How to write your own Dazzle plugin

Each plugin for Dazzle has to implement certain interfaces. Here we will show how to implement a Dazzle plugin that supports the DAS - features command, using the GFFFeatureSource interface. There are also other plugin mechanisms in Dazzle, but for the moment let’s only consider this one.

Required knowledge

For this turorial you should already know how to deploy Dazzle

The GFFFeatureSource interface

The Interface that needs to be implemented is the GFFFeatureSource interface.

What this means is that the DAS source provides a method called

GFFFeature getFeatures(String reference);

This method accepts a String as an argument, that represents either the chromosomal region or the accession code that is requested. It returns an array of GFFFeature objects that contain the data that should be transported.

When Dazzle gets a DAS - Features request for your DAS source, it will call this getFeatures method in order to obtain the data and then return it as DAS-XML.

The AbstractGFFFeatureSource class

For full DAS-specification support a couple of more methods are required, but they do not need to worry us right now, since there is a utility class available that contains most of the required code already. Your plugin simply needs to extend AbstractGFFFeatureSource.

A minimal plugin

A minimal plugin for Dazzle looks like this: let’s call the file below MyPlugin.java package org.dazzle;

import org.biojava.servlets.dazzle.datasource.AbstractGFFFeatureSource; import org.biojava.servlets.dazzle.datasource.DataSourceException; import org.biojava.servlets.dazzle.datasource.GFFFeature;

public class MyPlugin extends AbstractGFFFeatureSource {

   public GFFFeature[] getFeatures(String reference) 
   throws DataSourceException{
       System.out.println("got a features request for " + reference);
       return new GFFFeature[0];
   }

} </java>

and to enable this in Dazzle we add the following lines to dazzlecfg.xml :

 <datasource id="myplugin" jclass="org.dazzle.MyPlugin">
    <string name="name" value="My 1st Plugin" />
    <string name="description" value="a demo for how to write a Dazzle plugin" />
    <string name="version" value="1.0" />
  </datasource>

DAS - DSN request

Start your Dazzle instance. If you don’t know how you should do that, please see . Once Dazzle is running you can do the DAS - dsn (data source names) command, which lists all available datasources.

http://localhost:8080/dazzleDemo/dsn

note: Dazzle provides XSL stylesheets for a nice display of the XML response in your browser. To view the raw XML source code in the Firefox browser, add view-source: in front of the URL.

view-source:http://localhost:8080/dazzleDemo/dsn

You should get this response if you called your servlet dazzleDemo and your basic Dazzle installation is correct:

The DAS features command

Now you can also do a first DAS - features command:

http://localhost:8080/dazzleDemo/myplugin/features?segment=123

should give you now a very simple response, which will not contain features. (we did not return any, did we?)

Check your server logs it should say something like

got a features request for 123

If you see that, you mastered the first step!

Adding Features

So fare our response does not contain features. Let’s add one: