The following plugins are already provided within Dazzle and can be used to set up a DAS source very quickly by configuring dazzlecfg.xml. For more info on how to configure Dazzle see . For information on how to write your own Dazzle plugin see

The EMBL-file plugin

The EMBL-file plugin provides a DAS reference datasource backed by a standard EMBL-format flatfile. It is included in the basic Dazzle package, with classname

org.biojava.servlets.dazzle.datasource.EmblDataSource.

Properties of the EMBL plugin: Name Datatype Description name string The display name of the datasource description string A textual description of the datasource version string The version of the database being served (note that individual sequences are served with version numbers taken from the EMBL file stylesheet string Filename of a DAS stylesheet to associate with this datasource fileName string Name of an EMBL file which is read at startup.

The GFF plugin

The GFF plugin is a very lightweight annotation datasource, backed by a GFF version 2 file. It is very easy to set up, but has some limitations (no complex features, no links out to external data). A more sophisticated `general purpose’ annotation datasource should be released soon.

The GFF plugin has class name

org.biojava.servlets.dazzle.datasource.GFFAnnotationSource 

The following properties are available:

Name        Datatype    Description

name        string      The display name of the datasource
description     string      A textual description of the datasource
version     string      The version of the database being served. Individual sequences are served with version numbers copies from the reference server.
stylesheet  string      Filename of a DAS stylesheet to associate with this datasource
mapMaster   string      URL of a DAS reference server.
fileName    string      Name of a GFF file which is read at startup.
dotVersions     boolean     Interpret sequence names contains a '.' character as id.version.

Attributes

The following attributes in the GFF file can be used:

Atttribute  field
id      the feature ID
href:       the LINK href

Example

The Ldas plugin

The Ldas plugin is an annotation datasource which reads from a Bio::DB::GFF format database, and is largely compatible with the LDAS DAS server. This plugin is useful for existing LDAS users who want to consolidate on a single general purpose DAS server. It’s also a good choice for serving straightforward sets of features which are too large to serve up using the GFF plugin, but don’t already have their own database. Currently, there is only an Ldas annotation plugin. An equivalent for reference servers is possible in the future.

The Ldas plugin is included as standard with Dazzle 1.01 or later. But to use it, you will need to add several extra JAR files to your WEB-INF/lib directory:

   * commons-collections-2.1.jar
   * commons-dbcp-1.1.jar
   * commons-pool-1.1.jar
   * mysql-connector-java.jar

The first three files are distributed with BioJava. The MySQL database connector can be download from MySQL AB.. It should be possible to use the Ldas plugin with other relational databases, but this has not been tested – contact the author if in doubt.

See the LDAS installation page for instructions on creating a Bio::DB::GFF database and populating it with annotation data.

The Ldas plugin has class name

javaorg.biojava.servlets.dazzle.datasource.LdasDataSource

The following properties are available:

Name        Datatype    Description
name        string  The display name of the datasource
description     string  A textual description of the datasource
version     string  The version of the database being served.
stylesheet  string  Filename of a DAS stylesheet to associate with this datasource
mapMaster   string  URL of a DAS reference server.
dbURL       string  A JDBC-style URL specifying which database to use (e.g jdbc:mysql://localhost/dicty).
dbUser      string  The username to use when connecting to the database.
dbPass      string  The password to use when connecting to the database (may be an empty string).

The UniProt plugin

A Uniprot file can be easily used to set up a reference and annotation server. add the following config in your dazzlecfg.xml file:

the example.up file is the uniprot file contains the data.

To see how the UniProt plugin is written see .