Hack BEAST XML using DOM notation?

[Anaphory]

In #153, we mused about

hacking beast xml using some kind of DOM notation in the beastling config

Does that suggestion have any merit?

[Anaphory]

Actually, we might instead hack based on the ID. Something like

[hacking]
samplingProportionPriorFBD.t:beastlingTree, text=<Beta name="distr" alpha="20.0" beta="0.5" />

should be enough. In that example, I opted for , as the separator between ID and property – my choice would have been :, but that is overused in IDs, while , is guaranteed not to be a part of IDs because of BEAST limitations anyway.

This would be a uniform syntax to edit any attribute of any named BEAST object, and with text= we can also access its object hierarchy.

[Anaphory]

The things this syntax cannot do:

• Access unnamed objects (but nearly all of our objects have IDs)
• Delete an attribute vs. set it to the empty string (not that I have seen empty string attributes in BEAST)

Things that need more specification to do:

• Replace an entire object: Easy, no attribute specfied.
• Add something to an object, without having to re-iterate its current content: Maybe , tail like in Python XML APIs?
• Manipulate stuff more cleverly: Not the job of this hack.
• Change the tag: Why would you even do that? If you really need that, delete this object and add a variant, I guess. For most BEAST purposes, changing spec or name would be the better option, anyway, because of BEAST's philosophy of “there should be at least three ways to specifiy something in an XML, and don't you dare just use one of them!”