[Biojava-l] reading Nexus files

[Scooter Willis]

I would go with the Forester library. It has everything you need and then
some. You can download the source and take a look at the command line
examples. It is more of an application versus an API but that doesn't mean
you can integrate into your application. This is part of the motivation for
doing a biojava wrapper so that you can pass around biojava classes to the
forester application library to make it more of an API.


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?
> > >
> > > _______________________________________________
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> > >
> >
> >
> >
>
>
> 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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>