[Biojava-l] Newick parser

[Tiago Antão]

I can just easily solve 2679, as it is precisely on the file that I
was changing. In case there is interest I'll just solve it.

2009/11/16 Richard Holland <holland at eaglegenomics.com>:
> Patch applied to the trunk of biojava-live. Thanks for fixing it!
>
> cheers,
> Richard
>
> On 15 Nov 2009, at 23:19, Tiago Antão wrote:
>
>> Hi,
>>
>> I have made the changes as discussed, the code is attached to the
>> bugzilla bug concerning part of the issues that were found.
>> A few notes:
>>
>> 1. There is a ParserException raised on TreeBlock. Tough there is a
>> TreeBlockParser, most of the important parsing was (and still is!)
>> being made on TreeBlock. I would imagine that this is not the best
>> design, but I did not change it.
>> 2. I made some test cases. Also included.
>> 3. I don't mind producing some documentation, in case you accept the code.
>> 4. I noticed a few minor bugs more (like eating spaces in the names of
>> nodes). But they are really minor.
>> 5. The API was changed, but I suppose not many people were parsing
>> trees. If there were people parsing trees most probably the bug on not
>> being able to process trees that are not binary would have been
>> detected as it is pretty major.
>>
>> Tiago
>>
>> --
>> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci
>>
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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/
>
>



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