+ treeGroup.setName("Tree Group " + nrTreeGroups);
+ treeGroup.setIdColour(groupColour);
+
+ for (AlignmentPanel associatedPanel : associatedPanels)
+ {
+ AlignViewportI altViewport = associatedPanel
+ .getAlignViewport();
+
+ if (altViewport.getGlobalColourScheme() != null
+ && altViewport.getResidueShading()
+ .conservationApplied())
+ {
+ Conservation conserv = new Conservation(treeGroup.getName(),
+ treeGroup.getSequences(null), treeGroup.getStartRes(),
+ treeGroup.getEndRes());
+ conserv.calculate();
+ conserv.verdict(false, altViewport.getConsPercGaps());
+ treeGroup.getGroupColourScheme().setConservation(conserv);
+ }
+
+ altViewport.getAlignment().addGroup(treeGroup);
+ // TODO can we push all of the below into AlignViewportI?
+ final AlignViewportI codingComplement = altViewport
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(treeGroup,
+ parentAvport, codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq, groupColour.brighter());
+ }
+ }
+ }
+
+ }
+
+ }