[Biojava-l] A question about NexusFile and NewickTreeString

[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 :
> >> ===========================================================
> >>
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
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>
> --
> 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/
>
>