[Biojava-dev] Proposed change to RichFormat interface

[Richard Holland]

Go for it. It would be very helpful.

On Tue, 2006-06-06 at 14:45 +0800, mark.schreiber at novartis.com wrote:
> Hi all -
> 
> I would like to propose a change  to the RichFormat interface. I think we 
> should do this now as we haven't done a stable biojavax roll out yet so 
> interface 
> changes should still be allowed. The additional methods would be:
> 
> public String currentLine();
> public int currentLineNumber();
> 
> This would make debugging a lot easier, it would also make construction of 
> a RichSeqIOListener that logs and debugs much easier. I was trying to do 
> this a while back. I started a background process that parsed 6GB of 
> genbank records looking for records that failed. It worked ok but would be 
> 
> much better with the ability to query the RichFormat in the above way. We 
> might even be able to make it  a utility that people could run on suspect 
> files and generate standard bug reports to make it easier for us to debug 
> the parser code.
> 
> What do people think??
> - Mark
> 
> 
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416