[Biojava-l] Rooted trees in nexus files

[Peter Midford]

Tiago,
             If you return a directed graph, the root will be a node  
with no incoming edges.

Peter

On Nov 3, 2009, at 13:55, Tiago Antão wrote:

> But the point is that the class interface changes to the outside user:
> 1. How does one report back the root to the user?
> 2. Regarding the prefix stuff, should the user be allowed to specify a
> preferred prefix?
>
> Both this things imply interface changes visible to users.
> If you still need volunteers to do the change, I can do it. But I need
> to know what changes to the user interface are to be done.
> For 1, maybe a method getRoot, returning a string with the name of the
> root node?
> For 2, maybe an extended version of the parse function with a suffix
> as input parameter?
>
> 2009/11/3 Richard Holland <holland at eaglegenomics.com>:
>>> 1. Lack of knowledge of root node
>>
>> The Newick tree string is read as-is and is not parsed. It only  
>> gets parsed
>> at the point of conversion to a Undirected or WeightedGraph inside  
>> the
>> TreeBlocks.java source code (inside the two types of get-As-JGraphT
>> methods). It's at this point the string is parsed and it's here  
>> that root
>> note determination should take place. It's already known whether &R  
>> or &U
>> have been specified here, which should help the code work out what  
>> to do.
>>
>>> 2. The p* stuff.
>>
>> Exactly the same part of the code as described above. Wherever it  
>> pushes
>> values to the stack but prepends them with 'p' first, you'll need  
>> to change
>> the 'p' to some instance variable and provide a getter/setter to  
>> change it,
>> with 'p' being the default setting.
>>
>> cheers,
>> Richard
>>
>>>
>>> Tiago
>>> 2009/11/3 Richard Holland <holland at eaglegenomics.com>:
>>>>
>>>> Agreed that there is a bug. Now all we need is someone to go in  
>>>> and fix
>>>> it!
>>>> :)
>>>>
>>>> cheers,
>>>> Richard
>>>>
>>>> On 3 Nov 2009, at 18:16, Tiago Antão wrote:
>>>>
>>>>> 2009/11/3 Thasso Griebel <thasso.griebel at uni-jena.de>:
>>>>>>
>>>>>> There is a way to uniquely  get a root from a newick string.  
>>>>>> Usually a
>>>>>> rooted newick is surrounded with brackets, which indicates the  
>>>>>> root as
>>>>>> the
>>>>>> highest node in the tree. For example:
>>>>>>
>>>>>> (A, (B,C))
>>>>>>
>>>>>
>>>>> Agree, it is quite easy to get the root of the tree from the  
>>>>> newick
>>>>> representation. But it should be done on parsing and returned in  
>>>>> some
>>>>> way by the parsing system. If the user has to do it again, it  
>>>>> means
>>>>> that the user has to parse it again just to know the root node.
>>>>>
>>>>>> I would also suggest to generally parse trees as rooted trees  
>>>>>> (maybe
>>>>>> jsut
>>>>>> for th initial internal model). Creating an unrooted tree from  
>>>>>> a rooted
>>>>>>  one
>>>>>> is easy, remove the root and forget about directions. The other  
>>>>>> way
>>>>>> might
>>>>>> be
>>>>>> hard and ambiguous.
>>>>>
>>>>> 100% agree.
>>>>> The newick _representation_ always has a root by virtue of the  
>>>>> way it
>>>>> is done. If that root has meaning or not depends. Doing as you  
>>>>> suggest
>>>>> seems the most reasonable idea.
>>>>> I would add that even if it is an unrooted tree, the topology  
>>>>> might be
>>>>> of interest. In my case I am doing a comparative visualizer and it
>>>>> might be nice for the user to be able to visualize the topology as
>>>>> specified. It has no biological meaning, but in practice, for many
>>>>> users, it helps.
>>>>> I note that PhyloXML (even by virtue of being a XML format) always
>>>>> represents the phylogenies as trees (not weigthed DAGs). There an
>>>>> attribute rooted which can be true or false.
>>>>>
>>>>> But, anyway. Even assuming a very conservative view on this, the
>>>>> current parser, for rooted trees, does not allow to determine  
>>>>> where is
>>>>> the root. I think that there would be a consensus that that is a  
>>>>> bug?
>>>>>
>>>>> Tiago
>>>>
>>>> --
>>>> 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
>>
>> --
>> 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
>
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Peter E. Midford
Mesquite Developer
Peter.Midford at gmail.com