[Biojava-l] FeatureImpl

[Schreiber, Mark]

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
 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================