[Biojava-l] Rooted trees in nexus files

[Tiago Antão]

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