[Biojava-l] A question about NexusFile and NewickTreeString

[Andreas Prlic]

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
>
>
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