EDIT

    public Object execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection,

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

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

            final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();

            final WizardDialog dialog = new WizardDialog(shell, wizard);

            if (dialog.open() == IStatus.OK) {

                // Prepare writer parameters:

                ReadWriteParameterMap parameters = new ReadWriteParameterMap();

                parameters.put(ReadWriteParameterNames.KEY_APPLICATION_NAME, ApplicationUtil.getTitle());

                //parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion());  // Setting the version unnecessary, since its already contained in the title.

                parameters.put(ReadWriteParameterNames.KEY_APPLICATION_URL, "http://cybertaxonomy.eu/taxeditor/");  //TODO Specify URL obtained from a central class? //$NON-NLS-1$

                parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, wizard.getModel().getElongationToken());

                // Create and register object translator for writing pherogram alignment shifts:

                ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory();

                translatorFactory.addXSDTranslators(true);

                translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT);

                parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory);

                // Create writer and document adapters:

                JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());

                ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();

                document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel(),

                        wizard.getModel().isExportConsensusSequence(), wizard.getModel().isExportSingleReads()));

                // Write document:

                File file = new File(wizard.getModel().getFileName());

                if (!file.exists() || MessagingUtils.confirmDialog(Messages.exportSequenceToFileHandlerOverwriteTitle, String.format(

                        Messages.exportSequenceToFileHandlerOverwriteText, file.getAbsolutePath()))) {

                    try {

                        writer.writeDocument(document, file, parameters);

                    }

                    catch (IOException e) {

                        e.printStackTrace();

                        MessagingUtils.errorDialog(Messages.exportSequenceToFileHandlerIOErrorTitle, this,

                                String.format(Messages.exportSequenceToFileHandlerIOErrorMessage,

                                        file.getAbsolutePath()), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);

                    }

        return null;

    public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) TreeNode selectedTreeNode, MHandledMenuItem menuItem) {

        if(selectedTreeNode!=null){

            Object value = selectedTreeNode.getValue();

            canExecute = value instanceof Sequence;

        }