If somebody would provide the desired changes to the parser interface (wrt this bug and the other one reported previously), I might offer to to the grunt work.
But somebody has to say which interface changes are desired. I remember which problems exist: 1. Lack of knowledge of root node 2. The p* stuff. Tiago 2009/11/3 Richard Holland <[email protected]>: > Agreed that there is a bug. Now all we need is someone to go in and fix it! > :) > > cheers, > Richard > > On 3 Nov 2009, at 18:16, Tiago Antão wrote: > >> 2009/11/3 Thasso Griebel <[email protected]>: >>> >>> There is a way to uniquely get a root from a newick string. Usually a >>> rooted newick is surrounded with brackets, which indicates the root as >>> the >>> highest node in the tree. For example: >>> >>> (A, (B,C)) >>> >> >> Agree, it is quite easy to get the root of the tree from the newick >> representation. But it should be done on parsing and returned in some >> way by the parsing system. If the user has to do it again, it means >> that the user has to parse it again just to know the root node. >> >>> I would also suggest to generally parse trees as rooted trees (maybe jsut >>> for th initial internal model). Creating an unrooted tree from a rooted >>> one >>> is easy, remove the root and forget about directions. The other way might >>> be >>> hard and ambiguous. >> >> 100% agree. >> The newick _representation_ always has a root by virtue of the way it >> is done. If that root has meaning or not depends. Doing as you suggest >> seems the most reasonable idea. >> I would add that even if it is an unrooted tree, the topology might be >> of interest. In my case I am doing a comparative visualizer and it >> might be nice for the user to be able to visualize the topology as >> specified. It has no biological meaning, but in practice, for many >> users, it helps. >> I note that PhyloXML (even by virtue of being a XML format) always >> represents the phylogenies as trees (not weigthed DAGs). There an >> attribute rooted which can be true or false. >> >> But, anyway. Even assuming a very conservative view on this, the >> current parser, for rooted trees, does not allow to determine where is >> the root. I think that there would be a consensus that that is a bug? >> >> Tiago > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: [email protected] > http://www.eaglegenomics.com/ > > -- "The hottest places in hell are reserved for those who, in times of moral crisis, maintain a neutrality." - Dante _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
