}
}
}
- // for the case when no sequences are even visible
+
+ /*
+ * offer 'Reveal All'
+ * - in the IdPanel (seq not null) if any sequence is hidden
+ * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
+ */
if (alignPanel.av.hasHiddenRows())
{
+ boolean addOption = seq != null;
+ if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
+ {
+ addOption = true;
+ }
+ if (addOption)
{
menuItem = new JMenuItem(
MessageManager.getString("action.reveal_all"));
}
}
});
-
add(menuItem);
}
}
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
-
- HiddenColumns hidden = new HiddenColumns();
- BitSet inserts = new BitSet(), mask = new BitSet();
-
- // set mask to preserve existing hidden columns outside selected group
- if (ap.av.hasHiddenColumns())
- {
- ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
- }
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
boolean markedPopup = false;
// mark inserts in current selection
{
// mark just the columns in the selection group to be hidden
inserts.set(ap.av.getSelectionGroup().getStartRes(),
- ap.av.getSelectionGroup().getEndRes() + 1);
-
- // and clear that part of the mask
- mask.andNot(inserts);
+ ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
// now clear columns without gaps
for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
}
inserts.and(sq.getInsertionsAsBits());
}
- }
- else
- {
- // initially, mark all columns to be hidden
- inserts.set(0, ap.av.getAlignment().getWidth());
-
- // and clear out old hidden regions completely
- mask.clear();
+ hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes());
}
// now mark for sequence under popup if we haven't already done it
- if (!markedPopup && sequence != null)
+ else if (!markedPopup && sequence != null)
{
- inserts.and(sequence.getInsertionsAsBits());
- }
-
- // finally, preserve hidden regions outside selection
- inserts.or(mask);
+ inserts.or(sequence.getInsertionsAsBits());
- // and set hidden columns accordingly
- hidden.hideMarkedBits(inserts);
-
- ap.av.getAlignment().setHiddenColumns(hidden);
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
refresh();
}