[Biojava-l] Rooted trees in nexus files

[Tiago Antão]

2009/11/4 Thasso Griebel <thasso.griebel at uni-jena.de>:
>> Personally I would also alter the methods that return JGraphTs so that
>> they return their Directed equivalents if possible. I believe that these can
>> still be unrooted - you'd have to check the JGraphT documentation to make
>> sure.
>
> You have to change that method signature if you want to use the same method.
> The only relationship between JGraphTs UndirectedGraph and the DirectedGraph
> counterpart is that they both extend the Graph interface, but a
> DirectedGraph is not an UndirectedGraph. Switching to DirectedGraph
> definitely breaks the current API ! I don't know how you usually handle such
> situations in BioJava, but this clearly breaks compatibility. Maybe it would
> be better to introduce a new method that returns directed graphs ?

I also don't know how BioJava sorts these kinds of issues. But my
personal, outsider, opinion would be in your direction, ie:
a. Not break the current API
b. Add a new method with a directed graph
c. (extra) Add a new method boolean isRooted(void) to check is the
tree is rooted or not...

Best
Tiago