[Biojava-l] Parsing circular sequences

[Matthew Pocock]

Is there any will to replace the current monolithic parsers for 
embl/genbank/swissprot et.al. with modular event-based parsers based 
upon tag-value? If we did this then the location parsing module can just 
listen for sequence length events. I realy have no idea how the 
performance of the two aproaches would compare, but I'm willing to help 
with writing the tag-value embl parser and benchmarking the result.

Matthew

Schreiber, Mark wrote:
> Hi -
> 
> I have struggled with the circular sequence api for a long time. I can't
> think of any way to avoid parsing the length of the sequence as this is
> nescessary for converting the coordinates. If you can it would be really
> cool.
> 
> - Mark
> 
> 
> 
>>-----Original Message-----
>>From: Cox, Greg [mailto:gcox@cle.lionbioscience.com] 
>>Sent: Tuesday, 12 November 2002 5:11 a.m.
>>To: biojava
>>Subject: [Biojava-l] Parsing circular sequences
>>
>>
>>I'm taking a look at a circular genbank sequence of length n 
>>with a location n^1 on it.  I think that what has to happen 
>>is the size of the sequence and if it is circular have to be 
>>passed down to EmblLikeLocationParser, which will check each 
>>location and convert x..y on the sequence to a 
>>CircularLocation around RangedLocation x..y+n.  
>>
>>	This approach involves changing a lot of method 
>>signatures, since there are a lot of layers between the 
>>formatter and the location parser. That's something I'd like 
>>to avoid, but I've convinced myself it has to be done this 
>>way since at the least the location parser needs the length 
>>of the circular sequence.  I'd like a sanity check if someone 
>>has a better idea of how to work through this.
>>
>>Greg
>>_______________________________________________
>>Biojava-l mailing list  -  Biojava-l@biojava.org 
>>http://biojava.org/mailman/listinfo/biojava-l
>>
> 
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