[Biojava-dev] Region & Junction

[Michael Heuer]

Hello,

Just floating an idea that's been in my head for a bit.

What if for a "biojava next" we replace Sequence and typed Features etc.
with classes extending the two basic SOFA classes _region_ and
_junction_.  A region is a length of symbols and a junction is the space
between two symbols [1, 2].

At the API level Region would look something like a SymbolList but with
interbase (zero-based) coordinates.

Subclasses of _region_, such as _exon_ and _transposable_element_, and of
_junction_, like _insertion_site_, might be generated as java classes from
SOFA itself (or maybe an OWL representation thereof).  Methods could be
generated between these classes representing the various SOFA relationship
types (_kind_of_, _derives_from_, _part_of_).

Of course, in java land these class names would take on proper
JavaClassNameCapitalization instead of lowercase_with_underscores.

   michael


[1]
> http://song.sf.net

[2]
> http://genomebiology.com/2005/6/5/R44