[Biojava-l] The root node is missing when parsing nexus tree files from MrBayes

[Andreas Prlic]

Hi,

Tiago, I found a mail from 2009/11/16 which says that your patch got
committed. Is this the one you are referring to?  Martin, this would
mean that the patch is available through the biojava-legacy project
(biojava v. 1.8)

Andreas




2011/1/25 Tiago Antão <tiagoantao at gmail.com>:
> I think the patch that I submitted to the old newick module of biojava
> never really was released by the biojava team. So that example will
> not work with biojava (unless you track the svn release with the patch
> and use that, arguably not a good solution).
>
> More info can be supplied by the biojava maintainers. I just made the
> patch and the example.
>
> On Tue, Jan 25, 2011 at 5:35 PM, Martin Jones <martin.jones at ed.ac.uk> wrote:
>> Hi,
>>
>> I am using some of the code from here:
>>
>> http://tiago.org/cc/2009/11/17/reading-newicknexus-phylogenetic-trees-with-biojava/
>>
>> to parse nexus phylogenetic tree data. My nexus file is output from MrBayes:
>>
>> ------------------ snip-----------------
>> #NEXUS
>>
>> [ID: 7166567671]
>> begin trees;
>>   [Note: This tree contains information on the topology,
>>          branch lengths (if present), and the probability
>>          of the partition indicated by the branch.]
>>   tree con_50_majrule =
>> (27563:0.194008,(6843:0.233188,6960:0.229043)0.98:0.117649,(61985:0.217735,6657:0.275071)0.89:0.089314);
>>
>>   [Note: This tree contains information only on the topology
>>          and branch lengths (mean of the posterior probability density).]
>>   tree con_50_majrule =
>> (27563:0.194008,(6843:0.233188,6960:0.229043):0.117649,(61985:0.217735,6657:0.275071):0.089314);
>> end;
>>
>> -------------------------- snip -------------
>>
>> the file parses without any error, but when I get a list of vertices,
>> the first one (27563) is missing:
>>
>> def tree = getTree(nexus, 'con 50 majrule')
>> tree.vertexSet().each{
>>  println it
>> }
>>
>> output:
>>
>> 6843
>> p1
>> 6960
>> 61985
>> p3
>> 6657
>> p2
>>
>> ______________snip ___________
>>
>> The above code is Groovy, but hopefully is self-explanatory. Is the
>> first node being treated specially because it is the root? If so, can
>> I get it using some other method?
>>
>> Thanks,
>>
>> Martin
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> "If you want to get laid, go to college.  If you want an education, go
> to the library." - Frank Zappa
>
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