[Biojava-l] A question about NexusFile and NewickTreeString

[Thasso Griebel]

Hi,

now I am confused :)

I did my fixes on the SVN version from this repository:

svn://code.open-bio.org/biojava/biojava-live/trunk

The revision I was working on is 7269. This is the current HEAD  
including the NEW parser, isn't it ? Tiago, you are listed as author  
in the javadoc and the last commit comment on the TreesBlock  states  
that it contains your changes...so I am pretty sure I did my changes  
on the right version ?

cheers,
-thasso

On Dec 15, 2009, at 16:02 , Tiago Antão wrote:

> 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.
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>>
>>
>>
>
>
>
> -- 
> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci