[Biojava-l] Parsing circular sequences

[Schreiber, Mark]

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
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> 
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