{
alignmentToExport = viewport.getAlignment();
}
- alignmentStartEnd = alignmentToExport
- .getVisibleStartAndEndIndex(viewport.getAlignment()
- .getHiddenColumns()
- .getHiddenRegions());
+ alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
if (viewport.hasHiddenColumns())
{
hiddenColumns = new ArrayList<>();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes(),
- hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
for (int[] region : viewport.getAlignment().getHiddenColumns())
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)