ranges = null;
currentTree = null;
selectionGroup = null;
+ colSel = null;
setAlignment(null);
}
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
{
- return new AlignmentView(alignment, alignment.getHiddenColumns(),
- selectionGroup,
+ return getAlignmentViewWithComplement(selectedOnly,markGroups,true);
+ }
+
+ @Override
+ public jalview.datamodel.AlignmentView getAlignmentViewWithComplement(
+ boolean selectedOnly, boolean markGroups,boolean withComplment)
+ {
+ AlignmentView complementView = null;
+ if (withComplment)
+ {
+ if (codingComplement != null)
+ {
+ complementView = codingComplement.getAlignmentViewWithComplement(
+ selectedOnly, markGroups, false);
+ }
+ }
+ AlignmentView thisView = new AlignmentView(alignment,
+ alignment.getHiddenColumns(), selectionGroup,
alignment.getHiddenColumns() != null
&& alignment.getHiddenColumns().hasHiddenColumns(),
selectedOnly, markGroups);
+ thisView.setComplement(complementView);
+ return thisView;
}
@Override
codingComplement.setUpdateStructures(needToUpdateStructureViews);
}
}
+
+ @Override
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int start = 0;
+ int end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
+ }
}