[Biojava-dev] phylo code

[Thasso Griebel]

Hi,

thanks for the fast answer.

So, I would really like to contribute to the BioJava Phylogeny  
Package, but I will wait until the GSOC project is finished and I am  
back from my vacation ;) For now, I just took a look on the io  
package, especially the three classes concerning phylip io.
Some personal feeling about the naming.
I wouldn't mention "fire" and "events" in the documentation and   
rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler.  
For me, this was irritating. I started looking for a fireXXX method  
immediately and automatically started  thinking about the  
EventDispatchingThread and synchronization. As far as I see, this is  
a direct handler delegate, the parser delegates some method calls to  
a given handler callback method, no events are fired (there is not  
even an Event class that could be fired) and no event dispatching is  
involved.
Also, the io seem to focus on the output of alignment. What about  
trees and distance/character matrices ?
And a really important point is the name handling. The method

  private static String formatSequenceLabel(String label)

in PHYLIPFileFormat simply cuts names that are longer than 10  
characters. I know that phylip has this stupid  limitation. But  
cutting will not work in a lot of cases. If just two sequence names  
are identical over the first ten characters,  the resulting phylip  
file is corrupted and can not be used by most of the phylip  
executables. Maybe the handler can do a renaming and keep track of  
the map. Then one can use the parser to write some phylip file, start  
a phylip method on that file, read in the results and do an automatic  
remapping of the names ?

I also wanted to take a look on the tree model. Is this already in  
the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but  
it was empty ?

regards,

thasso



On 01.08.2007, at 20:03, Richard Holland wrote:

> Hi Thasso.
>
> Thanks for your interest! We always welcome all contributions of  
> code and
> documentation to the BioJava project.
>
> Our GSOC project is well under way and has a plan as you have already
> noticed. The items on that plan are what was agreed with our  
> student, Boh
> Yun Lee, and will be implemented by the time that GSOC is over (early
> September) - or at least, most of them will, and any that aren't  
> will be
> flagged as such.
>
> If you have suggestions to make about code already committed, we would
> welcome them. Such feedback is a necessary part of the development  
> cycle.
> Likewise we would welcome contributions of code not already  
> mentioned as
> being planned on the GSOC pages.
>
> However, if your existing code implements something that is on the  
> to-do
> list on the GSOC page, then the best thing would be to hang on till  
> the
> end of the GSOC project then contribute any items that did not get
> implemented.
>
> cheers,
> Richard
>
> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote:
>> hi,
>>
>> i recently explored the phylogeny code base in biojava. I am
>> currently working on a phylogeny framework similar to mesquite
>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add
>> some functionality using biojava (the sequence stuff and the nexus
>> parser).
>>
>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/
>> BioJava:PhyloSOC07 ) and i might be able to help out with some of the
>> methods, so is there a way to contribute ? Or is this closed to
>> participants of the google summer of code ?
>>
>> I have code for n-consensus and adams consensus methods and some
>> possible extensions for UPGMA (provide other distance computations,
>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and
>> rooting support ). As our research groups has a focus on supertree
>> construction, we have java implementations for several graph based
>> supertree methods (aho's build, mincut, modified mincut, ranked tree,
>> ancestral build).
>>
>>
>> Regards,
>>
>> Thasso
>>
>> --
>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer  
>> Bioinformatik
>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer  
>> Informatik
>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- 
>> Universitaet Jena
>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena,  
>> Germany
>>
>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
> -- 
> Richard Holland
> BioMart (http://www.biomart.org/)
> EMBL-EBI
> Hinxton, Cambridgeshire CB10 1SD, UK

--
Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik
Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik
Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena
Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany