[Biojava-l] RE: Going in circles (again)!

[Mark Schreiber]

On Fri, 7 Sep 2001, Cox, Greg wrote:

> Hi Mark, I'm glad to see someone else looking at this.  
> 
> I don't know what you mean by a "hospital pass," but handleDecorations() was

Sorry a hospital pass is a rugby term for passing the ball to someone who
can't do anything with it to avoid getting onesself nailed... just making
sure there where know great plans for handleDecorations() for some future
version.


> just a convenient way to encapsulate the decoration messiness.  It proably
> doesn't make sense to keep that method around, but that's your call.  There

I like this idea except that a number of methods from LocationTools call
handleDecorations(), is there some fancy way that a method can determined
who called it, perhaps through the reflection api??


> were bugs in how BioJava 1.1 handled circular locations, so I don't
> reccommend cutting and pasting directly.  How do you plan to handle
> operations on two circular sequences not in the same base?  For example,
> intersecting 95..10 on a 100 pair plasmid and 100..10 on a 105 pair plasmid?
> That's the case I'm not sure about, but don't have any use case for.
> 

I hadn't planned to handle this, even thinking about it is giving me a
head ache. This kind of thing could be useful for some kind of plasmid
cloning api, for my purposes I am interested in finding out if one
location on a circular sequence overlaps another so as an intermediate
step I might just limit things to locations from molecules with the same
length. Anyone interested in knocking out a plasmid cloning api?


Mark


> I like the idea for isDecorated changing.  I don't know enough about the
> guts of Java to know if it saves cycles, but it's cleaner.
> 
> Greg
> 
> > -----Original Message-----
> > From: Mark Schreiber [mailto:mark_s@sanger.otago.ac.nz]
> > Sent: Thursday, September 06, 2001 11:44 PM
> > To: biojava-l@biojava.org
> > Cc: gcox@netgenics.com
> > Subject: Going in circles (again)!
> > 
> > 
> > Hi -
> > 
> > I am in the process of making CircularLocations more 
> > compatible with the
> > biojava 1.2 api. I have made good progress but I have run aground with
> > LocationTools.handleDecorations() which doesn't.
> > 
> > Is this method intended as a hospital pass? or should it be used by
> > decorated methods when performing logical operations?
> > 
> > In biojava 1.1 the old CircularRangeLocation and CircularPointLocation
> > classes implemented the old requirements for 
> > Union/Intersection methods
> > etc, is there any reason why these could not be used in LocationTools.
> > 
> > Also would the LocationTools.isDecorated() method be more 
> > efficient if it
> > had the following signature
> > 
> > protected static boolean isDecorated(Location loc){
> >   return (loc instanceof AbstractLocationDecorator);
> > }
> > 
> > Mark
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Mark Schreiber			Ph: 64 3 4797875
> > Rm 218				email mark_s@sanger.otago.ac.nz
> > Department of Biochemistry	email m.schreiber@clear.net.nz
> > University of Otago		
> > PO Box 56
> > Dunedin
> > New Zealand
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > 
> _______________________________________________
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> 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Mark Schreiber			Ph: 64 3 4797875
Rm 218				email mark_s@sanger.otago.ac.nz
Department of Biochemistry	email m.schreiber@clear.net.nz
University of Otago		
PO Box 56
Dunedin
New Zealand
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~