[Biojava-dev] code contribution

[Konrad Büssow]

Hello Mark,

The ORFer software is already up and running. Take a look at

http://www.proteinstrukturfabrik.de/orfer
We have used some bioJava software to make it. However the new routines in the program have not been written with the BioJava structure in mind, e.g. the SeqIO model you mentioned. 
I will take up this hint and look at the SeqIO model and events, to see if there is a way to incorporate our code into this model.

Regards, Konrad 



Schreiber, Mark wrote:

>Hi Konrad,
> 
>The BioJava SeqIO model is largely event based. Probably the best way to parse GenBankXML would be to write a SAX parser that passes events to a SequenceBuilder or similar.
> 
>Good luck, I would be keen to see the final result.
> 
>- Mark
> 
>
>	-----Original Message----- 
>	From: Konrad Büssow [mailto:buessow at molgen.mpg.de] 
>	Sent: Sat 12/04/2003 2:48 a.m. 
>	To: biojava-dev at biojava.org 
>	Cc: 
>	Subject: [Biojava-dev] code contribution
>	
>	
>
>	Hello,
>	
>	I have been using BioJava for a while now and find it very useful. Now I
>	would like to contribute code to BioJava.
>	I was developing a Java program for parsing the GenBank XML format and
>	extraction of open reading frames: http://www.proteinstrukturfabrik.de/orfer
>	The source code might be useful for BioJava, but probably I will have to
>	re-write it to some extent to make to make it fit into the BioJava
>	structure. Any hint how to approach this would be welcome.
>	
>	Best Regards, Konrad Büssow
>	
>	
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