### Eclipse Workspace Patch 1.0
#P org.eclipse.pde.ui
Index: src/org/eclipse/pde/internal/ui/launcher/OSGiBundleBlock.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.pde.ui/src/org/eclipse/pde/internal/ui/launcher/OSGiBundleBlock.java,v
retrieving revision 1.14
diff -u -r1.14 OSGiBundleBlock.java
--- src/org/eclipse/pde/internal/ui/launcher/OSGiBundleBlock.java	12 Feb 2008 15:48:21 -0000	1.14
+++ src/org/eclipse/pde/internal/ui/launcher/OSGiBundleBlock.java	19 Feb 2008 02:44:56 -0000
@@ -32,8 +32,8 @@
 
 public class OSGiBundleBlock extends AbstractPluginBlock {
 
-	private HashMap levelColumnCache = null;
-	private HashMap autoColumnCache = null;
+	private HashMap levelColumnCache = new HashMap();
+	private HashMap autoColumnCache = new HashMap();
 	private TreeEditor levelColumnEditor = null;
 	private TreeEditor autoColumnEditor = null;
 
@@ -141,6 +141,7 @@
 							if (item.getChecked()) {
 								item.setText(2, combo.getText());
 								fTab.updateLaunchConfigurationDialog();
+								autoColumnCache.put(item.getData(), item.getText(2));
 							}
 						}
 					});
@@ -181,11 +182,13 @@
 		for (int i = 0; i < selected.length; i++) {
 			if (selected[i] instanceof IPluginModelBase) {
 				IPluginModelBase model = (IPluginModelBase) selected[i];
-				TreeItem item = (TreeItem) fPluginTreeViewer.testFindItem(model);
+				//TreeItem item = (TreeItem) fPluginTreeViewer.testFindItem(model);
 				if (model.getUnderlyingResource() == null) {
-					appendToBuffer(tBuffer, model, item);
+					//appendToBuffer(tBuffer, model, item);
+					appendToBuffer(tBuffer, model);
 				} else {
-					appendToBuffer(wBuffer, model, item);
+					//appendToBuffer(wBuffer, model, item);
+					appendToBuffer(wBuffer, model);
 				}
 			}
 		}
@@ -196,18 +199,19 @@
 		if (fAddWorkspaceButton.getSelection()) {
 			for (int i = 0; i < fWorkspaceModels.length; i++) {
 				if (!fPluginTreeViewer.getChecked(fWorkspaceModels[i])) {
-					appendToBuffer(buffer, fWorkspaceModels[i], null);
+					appendToBuffer(buffer, fWorkspaceModels[i]);
 				}
 			}
 		}
 		config.setAttribute(IPDELauncherConstants.DESELECTED_WORKSPACE_PLUGINS, buffer.length() > 0 ? buffer.toString() : (String) null);
 	}
 
-	private void appendToBuffer(StringBuffer buffer, IPluginModelBase model, TreeItem item) {
+	private void appendToBuffer(StringBuffer buffer, IPluginModelBase model) {
 		if (buffer.length() > 0)
-			buffer.append(","); //$NON-NLS-1$
-		String startLevel = item != null ? item.getText(1) : null;
-		String autoStart = item != null ? item.getText(2) : null;
+			buffer.append(","); //$NON-NLS-1$ 
+
+		String startLevel = levelColumnCache.get(model) != null ? levelColumnCache.get(model).toString() : null;
+		String autoStart = autoColumnCache.get(model) != null ? autoColumnCache.get(model).toString() : null;
 		String value = BundleLauncherHelper.writeBundles(model, startLevel, autoStart);
 		buffer.append(value);
 	}
@@ -237,6 +241,7 @@
 	}
 
 	private void resetGroup(NamedElement group) {
+		/*
 		Widget widget = fPluginTreeViewer.testFindItem(group);
 		if (widget instanceof TreeItem) {
 			TreeItem[] items = ((TreeItem) widget).getItems();
@@ -246,6 +251,19 @@
 				}
 			}
 		}
+		*/
+		Object[] children = group.getChildren();
+		if (children == null)
+			return;
+		for (int i = 0; i < children.length; i++) {
+			Object child = children[i];
+			if (child instanceof IPluginModelBase) {
+				if (fPluginTreeViewer.getChecked(child)) {
+					resetText((IPluginModelBase) child);
+				}
+			}
+		}
+
 	}
 
 	private void initWorkspacePluginsState(ILaunchConfiguration configuration) throws CoreException {
@@ -266,13 +284,27 @@
 
 	protected void handleGroupStateChanged(Object group, boolean checked) {
 		super.handleGroupStateChanged(group, checked);
-		Widget item = fPluginTreeViewer.testFindItem(group);
-		if (item instanceof TreeItem) {
-			TreeItem[] items = ((TreeItem) item).getItems();
-			for (int i = 0; i < items.length; i++) {
-				TreeItem child = items[i];
-				if (child.getChecked() == (child.getText(1).length() == 0))
-					resetText(items[i]);
+//		Widget item = fPluginTreeViewer.testFindItem(group);
+//		if (item instanceof TreeItem) {
+//			TreeItem[] items = ((TreeItem) item).getItems();
+//			for (int i = 0; i < items.length; i++) {
+//				TreeItem child = items[i];
+//				if (child.getChecked() == (child.getText(1).length() == 0))
+//					resetText(items[i]);
+//			}
+//		}
+		if (group instanceof NamedElement) {
+			NamedElement namedElement = (NamedElement) group;
+			Object[] children = namedElement.getChildren();
+			if (children == null)
+				return;
+			for (int i = 0; i < children.length; i++) {
+				Object child = children[i];
+				if (child instanceof IPluginModelBase) {
+					if (fPluginTreeViewer.getChecked(child) == (((String) (levelColumnCache.get(child))).length() == 0)) {
+						resetText((IPluginModelBase) child);
+					}
+				}
 			}
 		}
 	}
@@ -294,6 +326,7 @@
 	}
 
 	private void updateGroup(Object group) {
+		/*
 		Widget item = fPluginTreeViewer.testFindItem(group);
 		if (item instanceof TreeItem) {
 			TreeItem[] items = ((TreeItem) item).getItems();
@@ -303,6 +336,23 @@
 					resetText(items[i]);
 			}
 		}
+		*/
+		if (group instanceof NamedElement) {
+			NamedElement namedElement = (NamedElement) group;
+			Object[] children = namedElement.getChildren();
+			if (children == null) {
+				return;
+			}
+			for (int i = 0; i < children.length; i++) {
+				Object child = children[i];
+				if (child instanceof IPluginModelBase) {
+					if (fPluginTreeViewer.getChecked(child) == (((String) (levelColumnCache.get(child))).length() == 0)) {
+						resetText((IPluginModelBase) child);
+					}
+				}
+
+			}
+		}
 	}
 
 	private void setText(IPluginModelBase model, String value) {
@@ -310,15 +360,57 @@
 		if (widget instanceof TreeItem) {
 			TreeItem item = (TreeItem) widget;
 			int index = value == null ? -1 : value.indexOf(':');
-			item.setText(1, index == -1 ? "" : value.substring(0, index)); //$NON-NLS-1$
+			String levelValue = index == -1 ? "" : value.substring(0, index); //$NON-NLS-1$
+			String autoValue = null;
+			item.setText(1, levelValue);
 			if (model.isFragmentModel()) {
-				item.setText(2, "false"); //$NON-NLS-1$
+				autoValue = "false"; //$NON-NLS-1$
+				item.setText(2, autoValue);
 			} else {
-				item.setText(2, index == -1 ? "" : value.substring(index + 1)); //$NON-NLS-1$
+				autoValue = index == -1 ? "" : value.substring(index + 1); //$NON-NLS-1$
+				item.setText(2, autoValue);
+			}
+			levelColumnCache.put(model, levelValue);
+			autoColumnCache.put(model, autoValue);
+		}
+	}
+
+	private void resetText(IPluginModelBase model) {
+		String levelText = null;
+		String autoText = null;
+		Widget widget = fPluginTreeViewer.testFindItem(model);
+		if (fPluginTreeViewer.getChecked(model)) {
+			boolean isSystemBundle = "org.eclipse.osgi".equals(model.getPluginBase().getId()); //$NON-NLS-1$
+			if (!"default".equals(levelColumnCache.get(model))) //$NON-NLS-1$
+				levelText = isSystemBundle ? "" : "default"; //$NON-NLS-1$ //$NON-NLS-2$
+			if (!"default".equals(autoColumnCache.get(model))) //$NON-NLS-1$
+				autoText = isSystemBundle ? "" : "default"; //$NON-NLS-1$ //$NON-NLS-2$
+		} else {
+			if (((String) levelColumnCache.get(model)).length() > 0) {
+				levelText = ""; //$NON-NLS-1$
+			}
+			if (((String) autoColumnCache.get(model)).length() > 0) {
+				autoText = ""; //$NON-NLS-1$
+			}
+		}
+		if (model.isFragmentModel()) {
+			autoText = "false"; //$NON-NLS-1$
+		}
+		if (levelText != null) {
+			levelColumnCache.put(model, levelText);
+			if (widget instanceof TreeItem) {
+				((TreeItem) widget).setText(1, levelText);
+			}
+		}
+		if (autoText != null) {
+			autoColumnCache.put(model, autoText);
+			if (widget instanceof TreeItem) {
+				((TreeItem) widget).setText(2, autoText);
 			}
 		}
 	}
 
+	/*
 	private void resetText(IPluginModelBase model) {
 		Widget widget = fPluginTreeViewer.testFindItem(model);
 		if (widget instanceof TreeItem) {
@@ -344,6 +436,7 @@
 				item.setText(2, ""); //$NON-NLS-1$
 		}
 	}
+	*/
 
 	protected void handleRestoreDefaults() {
 		Object[] selected = fPluginTreeViewer.getCheckedElements();
@@ -384,33 +477,33 @@
 			autoColumnEditor.getEditor().dispose();
 		}
 
-		// Cache the current text
-		levelColumnCache = new HashMap();
-		autoColumnCache = new HashMap();
-		ArrayList allTreeItems = getAllTreeItems(treeView.getTree().getItems());
-		for (Iterator iterator = allTreeItems.iterator(); iterator.hasNext();) {
-			TreeItem item = (TreeItem) iterator.next();
-			levelColumnCache.put(item.getData(), item.getText(1));
-			autoColumnCache.put(item.getData(), item.getText(2));
-		}
-	}
-
-	/**
-	 * This gets all the tree items from a tree.  
-	 * 
-	 * This method must exist in some SWT util library, so it can probably be 
-	 * removed when I find it.
-	 * 
-	 * @param roots
-	 */
-	private ArrayList getAllTreeItems(TreeItem[] roots) {
-		ArrayList list = new ArrayList();
-		for (int i = 0; i < roots.length; i++) {
-			TreeItem item = roots[i];
-			list.add(item);
-			list.addAll(getAllTreeItems(item.getItems()));
-		}
-		return list;
-	}
+//		// Cache the current text
+//		levelColumnCache = new HashMap();
+//		autoColumnCache = new HashMap();
+//		ArrayList allTreeItems = getAllTreeItems(treeView.getTree().getItems());
+//		for (Iterator iterator = allTreeItems.iterator(); iterator.hasNext();) {
+//			TreeItem item = (TreeItem) iterator.next();
+//			levelColumnCache.put(item.getData(), item.getText(1));
+//			autoColumnCache.put(item.getData(), item.getText(2));
+//		}
+	}
+
+//	/**
+//	 * This gets all the tree items from a tree.  
+//	 * 
+//	 * This method must exist in some SWT util library, so it can probably be 
+//	 * removed when I find it.
+//	 * 
+//	 * @param roots
+//	 */
+//	private ArrayList getAllTreeItems(TreeItem[] roots) {
+//		ArrayList list = new ArrayList();
+//		for (int i = 0; i < roots.length; i++) {
+//			TreeItem item = roots[i];
+//			list.add(item);
+//			list.addAll(getAllTreeItems(item.getItems()));
+//		}
+//		return list;
+//	}
 
 }
Index: src/org/eclipse/pde/internal/ui/launcher/AbstractPluginBlock.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.pde.ui/src/org/eclipse/pde/internal/ui/launcher/AbstractPluginBlock.java,v
retrieving revision 1.28
diff -u -r1.28 AbstractPluginBlock.java
--- src/org/eclipse/pde/internal/ui/launcher/AbstractPluginBlock.java	16 Jan 2008 17:08:31 -0000	1.28
+++ src/org/eclipse/pde/internal/ui/launcher/AbstractPluginBlock.java	19 Feb 2008 02:44:56 -0000
@@ -27,6 +27,8 @@
 import org.eclipse.pde.internal.ui.*;
 import org.eclipse.pde.internal.ui.elements.DefaultContentProvider;
 import org.eclipse.pde.internal.ui.elements.NamedElement;
+import org.eclipse.pde.internal.ui.launcher.FilteredCheckboxTree.FilterableCheckboxTreeViewer;
+import org.eclipse.pde.internal.ui.launcher.FilteredCheckboxTree.PreRefreshNotifier;
 import org.eclipse.pde.internal.ui.util.PersistablePluginObject;
 import org.eclipse.pde.internal.ui.util.SWTUtil;
 import org.eclipse.pde.internal.ui.wizards.ListUtil;
@@ -42,11 +44,13 @@
 import org.eclipse.swt.widgets.*;
 import org.eclipse.ui.*;
 import org.eclipse.ui.dialogs.IWorkingSetSelectionDialog;
+import org.eclipse.ui.dialogs.PatternFilter;
 
 public abstract class AbstractPluginBlock {
 
 	protected AbstractLauncherTab fTab;
 
+	private FilteredCheckboxTree fPluginFilteredTree;
 	protected CheckboxTreeViewer fPluginTreeViewer;
 	protected NamedElement fWorkspacePlugins;
 	protected NamedElement fExternalPlugins;
@@ -249,7 +253,17 @@
 	}
 
 	protected void createPluginViewer(Composite composite, int span, int indent) {
-		fPluginTreeViewer = new CheckboxTreeViewer(composite, getTreeViewerStyle());
+
+		//fPluginTreeViewer = new CheckboxTreeViewer(composite, getTreeViewerStyle());
+		fPluginFilteredTree = new FilteredCheckboxTree(composite, getTreeViewerStyle(), new PatternFilter());
+		fPluginTreeViewer = (CheckboxTreeViewer) fPluginFilteredTree.getViewer();
+		((FilterableCheckboxTreeViewer) fPluginTreeViewer).addPerRefreshNotifier(new PreRefreshNotifier() {
+			public void preRefresh(FilterableCheckboxTreeViewer viewer) {
+				refreshTreeView(fPluginTreeViewer);
+
+			}
+		});
+
 		fPluginTreeViewer.addCheckStateListener(new ICheckStateListener() {
 
 			public void checkStateChanged(CheckStateChangedEvent event) {
@@ -299,13 +313,16 @@
 		GridData gd = new GridData(GridData.FILL_BOTH);
 		gd.horizontalSpan = span;
 		gd.horizontalIndent = indent;
-		fPluginTreeViewer.getTree().setLayoutData(gd);
+		fPluginFilteredTree.setLayoutData(gd);
 
 		Image siteImage = PDEPlugin.getDefault().getLabelProvider().get(PDEPluginImages.DESC_SITE_OBJ);
 
 		fWorkspacePlugins = new NamedElement(PDEUIMessages.AdvancedLauncherTab_workspacePlugins, siteImage);
 		fExternalPlugins = new NamedElement(PDEUIMessages.PluginsTab_target, siteImage);
 
+		fWorkspacePlugins.setChildren(fWorkspaceModels);
+		fExternalPlugins.setChildren(fExternalModels);
+
 		fPluginTreeViewer.addFilter(new Filter());
 	}
 
@@ -395,7 +412,6 @@
 	}
 
 	protected void handleFilterButton() {
-		refreshTreeView(fPluginTreeViewer);
 		fPluginTreeViewer.refresh();
 		fPluginTreeViewer.expandAll();
 	}
@@ -548,6 +564,7 @@
 
 	public void enableViewer(boolean enable) {
 		fPluginTreeViewer.getTree().setEnabled(enable);
+		fPluginFilteredTree.getFilterControl().setEnabled(enable);
 		fAddRequiredButton.setEnabled(enable);
 		fDefaultsButton.setEnabled(enable);
 		fWorkingSetButton.setEnabled(enable);
Index: src/org/eclipse/pde/internal/ui/elements/NamedElement.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.pde.ui/src/org/eclipse/pde/internal/ui/elements/NamedElement.java,v
retrieving revision 1.7
diff -u -r1.7 NamedElement.java
--- src/org/eclipse/pde/internal/ui/elements/NamedElement.java	3 May 2006 13:31:06 -0000	1.7
+++ src/org/eclipse/pde/internal/ui/elements/NamedElement.java	19 Feb 2008 02:44:56 -0000
@@ -18,6 +18,8 @@
 	private String name;
 
 	private IPDEElement parent;
+	
+	private Object[] children; 
 
 	public NamedElement(String name) {
 		this(name, null, null);
@@ -33,6 +35,21 @@
 		this.parent = parent;
 	}
 
+	/**
+	 * Sets the children of this element. The children are not copied
+	 * @param children
+	 */
+	public void setChildren(Object[] children) {
+		this.children = children;
+	}
+	
+	/**
+	 * Gets the children of this element.  The children are not copied
+	 */
+	public Object[] getChildren() {
+		return children;
+	}
+
 	public Image getImage() {
 		return image;
 	}
Index: src/org/eclipse/pde/internal/ui/launcher/FilteredCheckboxTree.java
===================================================================
RCS file: src/org/eclipse/pde/internal/ui/launcher/FilteredCheckboxTree.java
diff -N src/org/eclipse/pde/internal/ui/launcher/FilteredCheckboxTree.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/org/eclipse/pde/internal/ui/launcher/FilteredCheckboxTree.java	1 Jan 1970 00:00:00 -0000
@@ -0,0 +1,352 @@
+/*******************************************************************************
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     Ian Bull - initial API and implementation (Bug #207064)
+ *******************************************************************************/
+package org.eclipse.pde.internal.ui.launcher;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.eclipse.jface.viewers.CheckStateChangedEvent;
+import org.eclipse.jface.viewers.CheckboxTreeViewer;
+import org.eclipse.jface.viewers.ICheckStateListener;
+import org.eclipse.jface.viewers.TreeViewer;
+import org.eclipse.swt.widgets.Composite;
+import org.eclipse.swt.widgets.Item;
+import org.eclipse.swt.widgets.TreeItem;
+import org.eclipse.swt.widgets.Widget;
+import org.eclipse.ui.dialogs.FilteredTree;
+import org.eclipse.ui.dialogs.PatternFilter;
+
+/**
+ * A FilteredChecboxTree.  This tree stores all the tree elements internally, and keeps the
+ * check state in sync.  This way, even if an element is filtered, the caller can get and set the
+ * checked state.  
+ * 
+ * The internal representation is additive.  That is, elements are never removed from the internal
+ * representation.  This is OK since the PDE launch Dialog never changes the elements once
+ * the view is opened.  If any other tree is based on this code, they may want to address this issue. 
+ * 
+ * This is not public because it was customized for the Launch Dialog.
+ * 
+ * @author Ian Bull
+ */
+class FilteredCheckboxTree extends FilteredTree {
+
+	/**
+	 * The FilteredCheckboxTree Constructor.
+	 * @param parent The parent composite where this Tree will be placed.
+	 * @param treeStyle Tree styles
+	 * @param filter The pattern filter that wil be used to filter elements
+	 */
+	public FilteredCheckboxTree(Composite parent, int treeStyle, PatternFilter filter) {
+		super(parent, treeStyle, filter);
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * @see org.eclipse.ui.dialogs.FilteredTree#doCreateTreeViewer(org.eclipse.swt.widgets.Composite, int)
+	 */
+	protected TreeViewer doCreateTreeViewer(Composite parent, int style) {
+		return new FilterableCheckboxTreeViewer(parent, style);
+	}
+
+	/**
+	 * Classes which implement this interface deal with notifications from the
+	 * filtered checkbox tree viewer.  The notifications are fired before a refresh
+	 * happens. 
+	 */
+	interface PreRefreshNotifier {
+		public void preRefresh(FilterableCheckboxTreeViewer viewer);
+	}
+
+	/**
+	 * A CheckboxTreeViewer that maintains an internal representation of all the nodes.
+	 * 
+	 */
+	 class FilterableCheckboxTreeViewer extends CheckboxTreeViewer {
+		static final String NONE = "none";
+		static final String CHECKED = "checked";
+		static final String GREYED = "greyed";
+		static final String CHECKED_GREYED = "checked_greyed";
+
+		/**
+		 * The internal node for the FilterableCheckboxTreeViewer
+		 */
+		class FilteredCheckboxTreeItem {
+			Object data;    // Data element
+			String state;   // Checked State
+			List children = new ArrayList();
+			public FilteredCheckboxTreeItem(Object data, String state, Map itemCache, FilteredCheckboxTreeItem parent) {
+				this.data = data;
+				this.state = state;
+				itemCache.put(data, this);
+				if ( parent != null ) {
+					parent.children.add(this);
+				}
+			}
+		}
+
+		/* A cache of all the nodes */
+		Map itemCache = new HashMap();
+		
+		/* The preRefresh Listeners */
+		List refreshingListeners = new ArrayList();
+
+		/**
+		 * FilterableCheckboxTreeViewer constructor. This creates the tree part of the filtered tree.
+		 */
+		public FilterableCheckboxTreeViewer(Composite parent, int style) {
+			super(parent, style);
+			addCheckStateListener(new ICheckStateListener() {
+
+				public void checkStateChanged(CheckStateChangedEvent event) {
+					FilteredCheckboxTreeItem item = (FilteredCheckboxTreeItem) itemCache.get(event.getElement());
+					if ( item != null ) {
+						item.state = event.getChecked() ? CHECKED : NONE;
+					}
+				}
+			});
+		}
+
+	
+		/**
+		 * Allows clients to listen to the tree refresh.
+		 */
+		public void addPerRefreshNotifier(PreRefreshNotifier notifier) {
+			if (refreshingListeners.contains(notifier))return;
+			refreshingListeners.add(notifier);
+		}
+		
+	
+		/*
+		 * (non-Javadoc)
+		 * @see org.eclipse.jface.viewers.CheckboxTreeViewer#getChecked(java.lang.Object)
+		 */
+		public boolean getChecked(Object element) {
+			Widget testFindItem = getViewer().testFindItem(element);
+			testFindItem = null;
+			if  ( testFindItem == null ) {
+				if ( itemCache.containsKey(element)) {
+					FilteredCheckboxTreeItem item = (FilteredCheckboxTreeItem) itemCache.get(element);
+					if ( item.state.equals(CHECKED)) return true;
+					if ( item.state.equals(CHECKED_GREYED )) return true;
+					if ( item.state.equals(GREYED)) return true;
+					else if ( item.state.equals(NONE)) return false;
+				}
+			}
+			return super.getChecked(element);
+		}
+	
+		/*
+		 * (non-Javadoc)
+		 * @see org.eclipse.jface.viewers.CheckboxTreeViewer#getCheckedElements()
+		 */
+		public Object[] getCheckedElements() {
+			Iterator iterator = itemCache.values().iterator();
+			List checkedElements = new LinkedList();
+			while(iterator.hasNext()) {
+				FilteredCheckboxTreeItem item = (FilteredCheckboxTreeItem) iterator.next();
+				Widget testFindItem = getViewer().testFindItem(item.data);
+				testFindItem = null;
+				if ( testFindItem == null ) {
+					if ( item.state.equals(CHECKED) || item.state.equals(CHECKED_GREYED) || item.state.equals(GREYED)) {
+						checkedElements.add(item.data);
+					}
+				}
+				else {
+					if (((TreeItem)testFindItem).getChecked()) {
+						checkedElements.add(testFindItem.getData());
+					}
+				}
+			}
+			return checkedElements.toArray();
+		}
+	
+		/*
+		 * (non-Javadoc)
+		 * @see org.eclipse.jface.viewers.CheckboxTreeViewer#setChecked(java.lang.Object, boolean)
+		 */
+		public boolean setChecked(Object element, boolean state) {
+			if ( itemCache.containsKey(element) ) {
+				FilteredCheckboxTreeItem item = (FilteredCheckboxTreeItem) itemCache.get(element);
+				item.state = state ? CHECKED : NONE;
+			}
+			return super.setChecked(element, state);
+		}
+		
+		/*
+		 * (non-Javadoc)
+		 * @see org.eclipse.jface.viewers.CheckboxTreeViewer#setCheckedElements(java.lang.Object[])
+		 */
+		public void setCheckedElements(Object[] elements) {
+			Set s = new HashSet(itemCache.keySet());
+			s.removeAll(new HashSet(Arrays.asList(elements)));
+			for (int i = 0; i < elements.length; i++) {
+				FilteredCheckboxTreeItem item = (FilteredCheckboxTreeItem) itemCache.get(elements[i]);
+				if ( item != null ) {
+					item.state = CHECKED;
+				}
+			}
+			for (Iterator iterator = s.iterator(); iterator.hasNext();) {
+				Object object = iterator.next();
+				FilteredCheckboxTreeItem item = (FilteredCheckboxTreeItem) itemCache.get(object);
+				if ( item != null ) {
+					item.state = NONE;
+				}
+			}
+			super.setCheckedElements(elements);
+		}
+		
+		/*
+		 * (non-Javadoc)
+		 * @see org.eclipse.jface.viewers.CheckboxTreeViewer#setSubtreeChecked(java.lang.Object, boolean)
+		 */
+		public boolean setSubtreeChecked(Object element, boolean state) {
+			String newState = state ? CHECKED : NONE;
+			FilteredCheckboxTreeItem filteredCheckboxTreeItem = (FilteredCheckboxTreeItem) itemCache.get(element);
+			if ( filteredCheckboxTreeItem != null ) {
+				filteredCheckboxTreeItem.state = newState;
+				List children = filteredCheckboxTreeItem.children;
+				for (Iterator iterator = children.iterator(); iterator.hasNext();) {
+					FilteredCheckboxTreeItem child = (FilteredCheckboxTreeItem) iterator.next();
+					child.state = newState;
+				}
+			}
+			return super.setSubtreeChecked(element, state);
+		}
+
+		/*
+		 * (non-Javadoc)
+		 * @see org.eclipse.jface.viewers.CheckboxTreeViewer#preservingSelection(java.lang.Runnable)
+		 */
+		protected void preservingSelection(Runnable updateCode) {
+			super.preservingSelection(updateCode);
+			
+			// Re-apply the checked state
+			ArrayList allTreeItems = getAllTreeItems(treeViewer.getTree().getItems());
+			for (Iterator iterator = allTreeItems.iterator(); iterator.hasNext();) {
+				TreeItem item = (TreeItem) iterator.next();
+				doApplyCheckedState(item, item.getData());
+			}
+		}
+		
+
+		/*
+		 * (non-Javadoc)
+		 * @see org.eclipse.jface.viewers.AbstractTreeViewer#internalRefresh(java.lang.Object, boolean)
+		 */
+		protected void internalRefresh(Object element, boolean updateLabels) {
+			// Notify anybody who is listening for the refresh
+			for (Iterator iterator = refreshingListeners.iterator(); iterator.hasNext();) {
+				PreRefreshNotifier notifier = (PreRefreshNotifier) iterator.next();
+				notifier.preRefresh(FilterableCheckboxTreeViewer.this);
+			}
+			saveCheckedState();
+			super.internalRefresh(element, updateLabels);
+			treeViewer.expandAll();
+		}	
+
+		
+		/*
+		 * Set the checked state 
+		 */
+		private void doApplyCheckedState(Item item, Object element) {
+			// update the item first
+			super.doUpdateItem(item, element);
+			
+			// Update the checked state
+			TreeItem treeItem = (TreeItem) item;
+			if (itemCache.containsKey(element)) {
+				String state = ((FilteredCheckboxTreeItem)itemCache.get(element)).state;
+				if (state.equals(CHECKED_GREYED)) {
+					treeItem.setGrayed(true);
+					treeItem.setChecked(true);
+				} else if (state.equals(CHECKED)) {
+					treeItem.setChecked(true);
+					treeItem.setGrayed(false);
+				} else if (state.equals(GREYED)) {
+					treeItem.setGrayed(true);
+					treeItem.setChecked(false);
+				} else {
+					treeItem.setGrayed(false);
+					treeItem.setChecked(false);
+				}
+			}
+		}
+		
+		/*
+		 * A helper method to get all the items in the tree
+		 */
+		private ArrayList getAllTreeItems(TreeItem[] roots) {
+			ArrayList list = new ArrayList();
+			for (int i = 0; i < roots.length; i++) {
+				TreeItem item = roots[i];
+				list.add(item);
+				list.addAll(getAllTreeItems(item.getItems()));
+			}
+			return list;
+		}
+		
+		/**
+		 * Saves the checked state of all the elements in the tree
+		 */
+		private void saveCheckedState() {
+			TreeItem[] items = treeViewer.getTree().getItems();
+			for (int i = 0; i < items.length; i++) {
+				TreeItem item = items[i];
+				if (!itemCache.containsKey(item.getData())) {
+					new FilteredCheckboxTreeItem(item.getData(), getItemState(item), itemCache, null);
+				}
+				FilteredCheckboxTreeItem filteredCheckboxTreeItem = (FilteredCheckboxTreeItem) itemCache.get(item.getData());
+				filteredCheckboxTreeItem.state = getItemState(item);
+				saveCheckedState(filteredCheckboxTreeItem, item);
+			}
+		}
+		
+		/**
+		 * Saves the checked state of an item and all its children
+		 */
+		private void saveCheckedState(FilteredCheckboxTreeItem parent, TreeItem parentItem) {
+			TreeItem[] items = parentItem.getItems();
+			for (int i = 0; i < items.length; i++) {
+				TreeItem item = items[i];
+				if (!itemCache.containsKey(item.getData())) {
+					new FilteredCheckboxTreeItem(item.getData(), getItemState(item), itemCache, parent);
+				}
+				FilteredCheckboxTreeItem filteredCheckboxTreeItem = (FilteredCheckboxTreeItem) itemCache.get(item.getData());
+				filteredCheckboxTreeItem.state = getItemState(item);
+				saveCheckedState(filteredCheckboxTreeItem, item);
+			}
+		}
+		
+		/**
+		 * Computes the checked state from a tree item 
+		 */
+		private String getItemState(TreeItem item) {
+			if (item.getChecked() && item.getGrayed()) {
+				return CHECKED_GREYED;
+			} else if (item.getChecked()) {
+				return CHECKED;
+			} else if (item.getGrayed()) {
+				return GREYED;
+			} else {
+				return NONE;
+			}
+		}
+
+	} // end of FilterableCheckboxTreeViewer
+
+}