Changing parameter linking in a re-loaded xml file with Beauti 2

[dcmarshall]

In Beauti 2, if a previously saved xml file is loaded back in (File: Load), and if the xml file has the treemodel linked across the partitions, Beauti will not unlink the partitions when the "Unlink trees" button is clicked in the Partitions panel. Instead, the name of the linked treemodel changes to that of the last partition (in my case), but all partitions keep the same treemodel name, and there remains only one tree model in the priors panel. Going back-and-forth between linking and unlinked treemodels seems to work fine if the xml is a newly created one that has not yet been saved.

To illustrate the problem, one can open a partitioned nexus file (e.g., the Primates.nex in the provided Examples folder), link the trees across the two partitions, immediately save the file, load it back in to a new Beauti window, and then try to unlink the treemodels.

The same thing happens if it is the clock model that is linked. I haven't tested the site model linking/unlinking.

[walterxie]

cannot replicate now.

[rbouckaert]

The problem still exists: With v2.5.0, start BEAUti (uses Standard template) Import alignment Primates.nex Select both partitions, link trees Save file

Restart BEAUti Load file Select both partitions, unlink trees

Now, both trees are "secondhalf" instead of "firsthalf" and "secondhalf".