I noticed that there are quite a lot different between current version and the last version.
And if there is a "_" in the node's name, NexasParse will remove the "_" in the node's name and there will be an error thrown for exmple (a_1,a_2); will be changed to (a 1,a 2); 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. > > cheers, > Richard > > On 15 Dec 2009, at 05:04, [email protected] wrote: > > > Thanks for your reply > > > > Yes. > > > > But how to parse this kind of tree in BIOJava? > > > > > > 2009/12/15 Hilmar Lapp <[email protected]> > > > >> > >> On Dec 14, 2009, at 9:40 PM, Tiago Antão wrote: > >> > >> On Tue, Dec 15, 2009 at 2:19 AM, [email protected] > >>> <[email protected]> wrote: > >>> > >>>> Hi all, > >>>> > >>>> I have a NexusFile like this: > >>>> > >>>> #NEXUS > >>>> > >>>> Begin TREES; > >>>> tree test1 = (1,2); > >>>> tree test2 = (B:6.0,(A:5.0,C:3.0,E:4.0) > >>>> Ancestor1:5.0,D:11.0); > >>>> End; > >>>> How can I deal with this ? > >>>> > >>> > >>> There is a comma missing after the ) closing E:4.0) ie, > >>> > >>>> tree test2 = (B:6.0,(A:5.0,C:3.0,E:4.0), <-- NOTE COMMA > >>>> Ancestor1:5.0,D:11.0); > >>>> > >>> > >> Actually no. Ancestor1 is the node label of the ancestor node of A, C, > and > >> E. Node labels follow after a parenthesis without a comma. > >> > >> -hilmar > >> -- > >> =========================================================== > >> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > >> =========================================================== > >> > >> > >> > >> > >> > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: [email protected] > http://www.eaglegenomics.com/ > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
