Hi -
I have noticed that the following block of code in FeatureImpl:
try {
d.addImplementation(Feature.Template.class,
SimpleFeature.class);
d.addImplementation(StrandedFeature.Template.class,
SimpleStrandedFeature.class);
d.addImplementation(HomologyFeature.Template.class,
SimpleHomologyFeature.class);
d.addImplementation(SimilarityPairFeature.Template.class,
SimpleSimilarityPairFeature.class);
d.addImplementation(RemoteFeature.Template.class,
SimpleRemoteFeature.class);
} catch (BioException ex) {
throw new BioError(ex, "Couldn't initialize default
FeatureRealizer");
}
Needs to have d.addImplementation(FramedFeature.Template.class,
SimpleFramedFeature.class); added to it. I will check this into the
Biojava-live cvs. Someone might want to put it in the 1.2 branch. I
don't think many people will be affected as the uses of FramedFeature
are pretty esoteric (ie I invented it for my use but some others might
want it).
The only symptom of it not being there is that your FramedFeature can
sometimes become a StrandedFeature during filtering via the wonders of
reflection/introspection.
Cheers
Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
PH: +64 3 489 9175
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