[Biojava-l] A question about NexusFile and NewickTreeString

[Tiago Antão]

Hi Thasso,

I think you are using an old version (even the current stable is "old"
AFAIK)... I have changed TreeBlock quite a lot, as it was somewhat
problematic.

2009/12/15 Thasso Griebel <thasso.griebel at uni-jena.de>:
> Hi,
>
> I wanted to take a look at the parser anyways, so I took the opportunity.
>
> As far as i see this, the newline is just a minor part of the problem. I
> think the bigger issue here is parsing inner node labels. I attached a patch
> that fixes the problem, at least for inner nodes with label and inner nodes
> with label and weights. Wikipedia states that Newick allows leaves without
> any labels, but in case of phylogenetic trees I think one can safely ignore
> this, though the parser should maybe throw an exception.
>
> If you are interested I also updated the unit test.
>
> hope it helps, cheers,
> -thasso
>
> On Dec 15, 2009, at 12:43 , Tiago Antão wrote:
>
>> 2009/12/15 Richard Holland <holland at eaglegenomics.com>:
>>>
>>> Hi there.
>>>
>>> I believe the code used to be able to parse this kind of tree, but TIago
>>> recently rewrote it so I'm no longer certain.
>>>
>>> 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.
>>
>>
>> Yep, will take care of this over the weekend. Maybe before, but no
>> promises.
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>
>
>
>
>



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