[Biojava-l] A question about NexusFile and NewickTreeString

[Richard Holland]

Patched.

On 18 Dec 2009, at 23:14, Tiago Antão wrote:

> Just submitted a patch.
> 
> 2009/12/18 Richard Holland <holland at eaglegenomics.com>:
>> You could be right - it could be just the other problem.
>> 
>> cheers,
>> Richard
>> 
>> On 18 Dec 2009, at 12:04, Tiago Antão wrote:
>> 
>>> 2009/12/15 Richard Holland <holland at eaglegenomics.com>:
>>>> Tiago - your new code doesn't seem to be coping with the insertion of a newline at random points in the Tree string. I think you might need to modify your tokenize() method to handle this better? Could you also add a unit test using this particular tree.
>>> 
>>> Do you have any case that exposes this bug? I am trying with this:
>>> 
>>> #NEXUS
>>> 
>>> Begin TREES;
>>>       tree test1 =
>>> (
>>> 1
>>> ,
>>> 2
>>> )
>>> ;
>>> 
>>> End;
>>> 
>>> And it works out fine and dandy.
>>> Maybe the bug that you are spotting is really not a newline problem
>>> but an instance of the other bug (ie node name that happens after a
>>> newline and seems as a newline bug)?
>> 
>> --
>> 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/
>> 
>> 
> 
> 
> 
> -- 
> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci

--
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/