[Biojava-dev] phylo code

Tue Aug 7 07:48:05 UTC 2007

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Thanks for your feedback Thasso.

The fire/events thing is certainly a misnomer - guilty as charged (I
wrote the code...) - but I suppose I wasn't expecting the naming to
matter much. I'll bear that in mind for future code. We can't really
change the existing interfaces now as they've been released and it is
not nice to users for us to change public interfaces that might already
be in use.

The PHYLIP format handler was written by Jim Balhoff. Jim - do you have
any responses to Thasso's comments about the output options?

I like the sound of your PHYLIP short-name map. You could definitely go
ahead and contribute an update which implemented that. (Don't forget to
make your code clear the map between one file and the next!)

The tree model never materialised in the end. We chose instead to use
the external JGraphT package to represent our trees. The exact way in
which this is done will be documented by Boh-Yun as part of the GSOC
project.

cheers,
Richard

Thasso Griebel wrote:
> 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
> 
> 
> 
> _______________________________________________
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> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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