[Biojava-l] Rooted trees in nexus files

[Richard Holland]

Sounds great.

With regard to addTree you could add a new method with the signature  
that you propose, copy the existing method body into it and modify  
appropriately, then delete the existing method body and replace with a  
call to the new one instead, with a default topNode value that  
corresponds to the assumptions that the existing method currently makes.

cheers,
Richard

On 6 Nov 2009, at 11:30, Tiago Antão wrote:

> I've done a few changes to TreesBlock, namely implementing a version
> of what was talked here:
>
> 1. I maintained getTreeAsJGraphT and getTreeAsWeightedJGraphT as they
> are in terms of interface
> 2. There is now a new method getTopNode, stating which node is on the
> "top". I use the name getTopNode and not getRootNode to avoid
> misleading users: only rooted trees have a root, but for the nexus
> type of representation all have a "top" (which in rooted trees is the
> root)
> 3. There exist now setNodePrefix and getNodePrefix to be able to
> change the prefix (which defaults to p, as before)
>
> In my view these changes solve both problems: The issue with node
> names and the need to know the root/top of a nexus tree. It might not
> be the best solution, but it gets things on the right track without
> taking too much of my time. There are also no changes to the
> signatures of existing methods
>
> Now, there is still a problem:
> addTree(final String label, UndirectedGraph<String, DefaultEdge>  
> treegraph)
> Is highly dependent on the p* convention for internal nodes.
> Here I would be tempted to change the method signature to:
> addTree(final String label, UndirectedGraph<String, DefaultEdge>
> treegraph, String topNode)
>
> Interestingly there is no addTree with weighted graphs (for  
> distances).
>
> If nobody sees a problem with this, I will change addTree.
>
> I will then attach a patch to the currently open bug (along with test
> cases). And it should be done.
>
> 2009/11/4 Andreas Prlic <andreas at sdsc.edu>:
>> excellent, thanks for taking this on!
>> Andreas
>>
>> 2009/11/4 Tiago Antão <tiagoantao at gmail.com>
>>>
>>> Unless anyone with experience in biojava development wants to take  
>>> on
>>> this, I would volunteer to do this. I ended up using the PhyloXML
>>> forester-atv parser (and moving to phyloxml instead of nexus), but  
>>> as
>>> I reported this, I might as well sort it out...
>>>
>>> 2009/11/4 Richard Holland <holland at eaglegenomics.com>:
>>>> ah... except a problem! The parser does not know all names in the  
>>>> string
>>>> in
>>>> advance, so if it auto-assigns one that is then used later in the
>>>> string, we
>>>> have the same problem with name clashes as before.
>>>>
>>>> The names the parser assigns cannot totally avoid all clashes  
>>>> unless it
>>>> has
>>>> already parsed the string to find out what names were used in the  
>>>> string
>>>> itself already. So some kind of pre-parse would be necessary.
>>>>
>>>> On 4 Nov 2009, at 12:46, Richard Holland wrote:
>>>>
>>>>> Sounds good.
>>>>>
>>>>> On 4 Nov 2009, at 12:40, Tiago Antão wrote:
>>>>>
>>>>>> 2009/11/3 Richard Holland <holland at eaglegenomics.com>:
>>>>>>>
>>>>>>> The prefix for the parser currently is hardcoded as p. Two new
>>>>>>> methods -
>>>>>>> set
>>>>>>> and getDefaultPrefix which accept a string should be provided  
>>>>>>> (it
>>>>>>> should
>>>>>>> check that the string is valid, i.e. all alphanumeric and with  
>>>>>>> no
>>>>>>> spaces
>>>>>>> or
>>>>>>> other Newick-sensitive characters). The parser should be  
>>>>>>> changed to
>>>>>>> use
>>>>>>> the
>>>>>>> output from getDefaultPrefix() instead of the hardcoded p. The
>>>>>>> default
>>>>>>> behaviour should be such that it behaves the same as at present
>>>>>>> unless
>>>>>>> the
>>>>>>> user explicitly says otherwise by calling the setDefaultPrefix()
>>>>>>> method.
>>>>>>
>>>>>> This default behavior would still raise an exception with nodes  
>>>>>> called
>>>>>> p* . I would suggest a minor change: If there is a clash, the  
>>>>>> parser
>>>>>> would try the next p* (or whatever defaultPrefix) ...
>>>>>>
>>>>>> Example to make it clear: if there is a leaf called p2,  
>>>>>> internal nodes
>>>>>> generated would be p1, p3, p4, ....
>>>>>>
>>>>>> --
>>>>>> "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/
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>
>>>> --
>>>> 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/
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> "The hottest places in hell are reserved for those who, in times of
>>> moral crisis, maintain a neutrality." - Dante
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>
>
>
> -- 
> "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/