[Biojava-l] A question about NexusFile and NewickTreeString

[Tiago Antão]

If anyone wants to test with real data, please go ahead. There is some
free time, so if bugs are detected it is a good time to report them.

2009/12/21 Richard Holland <holland at eaglegenomics.com>:
> 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/
>
>



-- 
“Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci