int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
- .getListOfCols();
+ .getHiddenRegions();
if (hiddenCols != null)
{
alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
{
hiddenColumns = new ArrayList<int[]>();
for (int[] region : av.getAlignment().getHiddenColumns()
- .getListOfCols())
+ .getHiddenRegions())
{
hiddenColumns.add(new int[] { region[0], region[1] });
}