[Biojava-l] Rooted trees in nexus files

[Tiago Antão]

2009/11/3 Richard Holland <holland at eaglegenomics.com>:
> The prefix for the parser currently is hardcoded as p. Two new methods - set
> and getDefaultPrefix which accept a string should be provided (it should
> check that the string is valid, i.e. all alphanumeric and with no spaces or
> other Newick-sensitive characters). The parser should be changed to use the
> output from getDefaultPrefix() instead of the hardcoded p. The default
> behaviour should be such that it behaves the same as at present unless the
> user explicitly says otherwise by calling the setDefaultPrefix() method.

This default behavior would still raise an exception with nodes called
p* . I would suggest a minor change: If there is a clash, the parser
would try the next p* (or whatever defaultPrefix) ...

Example to make it clear: if there is a leaf called p2, internal nodes
generated would be p1, p3, p4, ....

-- 
"The hottest places in hell are reserved for those who, in times of
moral crisis, maintain a neutrality." - Dante