[DL-Learner SVN] SF.net SVN: dl-learner:[1513] trunk/src/dl-learner/org/dllearner/tools/ protege

[<hee...@us...>]

Revision: 1513
          http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1513&view=rev
Author:   heeroyuy
Date:     2008-11-14 15:04:06 +0000 (Fri, 14 Nov 2008)

Log Message:
-----------
-fixed updateproblem of the suggest panel after learning

Modified Paths:
--------------
    trunk/src/dl-learner/org/dllearner/tools/protege/ActionHandler.java
    trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
    trunk/src/dl-learner/org/dllearner/tools/protege/IndividualObject.java
    trunk/src/dl-learner/org/dllearner/tools/protege/MoreDetailForSuggestedConceptsPanel.java
    trunk/src/dl-learner/org/dllearner/tools/protege/OWLClassDescriptionEditorWithDLLearnerTab.java
    trunk/src/dl-learner/org/dllearner/tools/protege/OptionPanel.java
    trunk/src/dl-learner/org/dllearner/tools/protege/PosAndNegSelectPanel.java
    trunk/src/dl-learner/org/dllearner/tools/protege/PosAndNegSelectPanelHandler.java

Modified: trunk/src/dl-learner/org/dllearner/tools/protege/ActionHandler.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/ActionHandler.java	2008-11-14 11:48:57 UTC (rev 1512)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/ActionHandler.java	2008-11-14 15:04:06 UTC (rev 1513)
@@ -19,6 +19,7 @@
  */
 package org.dllearner.tools.protege;
 
+import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
@@ -26,7 +27,14 @@
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.util.Iterator;
+import java.util.List;
+import java.util.Timer;
+import java.util.TimerTask;
+import java.util.concurrent.ExecutionException;
 
+import javax.swing.DefaultListModel;
+import javax.swing.SwingUtilities;
+import javax.swing.SwingWorker;
 import javax.swing.event.ListDataEvent;
 import javax.swing.event.ListDataListener;
 import javax.swing.event.ListSelectionEvent;
@@ -37,7 +45,8 @@
 import org.protege.editor.owl.OWLEditorKit;
 
 /**
- * This class  processes input from the user. 
+ * This class processes input from the user.
+ * 
  * @author Christian Koetteritzsch
  * 
  */
@@ -59,6 +68,7 @@
 	private EvaluatedDescription evaluatedDescription;
 	// This is the view of the DL-Learner tab.
 	private OWLClassDescriptionEditorWithDLLearnerTab.DLLearnerView view;
+	private Timer timer;
 
 	/**
 	 * This is the constructor for the action handler.
@@ -71,7 +81,8 @@
 	 *            DLlearner tab
 	 * @param i
 	 *            id if it is a subclass or an equivalent class
-	 * @param editor OWLEditorKit
+	 * @param editor
+	 *            OWLEditorKit
 	 */
 	public ActionHandler(ActionHandler a, DLLearnerModel m,
 			OWLClassDescriptionEditorWithDLLearnerTab.DLLearnerView view,
@@ -86,34 +97,36 @@
 
 	/**
 	 * When a Button is pressed this method select the right.
-	 * @param z ActionEvent 
+	 * 
+	 * @param z
+	 *            ActionEvent
 	 */
 	public void actionPerformed(ActionEvent z) {
 
-			
 		if (z.getActionCommand().equals("Suggest " + id)) {
 			if (model.getAlreadyLearned()) {
 				model.unsetListModel();
 			}
-				view.getPosAndNegSelectPanel().setCheckBoxesEnable(false);
-				model.setKnowledgeSource();
-				model.setReasoner();
-				model.setPositiveAndNegativeExamples();
-				model.setLearningProblem();
-				model.setLearningAlgorithm();
-				this.dlLearner = new Thread(model);
-				dlLearner.start();
-				view.getRunButton().setEnabled(false);
-				view.renderErrorMessage("Learning started");
-				//view.getPosAndNegSelectPanel().unsetCheckBoxes();
-			
+			view.getRunButton().setEnabled(false);
+			view.renderErrorMessage("Learning started");
+			view.getPosAndNegSelectPanel().setCheckBoxesEnable(false);
+			final SuggestionRetriever retriever = new SuggestionRetriever();
+			//
+			// dlLearner.start();
+			retriever.execute();
+
 		}
 
 		if (z.getActionCommand().equals("ADD")) {
 			if (evaluatedDescription != null) {
-				model.changeDLLearnerDescriptionsToOWLDescriptions(evaluatedDescription.getDescription());
+				model
+						.changeDLLearnerDescriptionsToOWLDescriptions(evaluatedDescription
+								.getDescription());
 			} else {
-				model.changeDLLearnerDescriptionsToOWLDescriptions((Description) view.getSuggestClassPanel().getSuggestList().getSelectedValue());
+				model
+						.changeDLLearnerDescriptionsToOWLDescriptions((Description) view
+								.getSuggestClassPanel().getSuggestList()
+								.getSelectedValue());
 			}
 			String message = "Concept added";
 			view.renderErrorMessage(message);
@@ -144,47 +157,21 @@
 		return id;
 	}
 
-	
 	/**
 	 * select/deselect the Check boxes.
-	 * @param i ItemEvent
+	 * 
+	 * @param i
+	 *            ItemEvent
 	 */
 	public void itemStateChanged(ItemEvent i) {
-		if (i.getItem().toString().contains("Positive")) {
-			for (int j = 0; j < model.getPosVector().size(); j++) {
-				if (i.getItem().toString().contains(
-						model.getPosVector().get(j).getText().toString())) {
-					if (!model.getPosVector().get(j).isSelected()) {
-						model.getPosVector().get(j).setSelected(true);
-						break;
-					}
-					if (model.getPosVector().get(j).isSelected()) {
-						model.getPosVector().get(j).setSelected(false);
-						break;
-					}
-				}
-			}
-		}
-		if (i.getItem().toString().contains("Negative")) {
-			for (int j = 0; j < model.getNegVector().size(); j++) {
-				if (i.getItem().toString().contains(
-						model.getNegVector().get(j).getText().toString())) {
-					if (!model.getNegVector().get(j).isSelected()) {
-						model.getNegVector().get(j).setSelected(true);
-						break;
-					}
-					if (model.getNegVector().get(j).isSelected()) {
-						model.getNegVector().get(j).setSelected(false);
-						break;
-					}
-				}
-			}
-		}
+
 	}
-	
+
 	/**
 	 * Nothing happens here.
-	 * @param e ListSelectionEvent 
+	 * 
+	 * @param e
+	 *            ListSelectionEvent
 	 */
 	public void valueChanged(ListSelectionEvent e) {
 
@@ -192,30 +179,37 @@
 
 	/**
 	 * Nothing happens here.
-	 * @param m MouseEvent
+	 * 
+	 * @param m
+	 *            MouseEvent
 	 */
 	public void mouseReleased(MouseEvent m) {
 
 	}
 
- 	/**
+	/**
 	 * Nothing happens here.
-	 * @param m MouseEvent
+	 * 
+	 * @param m
+	 *            MouseEvent
 	 */
 	public void mouseEntered(MouseEvent m) {
 
 	}
 
 	/**
-	 * Choses the right EvaluatedDescription object after a concept is chosen in the list.
-	 * @param m MouseEvent
+	 * Choses the right EvaluatedDescription object after a concept is chosen in
+	 * the list.
+	 * 
+	 * @param m
+	 *            MouseEvent
 	 */
 	public void mouseClicked(MouseEvent m) {
 		EvaluatedDescription eDescription = null;
-		if (view.getSuggestClassPanel().getSuggestList()
-				.getSelectedValue() != null) {
-			SuggestListItem item = (SuggestListItem) view.getSuggestClassPanel().getSuggestList()
-			.getSelectedValue();
+		
+		if (view.getSuggestClassPanel().getSuggestList().getSelectedValue() != null) {
+			SuggestListItem item = (SuggestListItem) view
+					.getSuggestClassPanel().getSuggestList().getSelectedValue();
 			String desc = item.getValue();
 			if (model.getEvaluatedDescriptionList() != null) {
 				for (Iterator<EvaluatedDescription> i = model
@@ -223,28 +217,29 @@
 					eDescription = i.next();
 					if (desc.equals(eDescription.getDescription()
 							.toManchesterSyntaxString(
-									editorKit.getModelManager().getActiveOntology().getURI()
+									editorKit.getModelManager()
+											.getActiveOntology().getURI()
 											+ "#", null))) {
 						evaluatedDescription = eDescription;
+						
 						break;
 					}
 
 				}
 			}
-		
-		
-		if(m.getClickCount()==2) {
-			view.getMoreDetailForSuggestedConceptsPanel().renderDetailPanel(
-					evaluatedDescription);
+
+			if (m.getClickCount() == 2) {
+				view.getMoreDetailForSuggestedConceptsPanel()
+						.renderDetailPanel(evaluatedDescription);
+			}
 		}
-	} else {
-		
 	}
-	}
 
 	/**
 	 * Nothing happens here.
-	 * @param m MouseEvent
+	 * 
+	 * @param m
+	 *            MouseEvent
 	 */
 	public void mouseExited(MouseEvent m) {
 
@@ -252,15 +247,16 @@
 
 	/**
 	 * Sets the ADD button enable after a concept is chosen.
-	 * @param m MouseEvent
+	 * 
+	 * @param m
+	 *            MouseEvent
 	 */
 	public void mousePressed(MouseEvent m) {
-		if (view.getSuggestClassPanel().getSuggestList()
-				.getSelectedValue()!= null) {
+		if (view.getSuggestClassPanel().getSuggestList().getSelectedValue() != null) {
 			if (!view.getAddButton().isEnabled()) {
 				view.getAddButton().setEnabled(true);
-			} 
-		} 
+			}
+		}
 	}
 
 	/**
@@ -271,7 +267,7 @@
 	}
 
 	/**
-	 *  Resets the toggled Button after the plugin is closed.
+	 * Resets the toggled Button after the plugin is closed.
 	 */
 	public void resetToggled() {
 		toggled = false;
@@ -280,19 +276,131 @@
 	@Override
 	public void contentsChanged(ListDataEvent listEvent) {
 		System.out.println(listEvent);
-		
+
 	}
 
 	@Override
 	public void intervalAdded(ListDataEvent listEvent) {
 		// TODO Auto-generated method stub
-		
+
 	}
 
 	@Override
 	public void intervalRemoved(ListDataEvent listEvent) {
 		// TODO Auto-generated method stub
-		
+
 	}
 
+	class SuggestionRetriever extends
+			SwingWorker<List<EvaluatedDescription>, List<EvaluatedDescription>> {
+
+		public SuggestionRetriever() {
+
+		}
+
+		@Override
+		protected List<EvaluatedDescription> doInBackground() throws Exception {
+			// DefaultListModel descriptions = new DefaultListModel();
+			// List<Description> descriptionList =
+			// model.getLearningAlgorithm().getCurrentlyBestDescriptions();
+			// Iterator<Description> it = descriptionList.iterator();
+			timer = new Timer();
+			timer.schedule(new TimerTask() {
+
+				@SuppressWarnings("unchecked")
+				@Override
+				public void run() {
+					if (model.getLearningAlgorithm() != null) {
+						publish(model.getLearningAlgorithm()
+								.getCurrentlyBestEvaluatedDescriptions(30, 0.0,
+										true));
+					}
+				}
+
+			}, 1000, 2000);
+
+			dlLearner = new Thread(new Runnable() {
+
+				@Override
+				public void run() {
+
+					model.run();
+				}
+
+			});
+			dlLearner.start();
+
+			try {
+				dlLearner.join();
+			} catch (InterruptedException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+			List<EvaluatedDescription> result = model.getLearningAlgorithm()
+					.getCurrentlyBestEvaluatedDescriptions(
+							view.getPosAndNegSelectPanel().getOptionPanel()
+									.getNrOfConcepts(),
+							view.getPosAndNegSelectPanel().getOptionPanel()
+									.getMinAccuracy(), true);
+			
+
+			return result;
+		}
+
+		@Override
+		public void done() {
+
+			timer.cancel();
+			List<EvaluatedDescription> result = null;
+			try {
+				result = get();
+			} catch (InterruptedException e) {
+				e.printStackTrace();
+			} catch (ExecutionException e) {
+				e.printStackTrace();
+			}
+
+			view.getRunButton().setEnabled(true);
+			updateList(result);
+		}
+
+		@Override
+		protected void process(List<List<EvaluatedDescription>> resultLists) {
+
+			// panel4.getModel().clear();
+
+			for (List<EvaluatedDescription> list : resultLists) {
+				updateList(list);
+			}
+		}
+
+		private void updateList(final List<EvaluatedDescription> result) {
+
+			Runnable doUpdateList = new Runnable() {
+
+				DefaultListModel dm = new DefaultListModel();
+
+				public void run() {
+					model.setSuggestList(result);
+					// learnPanel.getListModel().clear();
+					Iterator<EvaluatedDescription> it = result.iterator();
+					//it.next().getDescription().toManchesterSyntaxString(baseURI, prefixes);
+					while (it.hasNext()) {
+						EvaluatedDescription eval = it.next();
+						if(model.isConsistent(eval)) {
+							dm.add(0, new SuggestListItem(Color.GREEN, eval.getDescription().toManchesterSyntaxString(model.getURI().toString()+"#", null)));
+						} else {
+							dm.add(0, new SuggestListItem(Color.RED, eval.getDescription().toManchesterSyntaxString(model.getURI().toString()+"#", null)));
+						}
+					}
+					view.getSuggestClassPanel().getSuggestList().setModel(dm);
+					
+				}
+			};
+			SwingUtilities.invokeLater(doUpdateList);
+
+		}
+
+	}
+
 }

Modified: trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java	2008-11-14 11:48:57 UTC (rev 1512)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java	2008-11-14 15:04:06 UTC (rev 1513)
@@ -32,7 +32,6 @@
 import java.util.Vector;
 
 import javax.swing.DefaultListModel;
-import javax.swing.JCheckBox;
 
 import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
 import org.dllearner.core.ComponentInitException;
@@ -86,14 +85,7 @@
 			"org.dllearner.algorithms.refexamples.ExampleBasedROLComponent",
 			"org.dllearner.algorithms.gp.GP" };
 
-	// This Vector stores the check boxes for the view.
 
-	private Vector<JCheckBox> positiv;
-
-	// This Vector stores the negative Examples.
-
-	private Vector<JCheckBox> negativ;
-
 	// Component Manager that manages the components of the DL-Learner
 
 	private ComponentManager cm;
@@ -204,7 +196,6 @@
 	// This is a List of evaluated descriptions to get more information of the
 	// suggested concept
 	private List<EvaluatedDescription> evalDescriptions;
-	private Vector<String> normalIndividuals;
 
 	/**
 	 * This is the constructor for DL-Learner model.
@@ -227,11 +218,8 @@
 		this.view = view;
 		ontologyURI = editor.getModelManager().getActiveOntology().getURI().toString()+"#";
 		owlDescription = new HashSet<OWLDescription>();
-		positiv = new Vector<JCheckBox>();
 		posListModel = new DefaultListModel();
 		negListModel = new DefaultListModel();
-		negativ = new Vector<JCheckBox>();
-		normalIndividuals = new Vector<String>();
 		ComponentManager.setComponentClasses(componenten);
 		individualVector = new Vector<IndividualObject>();
 		cm = ComponentManager.getInstance();
@@ -351,12 +339,12 @@
 		if (id.equals("equivalent classes")) {
 			// sets the learning problem to PosNegDefinitionLP when the
 			// dllearner should suggest an equivalent class
-			lp = cm.learningProblem(PosNegDefinitionLP.class, rs);
+			lp = cm.learningProblem(PosNegDefinitionLP.class, reasoner);
 		}
 		if (id.equals("super classes")) {
 			// sets the learning problem to PosNegInclusionLP when the dllearner
 			// should suggest a subclass
-			lp = cm.learningProblem(PosNegInclusionLP.class, rs);
+			lp = cm.learningProblem(PosNegInclusionLP.class, reasoner);
 		}
 		// adds the positive examples
 		cm.applyConfigEntry(lp, "positiveExamples", positiveExamples);
@@ -376,7 +364,7 @@
 		try {
 			// sets the learning algorithm to ROlearner
 			this.la = cm.learningAlgorithm(ExampleBasedROLComponent.class, lp,
-					rs);
+					reasoner);
 		} catch (LearningProblemUnsupportedException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
@@ -397,21 +385,25 @@
 	 */
 	public void run() {
 		error = "Learning succesful";
-		
+		setKnowledgeSource();
+		setReasoner();
+		setPositiveAndNegativeExamples();
+		setLearningProblem();
+		setLearningAlgorithm();
 		String message = "To view details about why a class description was suggested, please doubleclick on it.";
 		// start the algorithm and print the best concept found
 		la.start();
-		description = new Description[la.getCurrentlyBestEvaluatedDescriptions(view.getPosAndNegSelectPanel().getOptionPanel().getNrOfConcepts())
-				.size()];
-		addToListModel();
+		//description = new Description[la.getCurrentlyBestEvaluatedDescriptions(view.getPosAndNegSelectPanel().getOptionPanel().getNrOfConcepts())
+		//		.size()];
+		//addToListModel();
 		// renders the errormessage
 		view.renderErrorMessage(error);
 		view.setHintMessage(message);
 		// reenables the run button
-		view.getRunButton().setEnabled(true);
+		//view.getRunButton().setEnabled(true);
 		// disables the cancel button
-		view.getPosAndNegSelectPanel().setCheckBoxesEnable(true);
-		view.getSuggestClassPanel().setSuggestList(suggestModel);
+		//view.getPosAndNegSelectPanel().setCheckBoxesEnable(true);
+		//view.getSuggestClassPanel().setSuggestList(suggestModel);
 	}
 
 	/**
@@ -424,24 +416,6 @@
 	}
 
 	/**
-	 * This method returns the check boxes for the positive examples.
-	 * 
-	 * @return Vector of check boxes for positive examples
-	 */
-	public Vector<JCheckBox> getPosVector() {
-		return positiv;
-	}
-
-	/**
-	 * This method returns the check boxes for the negative examples.
-	 * 
-	 * @return Vector of check boxes for negative examples
-	 */
-	public Vector<JCheckBox> getNegVector() {
-		return negativ;
-	}
-
-	/**
 	 * This method gets an error message and storess it.
 	 * 
 	 * @param err
@@ -457,10 +431,10 @@
 	 */
 	public void setPosVector() {
 		setPositiveConcept();
-		for (Iterator<Individual> j = rs.getIndividuals().iterator(); j
+
+		for (Iterator<Individual> j = reasoner.getIndividuals().iterator(); j
 				.hasNext();) {
 			Individual ind = j.next();
-			normalIndividuals.add(ind.toString());
 			String indiv = ind.toString();
 			// checks if individual belongs to the selected concept
 			if (setPositivExamplesChecked(indiv)) {
@@ -486,6 +460,10 @@
 		}
 	}
 	
+	/**
+	 * This method returns the Vector of IndividualObjects.
+	 * @return individualVector Vector
+	 */
 	public Vector<IndividualObject> getIndividualVector() {
 		return individualVector;
 	}
@@ -495,11 +473,12 @@
 	 */
 	public void setPositiveConcept() {
 		SortedSet<Individual> individuals = null;
+		//System.out.println("TEST: " +  rs.getNamedClasses());
 		// checks if selected concept is thing when yes then it selects all
 		// individuals
 		if (!current.getRootObject().toString().equals("Thing")) {
-
-			for (Iterator<NamedClass> i = rs.getNamedClasses().iterator(); i
+			
+			for (Iterator<NamedClass> i = reasoner.getAtomicConceptsList().iterator(); i
 					.hasNext();) {
 				// if individuals is null
 				if (individuals == null) {
@@ -509,31 +488,35 @@
 							"#" + current.getRootObject().toString())) {
 						// if individuals is not null it gets all individuals of
 						// the concept
-						if (rs.getIndividuals(concept) != null) {
-							individual = rs.getIndividuals(concept);
+						if (reasoner.getIndividuals(concept) != null) {
+							individual = reasoner.getIndividuals(concept);
 							break;
 						}
 					}
 				}
 			}
 		} else {
-			individual = rs.getIndividuals();
+			individual = reasoner.getIndividuals();
 		}
 	}
-	public boolean hasIndividuals(OWLClass OWLConcept) {
+	
+	/**
+	 * This Method checks if the selected class has any individuals.
+	 * @param owlConcept OWLClass
+	 * @return boolean hasIndividuals
+	 */
+	public boolean hasIndividuals(OWLClass owlConcept) {
 		boolean hasIndividuals = false;
 		NamedClass concept = null;
 		NamedClass selectedConcept = null;
 		Iterator<NamedClass> it = reasoner.getNamedClasses().iterator();
 		while(it.hasNext()) {
 			concept = it.next();
-			if (concept.toManchesterSyntaxString(ontologyURI, prefixes).equals(OWLConcept.toString())) {
+			if (concept.toManchesterSyntaxString(ontologyURI, prefixes).equals(owlConcept.toString())) {
 				selectedConcept = concept;
 				break;
 			}
 		}
-		System.out.println("CON: "+ concept);
-		System.out.println("SIZE: "+ reasoner.getIndividuals(concept).size());
 		if (reasoner.getIndividuals(selectedConcept).size() > 0) {
 			hasIndividuals = true;
 		}
@@ -572,8 +555,6 @@
 		individualVector.removeAllElements();
 		posListModel.removeAllElements();
 		negListModel.removeAllElements();
-		positiv.removeAllElements();
-		negativ.removeAllElements();
 	}
 
 	/**
@@ -587,10 +568,18 @@
 		description = list;
 	}
 	
+	/**
+	 * This method returns the PosListModel.
+	 * @return DefaultListModel posListModel
+	 */
 	public DefaultListModel getPosListModel() {
 		return posListModel;
 	}
 	
+	/**
+	 * This method returns the NegListModel.
+	 * @return DefaultListModel negListModel
+	 */
 	public DefaultListModel getNegListModel() {
 		return negListModel;
 	}
@@ -605,30 +594,6 @@
 	}
 
 	/**
-	 * This method gets an integer to return the positive examples check box on
-	 * that position.
-	 * 
-	 * @param i
-	 *            integer for the position in the vector
-	 * @return Positive examples check box on position i.
-	 */
-	public JCheckBox getPositivJCheckBox(int i) {
-		return positiv.get(i);
-	}
-
-	/**
-	 * This method gets an integer to return the negative examples check box on
-	 * that position.
-	 * 
-	 * @param i
-	 *            integer for the position in the vector
-	 * @return Negative examples check box on position i.
-	 */
-	public JCheckBox getNegativJCheckBox(int i) {
-		return negativ.get(i);
-	}
-
-	/**
 	 * This method resets the array of concepts from the DL_Learner. It is
 	 * called after the DL-Learner tab is closed.
 	 */
@@ -639,27 +604,6 @@
 	}
 
 	/**
-	 * This method unchecks the checkboxes that are checked after the process of
-	 * learning.
-	 */
-	public void unsetJCheckBoxen() {
-		for (int j = 0; j < positiv.size(); j++) {
-			// unselect all check poxes of the positive examples
-			if (positiv.get(j).isSelected()) {
-				JCheckBox i = positiv.get(j);
-				i.setSelected(false);
-				positiv.set(j, i);
-			}
-			// unselect all check boxes of the negative examples
-			if (negativ.get(j).isSelected()) {
-				JCheckBox i = negativ.get(j);
-				i.setSelected(false);
-				negativ.set(j, i);
-			}
-		}
-	}
-
-	/**
 	 * This method resets the model for the suggest panel. It is called befor
 	 * the DL-Learner learns the second time or when the DL-Learner tab is
 	 * closed.
@@ -750,7 +694,7 @@
 	 */
 	private void setOldConceptOWLAPI() {
 		// gets all individuals
-		SortedSet<Individual> indi = rs.getIndividuals();
+		SortedSet<Individual> indi = reasoner.getIndividuals();
 		// Iterator of Individuals
 		for (Iterator<Individual> i = indi.iterator(); i.hasNext();) {
 			Individual indi2 = i.next();
@@ -823,7 +767,7 @@
 		return alreadyLearned;
 	}
 
-	private boolean isConsistent(EvaluatedDescription eDescription) {
+	public boolean isConsistent(EvaluatedDescription eDescription) {
 		boolean isConsistent = false;
 		if (eDescription.getNotCoveredPositives().isEmpty()) {
 			isConsistent = true;
@@ -841,4 +785,8 @@
 	public URI getURI() {
 		return editor.getModelManager().getActiveOntology().getURI();
 	}
+	
+	public void setSuggestList(List<EvaluatedDescription> list) {
+		evalDescriptions = list;
+	}
 }

Modified: trunk/src/dl-learner/org/dllearner/tools/protege/IndividualObject.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/IndividualObject.java	2008-11-14 11:48:57 UTC (rev 1512)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/IndividualObject.java	2008-11-14 15:04:06 UTC (rev 1513)
@@ -1,29 +1,74 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ * 
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
 package org.dllearner.tools.protege;
-
+/**
+ * This Class handles the manchester String, the normal string and if the Individual is a positive Individual. 
+ * @author Christian Koetteritzsch
+ *
+ */
 public class IndividualObject {
 
 	private String normalIndividual;
 	private String manchesterIndividual;
 	private boolean isPos;
 	
+	/**
+	 * Constructor for the IndividualObject.
+	 * @param normal String
+	 * @param manchester String
+	 * @param pos boolean
+	 */
 	public IndividualObject(String normal, String manchester, boolean pos) {
 		normalIndividual = normal;
 		manchesterIndividual = manchester;
 		isPos = pos;
 	}
 	
+	/**
+	 * This method returns the String of the Individual.
+	 * @return String normalIndividual
+	 */
 	public String getIndividualString() {
 		return normalIndividual;
 	}
 	
+	/**
+	 * This method returns the manchester String of the Individual.
+	 * @return String manchesterIndividual
+	 */
 	public String getManchesterIndividual() {
 		return manchesterIndividual;
 	}
 	
+	/**
+	 * This method returns if the Example is a positive Example.
+	 * @return boolean isPos
+	 */
 	public boolean isPositiveExample() {
 		return isPos;
 	}
 	
+	/**
+	 * This method sets the example positive or negative if changed to the othe list.
+	 * @param pos boolean
+	 */
 	public void setExamplePositive(boolean pos) {
 		isPos = pos;
 	}

Modified: trunk/src/dl-learner/org/dllearner/tools/protege/MoreDetailForSuggestedConceptsPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/MoreDetailForSuggestedConceptsPanel.java	2008-11-14 11:48:57 UTC (rev 1512)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/MoreDetailForSuggestedConceptsPanel.java	2008-11-14 15:04:06 UTC (rev 1513)
@@ -71,10 +71,6 @@
 	 
 	private JDialog detailPopup;
 	
-	 // Panel where the informations of the selected panel are rendered
-	 
-	//private JPanel examplePanel;
-	
 	 // Text area that shows the covered positive examples
 	 
 	private JTextArea posCoveredText;
@@ -135,8 +131,8 @@
 	 */
 	public void renderDetailPanel(EvaluatedDescription desc) {
 		eval = desc;
-		JPanel posBox = new JPanel(new GridLayout(0,2));
-		JPanel negBox = new JPanel(new GridLayout(0,2));
+		JPanel posBox = new JPanel(new GridLayout(0, 2));
+		JPanel negBox = new JPanel(new GridLayout(0, 2));
 		Box exampleBox = Box.createVerticalBox();
 		concept = new JTextArea("Class Description:");
 		concept.setEditable(false);
@@ -148,12 +144,12 @@
 		coveredNegativeExamples.setForeground(colorRed);
 		notCoveredNegativeExamples = new JLabel("Not Covered Negative Examples");
 		notCoveredNegativeExamples.setForeground(colorGreen);
-		conceptPanel = new JPanel(new GridLayout(0,1));
-		accuracyPanel = new JPanel(new GridLayout(0,1));
-		posCoveredPanel = new JPanel(new GridLayout(0,1));
-		posNotCoveredPanel = new JPanel(new GridLayout(0,1));
-		negCoveredPanel = new JPanel(new GridLayout(0,1));
-		negNotCoveredPanel = new JPanel(new GridLayout(0,1));
+		conceptPanel = new JPanel(new GridLayout(0, 1));
+		accuracyPanel = new JPanel(new GridLayout(0, 1));
+		posCoveredPanel = new JPanel(new GridLayout(0, 1));
+		posNotCoveredPanel = new JPanel(new GridLayout(0, 1));
+		negCoveredPanel = new JPanel(new GridLayout(0, 1));
+		negNotCoveredPanel = new JPanel(new GridLayout(0, 1));
 		accuracy = new JTextArea("Accuracy:");
 		accuracy.setEditable(false);
 		conceptText = new JTextArea();
@@ -178,7 +174,6 @@
 		//sets accuracy text area not editable
 		accuracyText.setEditable(false);
 		//panel for the informations of the selected concept
-		//examplePanel = new JPanel(new GridLayout(0,2));
 		//this method adds the informations for the selected concept to the panel
 		setInformation();
 		
@@ -225,28 +220,24 @@
 				JLabel posLabel = new JLabel(i.next().toManchesterSyntaxString(model.getURI().toString()+"#", null));
 				posLabel.setForeground(colorGreen);
 				posCoveredPanel.add(posLabel);
-				//posCoveredText.append(i.next().toManchesterSyntaxString(model.getURI().toString()+"#", null)+"\n");
 			}
 			//sets the positive examples that are not covered
 			for(Iterator<Individual> i = eval.getNotCoveredPositives().iterator(); i.hasNext();) {
 				JLabel posLabel = new JLabel(i.next().toManchesterSyntaxString(model.getURI().toString()+"#", null));
 				posLabel.setForeground(colorRed);
 				posNotCoveredPanel.add(posLabel);
-				//posNotCoveredText.append(i.next().toManchesterSyntaxString(model.getURI().toString()+"#", null)+"\n");
 			}
 			//sets the negative examples that are covered
 			for(Iterator<Individual> i = eval.getCoveredNegatives().iterator(); i.hasNext();) {
 				JLabel posLabel = new JLabel(i.next().toManchesterSyntaxString(model.getURI().toString()+"#", null));
 				posLabel.setForeground(colorRed);
 				negCoveredPanel.add(posLabel);
-				//negCoveredText.append(i.next().toManchesterSyntaxString(model.getURI().toString()+"#", null)+"\n");
 			}
 			//sets the negative examples that are not covered
 			for(Iterator<Individual> i = eval.getNotCoveredNegatives().iterator(); i.hasNext();) {
 				JLabel posLabel = new JLabel(i.next().toManchesterSyntaxString(model.getURI().toString()+"#", null));
 				posLabel.setForeground(colorGreen);
 				negNotCoveredPanel.add(posLabel);
-				//negNotCoveredText.append(i.next().toManchesterSyntaxString(model.getURI().toString()+"#", null)+"\n");
 			}
 		}
 	}

Modified: trunk/src/dl-learner/org/dllearner/tools/protege/OWLClassDescriptionEditorWithDLLearnerTab.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/OWLClassDescriptionEditorWithDLLearnerTab.java	2008-11-14 11:48:57 UTC (rev 1512)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/OWLClassDescriptionEditorWithDLLearnerTab.java	2008-11-14 15:04:06 UTC (rev 1513)
@@ -315,8 +315,6 @@
 
 		private JButton run;
 
-		// private JButton why;
-
 		// This is the label for the advanced button.
 
 		private JLabel adv;
@@ -360,7 +358,7 @@
 		private JTextArea hint;
 		// This is the Panel for more details of the suggested concept
 		private MoreDetailForSuggestedConceptsPanel detail;
-		OWLFrame<OWLClass> frame;
+		//private OWLFrame<OWLClass> frame;
 		private URL pluginURL;
 
 		/**
@@ -374,7 +372,7 @@
 		public DLLearnerView(OWLFrame<OWLClass> current, String label, OWLClassDescriptionEditorWithDLLearnerTab dlLearner) {
 			classSelectorPanel = new OWLClassSelectorPanel(editorKit);
 			mainWindow = dlLearner;
-			frame = current;
+			//frame = current;
 			try {
 				pluginURL = new URL("http://dl-learner.org/wiki/ProtegePlugin");
 			} catch (MalformedURLException e) {
@@ -549,7 +547,6 @@
 		 */
 		public void updateWindow() {
 			mainWindow.getHandler().handleEditingFinished(mainWindow.getEditedObjects());
-			mainWindow.dispose();
 		}
 		/**
 		 * Returns all added descriptions.
@@ -579,15 +576,8 @@
 			posPanel.unsetPosAndNegPanel();
 			learner.removeAll();
 		}
+
 		/**
-		 * This method returns the nummers of Individuals present in the Ontology.
-		 * @return int amount of Individuals in the Ontology
-		 */
-		public int getNrOfIndividuals() {
-			int counter = model.getPosVector().size();
-			return counter;
-		}
-		/**
 		 * Renders the error message when an error occured.
 		 * @param s String 
 		 */
@@ -615,7 +605,6 @@
 	    * Destroys the view after the plugin is closed.
 	    */
 		public void dispose() {
-			System.out.println("hier");
 			run.removeActionListener(action);
 			accept.removeActionListener(action);
 			advanced.removeActionListener(action);

Modified: trunk/src/dl-learner/org/dllearner/tools/protege/OptionPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/OptionPanel.java	2008-11-14 11:48:57 UTC (rev 1512)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/OptionPanel.java	2008-11-14 15:04:06 UTC (rev 1513)
@@ -1,3 +1,22 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ * 
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
 package org.dllearner.tools.protege;
 
 import java.awt.Dimension;
@@ -28,8 +47,8 @@
 	public OptionPanel() {
 
 		setPreferredSize(new Dimension(490, 120));
-		setLayout(new GridLayout(0,1));
-		optionPanel = new JPanel(new GridLayout(0,2));
+		setLayout(new GridLayout(0, 1));
+		optionPanel = new JPanel(new GridLayout(0, 2));
 		minAccuracyLabel = new JLabel("minimum accuracy");
 		maxExecutionTimeLabel = new JLabel("maximum execution time");
 		nrOfConceptsLabel = new JLabel("maximum number of results");

Modified: trunk/src/dl-learner/org/dllearner/tools/protege/PosAndNegSelectPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/PosAndNegSelectPanel.java	2008-11-14 11:48:57 UTC (rev 1512)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/PosAndNegSelectPanel.java	2008-11-14 15:04:06 UTC (rev 1513)
@@ -41,11 +41,6 @@
 
 	private static final long serialVersionUID = 23632947283479L;
 
-	// This is the Panel here the check boxes, the labels, and the help buttons
-	// are in.
-
-	//private JPanel posAndNegPanel;
-
 	// this is the Panel where the check boxes are.
 
 	private JPanel posAndNegSelectPanel;
@@ -93,9 +88,6 @@
 
 	// This is the Text area where the help message is displayed.
 	private OptionPanel optionPanel;
-	//private JComboBox optionBox;
-	//private JPanel optionBoxPanel;
-	//private ActionHandler action;
 	private DefaultListModel posListModel;
 	private DefaultListModel negListModel;
 	private JPanel examplePanel;
@@ -109,6 +101,7 @@
 	 *            DLLearnerModel
 	 * @param act
 	 *            ActionHandler
+	 * @param v DLLearnerView
 	 */
 	public PosAndNegSelectPanel(DLLearnerModel model, ActionHandler act, OWLClassDescriptionEditorWithDLLearnerTab.DLLearnerView v) {
 		//set layout for parent Panel
@@ -191,6 +184,8 @@
 	/**
 	 * This method adds the check boxes, the labels and the help buttons for
 	 * positive and negative examples.
+	 * @param posData DefaultListModel
+	 * @param negData DefaultListModel
 	 */
 	public void setExampleList(DefaultListModel posData, DefaultListModel negData) {
 		posListModel = posData;
@@ -199,10 +194,18 @@
 		negList.setModel(negListModel);
 	}
 	
+	/**
+	 * This method returns the pos button.
+	 * @return JButton
+	 */
 	public JButton getAddToPosPanelButton() {
 		return addToPosExamples;
 	}
 	
+	/**
+	 * This method returns the neg button.
+	 * @return JButton
+	 */
 	public JButton getAddToNegPanelButton() {
 		return addToNegExamples;
 	}
@@ -226,10 +229,18 @@
 
 	}
 	
+	/**
+	 * Nothing.
+	 * @param act ActionHandler
+	 */
 	public void removeListeners(ActionHandler act) {
 
 	}
 	
+	/**
+	 * Nothing.
+	 * @param enable boolean
+	 */
 	public void setCheckBoxesEnable(boolean enable) {
 	}
 	
@@ -244,14 +255,6 @@
 	}
 
 	/**
-	 * This method unselect the selected check boxes after learning.
-	 */
-	public void unsetCheckBoxes() {
-		// after the learning the check boxes will be unset.
-		model.unsetJCheckBoxen();
-	}
-
-	/**
 	 * This message displays the help message after the help button is pressed.
 	 * 
 	 * @param assistance String
@@ -262,12 +265,17 @@
 
 	}
 	
+	/**
+	 * this method sets the example to the other list when button is pressed.
+	 * @param toPos boolean
+	 * @param example String
+	 */
 	public void setExampleToOtherList(boolean toPos, String example) {
 		if (toPos) {
 			for(int i = 0; i < negListModel.size(); i++) {
 				if(negListModel.get(i).equals(example)) {
 					negListModel.remove(i);
-					for (int j = 0; j < model.getIndividualVector().size(); j++ ) {
+					for (int j = 0; j < model.getIndividualVector().size(); j++) {
 						if (model.getIndividualVector().get(j).getManchesterIndividual().equals(example)) {
 							model.getIndividualVector().get(j).setExamplePositive(true);
 							break;
@@ -281,7 +289,7 @@
 			for(int i = 0; i < posListModel.size(); i++) {
 				if(posListModel.get(i).equals(example)) {
 					posListModel.remove(i);
-					for (int j = 0; j < model.getIndividualVector().size(); j++ ) {
+					for (int j = 0; j < model.getIndividualVector().size(); j++) {
 						if (model.getIndividualVector().get(j).getManchesterIndividual().equals(example)) {
 							model.getIndividualVector().get(j).setExamplePositive(false);
 						}
@@ -300,8 +308,8 @@
 	/**
 	 * This method adds the Action listener to the help buttons.
 	 * 
-	 * @param a
-	 *            ActionHandler
+	 * @param handle
+	 *            PosAndNegSelectPanelHandler
 	 */
 	public void addHelpButtonListener(PosAndNegSelectPanelHandler handle) {
 		// adds listener to the help button for the positive examples
@@ -309,19 +317,35 @@
 		// adds listener to the help button for the negative examples
 		helpForNegExamples.addActionListener(handle);
 	}
-	
+	/**
+	 * This Method removes the listeners for the help button.
+	 * @param a ActionHandler
+	 */
 	public void removeHelpButtonListener(ActionHandler a) {
 		helpForPosExamples.removeActionListener(a);
 		helpForNegExamples.removeActionListener(a);
 	}
+	
+	/**
+	 * This method returns the option panel.
+	 * @return OptionPanel 
+	 */
 	public OptionPanel getOptionPanel() {
 		return optionPanel;
 	}
 	
+	/**
+	 * This method returns the list of positive examples.
+	 * @return JList posExampleList
+	 */
 	public JList getPosExampleList() {
 		return posList;
 	}
 	
+	/**
+	 * This method returns the list of negative examples.
+	 * @return JList negExampleList
+	 */
 	public JList getNegExampleList() {
 		return negList;
 	}

Modified: trunk/src/dl-learner/org/dllearner/tools/protege/PosAndNegSelectPanelHandler.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/PosAndNegSelectPanelHandler.java	2008-11-14 11:48:57 UTC (rev 1512)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/PosAndNegSelectPanelHandler.java	2008-11-14 15:04:06 UTC (rev 1513)
@@ -1,3 +1,22 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ * 
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
 package org.dllearner.tools.protege;
 
 import java.awt.event.ActionEvent;
@@ -2,7 +21,10 @@
 import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 
-
+/**
+ * This class handles the commands for the example panel.
+ * @author christian Koetteritzsch
+ *
+ */
 public class PosAndNegSelectPanelHandler implements ActionListener, MouseListener {
@@ -12,33 +34,29 @@
 
 // This is the DLLearnerModel.
 
-private DLLearnerModel model;
+//private DLLearnerModel model;
 private PosAndNegSelectPanel panel;
 // This is the view of the DL-Learner tab.
 private OWLClassDescriptionEditorWithDLLearnerTab.DLLearnerView view;
 
 /**
- * This is the constructor for the action handler.
- * 
- * @param a
- *            ActionHandler
+ * This is the constructor for the PosAndNegSelectPanelHandler.
  * @param m
  *            DLLearnerModel
- * @param view
- *            DLlearner tab
- * @param i
- *            id if it is a subclass or an equivalent class
- * @param editor OWLEditorKit
+ * @param v
+ *            OWLClassDescriptionEditorWithDLLearnerTab.DLLearnerView
+ * @param p
+ *            PosAndNegSelectPanel
  */
 public PosAndNegSelectPanelHandler(DLLearnerModel m, OWLClassDescriptionEditorWithDLLearnerTab.DLLearnerView v, PosAndNegSelectPanel p) {
-	model = m;
+	//model = m;
 	panel = p;
 	view = v;
 }
 
 /**
  * When a Button is pressed this method select the right.
- * @param z ActionEvent 
+ * @param action ActionEvent 
  */
 public void actionPerformed(ActionEvent action) {
 
@@ -66,44 +84,9 @@
 	}
 }
 
-/**
- * select/deselect the Check boxes.
- * @param i ItemEvent
- */
-public void itemStateChanged(ItemEvent i) {
-	if (i.getItem().toString().contains("Positive")) {
-		for (int j = 0; j < model.getPosVector().size(); j++) {
-			if (i.getItem().toString().contains(
-					model.getPosVector().get(j).getText().toString())) {
-				if (!model.getPosVector().get(j).isSelected()) {
-					model.getPosVector().get(j).setSelected(true);
-					break;
-				}
-				if (model.getPosVector().get(j).isSelected()) {
-					model.getPosVector().get(j).setSelected(false);
-					break;
-				}
-			}
-		}
-	}
-	if (i.getItem().toString().contains("Negative")) {
-		for (int j = 0; j < model.getNegVector().size(); j++) {
-			if (i.getItem().toString().contains(
-					model.getNegVector().get(j).getText().toString())) {
-				if (!model.getNegVector().get(j).isSelected()) {
-					model.getNegVector().get(j).setSelected(true);
-					break;
-				}
-				if (model.getNegVector().get(j).isSelected()) {
-					model.getNegVector().get(j).setSelected(false);
-					break;
-				}
-			}
-		}
-	}
-}
 
 
+
 /**
  * Nothing happens here.
  * @param m MouseEvent


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