eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AlignmentEditorCopyHandler.java

   1 package eu.etaxonomy.taxeditor.molecular.handler;
   2
   3
   4 import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
   5 import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
   6 import info.bioinfweb.libralign.model.AlignmentModel;
   7 import info.bioinfweb.libralign.model.tokenset.AbstractTokenSet;
   8
   9 import org.eclipse.core.commands.AbstractHandler;
  10 import org.eclipse.core.commands.ExecutionEvent;
  11 import org.eclipse.core.commands.ExecutionException;
  12 import org.eclipse.swt.dnd.Clipboard;
  13 import org.eclipse.swt.dnd.TextTransfer;
  14 import org.eclipse.swt.dnd.Transfer;
  15 import org.eclipse.swt.widgets.Display;
  16 import org.eclipse.ui.IEditorPart;
  17 import org.eclipse.ui.handlers.HandlerUtil;
  18
  19 import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
  20
  21
  22
  23 /**
  24  * Handler that copies the currently selected nucleotides from an alignment editor to the clipboard.
  25  * <p>
  26  * The copied contents either come from the single reads or the consensus sequence alignment area,
  27  * depending on which component currently has the focus. If none of these components has the focus,
  28  * nothing will be copied, even if nucleotides are currently selected.
  29  * <p>
  30  * If the selection contains parts of multiple sequence, these are separated by the line separator
  31  * if the current operating system.
  32  *
  33  * @author Ben Stöver
  34  * @date 25.08.2015
  35  */
  36 public class AlignmentEditorCopyHandler extends AbstractHandler {
  37     @Override
  38     public Object execute(ExecutionEvent event) throws ExecutionException {
  39         IEditorPart activeEditor = HandlerUtil.getActiveEditor(event);
  40         if(activeEditor instanceof AlignmentEditor){
  41             AlignmentArea focusedArea = ((AlignmentEditor)activeEditor).getFocusedArea();
  42             if (focusedArea != null) {
  43                 copySelectionAsString(focusedArea);
  44             }
  45         }
  46         return null;
  47     }
  48
  49
  50         @SuppressWarnings("unchecked")
  51     public static void copySelectionAsString(AlignmentArea area) {
  52         SelectionModel selection = area.getSelection();
  53         if (!selection.isEmpty()) {
  54             StringBuilder selectedCharacters = new StringBuilder();
  55                         AlignmentModel<Character> alignmentModel = (AlignmentModel<Character>)area.getAlignmentModel();
  56                 for (int row = selection.getFirstRow(); row <= selection.getLastRow(); row++) {
  57                 int id = area.getSequenceOrder().idByIndex(row);
  58                 for (int column = selection.getFirstColumn(); column <= selection.getLastColumn(); column++) {
  59                         if (alignmentModel.getSequenceLength(id) > column) {
  60                                 selectedCharacters.append(alignmentModel.getTokenAt(id, column));
  61                         }
  62                         else {  // Add gaps if selection is behind the end of the sequence.
  63                                 selectedCharacters.append(AbstractTokenSet.DEFAULT_GAP_REPRESENTATION);
  64                         }
  65                                 }
  66                 if (row < selection.getLastRow()) {
  67                         selectedCharacters.append(System.getProperty("line.separator"));
  68                 }
  69                         }
  70             new Clipboard(Display.getCurrent()).setContents(new Object[]{selectedCharacters.toString()},
  71                         new Transfer[]{TextTransfer.getInstance()});
  72         }
  73     }
  74 }