[Biojava-l] circular musings

[Schreiber, Mark]

Hi -

I have been thinking further about the Circular classes from biojava and I
have decided that CircularSequence is almost deprecated in favour of
CircularView with one minor reservation. There doesn't seem to be a way to
serialize view objects even though the underlying object may be.

Any ideas?

This will have the advantage of simplifying the casting of Circular Objects
from say a SequenceDB.

I also like the idea of having a CircularLocation as a decorator although I
would like to propose that it have a second constructor that creates its own
RangeLocation to wrap. This is because (for simplicity) a CircularLocation
should be allowed to have a max less than a min. This can be done by making
the max longer than the length of the sequence when making a RangeLocation
but it would be nice to hid the nescessary conversion.

Any thoughts or objections?

Mark

Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand

PH: +64 3 489 9175

 


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