[Biojava-l] Another API for vocabularies and KR

[Matthew Pocock]

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Hi.

I've finaly got some monograph code in some sort of shape. Sory for how 
slow this has been. It's very close to the proposal from Michael with 
differences as follows:

  * Not solely for structured vocabularies - can be used for other 
graphical data like database schemas, object models, frames or sematic 
networks.

  * Classes have different names - search/replace can fix this - I'd 
prefer to keep the names closer to that of graphs than of vocabularies.

  * Collections not iterators used (Michael says that he has no firm 
view about this).

  * The Visitor.Direction concept is expanded into the Link entities. 
These label the role of a node in a particular arc.

  * The constraints allow you to follow from an arc to a node with a 
namespace which tells you more about that relationship. It could give 
extra constraints, such as saying that a relation is 1-many. It could 
also be used to generate relationship types or instances from data, for 
example, auto-generating java beans from vocabulary types.

Anyway, I've attached source for some interfaces which you can use to 
build javadocs and classes. There's an in-memory and an SQL-backed 
implementation you can have if you ask nicely (I didn't want to send too 
big a file via e-mail).

Matthew

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