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
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