BioJava:CookBook:Distribution:Entropy

From BioJava

How can I find the amount of information or entropy in a Distribution?

The amount of information or entropy in a Distribution is a reflection of the redundancy of the Distribution. Shannon information and Entropy can be calculated using static methods from the DistributionTools class.

Shannon information is returned as a double and reflects the total information content. The entropy is returned as a HashMap between each Symbol and its corresponding entropy. The following program calculates both for a very biased Distribution.

import java.util.*;
 
import org.biojava.bio.dist.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
 
public class Entropy {
  public static void main(String[] args) {
 
    Distribution dist = null;
    try {
      //create a biased distribution
      dist =
          DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA());
 
      //set the weight of a to 0.97
      dist.setWeight(DNATools.a(), 0.97);
 
      //set the others to 0.01
      dist.setWeight(DNATools.c(), 0.01);
      dist.setWeight(DNATools.g(), 0.01);
      dist.setWeight(DNATools.t(), 0.01);
    }
    catch (Exception ex) {
      ex.printStackTrace();
      System.exit(-1);
    }
 
    //calculate the information content
    double info = DistributionTools.bitsOfInformation(dist);
    System.out.println("information = "+info+" bits");
    System.out.print("\n");
 
    //calculate the Entropy (using the conventional log base of 2)
    HashMap entropy = DistributionTools.shannonEntropy(dist, 2.0);
 
    //print the Entropy of each residue
    System.out.println("Symbol\tEntropy");
    for (Iterator i = entropy.entrySet().iterator(); i.hasNext(); ) {
      Map.Entry entry = (Map.Entry)i.next();
      Symbol sym = (Symbol)entry.getKey();
      Double val = (Double)entry.getValue();
      System.out.println(sym.getName()+ "\t" +val);
    }
  }
}