Re: [Treebase-devel] phylowidget issue

[William P. <wil...@ya...>]

On Oct 28, 2010, at 7:34 PM, Hilmar Lapp wrote:

> The trees at http://www.treebase.org/treebase-web/search/study/trees.html?id=10562 
>  won't display in the phylowidget link. Is that specific to this  
> study, these trees, or do we have a general issue with PhyloWidget  
> right now?

Looks like whenever one of these trees are downloaded, TreeBASE is neglecting to add a ";" to the end of the newick. 

e.g.:

http://purl.org/phylo/treebase/phylows/tree/TB2:Tr9408?format=nexus

Mesquite is very forgiving, and loads the tree properly anyway. Phylowidget and TreeViewX are not so forgiving. 

Why would this be the case for some trees but not others? I'm guessing that instead of writing the newick on the fly, TreeBASE is just grabbing the newick string from a stored version (table: phylotree field: newickstring), and for some reason the stored version is missing a semicolon (could be that the authors rerooted the trees using our reroot tool, and our reroot tool has a bug wherein it doesn't return a string with a semicolon -- hence why we don't see this problem with all trees). 

The temporary solution for this particular study is to go through records where phylotree_id is between 9407 and 9414 and check that the string stored in the newickstring field ends in a ";".  I would do this with Navicat, but I don't have access to the production database. 

bp