[Biojava-l] Null Model

[Ren, Zhen]

Thank you both.  Please let the list know when you finish adding these new features.  -Zhen

-----Original Message-----
From: Schreiber, Mark [mailto:mark.schreiber at agresearch.co.nz]
Sent: Tuesday, May 06, 2003 2:18 AM
To: Thomas Down; Ren, Zhen
Cc: biojava-l at biojava.org
Subject: RE: [Biojava-l] Null Model


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.
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