Hi Thasso, just to clarify: you are correct, that is the latest SVN head.
Andreas 2009/12/15 Thasso Griebel <[email protected]>: > Hi, > > now I am confused :) > > I did my fixes on the SVN version from this repository: > > svn://code.open-bio.org/biojava/biojava-live/trunk > > The revision I was working on is 7269. This is the current HEAD including > the NEW parser, isn't it ? Tiago, you are listed as author in the javadoc > and the last commit comment on the TreesBlock states that it contains your > changes...so I am pretty sure I did my changes on the right version ? > > cheers, > -thasso > > On Dec 15, 2009, at 16:02 , Tiago Antão wrote: > >> 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
