Hi Thasso, I think you are using an old version (even the current stable is "old" AFAIK)... I have changed TreeBlock quite a lot, as it was somewhat problematic.
2009/12/15 Thasso Griebel <[email protected]>: > Hi, > > I wanted to take a look at the parser anyways, so I took the opportunity. > > As far as i see this, the newline is just a minor part of the problem. I > think the bigger issue here is parsing inner node labels. I attached a patch > that fixes the problem, at least for inner nodes with label and inner nodes > with label and weights. Wikipedia states that Newick allows leaves without > any labels, but in case of phylogenetic trees I think one can safely ignore > this, though the parser should maybe throw an exception. > > If you are interested I also updated the unit test. > > hope it helps, cheers, > -thasso > > On Dec 15, 2009, at 12:43 , Tiago Antão wrote: > >> 2009/12/15 Richard Holland <[email protected]>: >>> >>> Hi there. >>> >>> I believe the code used to be able to parse this kind of tree, but TIago >>> recently rewrote it so I'm no longer certain. >>> >>> Tiago - your new code doesn't seem to be coping with the insertion of a >>> newline at random points in the Tree string. I think you might need to >>> modify your tokenize() method to handle this better? Could you also add a >>> unit test using this particular tree. >> >> >> Yep, will take care of this over the weekend. Maybe before, but no >> promises. >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > -- “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
