[Biojava-l] A question about NexusFile and NewickTreeString

[Tiago Antão]

Ok thanks for the clarifications. I no one else offers, I will sort
this out before Monday (and add test cases also).

2009/12/15 Andreas Prlic <andreas.prlic at gmail.com>:
> Hi Thasso,
>
> just to clarify: you are correct, that is the latest SVN head.
>
> Andreas
>
>
>
>
> 2009/12/15 Thasso Griebel <thasso.griebel at uni-jena.de>:
>> 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
>>
>>
>> _______________________________________________
>> 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