[Biojava-l] LocationTools + Decoratorated Locations = ?

[Cox, Greg]

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:mark.schreiber@agresearch.co.nz]
Sent: Thursday, June 07, 2001 7:47 PM
To: 'Cox, Greg'; 'biojava-l@biojava.org'
Subject: RE: [Biojava-l] LocationTools + Decoratorated Locations = ?


 

> -----Original Message-----
> From: Cox, Greg [mailto:gcox@netgenics.com]
> Sent: Friday, June 08, 2001 9:15 AM
> To: 'biojava-l@biojava.org'
> 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