I have implemented location formatting for remote features [i.e. join(5..10,
AL121903:(10..105))], but in doing so I had to introduce a new method to the
SeqFileFormer interface. Since there's an interface change, I'd like some
consensus before comitting to CVS. Right now, the only way to format a
location is via SeqFileFormer.formatLocation(StringBuffer, Location,
Strand). I added SeqFileFormer.formatLocation(Feature), which will detect a
RemoteFeature and format its location properly, and for non-remote features
it extracts the location field and formats that.
This is needed because the location field of the RemoteFeature class
doesn't completely describe the location of the feature, being the
projection of the feature onto the sequence it's attached to. A field
specific to RemoteFeature (RegionList) is needed to describe the complete
location of the feature. In the next few days, I hope to add the capability
to distinguish between order(a,b) and join(a,b) and this function will be
needed to format an order() style location.
Greg
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