BioJava:CookBook:Distribution:Emission

From BioJava

What is an easy way to tell if two Distributions have equal weights?

Testing two distributions for equal weights is a good way of telling if a training procedure has converged or if two Sequences are likely to come from the same organism. It is a bit tedious to loop through all the residues, especially in a large Alphabet. Fortunately there is a static method called areEmissionSpectraEqual() in DistributionTools that checks for you.

Using this method is demonstrated below.

import org.biojava.bio.dist.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.*;
import org.biojava.utils.*;
 
public class EqualDistributions {
  public static void main(String[] args) {
    FiniteAlphabet alpha = DNATools.getDNA();
 
    //make a uniform distribution
    Distribution uniform = new UniformDistribution(alpha);
 
    try {
      //make another Distribution with uniform weights
      Distribution dist = DistributionFactory.DEFAULT.createDistribution(alpha);
      dist.setWeight(DNATools.a(), 0.25);
      dist.setWeight(DNATools.c(), 0.25);
      dist.setWeight(DNATools.g(), 0.25);
      dist.setWeight(DNATools.t(), 0.25);
 
      //test to see if the weights are equal
      boolean equal = DistributionTools.areEmissionSpectraEqual(uniform, dist);
      System.out.println("Are 'uniform' and 'dist' equal? "+ equal);
    }
    catch (Exception ex) {
      ex.printStackTrace();
    }
  }
}