newick exportation does not reflect manual rotations

[GoogleCodeExporter]

The newick exportation feature seems not to respect rotations that were 
manually imposed within the program.
For example, in the attached dummy files, a.nexus and b.nexus differ by a 
rotation.
But when I do the following for each: file… export trees… format = 
newick… save as currently displayed = checked,
the resulting newick outputs (a.nwk & b.nwk) are identical. That is, b.nwk does 
not reflect the rotation.

Original issue reported on code.google.com by [email protected] on 27 Aug 2014 at 7:08

[lczech]

The same is true for manually rooting the tree. Saving a re-rooted tree and then opening it again shows the original tree again.

The nexus file contains:

set trees.rooting=true;
set trees.rootingType="User Selection";

but it does not seem to contain a notion of the branch being used for rooting.