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package eu.etaxonomy.taxeditor.molecular.handler;
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import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
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import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
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import info.bioinfweb.libralign.model.AlignmentModel;
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import info.bioinfweb.libralign.model.tokenset.AbstractTokenSet;
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import org.eclipse.core.commands.AbstractHandler;
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import org.eclipse.core.commands.ExecutionEvent;
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import org.eclipse.core.commands.ExecutionException;
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import org.eclipse.swt.dnd.Clipboard;
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import org.eclipse.swt.dnd.TextTransfer;
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import org.eclipse.swt.dnd.Transfer;
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import org.eclipse.swt.widgets.Display;
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import org.eclipse.ui.IEditorPart;
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import org.eclipse.ui.handlers.HandlerUtil;
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import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
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/**
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* Handler that copies the currently selected nucleotides from an alignment editor to the clipboard.
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* <p>
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* The copied contents either come from the single reads or the consensus sequence alignment area,
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* depending on which component currently has the focus. If none of these components has the focus,
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* nothing will be copied, even if nucleotides are currently selected.
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* <p>
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* If the selection contains parts of multiple sequence, these are separated by the line separator
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* if the current operating system.
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*
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* @author Ben Stöver
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* @date 25.08.2015
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*/
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public class AlignmentEditorCopyHandler extends AbstractHandler {
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@Override
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public Object execute(ExecutionEvent event) throws ExecutionException {
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IEditorPart activeEditor = HandlerUtil.getActiveEditor(event);
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if(activeEditor instanceof AlignmentEditor){
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AlignmentArea focusedArea = ((AlignmentEditor)activeEditor).getFocusedArea();
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if (focusedArea != null) {
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copySelectionAsString(focusedArea);
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}
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}
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return null;
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}
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@SuppressWarnings("unchecked")
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public static void copySelectionAsString(AlignmentArea area) {
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SelectionModel selection = area.getSelection();
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if (!selection.isEmpty()) {
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StringBuilder selectedCharacters = new StringBuilder();
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AlignmentModel<Character> alignmentModel = (AlignmentModel<Character>)area.getAlignmentModel();
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for (int row = selection.getFirstRow(); row <= selection.getLastRow(); row++) {
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int id = area.getSequenceOrder().idByIndex(row);
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for (int column = selection.getFirstColumn(); column <= selection.getLastColumn(); column++) {
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if (alignmentModel.getSequenceLength(id) > column) {
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selectedCharacters.append(alignmentModel.getTokenAt(id, column));
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}
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else { // Add gaps if selection is behind the end of the sequence.
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selectedCharacters.append(AbstractTokenSet.DEFAULT_GAP_REPRESENTATION);
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}
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}
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if (row < selection.getLastRow()) {
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selectedCharacters.append(System.getProperty("line.separator"));
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}
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}
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new Clipboard(Display.getCurrent()).setContents(new Object[]{selectedCharacters.toString()},
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new Transfer[]{TextTransfer.getInstance()});
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}
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}
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}
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