[Biojava-l] Rooted trees in nexus files

[Richard Holland]

Sounds good.

On 4 Nov 2009, at 12:40, Tiago Antão wrote:

> 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

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/