- if (aps[a].av.getGlobalColourScheme() != null
- && aps[a].av.getGlobalColourScheme().conservationApplied())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
-
- c.calculate();
- c.verdict(false, aps[a].av.getConsPercGaps());
- sg.cs.setConservation(c);
- }
-
- aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
- // TODO can we push all of the below into AlignViewportI?
- final AlignViewportI codingComplement = aps[a].av
- .getCodingComplement();
- if (codingComplement != null)
- {
- if (codingComplement != null)
+ int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()-1+colm) : colm;
+
+ if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ {
+ if (cs.contains(offp))