[Biojava-l] reading Nexus files

[Tiago Antão]

I actually found the code here:
http://code.open-bio.org/svnweb/index.cgi/biojava/view/biojava-live/trunk/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/TreesBlock.java

But I absolutely have now idea if it was distributed or packaged for
the general public. Clearly the API docs do not have that version.

Tiago (not a biojava developer, just someone who heavily patched the
nexus parser long time ago)

2010/11/1 filip <fbielejec at gmail.com>:
> On Mon, 1 Nov 2010 17:39:03 +0000
> Tiago Antão <tiagoantao at gmail.com> wrote:
>
>> Hi,
>>
>> Biojava does have org.biojavax.bio.phylo.io.nexus. Sometime ago I
>> refactored that code and made an example with it:
>> http://tiago.org/cc/2009/11/17/reading-newicknexus-phylogenetic-trees-with-biojava/
>> I don't know if this suites you needs.
>> If you find a bug with the code, just drop an email here on the list
>> and I will take care of it (time permitting).
>>
>> On Mon, Nov 1, 2010 at 4:20 PM, filip <fbielejec at gmail.com> wrote:
>> > Hi,
>> > I would like to write a class with methods for parsing tip labels,
>> > edges (parent-sibling) and edge lengths from nexus tree file (single
>> > tree block). Could You point me to some biojava classes I could use?
>> >
>> > _______________________________________________
>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>>
>>
>>
>
>
> Hi,
>
> Thank You for the swift response - I tried the code snippets from
> Tiago's blog. It seems that the version of API I posess does not
> have "getTopNode()" method for TreesBlock class:
>
>        TreesBlock node = getTreeNode(nexus);
>        WeightedGraph<String, DefaultWeightedEdge> graph =
>        node.getTreeAsWeightedJGraphT(name); topNode =
>        node.getTopNode();
>
> My quick search through the sources confirms that.
>
> I will also take a look at forester libs - thank You for the tip. Are
> there any code examples for those I can look at?
>
>
> --
> while(!succeed) { try(); }
>



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