alignmentStartEnd = alignmentToExport
.getVisibleStartAndEndIndex(viewport.getAlignment()
.getHiddenColumns()
- .getListOfCols());
+ .getHiddenRegions());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
.getSelectionGroup().getEndRes();
for (int[] region : viewport.getAlignment().getHiddenColumns()
- .getListOfCols())
+ .getHiddenRegions())
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() > 0)
{
- if (viewport.getSelectionGroup().getSize() < 3)
- {
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager
- .getString("label.not_enough_sequences"),
- JvOptionPane.WARNING_MESSAGE);
- return;
- }
-
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */