Reference type (extension point)

Identifier

ru.biosoft.access.referenceType

Plugin

ru.biosoft.access

Registry

ReferenceTypeRegistry

Description

This extension point allows you to define new reference type which may appear in tables and other places.

Configuration Markup

<!ELEMENT type>
<!ATTLIST type
     typeClass     CDATA #REQUIRED
     urlTemplate   CDATA #IMPLIED
>

typeClass

Fully-qualified name of the reference type class.

urlTemplate

Template for the URL to the external database describing elements of this type. Two options are available here:

• Complete URL where $id$ will be expanded to the identifier: https://www.affymetrix.com/LinkServlet?probeset=$id$
• Internal BioUML URL pointing to some database like "de:databases/MyDatabase/genes/$id$"
• MIRIAM DB link like MIR:00000003

Example

<extension id="EnsemblGeneTableType" point="ru.biosoft.access.referenceType">
   <type typeClass="biouml.plugins.ensembl.tabletype.EnsemblGeneTableType" urlTemplate="MIR:00000003"/>
</extension>

This extension registers type for Ensembl Gene using MIRIAM URL template.

Notes

• Your reference type class must implement ReferenceType interface. It's highly recommended to subclass ReferenceTypeSupport abstract class.
• If URLs for your type has more complex structure and cannot be generated using the urlTemplate parameter, you may omit urlTemplate and override getURL method in your ReferenceType class to generate URLs in custom way.
• You can specify @ClassIcon annotation for your reference type class pointing to the icon file. This icon will be used to represent the tables of given type.