[pygr-notify] Issue 59 in pygr: Move annotation classes to a separate module

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Status: Accepted
Owner: cjlee112
CC: marecki
Labels: Type-Enhancement Priority-Low Milestone-Release0.8

New issue 59 by cjlee112: Move annotation classes to a separate module
http://code.google.com/p/pygr/issues/detail?id=59

We should move annotation functionality out of seqdb into a new module
(annotate.py or annotation.py?). AnnotationDB doesn't depend on seqdb; I
don't think the prospective annotation.py would even need to import
seqdb...  Their association is purely conceptual.

One consideration: backwards compatibility for unpickling and thus
pygr.Data.  Unpickling looks for classes based on the module location saved
when the object was originally pickled, so to maintain the ability to
unpickle (e.g. retrieve from pygr.Data) existing annotation resources, we'd
have seqdb import a few key classes (AnnotationDB and kin) from
annotation.py, so that those names continue to be accessible from the seqdb
namespace as before.

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