[Biojava-l] A question about NexusFile and NewickTreeString

[Tiago Antão]

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 huijieqiao at gmail.com <huijieqiao at gmail.com>:
> 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 <holland at eaglegenomics.com>
>>
>> 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, huijieqiao at gmail.com wrote:
>>
>> > Thanks for your reply
>> >
>> > Yes.
>> >
>> > But how to parse this kind of tree in BIOJava?
>> >
>> >
>> > 2009/12/15 Hilmar Lapp <hlapp at drycafe.net>
>> >
>> >>
>> >> On Dec 14, 2009, at 9:40 PM, Tiago Antão wrote:
>> >>
>> >> On Tue, Dec 15, 2009 at 2:19 AM, huijieqiao at gmail.com
>> >>> <huijieqiao at gmail.com> 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  -  Biojava-l at lists.open-bio.org
>> > 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: holland at eaglegenomics.com
>> http://www.eaglegenomics.com/
>>
>
>



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“Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci