I'm not sure I understand what you're saying. You question why anyone would want to check overlaps of circular regions of different length; and then you come up with the best use case I've seen for it. My reading is that you feel that's the only case, and it's not strong enough to justify the headache of implementing this, is that accurate? Greg -----Original Message----- From: Schreiber, Mark [mailto:[EMAIL PROTECTED]] Sent: Thursday, June 07, 2001 7:47 PM To: 'Cox, Greg'; '[EMAIL PROTECTED]' Subject: RE: [Biojava-l] LocationTools + Decoratorated Locations = ? > -----Original Message----- > From: Cox, Greg [mailto:[EMAIL PROTECTED]] > Sent: Friday, June 08, 2001 9:15 AM > To: '[EMAIL PROTECTED]' > Subject: [Biojava-l] LocationTools + Decoratorated Locations = ? > > > I'm feeling masochistic and ready to tackle the issue of how > the location > semantics apply to decorated locations (currently circular > and 'between' > locations). > Circular Locations: > The problem: > Circular locations essentially redefine the coordinate > system. The > semantics are perfectly clear when dealing with locations > that are circular > with the same circular length. However, it's not clear what > the result > should be when a location on a circular sequence of length 50 > is intersected > with a location on a circular sequence of length 40. > Excuse my ignorance but why on earth would you ever want to do this? The physical aspects of circular sequences suggests that locations on sequences of differing lengths should not be allowed to intersect. One particular application might be where does location 700-900 lie on a new circular plasmid after a 200 bp fragment has been inserted at location 755-761. I think this is a little beyond the capabilities of the intersection/ union methods Mark _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
