}
setOldHiddenColumns(av.getAlignment().getHiddenColumns());
adjusting = true;
- Vector<String> list = new Vector<String>();
+ Vector<String> list = new Vector<>();
int index = 1;
for (int i = 0; i < anns.length; i++)
{
HiddenColumns oldHidden = av
.getAnnotationColumnSelectionState()
.getOldHiddenColumns();
- if (oldHidden != null && oldHidden.getListOfCols() != null
- && !oldHidden.getListOfCols().isEmpty())
+ if (oldHidden != null
+ && !oldHidden.getHiddenRegions().isEmpty())
{
- for (Iterator<int[]> itr = oldHidden.getListOfCols()
+ for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
.iterator(); itr.hasNext();)
{
int positions[] = itr.next();
// build filter params
filterParams
.setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
- if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+ if (getCurrentAnnotation().isQuantitative())
{
filterParams
.setThresholdValue(getCurrentAnnotation().threshold.value);
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
- .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
+ .getSelectedIndex()].isQuantitative())
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
}