EDIT

eclipseprojects/eu.etaxonomy.taxeditor/src/eu/etaxonomy/taxeditor/model/NameTreeContentProvider.java -text

eclipseprojects/eu.etaxonomy.taxeditor/src/eu/etaxonomy/taxeditor/model/TaxTreeContentProvider.java -text

		boolean initialized = getPreferenceStore()

				.getBoolean(ITaxEditorConstants.INITIALIZED);

//		initialized = false; // to re-init db, uncomment this line

			initDatastore = true;

		} else {

			logger.warn("Datastore already initialized");

		if (initDatastore) {

			dbSchemaValidation = DbSchemaValidation.CREATE;

			initDatastore();

		}

		cdmApp = getCdmApp();

//		if (initDatastore) {

//			initDatastore();

//		}

		stopTransaction();

//					 CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_andreasM2", "edit", "wp5");

				 // Is this the problem?

				 Object txStatus = cdmApp.startTransaction();

	public void stopTransaction() {

					 new Color(null, 246, 246, 246));

import eu.etaxonomy.taxeditor.model.CdmUtil;

				// BUG beware of phantom taxon relations with a "NULL" fromTaxon

		// TODO delete taxon from CDM, tree, recent names list		

	private static String newTaxonText = "Open new taxon";

		draggableLabel.setLayoutData(new TableWrapData(TableWrapData.CENTER, TableWrapData.MIDDLE));

//			addPage(1, new EmptyEditorView(), getEditorInput());

		logger.warn("Calling doSave");

					CdmUtil.parseFullReference(nonViralName, text, null, true);

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy 

* http://www.e-taxonomy.eu

* 

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.taxeditor.model;

import java.util.Set;

import org.apache.log4j.Logger;

import org.eclipse.core.databinding.observable.Realm;

import org.eclipse.core.databinding.observable.list.IListChangeListener;

import org.eclipse.core.databinding.observable.list.IObservableList;

import org.eclipse.core.databinding.observable.list.ListChangeEvent;

import org.eclipse.core.databinding.observable.list.ListDiffEntry;

import org.eclipse.core.databinding.observable.list.WritableList;

import org.eclipse.core.databinding.observable.set.IObservableSet;

import org.eclipse.core.databinding.observable.set.WritableSet;

import org.eclipse.core.runtime.Assert;

import org.eclipse.jface.databinding.swt.SWTObservables;

import org.eclipse.jface.databinding.viewers.ObservableListContentProvider;

import org.eclipse.jface.viewers.ITreeContentProvider;

import org.eclipse.jface.viewers.TreeViewer;

import org.eclipse.jface.viewers.Viewer;

import org.eclipse.swt.widgets.Display;

import org.eclipse.ui.model.WorkbenchContentProvider;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.taxeditor.TaxEditorPlugin;

/**

 * Adds tree functionality (get parent, get children) to ObservableListContentProvider;

 *  much code was copied almost in tact from parent class due to

 *  viewer type restrictions and private settings of variables and methods

 * 

 * @author p.ciardelli

 * @created 14.05.2008

 * @version 1.0

 */

public class NameTreeContentProvider extends ObservableListContentProvider 

//		implements ILazyTreeContentProvider {

		implements ITreeContentProvider {

	private static final Logger logger = Logger.getLogger(NameTreeContentProvider.class);

	public Object[] getChildren(Object parentElement) {

		Taxon parentTaxon = (Taxon) parentElement;

//		Set<Taxon> children = TaxEditorPlugin.getDefault().getTaxonomicChildren(parentTaxon);

		Set<Taxon> children = parentTaxon.getTaxonomicChildren();

//		for (Taxon childTaxon : children) {

//			observableList.add(childTaxon);

//		}

		// TODO: suppress notify

		observableList.addAll(children);

		return children == null ? new Object[0] : children.toArray();

	}

	@Override

	public Object getParent(Object element) {

		return ((Taxon) element).getTaxonomicParent();

	}

	public boolean hasChildren(Object element) {

		return ((Taxon) element).hasTaxonomicChildren();

	}

	private IObservableList observableList;

	private Viewer viewer;

	private IListChangeListener listener = new IListChangeListener() {

		public void handleListChange(ListChangeEvent event) {

			if (viewer.getControl().isDisposed()) {

				return;

			}

			ListDiffEntry[] differences = event.diff.getDifferences();

			for (int i = 0; i < differences.length; i++) {

				ListDiffEntry entry = differences[i];

				if (entry.isAddition()) {

					knownElements.add(entry.getElement());

					Taxon newTaxon = (Taxon) entry.getElement();

					Taxon parent = newTaxon.getTaxonomicParent();

					((TreeViewer) viewer).add(parent, newTaxon);

				} else {

					knownElements.remove(entry.getElement());

					((TreeViewer) viewer).remove(entry.getElement());

				}

			}

		}

	};

	private IObservableSet knownElements;

	/**

	 * 

	 */

	public NameTreeContentProvider() {

		Assert.isNotNull(Realm.getDefault());

		observableList = new WritableList(SWTObservables.getRealm(Display.getDefault()));

		knownElements = new WritableSet(SWTObservables.getRealm(Display.getDefault()));

	}

	public Object[] getElements(Object inputElement) {

		return observableList.toArray();

	}

	public void dispose() {

		observableList.removeListChangeListener(listener);

	}

	public void inputChanged(Viewer viewer, Object oldInput, Object newInput) {

		this.viewer = viewer;

		if (newInput != null && !(newInput instanceof IObservableList)) {

			throw new IllegalArgumentException(

					"This content provider only works with input of type IObservableList"); //$NON-NLS-1$

		}

		setInput((IObservableList) newInput);

	}

	/**

	 * @param list

	 */

	private void setInput(IObservableList list) {

//		list = null;

		if (list == null) {

			list = new WritableList(SWTObservables.getRealm(Display.getDefault()));

//			list.addAll(TaxEditorPlugin.getDefault().getCdmApp().getTaxonService().getRootTaxa(null));

		}

		if (observableList != null) {

			observableList.removeListChangeListener(listener);

		}

		observableList = list; // this sets observablelist to TaxEditorPlugin.getDefault().getObservableTaxonTreeList()

		/*

		 * So then the question is: what's the first call that gets made to the content provider?

		 */

		observableList.addListChangeListener(listener);

		knownElements.clear();		

//		knownElements.addAll(list);

		knownElements.addAll(TaxEditorPlugin.getDefault().getCdmApp().getTaxonService().getRootTaxa(null));

	}

	/**

	 * @return the set of elements known to this content provider. Label providers may track

	 * this set if they need to be notified about additions before the viewer sees the added

	 * element, and notified about removals after the element was removed from the viewer.

	 */

	public IObservableSet getKnownElements() {

		return knownElements;

	}

}

/**

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy 

 * http://www.e-taxonomy.eu

 * 

 * The contents of this file are subject to the Mozilla Public License Version 1.1

 * See LICENSE.TXT at the top of this package for the full license terms.

 */

package eu.etaxonomy.taxeditor.model;

import java.util.ArrayList;

import java.util.Collection;

import java.util.List;

import java.util.Set;

import org.apache.log4j.Logger;

import org.eclipse.jface.viewers.ITreeContentProvider;

import org.eclipse.jface.viewers.Viewer;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.taxeditor.TaxEditorPlugin;

/**

 * @author p.ciardelli

 * @created 27.06.2008

 * @version 1.0

 */

public class TaxTreeContentProvider implements ITreeContentProvider {

	private static final Logger logger = Logger

			.getLogger(TaxTreeContentProvider.class);

	/*

	 * (non-Javadoc)

	 * 

	 * @see org.eclipse.jface.viewers.ITreeContentProvider#getChildren(java.lang.Object)

	 */

	@Override

	public Object[] getChildren(Object parentElement) {

		if (parentElement instanceof Taxon) {

			return getTaxonChildren((Taxon) parentElement).toArray();

		}

		if (!(parentElement instanceof Collection)) {

			throw new IllegalArgumentException(

					"getChildren() expects either a Collection or a Taxon object."); //$NON-NLS-1$	

		}

		List<Taxon> children = new ArrayList<Taxon>();

		for (Object parent : (Collection) parentElement) {

			if (!(parent instanceof Taxon)) {

				throw new IllegalArgumentException(

						"parentElement Collection can only contain Taxon objects."); //$NON-NLS-1$				

			}

			children.addAll(getTaxonChildren((Taxon) parent));

		}

		return children.toArray();

	}

	public Set<Taxon> getTaxonChildren(Taxon parentTaxon) {

		return TaxEditorPlugin.getDefault().getSessionTaxonomicChildren(

				parentTaxon);

	}

	/*

	 * (non-Javadoc)

	 * 

	 * @see org.eclipse.jface.viewers.ITreeContentProvider#getParent(java.lang.Object)

	 */

	@Override

	public Object getParent(Object element) {

		if (!(element instanceof Taxon)) {

			throw new IllegalArgumentException(

					"getParent() expects a Taxon object."); //$NON-NLS-1$				

		}

		return ((Taxon) element).getTaxonomicParent();

	}

	/*

	 * (non-Javadoc)

	 * 

	 * @see org.eclipse.jface.viewers.ITreeContentProvider#hasChildren(java.lang.Object)

	 */

	@Override

	public boolean hasChildren(Object element) {

		if (!(element instanceof Taxon)) {

			throw new IllegalArgumentException(

					"getParent() expects a Taxon object."); //$NON-NLS-1$				

		}

		// This seems a bit buggy

//		return ((Taxon) element).hasTaxonomicChildren();

		// Replace with this for now:

		return getChildren(element).length > 0;

	}

	/*

	 * (non-Javadoc)

	 * 

	 * @see org.eclipse.jface.viewers.IStructuredContentProvider#getElements(java.lang.Object)

	 */

	@Override

	public Object[] getElements(Object inputElement) {

		// BIG QUESTION: should getElements return only root taxa, or all taxa?

		// CONFLICTING INFO ONLINE!!!

//		return TaxEditorPlugin.getDefault().getObservableSessionTaxa().toArray();

		return TaxEditorPlugin.getDefault().getSessionRootTaxa().toArray();

	}

	/*

	 * (non-Javadoc)

	 * 

	 * @see org.eclipse.jface.viewers.IContentProvider#dispose()

	 */

	@Override

	public void dispose() {}

	/*

	 * (non-Javadoc)

	 * 

	 * @see org.eclipse.jface.viewers.IContentProvider#inputChanged(org.eclipse.jface.viewers.Viewer,

	 *      java.lang.Object, java.lang.Object)

	 */

	@Override

	public void inputChanged(Viewer viewer, Object oldInput, Object newInput) {

		// TODO Auto-generated method stub

	}

}

import org.eclipse.core.databinding.observable.set.IObservableSet;

import org.eclipse.core.databinding.observable.set.ISetChangeListener;

import org.eclipse.core.databinding.observable.set.SetChangeEvent;

import org.eclipse.jface.viewers.TreeViewer;

 * An implementation of ITreeContentProvider which adds taxa displayed in the tree

 *  to the Editor session on an as-loaded basis. Listens for any changes to the 

 *  set of session taxa, updates the TreeViewer accordingly.

 * <p> 

 * Could be re-written to implement ILazyTreeContentProvider at some point in the future. 

 *  NO: sorting not possible with lazy tree.

 * 

 * @created 28.05.2008

	TreeViewer viewer;

	/* (non-Javadoc)

		if (!(parentElement instanceof Taxon)) {

			logger.error("Method getChildren() expects a parentElement of type Taxon");

			return new Object[0];

		Taxon parentTaxon = (Taxon) parentElement;

		// If this does not return null, the taxon's children have already

		//	been requested during this session

		Set<Taxon> childTaxa = TaxEditorPlugin.getDefault()

				.getSessionTaxonomicChildren(parentTaxon);

		if (childTaxa == null) {

			removeSessionTaxaListener();

			// Request this taxon's children for the first time 

			//	during this session

			childTaxa = parentTaxon.getTaxonomicChildren();

			TaxEditorPlugin.getDefault().addSessionTaxa(childTaxa);

			addSessionTaxaListener();

		logger.warn("returning " + childTaxa.toString());

		return childTaxa.toArray();

			return null;			

			return false;			

		return ((Taxon) element).hasTaxonomicChildren();

//		logger.warn("Get elements for " + inputElement.toString() + " with class " + inputElement.getClass());

//		List elements = new ArrayList();

//		if (inputElement instanceof Collection) {

//			logger.warn("instanceof collection");

////			elements.addAll((Collection) inputElement);

//			for (Object parentElement : (Collection) inputElement) {

//				if (parentElement instanceof Taxon) {

//					for (Object childElement : getChildren(parentElement)) {

//						elements.add(childElement);

//					}

//				}

//			}

//		}

////		return TaxEditorPlugin.getDefault().getSessionRootTaxa().toArray();

////		return getChildren(inputElement);

//		logger.warn("elements have " + elements.size());

//		return elements.toArray();

		return null;

	public void dispose() {

		removeSessionTaxaListener();

	}

		if (!(viewer instanceof TreeViewer)) {

			throw new IllegalArgumentException(

					"This content provider only works with viewer of type TreeViewer"); //$NON-NLS-1$			

		}

		this.viewer = (TreeViewer) viewer;

		if (newInput != null && !(newInput instanceof Collection)) {

			throw new IllegalArgumentException(

					"This content provider only works with input of type Collection<Taxon>"); //$NON-NLS-1$

		}

		try {

			Collection<Taxon> input = (Collection<Taxon>) newInput;

			setInput(input);

		} catch (ClassCastException e) {

			throw new IllegalArgumentException(

				"This content provider only works with input of type Collection<Taxon>"); //$NON-NLS-1$

		}

	private void setInput(Collection<Taxon> input) {

		removeSessionTaxaListener();

		if (input != null) {

			TaxEditorPlugin.getDefault().addSessionTaxa(input);

		}

		addSessionTaxaListener();

	}

	private IObservableSet getObservableSessionTaxonSet() {

		return TaxEditorPlugin.getDefault().getObservableSessionTaxa();

	}

	private void addSessionTaxaListener() {

		getObservableSessionTaxonSet().addSetChangeListener(listener);

	}

	private void removeSessionTaxaListener() {

		getObservableSessionTaxonSet().removeSetChangeListener(listener);

	}

	private ISetChangeListener listener = new ISetChangeListener() {

		@Override

		public void handleSetChange(SetChangeEvent event) {

			if (viewer.getControl().isDisposed()) {

				return;

			}

			for (Object addition : event.diff.getAdditions()) {

				if (addition instanceof Taxon) {

					Taxon taxon = (Taxon) addition;

					Taxon parentTaxon = taxon.getTaxonomicParent();

					if (parentTaxon == null) {

						// If a new root item has been added, 

						//  set it as the viewer's input

						List<Taxon> newInput = new ArrayList<Taxon>();

						newInput.add(taxon);

						viewer.setInput(newInput);

//						viewer.setInput(TaxEditorPlugin.getDefault().getSessionRootTaxa());

					} else {

						viewer.add(parentTaxon, taxon);

					}

				}

			}

			for (Object removal : event.diff.getRemovals()) {

				if (removal instanceof Taxon) {

					Taxon taxon = (Taxon) removal; 

					viewer.remove(taxon);

				}

			}

//			viewer.getControl().setRedraw(true);

			viewer.refresh();

		}

	};

}

import org.eclipse.swt.events.SelectionAdapter;

import org.eclipse.swt.events.SelectionEvent;

import eu.etaxonomy.cdm.model.name.BotanicalName;

import eu.etaxonomy.cdm.model.name.Rank;

import eu.etaxonomy.taxeditor.model.TaxTreeContentProvider;

		// IContentProvider viewerContentProviderList = new

		// TaxonomicTreeContentProvider();

		IContentProvider viewerContentProviderList = new TaxTreeContentProvider();

		this

				.setLabelProvider(new TaxonomicTreeLabelProvider(

import eu.etaxonomy.taxeditor.TaxEditorPlugin;

	private boolean doReinitialize;

		final Button btnInit = new Button(container, SWT.CHECK);

			public void widgetSelected(final SelectionEvent e) {

				setDoReinitialize(btnInit.getSelection());

		btnInit.setText("Initialize datastore on next application start");

		setPreferenceStore(TaxEditorPlugin.getDefault().getPreferenceStore());

	public boolean performOk() {

		logger.warn("Setting init'ed to " + doReinitialize);

		TaxEditorPlugin.getDefault().getPreferenceStore().

				setValue(ITaxEditorConstants.INITIALIZED, !doReinitialize);

		return true;

	private void setDoReinitialize(boolean doReinitialize) {

		this.doReinitialize = doReinitialize;