[Biojava-dev] Developing LD visualizer

[Takaho A. Endo]

Hi Mark,

   Thanks for your reply despite my poor English.
   Another problems of my codes are that I did not follow manners of 
BioJava and I did not use useful libraries of it because I felt they 
are too general for my specific purpose at the time when I was 
developing.
   Do I have to change my codes to apply Symbol and Sequence APIs in 
order to avoid code-duplication?
   It is easy to modify package names of my source codes into the same 
as BioJava codes,  and I intend to.  However, I will ask you for advice 
to apply BioJava AIPs if required.

   Thanks.
--
Takaho A. Endo, Toaki University, Japan.




On 2003.9.8, at 11:17 Asia/Tokyo, Schreiber, Mark wrote:

> Hi -
>
> The development version of biojava is targetting Java 1.4 so this 
> shouldn't be a problem. If you take a look at the core Symbol and 
> Sequence API's you'll probably get some idea of how you might be able 
> to integrate you LD work.
>
> If you get stuck, just ask some questions on the list.
>
> - Mark
>
>
> 	-----Original Message-----
> 	From: Takaho A. Endo [mailto:endo at genetix-h.com]
> 	Sent: Mon 8/09/2003 12:19 p.m.
> 	To: biojava-dev at biojava.org
> 	Cc:
> 	Subject: [Biojava-dev] Developing LD visualizer
> 	
> 	
>
> 	Dear all,
> 	
> 	   I am studying in medical faculty of Tokai University, Japan.
> 	   For a certain sake I have developed a visualizing application of
> 	linkage disequilibrium.
> 	
> 	   The name of the application is ALDER (autonomic linkage
> 	disequilibrium (LD) expression resources). This is a GOLD(1)-like but
> 	finer application written in Java, which calculates LD by itself and
> 	shows LD graphs reflecting marker distance.
> 	
> 	   Due to current trend, we are required to show haplotype blocks in
> 	papers of linkage/association studies.
> 	   I think my application is useful for such purposes.
> 	
> 	   You can download binary, sample data and source codes from my
> 	personal site (2).
> 	   I would like to contribute to BioJava project with my program if 
> you
> 	accept, although it requires JRE 1.4 or more which is different from
> 	other codes in your project.
> 	   I am glad with any opinions and comments for my program.
> 	
> 	   Best regards.
> 	
> 	
> 	1) http://www.sph.umich.edu/csg/abecasis/GOLD/download/index.html
> 	2) http://homepage.mac.com/takaho_e/biology/alder/index.html
> 	
> 	---
> 	Takaho A. Endo
> 	
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> 	biojava-dev at biojava.org
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> 	
>
>
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