[Biojava-l] Rooted trees in nexus files

[Tiago Antão]

Unless anyone with experience in biojava development wants to take on
this, I would volunteer to do this. I ended up using the PhyloXML
forester-atv parser (and moving to phyloxml instead of nexus), but as
I reported this, I might as well sort it out...

2009/11/4 Richard Holland <holland at eaglegenomics.com>:
> 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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>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> 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/
>
>



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