Documentation

From BioDOM

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Application Programming Interface (API)

First of all you should check our API. The BioDOM-API was generated using doxygen.

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Class hierachy

This diagram shows an inheritance graph of the BioDOM classes. All classes possess an interface, which defines the public methods. The interfaces are used for testing purposes mainly, therefore it is not required to use the interfaces to access a BioDOM class.

AbstractBioDOM is the abstract superclass of all BioDOM classes. It specifies methods, variables and finals used by all classes. SequenceML, AlignmentML, RNAStructML and RNAStructAlignmentML are classes that correspond to a specific XSD schema. If you want to use BioDOM as a converter, than you probably want to instance one of these classes. They provide the full conversion functionality, along with several useful methods inherited by AbstractBioDOM.

Note that we have used plenty log4j log messages in our sourcecode. This allows easy debugging of your programs, since you can always control what is going on. Another helpfull function for debugging might be the toString()-method defined on all our BioDOM classes. This function returns a human readable string representation of the XML object currently in the memory, allowing you to get even better insight into your program flows.

biodom_inherit_graph_small.png
(Click on this link for a larger image.)


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Under development

Bug fixes / changes in version 1.2:

  • usage of ONLY JAXP interfaces for XML work, thereby dropping dependence on any particular Java XML implementation
  • correction of regular expression constants for sequence characters
  • global DocumentBuilder
  • changed default validation state for getDom method to 'ON'
  • own Resolver implementation (optionally, an external Resolver is used if available)
  • several new XSL-based import filters.
  • Bugfixes, comments, etc...

Bug fixes / changes in version 1.1:

  • XSL based transformation of supported XML Schemas
  • all supported XSDs in all (former and current) versions are now included in the release files for easy validation of XML files
  • removed dependencies on 3rd party libraries (log4j, resolver)
  • properties-based configuration of XML namespaces and namespace locations

As a legacy to the HOBIT meeting some nice lonely sentences for the documentation page remained.

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