[Biojava-dev] Annotation conversions

[Len Trigg]

Matthew Pocock wrote:
> Enum away. Use the type-safe enum design pattern?

Yep. I started having a crack at it, and the stuff in the seq/io
package seemed pretty straightforward. I introduced a translation
table to the *Processors and simplified the *FileFormats to only look
for the canonical keys.

My current point of difficulty is with biosql. First, what to do with
sequences that have been previously stored. Basically it needs a
translation table that handles either embl or genbank formats and
converts to the canonical key.

The second problem is what to do when storing sequences. I was
initially just going to use the name associated with the canonical key
(and map from this string to the required object when
reading). However, that's bad juju for compatibility with BioPerl etc,
who won't know how to interpret them correctly. Maybe have an idea of
the preferred format for the sequence and use that? It's getting back
to the reason for introducing the canonical keys in the first
place. Ewww. Suggestions?


Cheers,
Len.