import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
orders[j] = null;
}
SequenceI[] alignment = (SequenceI[]) newview[0];
- ColumnSelection columnselection = (ColumnSelection) newview[1];
+ HiddenColumns hidden = (HiddenColumns) newview[1];
Alignment al = new Alignment(alignment);
// TODO: add 'provenance' property to alignment from the method notes
if (lastProgram != null)
if (newFrame)
{
- displayInNewFrame(al, alorders, columnselection);
+ displayInNewFrame(al, alorders, hidden);
}
else
* @param columnselection
*/
protected void displayInNewFrame(AlignmentI al,
- List<AlignmentOrder> alorders, ColumnSelection columnselection)
+ List<AlignmentOrder> alorders, HiddenColumns hidden)
{
- AlignFrame af = new AlignFrame(al, columnselection,
+ AlignFrame af = new AlignFrame(al, hidden,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// initialise with same renderer settings as in parent alignframe.
// becomes null if the alignment window was closed before the alignment
// job finished.
AlignmentI copyComplement = new Alignment(complement);
+ // todo should this be done by copy constructor?
+ copyComplement.setGapCharacter(complement.getGapCharacter());
+ // share the same dataset (and the mappings it holds)
+ copyComplement.setDataset(complement.getDataset());
copyComplement.alignAs(al);
if (copyComplement.getHeight() > 0)
{