public void updateConservation(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (alignment.isNucleotide() || conservation == null
+ if (alignment.isNucleotide()
+ || (conservation == null && quality == null)
|| !autoCalculateConsensus)
{
return;
}
@Override
+ public boolean hasSelectedColumns()
+ {
+ ColumnSelection columnSelection = getColumnSelection();
+ return columnSelection != null && columnSelection.hasSelectedColumns();
+ }
+
+ @Override
public boolean hasHiddenColumns()
{
return colSel != null && colSel.hasHiddenColumns();
if (sg != null
&& (sgs = sg.getStartRes()) >= 0
&& sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
+ && !this.hasSelectedColumns())
{
if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
{
}
}
+ /**
+ * hold status of current selection group - defined on alignment or not.
+ */
+ private boolean selectionIsDefinedGroup = false;
+ @Override
+ public boolean isSelectionDefinedGroup()
+ {
+ if (selectionGroup == null)
+ {
+ return false;
+ }
+ if (isSelectionGroupChanged(true))
+ {
+ selectionIsDefinedGroup = false;
+ List<SequenceGroup> gps = alignment.getGroups();
+ if (gps == null || gps.size() == 0)
+ {
+ selectionIsDefinedGroup = false;
+ }
+ else
+ {
+ selectionIsDefinedGroup = gps.contains(selectionGroup);
+ }
+ }
+ return selectionGroup.getContext() == alignment
+ || selectionIsDefinedGroup;
+ }
}