- if (reply == JOptionPane.YES_OPTION)
- {
- // export only visible region
- omitHidden = viewport.getViewAsString(false);
- alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
- .getColumnSelection().getHiddenColumns());
- viewport.setIncludeHiddenRegion(false);
- }
- else
- {
- // export all region including visible
- alignmentToExport = hiddenSeqs.getFullAlignment();
- viewport.setIncludeHiddenRegion(true);
- }
+ if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+ {
+ omitHidden = viewport.getViewAsString(false);