[Biojava-l] Newick/Nexus processing of non-binary trees

[Richard Holland]

i'm all for that.

The original code was developed by a Google Summer of Code student, who we haven't heard much from since. :(

cheers,
Richard

On 13 Nov 2009, at 12:25, Tiago Antão wrote:

> Hi,
> 
>> My suggestion: for somebody else to verify my findings. I might be
>> doing something stupidly wrong. Maybe things are correct. Just a
>> simple tree like (1,2,3) (as long as it is not binary) - should expose
>> the problem.
>> 
> 
> Has nobody answered here is my take:
> 
> 1. The error reported probably exists
> 2. Most probably nobody is using the parser (as it only supports binary trees).
> 
> In this light, changing the API should not be a problem at all.
> 
> I would not mind correcting the problem (I have already corrected the
> previous 2 ones in my local version).
> I would suggest removing the call to the unweighted graph. Reasons:
> 1. A weighted version is enough. If branch lengths are not specified,
> then weights could be set to 0. There there would not be a decrease in
> functionality.
> 2. Severely reducing the size of the code is important. Clearly the
> code is not much maintained (and I am not offering to maintain it in
> the long run, just putting it in good shape) and not much used.
> Therefore a smaller, more easy to manage code base makes even more
> sense.
> 
> If you accept a solution along these lines. I would correct all the
> bugs and also include test code (which is also missing).
> 
> 
> 
> -- 
> "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/