import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
{
if (sequence != null)
{
- ColumnSelection cs = ap.av.getColumnSelection();
- if (cs == null)
+ /* ColumnSelection cs = ap.av.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+ cs.hideInsertionsFor(sequence);
+ ap.av.setColumnSelection(cs);*/
+
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ if (hidden == null)
{
- cs = new ColumnSelection();
+ hidden = new HiddenColumns();
}
- cs.hideInsertionsFor(sequence);
- ap.av.setColumnSelection(cs);
+ hidden.hideInsertionsFor(sequence);
+ ap.av.getAlignment().setHiddenColumns(hidden);
}
refresh();
}
if (start <= end)
{
seqs.add(sg.getSequenceAt(i).getDatasetSequence());
- features.add(new SequenceFeature(null, null, null, start, end,
- "Jalview"));
+ features.add(new SequenceFeature(null, null, null, start, end, null));
}
}
if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap, null))
+ features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
ap.highlightSearchResults(null);