[Biojava-l] Null Model

[Schreiber, Mark]

Hi -
 
DistributionTools has methods to read and write Distributions to and from XML called writeToXML and readFromXML the reader uses a SAX parser. They also handle OrderNDistributions. The format is similar to Thomas's

	-----Original Message----- 
	From: Thomas Down [mailto:thomas at derkholm.net] 
	Sent: Wed 7/05/2003 7:57 a.m. 
	To: Ren, Zhen 
	Cc: biojava-l at biojava.org 
	Subject: Re: [Biojava-l] Null Model
	
	

	Once upon a time, Ren, Zhen wrote:
	>
	> My question is how I would create a null model like this instead
	> of 1/20 (5.00%) as the null weight for each.  Using the snippet
	> below certainly would do the job, but it is a little awkward,
	> isn't it?
	
	Well, for something like that, you're probably going to
	want to read the Distribution in from some kind of a file.
	To get you started, here's a simple method from one of my
	programs which loads a Distribution from a DOM tree:
	
	    public Distribution readSymDistribution(Element cons)
	        throws Exception
	    {
	            Alphabet alph = AlphabetManager.instance().alphabetForName(cons.getAttribute("alphabet"));
	            SymbolTokenization nameParser = alph.getTokenization("name");
	            Distribution dist = DistributionFactory.DEFAULT.createDistribution(alph);
	
	            Node chld2 = cons.getFirstChild();
	            while (chld2 != null) {
	                if (chld2 instanceof Element) {
	                    Element weight = (Element) chld2;
	                    String sName = weight.getAttribute("symbol");
	                    Symbol sym = nameParser.parseToken(sName);
	                   
	                    double w = Double.parseDouble(weight.getAttribute("weight"));
	                    try {
	                        dist.setWeight(sym, w);
	                    } catch (ChangeVetoException ex) {
	                        throw new BioError(ex);
	                    }
	                }
	                chld2 = chld2.getNextSibling();
	            }
	
	            return dist;
	    }
	
	Sorry, it's rather old and not the last word in elegance
	(I actually tend to avoid the DOM APIs these days) but it
	does work.  The XML looks like:
	
	        <distribution alphabet="DNA">
	          <weight symbol="thymine" weight="0.2881944444444444" />
	          <weight symbol="adenine" weight="0.5011574074074073" />
	          <weight symbol="cytosine" weight="0.10300925925925926" />
	          <weight symbol="guanine" weight="0.10763888888888888" />
	        </distribution>
	
	There will be some similar code in the BioJava XmlMarkovModel
	class, which loads and saves MarkovModel objects.  But it doesn't
	public methods for loading a single distribution.  Maybe it
	should.
	
	     Thomas.
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