[Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2941





------- Comment #1 from holland at ebi.ac.uk  2009-11-02 12:52 EST -------
The reason this is happening is because JGraphT expects all nodes to have a
name, but the tree strings in Nexus files don't have names for all nodes (in
your case, the tree string you provide does not have a name for the sub-tree
mapped to :0.15).

  ((1:0.1,2:0.2):0.15,p1:0.3)

The 'p' notation is used internally to assign names to grouped nodes that don't
have names explicitly set in the tree string. It would be good to have this as
a modifiable setting, but it would still have to be set to something by
default, and users would still have to check that the setting they use does not
clash with any of their existing names. 

Volunteers to modify please?


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