EDIT

eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AlignmentEditorPasteHandler.java -text

         <handler

               class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorPasteHandler"

               commandId="org.eclipse.ui.edit.paste">

            <activeWhen>

               <with

                     variable="activePartId">

                  <equals

                        value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">

                  </equals>

               </with>

            </activeWhen>

         </handler>

	private static final String[] IDS = {ActionFactory.COPY.getCommandId(), ActionFactory.CUT.getCommandId(), 

		ActionFactory.PASTE.getCommandId()};

	private void updateEvents() {

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

	        service.refreshElements(IDS[i], null);

            updateEvents();

				updateEvents();

package eu.etaxonomy.taxeditor.molecular.handler;

import java.util.ArrayList;

import java.util.List;

import java.util.Map;

import java.util.Scanner;

import info.bioinfweb.libralign.alignmentarea.AlignmentArea;

import info.bioinfweb.libralign.alignmentarea.order.SequenceOrder;

import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;

import info.bioinfweb.libralign.model.AlignmentModel;

import info.bioinfweb.libralign.model.AlignmentModelUtils;

import org.eclipse.core.commands.ExecutionEvent;

import org.eclipse.jface.dialogs.MessageDialog;

import org.eclipse.swt.dnd.TextTransfer;

import org.eclipse.ui.commands.IElementUpdater;

import org.eclipse.ui.handlers.HandlerUtil;

import org.eclipse.ui.menus.UIElement;

import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;

/**

 * Handler that pastes the current contents of the clipboard into an active instance of {@link AlignmentEditor}.

 * 

 * @author Ben Stöver

 * @date 26.08.2015

 */

public class AlignmentEditorPasteHandler extends AbstractFocusedAlignmentAreaHandler implements IElementUpdater {

	private void pasteString(AlignmentArea area, int sequenceID, String content) {

		AlignmentModel<Object> alignmentModel = (AlignmentModel<Object>)area.getAlignmentModel();

		List<Object> tokens = AlignmentModelUtils.charSequenceToTokenList(content, alignmentModel.getTokenSet(),

				true, alignmentModel.getTokenSet().getGapToken()); 

		area.getActionProvider().deleteSelection();  // Overwrite selected tokens.

		area.getActionProvider().elongateSequence(sequenceID, area.getSelection().getCursorColumn());

		alignmentModel.insertTokensAt(sequenceID, area.getSelection().getCursorColumn(), tokens);

	}

	@Override

	protected void doExecute2(ExecutionEvent event, AlignmentEditor editor, AlignmentArea focusedArea) {

		SelectionModel selection = focusedArea.getSelection();

		String clipboardText = (String)editor.CLIPBOARD.getContents(TextTransfer.getInstance());

		if (clipboardText != null) {

			List<String> lines = new ArrayList<String>();

			Scanner scanner = new Scanner(clipboardText);

			try {

				while (scanner.hasNext()) {

					lines.add(scanner.nextLine());

				}

				if (lines.get(lines.size() - 1).equals("")) {

					lines.remove(lines.size() - 1);

				}

			}

			finally {

				scanner.close();

			}

			if (!lines.isEmpty()) { //TODO Can lines be empty? (Can an empty string "" be copied to the clipboard?)

				if (selection.getCursorHeight() == 1) {  // If the consensus sequence is focused, this is the only possible case.

					int sequenceID = focusedArea.getSequenceOrder().idByIndex(selection.getCursorRow());

					if (lines.size() == 1) {

						pasteString(focusedArea, sequenceID, lines.get(0));

					}

					else {

						MessageDialog dialog = new MessageDialog(HandlerUtil.getActiveWorkbenchWindow(event).getShell(),  //TODO Can the window be null? 

								"Pasting multiple lines", null,

								"The text to be pasted contains mutlitple lines (" + lines.size() + 

								") although the current cursor height is one. What do you want to do?", 

								MessageDialog.QUESTION, 

								new String[]{"Ingnore line breaks and paste as one sequence", 

										"Only paste the first line from the clipboard", "Cancel"}, 

								0);

						//TODO Does the dialog have to be disposed in some way?

						switch (dialog.open()) {

							case 0:  // Paste all lines in one sequence.

								pasteString(focusedArea, sequenceID, clipboardText);

								break;

							case 1:  // Paste only first line.

								pasteString(focusedArea, sequenceID, lines.get(0));

								break;

						}

					}

				}

				else {

					if (selection.getCursorHeight() == lines.size()) {

						SequenceOrder order = focusedArea.getSequenceOrder();

						for (int i = 0; i < selection.getCursorHeight(); i++) {

							pasteString(focusedArea, order.idByIndex(selection.getCursorRow() + i), lines.get(i));  // Multiple calls of deleteSelection() in here are unnecessary, but should have no effect.

						}

					}

					else {

						MessageDialog.openError(HandlerUtil.getActiveWorkbenchWindow(event).getShell(),  //TODO Can the window be null?

								"Unable to paste multiple lines", 

								"The current cursor height (" + selection.getCursorHeight() + 

								") does not match the number of lines to be pasted (" + lines.size() + ")." + 

								System.getProperty("line.separator") + System.getProperty("line.separator") + 

								"You can either change the cursor height accordingly or set the cursor height to one "

								+ "allowing you to paste all lines from the clipboad into one sequence.");

					}

				}

			}

		}

	}

	@Override

	public boolean isEnabled() {

		AlignmentEditor editor = getActiveAlignmentEditor();

		if (editor != null) {

			AlignmentArea focusedArea = editor.getFocusedArea();

			return (focusedArea != null);

		}

		else {

			return false;

		}

	}

	@Override

	public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {

		setBaseEnabled(isEnabled());

    }

}