Hi again, Just to make things clear, it would be nice if people stated if they are using the latest release version or the version in the subversion head. As they are totally different in tree processing as the SVN version is mostly a reimplementation (TreeBlock only).
2009/12/15 [email protected] <[email protected]>: > 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/ >> > > -- “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
