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.

```java 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);
   }
 }

} ```