Ok thanks for the clarifications. I no one else offers, I will sort this out before Monday (and add test cases also).
2009/12/15 Andreas Prlic <[email protected]>: > 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 >> > -- “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
