[Biojava-l] Null Model

[Schreiber, Mark]

I'd second both of those proposals
 
- Mark

	-----Original Message----- 
	From: Thomas Down [mailto:thomas at derkholm.net] 
	Sent: Tue 6/05/2003 9:01 p.m. 
	To: Ren, Zhen 
	Cc: biojava-l at biojava.org 
	Subject: Re: [Biojava-l] Null Model
	
	

	Once upon a time, on a computer far far away, Ren, Zhen wrote:
	>
	> The second part of the question is how to do this shown above using
	> BioJava API.  Notice although there is a null model behind this,
	> it is actually never used.  How would I use the null model here?
	
	Well, it's easy to write some code which uses log odds.
	
	     Distribution dist = ...
	     Symbol sym = ...
	     double logodds = Math.log(dist.getWeight(sym)) -
	                      Math.log(dist.getNullModel().getWeight(sym));
	
	I guess it wouldn't be a bad thing to have a utility
	method on DistributionTools to do this.  I'll add it,
	if nobody objects.
	
	WeightMatrixAnnotator doesn't seem to support log odds.
	I guess it's because it came from a DNA world, where using
	odds scores often (although no always) makes very little
	difference.  It should probably be more flexible.  A neat
	way to do this, mirroring the way the dynamic programming
	algorithms handle this issue, would be to use the ScoreType
	objects
	
	Sound reasonable?
	
	     Thomas.
	_______________________________________________
	Biojava-l mailing list  -  Biojava-l at biojava.org
	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.
=======================================================================