package org.biojava.bio.program.hmmer;

import org.biojava.bio.Annotation;
import org.biojava.bio.dist.Distribution;
import org.biojava.bio.dp.SimpleEmissionState;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.bio.symbol.Symbol;

/**
 * A state in a HMMer model.
 */

public class ProfileEmissionState extends SimpleEmissionState{
	
	public ProfileEmissionState(String str, Annotation ann, int[] adv, Distribution dis){
	  super(str, ann,adv, dis);
	}
	
	public double logProb(Symbol sym) throws IllegalSymbolException{
	 return log2(getDistribution().getWeight(sym)); 
	}
	
	protected static double log2(double x){
		return Math.log(x)/Math.log(2);
	}
    
}