[Biojava-l] Rooted trees in nexus files

[Richard Holland]

ah... except a problem! The parser does not know all names in the  
string in advance, so if it auto-assigns one that is then used later  
in the string, we have the same problem with name clashes as before.

The names the parser assigns cannot totally avoid all clashes unless  
it has already parsed the string to find out what names were used in  
the string itself already. So some kind of pre-parse would be necessary.

On 4 Nov 2009, at 12:46, Richard Holland wrote:

> 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/
>
>
> _______________________________________________
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--
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/