On Mon, 1 Nov 2010 17:39:03 +0000 Tiago Antão <[email protected]> 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 <[email protected]> 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 - [email protected] > > 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(); } _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
