- @Override
- public void run()
- {
-
- /*
- * ensure feature display is turned on to show the new features,
- * and remove them as highlighted regions
- */
- ap.alignFrame.showSeqFeatures.setSelected(true);
- av.setShowSequenceFeatures(true);
- ap.highlightSearchResults(null);
- }
- });
+ return; // shouldn't happen
+ }
+ List<SequenceI> seqs = new ArrayList<>();
+
+ String searchString = searchBox.getUserInput();
+ String desc = "Search Results";
+
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ for (SearchResultMatchI match : searchResults.getResults())
+ {
+ SequenceI seq = match.getSequence();
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()),
+ seq.findIndex(match.getEnd()) + 1));
+ }
+ Desktop.jalviewClipboard = new Object[] {
+ seqs.toArray(new SequenceI[0]), ap.av.getAlignment().getDataset(),
+ ap.av.getAlignment().getHiddenColumns() };