[Bioperl-l] Feature/Annotation rollback finished
cjfields at uiuc.edu
Tue Aug 28 17:05:10 EDT 2007
I'm now wrapping up the Feature/Annotation rollback. I will probably
start merging back to the main branch in the next day or two., as
soon as interested parties (*cough*devs*cough*) look over the last
batch of changes.
I have also added a small benchmark test which indicates a decrease
in parsing time in SeqIO::genbank with all tests passing. I expect
this will translate over to any Bio::SeqFeature::Generic-using class
(open mouth, prepare to insert foot....).
It is also possible there are still some instances where overloading
is expected lurking about in the ~1000 or so modules, so I'll leave
the exceptions I added to all Bio::AnnotationI; we can remove them
down the line, maybe prior to rel1.6, after more tests are added or
if they get particularly annoying. My guess is I caught 99.99% of
them (prepare to insert other foot....).
The key change in this last round is the addition of several class
*dbxref* methods to Bio::Ontology::Term and
Bio::Annotation::OntologyTerm, all of which are capable of working
with either DBLink instances or simple scalars. This was primarily
done in order to clear up inconsistencies in the older *dblink*
methods, which were ambiguous (some indicates simple scalar
arguments, others DBLink objects); operator overloading was used
extensively in these cases, which led to several issues. I have
added deprecation warnings to the older methods which now map to
using the newer methods. All tests pass with the exception of a few
already failing on the MAIN branch; the single test which needs to be
fixed is a round-tripping error in swiss.t (now a TODO), which can be
fixed after merging back.
Please respond to this if there are any questions or if I need to
clarify the changes I made a bit more.
More information about the Bioperl-l