[Biojava-l] Newick parser

[Richard Holland]

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
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