearningProblem lp = cm.learningProblem(ClassLearningProblem.class, reasoner);
 							lp.getConfigurator().setClassToDescribe(nc.getURI().toURL());
+							lp.getConfigurator().setCheckConsistency(false);
 							if (j == 0) {
 								lp.getConfigurator().setType("equivalence");
 								System.out.println("Learning equivalentClass expressions");
@@ -373,6 +446,7 @@
 							);
 					ClassLearningProblem lp = cm.learningProblem(ClassLearningProblem.class, reasoner);
 					lp.getConfigurator().setClassToDescribe(nc.getURI().toURL());
+					lp.getConfigurator().setCheckConsistency(false);
 					for (int j = 0; j <= 1; j++) {
 						if (j == 0) {
 							if(!equivalentReducedClassesSet.contains(nc)){
@@ -429,7 +503,7 @@
 			}
 			cm.freeComponent(reasoner);
 		}
-		cm.freeComponent(reasoner);
+//		cm.freeComponent(reasoner);
 		cm.freeComponent(lp);
 		cm.freeComponent(celoe);
 	}
@@ -459,6 +533,7 @@
 						+ " with " + instanceCount + " instances");
 				ClassLearningProblem lp = cm.learningProblem(ClassLearningProblem.class, reasoner);
 				lp.getConfigurator().setClassToDescribe(nc.getURI().toURL());
+				lp.getConfigurator().setCheckConsistency(false);
 				for (int i = 0; i <= 1; i++) {
 					if (i == 0) {
 						lp.getConfigurator().setType("equivalence");
@@ -543,7 +618,7 @@
 		if(args[0].startsWith("http")){
 			fileURL = new URL(args[0]);
 		} else {
-			fileURL = new File(args[0]).toURI().toURL();
+			fileURL = new File(new URL(args[0]).toURI()).toURI().toURL();
 		}
 		long startTime = System.currentTimeMillis();
 		new EvaluationComputingScript(fileURL);

Modified: trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationGUI.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationGUI.java	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationGUI.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -15,10 +15,15 @@
 import java.awt.event.MouseMotionListener;
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.OutputStream;
 import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -55,6 +60,7 @@
 import org.dllearner.tools.ore.ui.GraphicalCoveragePanel;
 import org.dllearner.tools.ore.ui.MarkableClassesTable;
 import org.dllearner.tools.ore.ui.ResultTable;
+import org.dllearner.tools.ore.ui.SelectableClassExpressionsTable;
 import org.mindswap.pellet.utils.SetUtils;
 import org.semanticweb.owl.model.OWLDescription;
 
@@ -66,6 +72,8 @@
 	 * 
 	 */
 	private static final long serialVersionUID = -3097551929270352556L;
+	
+	private File inputFile;
 
 	private RatingTablePanel tab1;
 	private RatingTablePanel tab2;
@@ -78,7 +86,11 @@
 	private RatingTablePanel tab9;
 	private RatingTablePanel tab10;
 
-	private ResultTable defaultTab;
+	private SelectableClassExpressionsTable defaultTab;
+	private static String INCONSISTENCYWARNING = "<html><font color=red>" +
+	"Warning. Selected class expressions leads to an inconsistent ontology!" +
+	"</font></html>";
+	private JLabel inconsistencyLabel;
 	private JCheckBox noSuggestionCheckBox;
 	private JCheckBox alternateSuggestionCheckBox;
 	private ButtonGroup bg;
@@ -142,12 +154,14 @@
 	private Map<NamedClass, Set<OWLDescription>> assertedEquivalentClasses = new HashMap<NamedClass, Set<OWLDescription>>();
 	private Map<NamedClass, Set<OWLDescription>> assertedSuperClasses = new HashMap<NamedClass, Set<OWLDescription>>();
 
-	private Map<NamedClass, EvaluatedDescriptionClass> selectedEquivalenceMap = new HashMap<NamedClass, EvaluatedDescriptionClass>();
-	private Map<NamedClass, EvaluatedDescriptionClass> selectedSuperMap = new HashMap<NamedClass, EvaluatedDescriptionClass>();
+	
+	private Map<NamedClass, String> selectedEquivalenceMap = new HashMap<NamedClass, String>();
+	private Map<NamedClass, String> selectedSuperMap = new HashMap<NamedClass, String>();
 
 	public EvaluationGUI(File input) throws ComponentInitException, MalformedURLException,
 			LearningProblemUnsupportedException {
 		super();
+		inputFile = input;
 		loadResults(input);
 		setTitle(input.getName());
 		createUI();
@@ -224,6 +238,15 @@
 
 		return messageTablesPanel;
 	}
+	
+	private void showInconsistencyWarning(boolean show){
+		if(show){
+			inconsistencyLabel.setText(INCONSISTENCYWARNING);
+		} else {
+			inconsistencyLabel.setText(" ");
+		}
+		
+	}
 
 	private JPanel createSingleTablePanel() {
 		JPanel panel = new JPanel(new GridBagLayout());
@@ -232,13 +255,21 @@
 		c.gridwidth = GridBagConstraints.REMAINDER;
 		c.weightx = 1.0;
 		c.weighty = 0.0;
-		JPanel tableHolderPanel = new JPanel(new BorderLayout());
-		defaultTab = new ResultTable();
+		JPanel tableHolderPanel = new JPanel(new GridBagLayout());
+		GridBagConstraints gbc = new GridBagConstraints();
+		gbc.fill = GridBagConstraints.HORIZONTAL;
+		gbc.weightx = 1.0;
+		defaultTab = new SelectableClassExpressionsTable();
 		defaultTab.getSelectionModel().addListSelectionListener(this);
-		tableHolderPanel.add(defaultTab);
+		tableHolderPanel.add(new JScrollPane(defaultTab), gbc);
 		graphPanel = new GraphicalCoveragePanel("");
-		tableHolderPanel.add(graphPanel, BorderLayout.EAST);
+		gbc.weightx = 0.0;
+		tableHolderPanel.add(graphPanel, gbc);
 		panel.add(tableHolderPanel, c);
+		
+		inconsistencyLabel = new JLabel();
+		panel.add(inconsistencyLabel, c);
+		inconsistencyLabel.setText(" ");
 
 		c.weightx = 1.0;
 		c.weighty = 0.0;
@@ -255,7 +286,9 @@
 			@Override
 			public void actionPerformed(ActionEvent e) {
 				defaultTab.clearSelection();
+				defaultTab.removeSelection();
 				graphPanel.clear();
+				showInconsistencyWarning(false);
 			}
 		});
 		panel.add(noSuggestionCheckBox, c);
@@ -272,7 +305,9 @@
 			@Override
 			public void actionPerformed(ActionEvent e) {
 				defaultTab.clearSelection();
+				defaultTab.removeSelection();
 				graphPanel.clear();
+				showInconsistencyWarning(false);
 			}
 		});
 		panel.add(alternateSuggestionCheckBox, c);
@@ -280,6 +315,7 @@
 		bg = new ButtonGroup();
 		bg.add(alternateSuggestionCheckBox);
 		bg.add(noSuggestionCheckBox);
+		noSuggestionCheckBox.setSelected(true);
 		return panel;
 	}
 
@@ -481,6 +517,9 @@
 	public void actionPerformed(ActionEvent e) {
 		if (e.getActionCommand().equals("next")) {
 			NamedClass nc = classesTable.getSelectedClass(currentClassIndex);
+			if(!showingMultiTables){
+				traceInput();
+			}
 			if (showingMultiTables && showingEquivalentSuggestions) {
 				if (defaultSuperMap.get(nc) != null) {
 					showSuperSuggestions(nc);
@@ -514,7 +553,7 @@
 				}
 
 			} else if (!showingMultiTables && !showingEquivalentSuggestions) {
-				if (owlEquivalenceStandardMap.get(nc) != null) {
+				if (owlSuperStandardMap.get(nc) != null) {
 					showMultiTables();
 
 				} else {
@@ -542,17 +581,79 @@
 				showSingleTable();
 			}
 			setFinished();
+			resetSingleTablePanel();
 
 		} else if (e.getActionCommand().equals("finish")) {
-
+			if(!showingMultiTables){
+				traceInput();
+			}
 			closeDialog();
+			saveInput();
 		}
 
 	}
+	
+	private void resetSingleTablePanel(){
+		bg.clearSelection();
+		noSuggestionCheckBox.setSelected(true);
+		showInconsistencyWarning(false);
+	}
+	
+	private void traceInput(){
+		NamedClass currentClass = classesTable.getSelectedClass(currentClassIndex);
+		if(alternateSuggestionCheckBox.isSelected()){
+			if(showingEquivalentSuggestions){
+				selectedEquivalenceMap.put(currentClass, "m");
+			} else {
+				selectedSuperMap.put(currentClass, "m");
+			}
+		} else if(noSuggestionCheckBox.isSelected()){
+			if(showingEquivalentSuggestions){
+				selectedEquivalenceMap.put(currentClass, "n");
+			} else {
+				selectedSuperMap.put(currentClass, "n");
+			}
+		} else {
+			int position = defaultTab.getSelectedPosition() - 1;
+			if(showingEquivalentSuggestions){
+				selectedEquivalenceMap.put(currentClass, String.valueOf(position));
+			} else {
+				selectedSuperMap.put(currentClass, String.valueOf(position));
+			}
+		}
+	}
+	
+	
+	private void saveInput(){
+		OutputStream fos = null;
+		int index = inputFile.getName().lastIndexOf('.');
+		String fileName = "test.inp";
+	    if (index>0&& index <= inputFile.getName().length() - 2 ) {
+	    	  fileName = inputFile.getName().substring(0, index) + ".inp";
+	    }  
+		File file = new File(fileName);
+		try {
+			fos = new FileOutputStream(file);
+			ObjectOutputStream o = new ObjectOutputStream(fos);
+			
+			o.writeObject(selectedEquivalenceMap);
+			o.writeObject(selectedSuperMap);
+			
+			o.flush();
+			o.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		} finally {
+			try {
+				fos.close();
+			} catch (Exception e) {
+			}
+		}
+	}
 
 	private void setFinished() {
 		NamedClass nc = classesTable.getSelectedClass(currentClassIndex);
-		if (currentClassIndex == SetUtils.union(defaultEquivalenceMap.keySet(), defaultSuperMap.keySet()).size()) {
+		if (currentClassIndex == SetUtils.union(defaultEquivalenceMap.keySet(), defaultSuperMap.keySet()).size() - 1) {
 			if (showingEquivalentSuggestions && owlEquivalenceStandardMap.get(nc) == null
 					&& defaultSuperMap.get(nc) == null || showingEquivalentSuggestions && showingMultiTables
 					&& defaultSuperMap.get(nc) == null || !showingEquivalentSuggestions
@@ -567,12 +668,51 @@
 	@Override
 	public void valueChanged(ListSelectionEvent e) {
 		if (!e.getValueIsAdjusting() && defaultTab.getSelectedRow() >= 0) {
-			graphPanel.setNewClassDescription(defaultTab.getSelectedValue());
-			bg.clearSelection();
+			EvaluatedDescriptionClass cl = defaultTab.getSelectedValue();
+			showInconsistencyWarning(!cl.isConsistent());
+			graphPanel.setNewClassDescription(cl);
+			if(defaultTab.getSelectedClassExpression() != null){
+				bg.clearSelection();
+			}
+			
 		}
 
 	}
+	
 
+	@Override
+	public void mouseDragged(MouseEvent e) {
+
+	}
+
+	@Override
+	public void mouseMoved(MouseEvent e) {
+		if (e.getSource() instanceof ResultTable) {
+			ResultTable result = ((ResultTable) e.getSource());
+			int column = result.columnAtPoint(e.getPoint());
+			int row = result.rowAtPoint(e.getPoint());
+
+			if (column == 0 && row >= 0) {
+				if (mouseOverTable != result || row != oldRow) {
+					mouseOverTable = result;
+					oldRow = row;
+					EvaluatedDescriptionClass ec = result.getValueAtRow(row);
+					graphPanel2.clear();
+					graphPanel2.setNewClassDescription(ec);
+					setCoverageLocationRelativeTo(result);
+					showCoveragePanel(true);
+				} else {
+					showCoveragePanel(true);
+				}
+			} else {
+				showCoveragePanel(false);
+			}
+		} else {
+			showCoveragePanel(false);
+		}
+
+	}
+
 	/**
 	 * @param args
 	 * @throws ComponentInitException
@@ -582,10 +722,11 @@
 	 * @throws IllegalAccessException
 	 * @throws InstantiationException
 	 * @throws ClassNotFoundException
+	 * @throws URISyntaxException 
 	 */
 	public static void main(String[] args) throws ComponentInitException, MalformedURLException,
 			LearningProblemUnsupportedException, ClassNotFoundException, InstantiationException,
-			IllegalAccessException, UnsupportedLookAndFeelException {
+			IllegalAccessException, UnsupportedLookAndFeelException, URISyntaxException {
 
 		UIManager.setLookAndFeel(new PlasticLookAndFeel());
 
@@ -593,7 +734,7 @@
 			System.out.println("You need to give an file as argument.");
 			System.exit(0);
 		}
-		final File input = new File(args[0]);
+		final File input = new File(new URL(args[0]).toURI());
 		SwingUtilities.invokeLater(new Runnable() {
 
 			@Override
@@ -613,39 +754,7 @@
 
 	}
 
-	@Override
-	public void mouseDragged(MouseEvent e) {
 
-	}
-
-	@Override
-	public void mouseMoved(MouseEvent e) {
-		if (e.getSource() instanceof ResultTable) {
-			ResultTable result = ((ResultTable) e.getSource());
-			int column = result.columnAtPoint(e.getPoint());
-			int row = result.rowAtPoint(e.getPoint());
-
-			if (column == 0 && row >= 0) {
-				if (mouseOverTable != result || row != oldRow) {
-					mouseOverTable = result;
-					oldRow = row;
-					EvaluatedDescriptionClass ec = result.getValueAtRow(row);
-					graphPanel2.clear();
-					graphPanel2.setNewClassDescription(ec);
-					setCoverageLocationRelativeTo(result);
-					showCoveragePanel(true);
-				} else {
-					showCoveragePanel(true);
-				}
-			} else {
-				showCoveragePanel(false);
-			}
-		} else {
-			showCoveragePanel(false);
-		}
-
-	}
-
 	class RatingTablePanel extends JPanel {
 
 		/**

Added: trunk/src/dl-learner/org/dllearner/scripts/evaluation/StatsGenerator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/evaluation/StatsGenerator.java	                        (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/evaluation/StatsGenerator.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -0,0 +1,421 @@
+package org.dllearner.scripts.evaluation;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.FileInputStream;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.ObjectInputStream;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.learningproblems.EvaluatedDescriptionClass;
+import org.dllearner.utilities.statistics.Stat;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyCreationException;
+import org.semanticweb.owl.model.OWLOntologyManager;
+
+
+public class StatsGenerator {
+	
+
+	private Map<NamedClass, List<EvaluatedDescriptionClass>> equivalentSuggestions;
+	private Map<NamedClass, List<EvaluatedDescriptionClass>> superSuggestions;
+	
+	private Map<NamedClass, String> equivalentInput;
+	private Map<NamedClass, String> superInput;
+	
+	private StringBuilder latex;
+	
+	//general stats
+	private Stat acceptedGlobalStat = new Stat();
+	private Stat rejectedGlobalStat = new Stat();
+	private Stat failedGlobalStat = new Stat();
+	
+	//equivalent class stats
+	private Stat acceptedStat = new Stat();
+	private Stat rejectedStat = new Stat();
+	private Stat failedStat = new Stat();
+	private Set<Stat> moreInstancesCountStats = new HashSet<Stat>();
+	private Set<Stat> accStats = new HashSet<Stat>();
+	private Set<Stat> accSelectedStats = new HashSet<Stat>();
+	private Set<Stat> accAboveThresholdStats = new HashSet<Stat>();
+	private Set<Stat> positionStats = new HashSet<Stat>();
+	
+	//super class stats
+	private Stat acceptedStatSC = new Stat();
+	private Stat rejectedStatSC = new Stat();
+	private Stat failedStatSC = new Stat();
+	private Set<Stat> moreInstancesCountStatsSC = new HashSet<Stat>();
+	private Set<Stat> accStatsSC = new HashSet<Stat>();
+	private Set<Stat> accSelectedStatsSC = new HashSet<Stat>();
+	private Set<Stat> accAboveThresholdStatsSC = new HashSet<Stat>();
+	private Set<Stat> positionStatsSC = new HashSet<Stat>();
+	
+	private int suggestionListsCount;
+	private int logicalAxiomCount;
+	
+	
+	public StatsGenerator(File directory){
+		//begin latex table with headers
+		beginTable();
+		//for each ontology
+		for(File suggestionFile : directory.listFiles(new ResultFileFilter())){
+			clearStats();
+			loadSuggestions(suggestionFile);
+			loadOntology(suggestionFile);
+			//for each user evaluation input file
+			for(File inputFile : directory.listFiles(new NameFilter(suggestionFile))){
+				loadUserInput(inputFile);
+				makeSingleStat();
+				printStats();
+				
+			}
+			//add row to the latex table for current ontology
+			addTableRow();
+		}
+		//end latex table
+		endTable();
+		printLatexCode();
+		
+		
+	}
+	
+	private void loadOntology(File file){
+		String ontologyPath = file.toURI().toString().substring(0, file.toURI().toString().lastIndexOf('.') ) + ".owl";
+		OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+		try {
+			OWLOntology ont = man.loadOntologyFromPhysicalURI(URI.create(ontologyPath));
+			logicalAxiomCount = ont.getLogicalAxiomCount();
+		} catch (OWLOntologyCreationException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+	}
+	
+	private void clearStats(){
+		acceptedGlobalStat = new Stat();
+		rejectedGlobalStat = new Stat();
+		failedGlobalStat = new Stat();
+		
+		moreInstancesCountStats.clear();
+		accStats.clear();
+		accSelectedStats.clear();
+		accAboveThresholdStats.clear();
+		positionStats.clear();
+		
+		moreInstancesCountStatsSC.clear();
+		accStatsSC.clear();
+		accSelectedStatsSC.clear();
+		accAboveThresholdStatsSC.clear();
+		positionStatsSC.clear();
+	}
+	
+	private void makeSingleStat(){
+		// equivalence classes
+		int candidatesAboveThresholdCount = 0;
+		int missesCount = 0;
+		int foundDescriptionCount = 0;
+		int noSensibleDescriptionCount = 0;
+		int inconsistencyDetected = 0;
+		int moreInstancesCount = 0;
+		int nonPerfectCount = 0;
+		Stat moreInstancesCountStat = new Stat();
+		Stat accStat = new Stat();
+		Stat accSelectedStat = new Stat();
+		Stat accAboveThresholdStat = new Stat();
+		Stat positionStat = new Stat();
+
+		// super classes
+		int candidatesAboveThresholdCountSC = 0;
+		int missesCountSC = 0;
+		int foundDescriptionCountSC = 0;
+		int noSensibleDescriptionCountSC = 0;
+		int inconsistencyDetectedSC = 0;
+		int moreInstancesCountSC = 0;
+		int nonPerfectCountSC = 0;
+		Stat moreInstancesCountStatSC = new Stat();
+		Stat accStatSC = new Stat();
+		Stat accSelectedStatSC = new Stat();
+		Stat accAboveThresholdStatSC = new Stat();
+		Stat positionStatSC = new Stat();
+		
+		//analysing input for equivalent class expressions
+		for (Entry<NamedClass, String> e : equivalentInput.entrySet()) {
+			NamedClass currentClass = e.getKey();
+			String input = e.getValue();
+			if (input.equals("m")) {
+				missesCount++;
+			} else if (input.equals("n")) {
+				noSensibleDescriptionCount++;
+			} else {
+				int selectedIndex = Integer.parseInt(input);
+				EvaluatedDescriptionClass selectedExpression = equivalentSuggestions.get(currentClass).get(
+						selectedIndex);
+				double bestAcc = equivalentSuggestions.get(currentClass).get(0).getAccuracy();
+				int selectedNr = selectedIndex + 1;
+				boolean isConsistent = selectedExpression.isConsistent();
+				Set<Individual> addInst = selectedExpression.getAdditionalInstances();
+				int additionalInstances = addInst.size();
+
+				accSelectedStat.addNumber(selectedExpression.getAccuracy());
+				positionStat.addNumber(selectedNr);
+				foundDescriptionCount++;
+				if (!isConsistent) {
+					inconsistencyDetected++;
+				}
+				if (additionalInstances > 0) {
+					moreInstancesCount++;
+					moreInstancesCountStat.addNumber(additionalInstances);
+				}
+				if (bestAcc < 0.9999) {
+					nonPerfectCount++;
+				}
+			}
+		}
+		acceptedStat.addNumber(foundDescriptionCount);
+		rejectedStat.addNumber(noSensibleDescriptionCount);
+		failedStat.addNumber(missesCount);
+		moreInstancesCountStats.add(moreInstancesCountStat);
+		accStats.add(accStat);
+		accSelectedStats.add(accSelectedStat);
+		accAboveThresholdStats.add(accSelectedStat);
+		positionStats.add(positionStat);
+		
+		//analysing input for super class expressions
+		for (Entry<NamedClass, String> e : superInput.entrySet()) {
+			NamedClass currentClass = e.getKey();
+			if (e.getValue().equals("m")) {
+				missesCountSC++;
+			} else if (e.getValue().equals("n")) {
+				noSensibleDescriptionCountSC++;
+			} else {
+				int selectedIndex = Integer.parseInt(e.getValue());
+				EvaluatedDescriptionClass selectedExpression = superSuggestions.get(currentClass).get(selectedIndex);
+				double bestAcc = superSuggestions.get(currentClass).get(0).getAccuracy();
+				int selectedNr = selectedIndex + 1;
+				boolean isConsistent = selectedExpression.isConsistent();
+				Set<Individual> addInst = selectedExpression.getAdditionalInstances();
+				int additionalInstances = addInst.size();
+
+				accSelectedStatSC.addNumber(selectedExpression.getAccuracy());
+				positionStatSC.addNumber(selectedNr);
+				foundDescriptionCountSC++;
+				if (!isConsistent) {
+					inconsistencyDetectedSC++;
+				}
+				if (additionalInstances > 0) {
+					moreInstancesCountSC++;
+					moreInstancesCountStatSC.addNumber(additionalInstances);
+				}
+				if (bestAcc < 0.9999) {
+					nonPerfectCountSC++;
+				}
+			}
+		}
+		acceptedStatSC.addNumber(foundDescriptionCountSC);
+		rejectedStatSC.addNumber(noSensibleDescriptionCountSC);
+		failedStatSC.addNumber(missesCountSC);
+		moreInstancesCountStatsSC.add(moreInstancesCountStatSC);
+		accStatsSC.add(accStatSC);
+		accSelectedStatsSC.add(accSelectedStatSC);
+		accAboveThresholdStatsSC.add(accSelectedStatSC);
+		positionStatsSC.add(positionStatSC);
+		
+		acceptedGlobalStat.addNumber(foundDescriptionCount + foundDescriptionCountSC);
+		rejectedGlobalStat.addNumber(noSensibleDescriptionCountSC + noSensibleDescriptionCount);
+		failedGlobalStat.addNumber(missesCountSC + missesCount);
+		
+		System.out.println("statistics for equivalence axioms:");
+		System.out.println("classes above 85% threshold: " + candidatesAboveThresholdCount);
+		System.out.println("axioms learned succesfully: " + foundDescriptionCount);
+		System.out.println("axioms missed: " + missesCount);
+		System.out.println("class with no sensible axioms: " + noSensibleDescriptionCount);
+		System.out.println("inconsistencies detected: " + inconsistencyDetected);
+		System.out.println("additional instances found: " + moreInstancesCountStat.prettyPrint(""));
+		System.out.println("average accuracy overall: " + accStat.prettyPrint(""));
+		System.out.println("average accuracy of selected expressions: " + accSelectedStat.prettyPrint(""));
+		System.out.println("average accuracy of expressions above threshold: " + accAboveThresholdStat.prettyPrint(""));
+		System.out.println("non-perfect (not 100% accuracy) axioms selected: " + nonPerfectCount);
+		System.out.println("average number typed by user: " + positionStat.prettyPrint(""));
+		System.out.println();
+
+		System.out.println("statistics for super class axioms:");
+		System.out.println("classes above 85% threshold: " + candidatesAboveThresholdCountSC);
+		System.out.println("axioms learned succesfully: " + foundDescriptionCountSC);
+		System.out.println("axioms missed: " + missesCountSC);
+		System.out.println("class with no sensible axioms: " + noSensibleDescriptionCountSC);
+		System.out.println("inconsistencies detected: " + inconsistencyDetectedSC);
+		System.out.println("additional instances found: " + moreInstancesCountStatSC.prettyPrint(""));
+		System.out.println("average accuracy overall: " + accStatSC.prettyPrint(""));
+		System.out.println("average accuracy of selected expressions: " + accSelectedStatSC.prettyPrint(""));
+		System.out.println("average accuracy of expressions above threshold: "
+				+ accAboveThresholdStatSC.prettyPrint(""));
+		System.out.println("non-perfect (not 100% accuracy) axioms selected: " + nonPerfectCountSC);
+		System.out.println("average number typed by user: " + positionStatSC.prettyPrint(""));
+		System.out.println();
+
+		System.out.println("merged statistics for equivalence/superclass:");
+		System.out.println("classes above 85% threshold: "
+				+ (candidatesAboveThresholdCount + candidatesAboveThresholdCountSC));
+		System.out.println("axioms learned succesfully: " + (foundDescriptionCount + foundDescriptionCountSC));
+		System.out.println("axioms missed: " + (missesCount + missesCountSC));
+		System.out.println("class with no sensible axioms: "
+				+ (noSensibleDescriptionCount + noSensibleDescriptionCountSC));
+		System.out.println("inconsistencies detected: " + (inconsistencyDetected + inconsistencyDetectedSC));
+		System.out.println("additional instances found: "
+				+ new Stat(moreInstancesCountStat, moreInstancesCountStatSC).prettyPrint(""));
+		System.out.println("average accuracy overall: " + new Stat(accStat, accStatSC).prettyPrint(""));
+		System.out.println("average accuracy of selected expressions: "
+				+ new Stat(accSelectedStat, accSelectedStatSC).prettyPrint(""));
+		System.out.println("average accuracy of expressions above threshold: "
+				+ new Stat(accAboveThresholdStat, accAboveThresholdStatSC).prettyPrint(""));
+		System.out.println("non-perfect (not 100% accuracy) axioms selected: " + (nonPerfectCount + nonPerfectCountSC));
+		System.out.println("average number typed by user: " + new Stat(positionStat, positionStatSC).prettyPrint(""));
+		System.out.println();
+	}
+	
+	
+	private void printStats() {
+
+		
+	}
+	
+	private void printLatexCode(){
+		System.out.println(latex.toString());
+	}
+	
+	private void addTableRow(){
+		double accept = acceptedGlobalStat.getMean() / suggestionListsCount * 100;
+		double reject = rejectedGlobalStat.getMean() /suggestionListsCount * 100;
+		double fail = failedGlobalStat.getMean() /suggestionListsCount * 100;
+		latex.append(logicalAxiomCount + " & " + suggestionListsCount + " & " + 
+				accept + " & " + reject + " & " + fail + " & " + new Stat(positionStats).getMean() +"\\\\\n");
+	}
+	
+	private void beginTable(){
+		latex = new StringBuilder();
+		latex.append("\\begin{tabular}{ c | c | c | c | c | c } \n");
+		latex.append("\\rotatebox{90}{\\#logical axioms} & ");
+		latex.append("\\rotatebox{90}{\\#suggestions lists} & ");
+		latex.append("\\rotatebox{90}{accept} & ");
+		latex.append("\\rotatebox{90}{reject} & ");
+		latex.append("\\rotatebox{90}{fail} & ");
+		latex.append("\\rotatebox{90}{selected positions}");
+		latex.append(" \\\\\n");
+		latex.append("\\hline\n");
+	}
+	
+	private void endTable(){
+		latex.append("\\hline\n");
+		latex.append("\\end{tabular}");
+	}
+	
+	private void loadSuggestions(File resultFile) {
+		InputStream fis = null;
+
+		try {
+			fis = new FileInputStream(resultFile);
+			ObjectInputStream o = new ObjectInputStream(fis);
+			for (int i = 0; i < 20; i++) {
+				o.readObject();
+			}
+			equivalentSuggestions = (Map<NamedClass, List<EvaluatedDescriptionClass>>) o.readObject();
+			superSuggestions = (Map<NamedClass, List<EvaluatedDescriptionClass>>) o.readObject();
+			
+		} catch (IOException e) {
+			System.err.println(e);
+		} catch (ClassNotFoundException e) {
+			System.err.println(e);
+		} finally {
+			try {
+				fis.close();
+			} catch (Exception e) {
+			}
+		}
+		suggestionListsCount = equivalentSuggestions.size() + superSuggestions.size();
+	}
+	
+	private void loadUserInput(File input){
+		InputStream fis = null;
+
+		try {
+			fis = new FileInputStream(input);
+			ObjectInputStream o = new ObjectInputStream(fis);
+
+			equivalentInput = (Map<NamedClass, String>) o.readObject();
+			superInput = (Map<NamedClass, String>) o.readObject();
+		} catch (IOException e) {
+			System.err.println(e);
+		} catch (ClassNotFoundException e) {
+			System.err.println(e);
+		} finally {
+			try {
+				fis.close();
+			} catch (Exception e) {
+			}
+		}
+	}
+
+	/**
+	 * @param args
+	 * @throws URISyntaxException 
+	 * @throws MalformedURLException 
+	 */
+	public static void main(String[] args) throws MalformedURLException, URISyntaxException {
+		File directory = new File(new URL(args[0]).toURI());
+		new StatsGenerator(directory);
+	}
+
+}
+
+class ResultFileFilter implements FileFilter {
+
+	public boolean accept(File pathname) {
+
+		if (pathname.getName().endsWith(".res")) {
+			return true;
+		}
+		return false;
+	}
+}
+
+class InputFileFilter implements FileFilter {
+
+	public boolean accept(File pathname) {
+
+		if (pathname.getName().endsWith(".inp")) {
+			return true;
+		}
+		return false;
+	}
+}
+
+class NameFilter implements FilenameFilter {
+	private File file;
+	
+	public NameFilter(File file){
+		this.file = file;
+	}
+
+	@Override
+	public boolean accept(File dir, String name) {
+		if(name.endsWith("inp")){
+			if(name.substring(0, name.indexOf('.')).startsWith(file.getName().substring(0, file.getName().indexOf('.')))){
+				return true;
+			}
+		}
+		return false;
+	}
+}

Added: trunk/src/dl-learner/org/dllearner/scripts/evaluation/father.ser
===================================================================
(Binary files differ)


Property changes on: trunk/src/dl-learner/org/dllearner/scripts/evaluation/father.ser
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Deleted: trunk/src/dl-learner/org/dllearner/scripts/evaluation/test.ser
===================================================================
(Binary files differ)

Deleted: trunk/src/dl-learner/org/dllearner/tools/ore/ui/ReasonerProgressUI.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/ReasonerProgressUI.java	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/ReasonerProgressUI.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -1,265 +0,0 @@
-package org.dllearner.tools.ore.ui;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.Toolkit;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.AbstractAction;
-import javax.swing.Action;
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-
-import javax.swing.SwingUtilities;
-import javax.swing.Timer;
-
-import org.mindswap.pellet.utils.progress.ProgressMonitor;
-
-
-
-
-/**
- * Author: Matthew Horridge<br>
- * The University Of Manchester<br>
- * Medical Informatics Group<br>
- * Date: 10-Oct-2006<br><br>
- * <p/>
- * mat...@cs...<br>
- * www.cs.man.ac.uk/~horridgm<br><br>
- */
-public class ReasonerProgressUI implements ProgressMonitor {
-
-
-    private JLabel label;
-
-    private JProgressBar progressBar;
-
-    private JDialog window;
-
-    private boolean cancelled;
-
-    private Action cancelledAction;
-
-    private String currentClass;
-
-    private static final int CANCEL_TIMEOUT_MS = 5000;
-
-    private Timer cancelTimeout;
-    
-    private int progress;
-    private int progressLength;
-
-    public ReasonerProgressUI(JFrame frame) {
-        JPanel panel = new JPanel(new BorderLayout(7, 7));
-        progressBar = new JProgressBar();
-        panel.add(progressBar, BorderLayout.SOUTH);
-        panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
-        label = new JLabel("Classifying...");
-        panel.add(label, BorderLayout.NORTH);
-        
-        window = new JDialog(frame,"Reasoner progress",true);
-        cancelledAction = new AbstractAction("Cancel") {
-            public void actionPerformed(ActionEvent e) {
-                setCancelled(true);
-            }
-        };
-        JButton cancelledButton = new JButton(cancelledAction);
-
-        window.setLocation(400, 400);
-        JPanel holderPanel = new JPanel(new BorderLayout(7, 7));
-        holderPanel.add(panel, BorderLayout.NORTH);
-        holderPanel.add(cancelledButton, BorderLayout.EAST);
-        holderPanel.setBorder(BorderFactory.createEmptyBorder(5, 10, 10, 10));
-        window.getContentPane().setLayout(new BorderLayout());
-        window.getContentPane().add(holderPanel, BorderLayout.NORTH);
-        window.pack();
-        Dimension windowSize = window.getSize();
-        window.setSize(400, windowSize.height);
-        window.setResizable(false);
-
-        cancelTimeout = new Timer(CANCEL_TIMEOUT_MS, new ActionListener() {
-            public void actionPerformed(ActionEvent event) {
-            }
-        });
-        cancelTimeout.setRepeats(false);
-    }
-
-
-
-
-    public void setIndeterminate(boolean b) {
-        progressBar.setIndeterminate(b);
-    }
-
-
-    private void setCancelled(boolean b) {
-        cancelled = b;
-        if (currentClass != null) {
-            JOptionPane.showMessageDialog(window,
-                                          "Cancelled while classifying " + currentClass,
-                                          "Cancelled classification",
-                                          JOptionPane.INFORMATION_MESSAGE);
-        }
-        if (b){
-            label.setText("Cancelling...");
-            cancelTimeout.start();
-        }
-        else{
-            cancelTimeout.stop();
-        }
-    }
-
-    public void setProgressIndeterminate(boolean b) {
-        progressBar.setIndeterminate(b);
-    }
-
-    public boolean isCancelled() {
-        return cancelled;
-    }
-
-
-    private void showWindow() {
-        SwingUtilities.invokeLater(new Runnable() {
-            public void run() {
-                Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-                window.setLocation(screenSize.width / 2 - window.getWidth() / 2,
-                                   screenSize.height / 2 - window.getHeight() / 2);
-                window.setVisible(true);
-            }
-        });
-    }
-
-
-    private void hideWindow() {
-
-        SwingUtilities.invokeLater(new Runnable() {
-            public void run() {
-                if (cancelled && currentClass != null) {
-                    JOptionPane.showMessageDialog(window,
-                                                  "Cancelled while classifying " + currentClass,
-                                                  "Cancelled classification",
-                                                  JOptionPane.INFORMATION_MESSAGE);
-                }
-                window.setVisible(false);
-            }
-        });
-    }
-
-
-	@Override
-	public int getProgress() {
-		return progress;
-	}
-
-
-	@Override
-	public int getProgressPercent() {
-		return (int)(progress * 100.0) / progressBar.getMaximum();
-	}
-
-
-	@Override
-	public void incrementProgress() {
-		SwingUtilities.invokeLater(new Runnable() {
-            public void run() {
-                progressBar.setValue(progress++);
-//                double percentDone = (progress * 100.0) / progressBar.getMaximum();
-//                if(percentDone / 100.0 == 0) {
-//                label.setText("Classifying ontology " + getProgressPercent() + " %");
-//                }
-            }
-        });
-	}
-
-
-	@Override
-	public boolean isCanceled() {
-		return cancelled;
-	}
-
-
-	@Override
-	public void setProgress(int progr) {
-		this.progress = progr;
-		SwingUtilities.invokeLater(new Runnable() {
-            public void run() {
-                progressBar.setValue((int) progress);
-                double percentDone = (progress * 100.0) / progressBar.getMaximum();
-//                if(percentDone / 100.0 == 0) {
-//                label.setText("Classifying ontology " + ((int) percentDone) + " %");
-//                }
-            }
-        });
-		
-	}
-
-
-	@Override
-	public void setProgressLength(int length) {
-		this.progressLength = length;
-		SwingUtilities.invokeLater(new Runnable() {
-            public void run() {
-                progressBar.setValue(0);
-                progressBar.setMaximum((int) progressLength);
-            }
-        });
-		
-	}
-
-
-	@Override
-	public void setProgressMessage(final String message) {
-		 SwingUtilities.invokeLater(new Runnable() {
-	            public void run() {
-	                label.setText(message);
-	            }
-	        });
-		
-	}
-
-
-	@Override
-	public void setProgressTitle(final String title) {
-		 SwingUtilities.invokeLater(new Runnable() {
-	            public void run() {
-	            	window.setTitle(title);
-	            }
-	        });
-		
-		
-	}
-
-
-	@Override
-	public void taskFinished() {
-		cancelTimeout.stop();
-        hideWindow();
-        currentClass = null;
-        progress = 0;
-        SwingUtilities.invokeLater(new Runnable() {
-            public void run() {
-            	 progressBar.setValue(progress);
-            }
-        });
-	
-       
-		
-	}
-
-
-	@Override
-	public void taskStarted() {
-//		label.setText("Classifying ontology                    ");
-        currentClass = null;
-        setCancelled(false);
-        showWindow();
-		
-	}
-}

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/SelectableClassExpressionsTable.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/SelectableClassExpressionsTable.java	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/SelectableClassExpressionsTable.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -45,6 +45,10 @@
 		((SelectableClassExpressionsTableModel)getModel()).clear();
 	}
 	
+	public void removeSelection(){
+		((SelectableClassExpressionsTableModel)getModel()).removeSelection();
+	}
+	
 	public void addResults(List<EvaluatedDescriptionClass> resultList){
 		
 		if(getSelectedRow() >= 0){
@@ -64,6 +68,18 @@
 		return ((SelectableClassExpressionsTableModel)getModel()).getSelectedValue(getSelectedRow());
 	}
 	
+	public EvaluatedDescriptionClass getSelectedClassExpression(){
+		return ((SelectableClassExpressionsTableModel)getModel()).getSelectedClassExpression();
+	}
+	
+	public EvaluatedDescriptionClass getBestClassExpression(){
+		return ((SelectableClassExpressionsTableModel)getModel()).getBestClassExpression();
+	}
+	
+	public int getSelectedPosition(){
+		return ((SelectableClassExpressionsTableModel)getModel()).getSelectedPosition();
+	}
+	
 	public List<EvaluatedDescriptionClass> getSelectedDescriptions(){
 		return ((SelectableClassExpressionsTableModel)getModel()).getSelectedDescriptions();
 	}

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/SelectableClassExpressionsTableModel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/SelectableClassExpressionsTableModel.java	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/SelectableClassExpressionsTableModel.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -2,12 +2,14 @@
 
 import java.text.DecimalFormat;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.table.AbstractTableModel;
 
 import org.dllearner.core.owl.Description;
 import org.dllearner.learningproblems.EvaluatedDescriptionClass;
+import org.protege.editor.owl.ui.view.SelectedEntityCardView;
 
 public class SelectableClassExpressionsTableModel extends AbstractTableModel {
 
@@ -19,6 +21,7 @@
 	private List<EvaluatedDescriptionClass> resultList;
 	private DecimalFormat df;
 	private List<Boolean> selectionList;
+	private EvaluatedDescriptionClass selectedClassExpression;
 
 	public SelectableClassExpressionsTableModel(){
 		super();
@@ -54,10 +57,16 @@
 	
 	@Override
 	public void setValueAt(Object value, int rowIndex, int columnIndex) {
+		if(!selectionList.get(rowIndex).booleanValue()){
+			selectedClassExpression = resultList.get(rowIndex);
+			for(int i = 0; i < selectionList.size(); i++){
+				selectionList.set(i, Boolean.FALSE);
+			}
+			selectionList.set(rowIndex, (Boolean)value);
+				
+			super.fireTableCellUpdated(rowIndex, columnIndex);
+		}
 		
-		selectionList.set(rowIndex, (Boolean)value);
-			
-		super.fireTableCellUpdated(rowIndex, columnIndex);
 		
 	}
 	
@@ -94,6 +103,14 @@
 		fireTableDataChanged();
 	}
 	
+	public void removeSelection(){
+		for(int i = 0; i < selectionList.size(); i++){
+			selectionList.set(i, Boolean.FALSE);
+		}
+		selectedClassExpression = null;
+		fireTableDataChanged();
+	}
+	
 	public void addResults(List<EvaluatedDescriptionClass> resultList){
 		this.resultList.clear();
 		this.selectionList.clear();
@@ -113,6 +130,18 @@
 		return resultList.indexOf(e);
 	}
 	
+	public EvaluatedDescriptionClass getSelectedClassExpression(){
+		return selectedClassExpression;
+	}
+	
+	public EvaluatedDescriptionClass getBestClassExpression(){
+		return resultList.get(0);
+	}
+	
+	public int getSelectedPosition(){
+		return resultList.indexOf(selectedClassExpression) + 1;
+	}
+	
 	public List<EvaluatedDescriptionClass> getSelectedDescriptions(){
 		List<EvaluatedDescriptionClass> selected = new ArrayList<EvaluatedDescriptionClass>();
 		for(int i = 0; i < selectionList.size(); i++){

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	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/AutoLearnPanelDescriptor.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -262,7 +262,7 @@
 	    private final double threshold = OREManager.getInstance().getThreshold();
 
 		@Override
-		public Void doInBackground() {System.out.println("Learning super class for " + OREManager.getInstance().getCurrentClass2Learn());
+		public Void doInBackground() {
 			OREManager.getInstance().setLearningType("superClass");
 			OREManager.getInstance().setLearningProblem();
 		    OREManager.getInstance().setLearningAlgorithm();

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	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ManualLearnPanelDescriptor.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -110,11 +110,8 @@
 		if (!e.getValueIsAdjusting() && learnPanel.getResultTable().getSelectedRow() >= 0 && 
 				(learningTask.isDone() || learningTask.isCancelled())){
 			EvaluatedDescriptionClass selectedClassExpression = learnPanel.getResultTable().getSelectedValue();
-//			if(!selectedClassExpression.isConsistent()){
-//				learnPanel.add(new JLabel("Selected class expression may lead to an inconsistent knowledgebase."));
-//			}
+			learnPanel.showInconsistencyWarning(!selectedClassExpression.isConsistent());
 			OREManager.getInstance().setNewClassDescription(selectedClassExpression);
-			
 			learnPanel.updateCurrentGraphicalCoveragePanel(OREManager.getInstance().getNewClassDescription());
 		}
 		

Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ManualLearnPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ManualLearnPanel.java	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ManualLearnPanel.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -30,6 +30,7 @@
 import javax.swing.ButtonGroup;
 import javax.swing.JButton;
 import javax.swing.JFrame;
+import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
 import javax.swing.JScrollPane;
@@ -57,6 +58,8 @@
 	private ResultTable resultTable;
 	private JScrollPane tableScrollPane;
 	private JPanel resultPanel;
+	
+	private JLabel inconsistencyLabel;
 
 	private JButton stopButton;
 	private JButton startButton;
@@ -70,6 +73,10 @@
 	private JRadioButton superClassButton;
 	
 	private GridBagConstraints c;
+	
+	private static String INCONSISTENCYWARNING = "<html><font color=red>" +
+	"Warning! Adding selected class expression leads to an inconsistent ontology." +
+	"</font></html>";
 
 
 	public ManualLearnPanel() {
@@ -98,6 +105,8 @@
 		resultPanel.setLayout(new BorderLayout());
 		resultPanel.add(tableScrollPane);
 		resultPanel.setBorder(new TitledBorder("Learned class expressions"));
+		inconsistencyLabel = new JLabel(" ");
+		resultPanel.add(inconsistencyLabel, BorderLayout.SOUTH);
 
 		add(resultPanel, c);
 	}
@@ -216,9 +225,18 @@
 		return equivalentClassButton.isSelected();
 	}
 	
+	public void showInconsistencyWarning(boolean show){
+		if(show){
+			inconsistencyLabel.setText(INCONSISTENCYWARNING);
+		} else {
+			inconsistencyLabel.setText(" ");
+		}
+	}
+	
 	public void reset(){
 		graphicPanel.clear();
 		resultTable.clear();
+		showInconsistencyWarning(false);
 	}
 	
 	public static void main(String[] args){

Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java	2009-12-29 15:39:49 UTC (rev 1961)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Stat.java	2009-12-29 18:00:50 UTC (rev 1962)
@@ -21,6 +21,7 @@
 package org.dllearner.utilities.statistics;
 
 import java.text.DecimalFormat;
+import java.util.Set;
 
 /**
  * Utility class for calculating the mean and standard deviation of a given set
@@ -59,6 +60,23 @@
     }
     
     /**
+     * Creates a new stat object by merging several stat objects. The result is the same as if
+     * the numbers, which have been added to each stat would have been added to this
+     * stat object.
+     * @param stat1 Statistical object 1.
+     * @param stat2 Statistical object 2.
+     */
+    public Stat(Set<Stat> stats) {
+    	for(Stat stat : stats){
+    		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.
      * 
      * @param number


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