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);
}
}

} ```