2009/11/4 Thasso Griebel <[email protected]>: >> 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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
