From BioJava

How to write a plugin for Dazzle

The source code

The full source code for this example is available from the dazzle svn repository

How to set up a Reference and Annotation server

This example demonstrates how to set up a reference & annotation server for Dazzle using the BioJava sequence model. There is also a second way to provide features, which is using a simple GFF style bean object. (Documentation to follow).

Step 1: declare what we want to implement. As you can see below, we want to implement a ReferenceSource and we use the convenience class AbstractDataSource, so we safe some time for the implmementation.

public class UniProtDataSource extends AbstractDataSource implements DazzleReferenceSource {

These objects will collect the data:

private Map seqs; // contains all the BioJava Sequence objects.
	private Set allTypes; // all annotation types.
	String fileName; // the filename to parse 

When the DAs source is requested, Dazzle will initiate this plugin. For this the init method is called:

public void init(ServletContext ctx) 
	throws DataSourceException
	{
		super.init(ctx);
		try {

Now we init the variables and use BioJava to parse the uniprot file:

seqs = new HashMap();
			allTypes = new HashSet();
			BufferedReader br = new BufferedReader(new InputStreamReader(ctx.getResourceAsStream(fileName)));
 
//			read the SwissProt File
			SequenceIterator sequences = SeqIOTools.readSwissprot(br);
 
 
			//iterate through the sequences
			while(sequences.hasNext()){
 
				Sequence seq = sequences.nextSequence();
			
				seqs.put(seq.getName(), seq);
			}

If something goes wrong, we throw a DataSourceException

} catch (Exception ex) {
			throw new DataSourceException(ex, "Couldn't load sequence file");
		}
	}
 
	/** try to parse a score out of the feature notes
	 * 
	 */
	public String getScore(Feature f) {
		String score = "-";
 
		Annotation a = f.getAnnotation();
		try {
			
			String note = (String) a.getProperty("swissprot.featureattribute");
			
			int scorePos =note.indexOf("Score: "); 
			if (  scorePos > 0 ) {
 
				String sc = note.substring(scorePos+7,note.length());
				//System.out.println("parsed " + sc);
				try {
					double scp  = Double.parseDouble(sc);
					score = "" + scp;
				} catch (Exception e){
					e.printStackTrace();
				}
				try {
					int scp = Integer.parseInt(sc);
					score = "" + scp;
				} catch (Exception e){ 
					e.printStackTrace();
				}
				
			}
			
			//score = ""+ (Double)a.getProperty(SCORE);
			System.out.println("found score " + score);
		} catch (NoSuchElementException e){
			// igonre in this case...
		}
		return score;
 
	}

Now some simple methods to provide some data to be returned to the user.

public String getDataSourceType() {
 
		return "UniProtFile";
	}
 
	public String getDataSourceVersion() {
 
		return "1.00";
	}

This method is called, since in dazzecfg.xml we configured the filename attribute.

public void setFileName(String s) {
		fileName = s;
	}

And this method is called when the DAS - SEQUENCE command is being called:

public Sequence getSequence(String ref) throws DataSourceException, NoSuchElementException {
		Sequence seq = (Sequence) seqs.get(ref);
		if (seq == null) {
			throw new NoSuchElementException("No sequence " + ref);
		}
		return seq;
	}
 
	public Set getAllTypes() {
		return Collections.unmodifiableSet(allTypes);
	}

and here now the method that is used for the ENTRYPOINTS command

public Set getEntryPoints() {
		return seqs.keySet();
	}
 
 
 
	public String getMapMaster() {
		// TODO Auto-generated method stub
		return null;
	}
 
 
 
	public String getLandmarkVersion(String ref) throws DataSourceException, NoSuchElementException {
		// TODO Auto-generated method stub
		return null;
	}
 
}