EDIT

* 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.editor.view.media;

import java.util.HashSet;

				MessagingUtils.error(getClass(), "Taxon is null", null); //$NON-NLS-1$

				return NO_CHILDREN;

			}

			for(DescriptionBase<?> description : taxon.getDescriptions()){

				if(description.isImageGallery()){

					imageGalleries.add(description);

import java.io.File;

import java.io.IOException;

import java.io.InputStream;

import java.util.ArrayList;

import java.util.Collection;

import java.util.Collections;

import info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider;

import info.bioinfweb.tic.SWTComponentFactory;

/**

 * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to

 * a consensus sequence.

    private MultipleAlignmentsContainer alignmentsContainer = null;

    @Inject

    private MDirtyable dirty;

    public AlignmentEditorE4() {

    }

    private void refreshToolbarElement(String id) {

		ICommandService commandService =

				PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class);

		}

    }

    private void registerEditSettingListener(MultipleAlignmentsContainer container) {

        container.getEditSettings().addListener(new EditSettingsListener() {

            @Override

        });

    }

    private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) {

		AlignmentArea result = new AlignmentArea(container);

		result.setAllowVerticalScrolling(false);

		return result;

    }

    private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {

		AlignmentArea result = new AlignmentArea(container);

		result.setAllowVerticalScrolling(allowVerticalScrolling);

		return result;

	}

    private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,

    		AlignmentArea labeledArea) {

		return result;

    }

    private MultipleAlignmentsContainer getAlignmentsContainer() {

    	if (alignmentsContainer == null) {

    		alignmentsContainer = new MultipleAlignmentsContainer();

    	}

    }

    /**

     * Checks whether the specified alignment area or one of its subcomponents currently has the

     * focus.

    	return SWTUtils.childHasFocus((Composite)area.getToolkitComponent());

    }

    public boolean hasPherogram(String sequenceID) {

        return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX;

    }

    public PherogramArea getPherogramArea(String sequenceID) {

        if (hasPherogram(sequenceID)) {

            return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX);

        }

    }

    private ConsensusSequenceArea getConsensusHintDataArea() {

        return (ConsensusSequenceArea)getAlignmentsContainer().getAlignmentAreas().

                get(CONSENSUS_HINT_AREA_INDEX).getDataAreas().getBottomAreas().

                get(CONSENSUS_DATA_AREA_INDEX);

    }

    @Deprecated  //TODO Remove as soon as testing period is over

    private void createTestContents() {

		// Just for testing:

		}

    }

    	//TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated).

		// Add reads:

		//TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?

    }

    @PostConstruct

    public void createPartControl(Composite parent) {

        if (CdmStore.isActive()){

            if(sequenceNode!=null && sequenceNode.getId()!=0){

                sequenceNode = CdmStore.getService(ISequenceService.class).load(sequenceNode.getUuid());

            }

        }

        else {

            createTestContents();  // This case will removed after the test phase and an exception should probably be thrown.

import eu.etaxonomy.cdm.model.media.MediaRepresentation;

import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;

import eu.etaxonomy.cdm.model.media.Rights;

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

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

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

//            }

        } else if (entity instanceof Identifier) {

            if(parentElement instanceof AbstractSampleDesignationDetailSection){

            }

            else{

                element = new IdentifierElement(this, parentElement, (Identifier) entity, removeListener, style);

 *

 * @author n.hoffmann

 * @created Oct 13, 2010

 */

public abstract class AbstractDeterminationEventDetailSection extends

		AbstractEntityCollectionSection<DerivedUnitFacade, DeterminationEvent> {

	public AbstractDeterminationEventDetailSection(CdmFormFactory formFactory,

			ConversationHolder conversation, ICdmFormElement parentElement,

			String title, int style) {

		super(formFactory, conversation, parentElement, title, style);

	}

	@Override

	public DeterminationEvent createNewElement() {

		DeterminationEvent instance = DeterminationEvent.NewInstance();

		return instance;

	}

	@Override

	public void addElement(DeterminationEvent determination) {

		getEntity().addDetermination(determination);

	}

	@Override

	public void removeElement(DeterminationEvent determination) {

		getEntity().removeDetermination(determination);

	}

	@Override

	public String getEmptyString() {

		return "No determinations yet.";

	}

* 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.ui.section.occurrence;

import java.util.Arrays;

public class CurrentDeterminationDetailSection extends

		AbstractDeterminationEventDetailSection {

	public CurrentDeterminationDetailSection(CdmFormFactory formFactory,

			ConversationHolder conversation, ICdmFormElement parentElement,

			int style) {

		return newElement;

	}

	@Override

	protected String getTooltipString() {

		return "Create new current determination event";

	}

    @Override

    public DeterminationEvent addExisting() {

        return null;

    }

    @Override

    public boolean allowAddExisting() {

        return false;

    }

* 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.ui.section.occurrence;

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;

/**

 * @author n.hoffmann

 * @created May 11, 2011

 */

public class DeterminationDetailElement extends AbstractCdmDetailElement<DerivedUnitFacade> {

	private DeterminationHistoryDetailSection section_determinationHistory;

	public DeterminationDetailElement(CdmFormFactory formFactory,

			ICdmFormElement formElement) {

		super(formFactory, formElement);

	}

	@Override

	protected void createControls(ICdmFormElement formElement,

			DerivedUnitFacade entity, int style) {

	}

	@Override

	public void handleEvent(Object eventSource) {

		if(eventSource == section_currentDetermination){

			section_determinationHistory.refresh();

		}

	}

* 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.ui.section.occurrence;

import org.eclipse.jface.viewers.ISelectionProvider;

/**

 * @author n.hoffmann

 * @created May 11, 2011

 */

public class DeterminationDetailSection extends AbstractCdmDetailSection<DerivedUnitFacade> implements IDerivedUnitFacadeDetailSection {

	public DeterminationDetailSection(CdmFormFactory formFactory,

			ConversationHolder conversation, ICdmFormElement parentElement,

			ISelectionProvider selectionProvider, int style) {

		super(formFactory, conversation, parentElement, selectionProvider, style);

	}

	@Override

	public String getHeading() {

		String sectionTitle = "Determinations";

		if(getEntity()!=null && getEntity().getDeterminations().size()>0){

		}

		return sectionTitle;

	}

	@Override

	protected AbstractCdmDetailElement<DerivedUnitFacade> createCdmDetailElement(AbstractCdmDetailSection<DerivedUnitFacade> parentElement, int style) {

	    return formFactory.createDeterminationDetailElement(parentElement);

	}

* 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.ui.section.occurrence;

import java.util.Collection;

public class DeterminationHistoryDetailSection extends

		AbstractDeterminationEventDetailSection {

	public DeterminationHistoryDetailSection(CdmFormFactory formFactory,

			ConversationHolder conversation, ICdmFormElement parentElement,

			int style) {

		internalUpdateSection(false);

	}

	@Override

	protected String getTooltipString() {

		return "Add a determination event to the history";

	}

    @Override

    public DeterminationEvent addExisting() {

        return null;

    }

    @Override

    public boolean allowAddExisting() {

        return false;

    }

* 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.ui.section.occurrence.dna;

import java.util.Collection;

import eu.etaxonomy.taxeditor.view.search.derivative.DerivateLabelProvider;

/**

 * @author pplitzner

 * @date Oct 16, 2014

 */

public class CurrentSampleDesignationDetailSection extends AbstractSampleDesignationDetailSection {

        return new DefaultCdmBaseComparator<>();

	}

	@Override

	protected String getTooltipString() {

		return "Create new current sample designation";

	}

    @Override

    public void addElement(Identifier sampleDesignation) {

        //The current sample designation is always the first one found.

        getEntity().addIdentifier(0, sampleDesignation);

    }

    @Override

    public Identifier addExisting() {

        return null;

    }

    @Override

    public boolean allowAddExisting() {

        return false;

    }

        }

        else if(eventSource==dateQualityCheck.getController()){

            DateTime dateTime = dateQualityCheck.getController().getDateTime();

            dnaQuality.setQualityCheckDate(dateTime);

        }

    }

/**

 * @author pplitzner

 * @date 05.03.2014

 */

public class DnaQualityDetailSection extends AbstractCdmDetailSection<DerivedUnitFacade> {

    public DnaQualityDetailSection(CdmFormFactory formFactory,

            ConversationHolder conversation, ICdmFormElement parentElement,

            ISelectionProvider selectionProvider, int style) {

        super(formFactory, conversation, parentElement, selectionProvider, style);

    }

    @Override

    public String getHeading() {

        return "DNA Quality";

    }

    @Override

    protected AbstractCdmDetailElement<DerivedUnitFacade> createCdmDetailElement(AbstractCdmDetailSection<DerivedUnitFacade> parentElement, int style) {

        return formFactory.createDnaQualityDetailElement(parentElement);

    }

 * 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.ui.section.occurrence.dna;

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;

/**

 * @author pplitzner

 * @date 16.12.2013

 */

public class DnaSamplePreparationPreservationDetailElement extends AbstractCdmDetailElement<DerivedUnitFacade> {

    private NumberWithLabelElement numberPreservationTemperature;

    private TextWithLabelElement txtMaterialOrMethods;

    public DnaSamplePreparationPreservationDetailElement(CdmFormFactory formFactory, ICdmFormElement formElement) {

        super(formFactory, formElement);

    }

    @Override

    protected void createControls(ICdmFormElement formElement, DerivedUnitFacade facade, int style) {

        Institution institution = null;

    }

    @Override

    public void handleEvent(Object eventSource) {

        DnaSample entity = (DnaSample)getEntity().innerDerivedUnit();

/**

 * @author pplitzner

 * @date 12.12.2013

 */

public class DnaSamplePreparationPreservationSection extends AbstractCdmDetailSection<DerivedUnitFacade> {

        super(formFactory, conversation, parentElement, selectionProvider, style);

    }

    @Override

    public String getHeading() {

        return "Preparation/Preservation";

    protected AbstractCdmDetailElement<DerivedUnitFacade> createCdmDetailElement(AbstractCdmDetailSection<DerivedUnitFacade> parentElement, int style) {

        return formFactory.createDnaSamplePreparationPreservationDetailElement(parentElement);

    }

* 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.ui.section.occurrence.dna;

import org.eclipse.jface.viewers.ISelectionProvider;

/**

 * @author n.hoffmann

 * @created May 11, 2011

 */

public class SampleDesignationDetailSection extends AbstractCdmDetailSection<DerivedUnitFacade> {

	public SampleDesignationDetailSection(CdmFormFactory formFactory,

			ConversationHolder conversation, ICdmFormElement parentElement,

			ISelectionProvider selectionProvider, int style) {

		super(formFactory, conversation, parentElement, selectionProvider, style);

	}

	@Override

	public String getHeading() {

		return "Sample Designations";

	    setTextClient(createToolbar());

	}

	@Override

	protected AbstractCdmDetailElement<DerivedUnitFacade> createCdmDetailElement(AbstractCdmDetailSection<DerivedUnitFacade> parentElement, int style) {

	    return formFactory.createSampleDesignationDetailElement(parentElement);

	}

* 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.ui.section.occurrence.dna;

import java.util.Collection;

/**

 * @author n.hoffmann

 * @created May 11, 2011

 */

public class SampleDesignationHistoryDetailSection extends AbstractSampleDesignationDetailSection {

	public SampleDesignationHistoryDetailSection(CdmFormFactory formFactory,

			ConversationHolder conversation, ICdmFormElement parentElement,

			int style) {

		super(formFactory, conversation, parentElement, "Sample Designation History", style);

	}

	@Override

	public Collection<Identifier> getCollection(IdentifiableEntity<?> entity) {

	    LinkedList<Identifier> sampleDesignations = new LinkedList<>();

		internalUpdateSection(false);

	}

	@Override

	protected String getTooltipString() {

		return "Add a sample designation to the history";

	}

    @Override

    public void addElement(Identifier sampleDesignation) {

        //The current sample designation is always the first one found.

        getEntity().addIdentifier(indexOfCurrentSampleDesignation+1, sampleDesignation);

    }

    @Override

    public Identifier addExisting() {

        return null;

    }

    @Override

    public boolean allowAddExisting() {

        return false;

    }

        if(entity.getPreservation()!=null){

            preservationMedium = entity.getPreservation().getMedium();

        }

                formElement, "Institution", institution, EntitySelectionElement.ALL, style);

                formElement, "Staff", staff, EntitySelectionElement.ALL,style);

        datePreparation = formFactory.createTimePeriodElement(formElement, "Preparation date", preparationDate, style);

        comboPreservationMedium = formFactory.createDefinedTermComboElement(TermType.MaterialOrMethod, formElement, "Preservation medium", preservationMedium, style);

                formElement, "Collection", entity.getCollection(), EntitySelectionElement.ALL, style);

        textAccessionNumber = formFactory.createTextWithLabelElement(formElement, "Accession Number", entity.getAccessionNumber(), style);

        textBarcode = formFactory.createTextWithLabelElement(formElement, "Barcode", entity.getBarcode(), style);

        }

        destroySections();

        if (input instanceof TaxonBase) {

                createEmptySection(Messages.DetailsViewerE4_TAXON_HAS_NO_NAME, rootElement);

            }

            else{

            else if(facade.getType()==SpecimenOrObservationType.DnaSample){

                if(facade.innerDerivedUnit().getRecordBasis()==SpecimenOrObservationType.TissueSample){

                    createTissueSampleSection(rootElement);

                }

                else if(facade.innerDerivedUnit().getRecordBasis()==SpecimenOrObservationType.DnaSample){

        else if(derivate instanceof DnaSample

                && ((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){

            DnaSample dnaSample = (DnaSample)derivate;

                if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){

                    label += currentSampleDesignation.getIdentifier()+separator;

                }

                if(derivedUnit.getKindOfUnit()!=null){

                    label += derivedUnit.getKindOfUnit()+separator;

                }

                if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){

                    label += currentSampleDesignation.getIdentifier() + separator;

                }

        //Sequence

        else if(derivate instanceof Sequence){

            Sequence sequence = (Sequence)derivate;

            if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){

                label += currentSampleDesignation.getIdentifier()+separator;

            }

            SingleRead singleRead = (SingleRead)derivate;

            if(parentNode!=null && parentNode.getValue() instanceof Sequence){

                Sequence sequence = (Sequence) parentNode.getValue();

                if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){

                    label = currentSampleDesignation.getIdentifier()+separator;

                }

        return ImageResources.getImage(ImageResources.DEFAULT_DERIVATIVE);

    }

        if(entity.isInstanceOf(DnaSample.class)){

            DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class);

                if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){

                    //first sample designation is the current

                    return identifier;