How can I write a Distribution to XML?

If you frequently construct Distributions from large training sets for later analysis it is desirable to be able to store these Distributions for latter use. One possibility is to serialize the Distribution to binary. Serialization, while ideal for short term storage or communication between Java VMs, is fragile and likely to break between different versions of BioJava. It is also impossible to inspect by eye.

A better solution is write the Distribution to XML, providing a long term, human readable and language independent solution. The following example shows how a Distribution can be written to XML and read back again. The example requires a fairly recent version of BioJava as the readFromXML() and writeToXML() methods in DistributionTools are fairly new features. The cvs version or version 1.3 (when released) will be adequate.

```java import java.io.*;

import org.biojava.bio.dist.*; import org.biojava.bio.seq.*;

public class Dist2XMLAndBack{

 public static void main(String[] args){

     try{
       File temp = File.createTempFile("xmltemp", ".xml");

       //create a Distribution to write
       Distribution d = DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA());

       //give the Distribution some random values
       DistributionTools.randomizeDistribution(d);

       //write it to 'temp'
       DistributionTools.writeToXML(d, new FileOutputStream(temp));

       //read it back in
       Distribution d2 = DistributionTools.readFromXML(new FileInputStream(temp));

       //check that the weights are reproduced
       boolean b = DistributionTools.areEmissionSpectraEqual(d, d2);

       System.out.println("Are values reproduced? " + b);
     } catch(Exception ex){
       ex.printStackTrace();
     }

 }

} ```