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)
{