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 - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
