if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{
- viewport.setExportHiddenSeqs(settings.isExportHiddenSequences());
- omitHidden = viewport.getViewAsString(false);
+ omitHidden = viewport.getViewAsString(false,
+ settings.isExportHiddenSequences());
}
int[] alignmentStartEnd = new int[2];
else
{
alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = viewport.getAlignment()
- .getVisibleStartAndEndIndex(
- viewport.getColumnSelection().getHiddenColumns());
}
+ alignmentStartEnd = alignmentToExport
+ .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+ .getHiddenColumns());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;