Difference between revisions of "Reference type (extension point)"
From BioUML platform
Tagir Valeev (Talk | contribs) (Created page with "{{Extension point|referenceType|ru.biosoft.access|registry=ru.biosoft.access.biohub.ReferenceTypeRegistry}} === Description === This extension point allows you to define new t...") |
Tagir Valeev (Talk | contribs) (Reference types information is moved to separate page.) |
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{{Extension point|referenceType|ru.biosoft.access|registry=ru.biosoft.access.biohub.ReferenceTypeRegistry}} | {{Extension point|referenceType|ru.biosoft.access|registry=ru.biosoft.access.biohub.ReferenceTypeRegistry}} | ||
=== Description === | === Description === | ||
− | This extension point allows you to define new type | + | This extension point allows you to define new [[reference type]] which may appear in tables and other places. |
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=== Configuration Markup === | === Configuration Markup === | ||
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=== Notes === | === Notes === | ||
− | * Your reference type class must implement | + | * Your reference type class must implement {{Class|ru.biosoft.access.biohub.ReferenceType}} interface. It's highly recommended to subclass {{Class|ru.biosoft.access.biohub.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. | * 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 | + | * You can specify {{Annotation|ru.biosoft.access.repository.ClassIcon}} annotation for your reference type class pointing to the icon file. This icon will be used to represent the tables of given type. |
Latest revision as of 10:36, 15 May 2013
- Identifier
- ru.biosoft.access.referenceType
- Plugin
- ru.biosoft.access
- Registry
ReferenceTypeRegistry
[edit] Description
This extension point allows you to define new reference type which may appear in tables and other places.
[edit] 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
- Complete URL where $id$ will be expanded to the identifier:
[edit] 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.
[edit] Notes
- Your reference type class must implement
ReferenceType
interface. It's highly recommended to subclassReferenceTypeSupport
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.