*/
package jalview.controller;
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.util.BitSet;
-import java.util.List;
-
public class AlignViewController implements AlignViewControllerI
{
AlignViewportI viewport = null;
return false;
}
+ @Override
+ public boolean copyHighlightedRegionsToClipboard()
+ {
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+
+ SearchResultsI searchResults = viewport.getSearchResults();
+ if (searchResults.isEmpty())
+ {
+ return false; // shouldn't happen
+ }
+ List<SequenceI> seqs = searchResults.getMatchingSubSequences();
+
+ // TODO: pass in hiddenColumns according to intersection of searchResults
+ // and visible columns. Currently this isn't done, since each contig becomes
+ // a single subsequence
+ Desktop.jalviewClipboard = new Object[] {
+ seqs.toArray(new SequenceI[0]),
+ alignPanel.getAlignment().getDataset(), null };
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", seqs.size()));
+ // Technically we should return false, since view has not changed
+ return false;
+ }
}