[Biojava-l] changed (improved) SequenceDB and stuff

[hilmar.lapp@pharma.Novartis.com]

> Though minor in nature, the addition of the getName() method to
> interface SequenceDB will result in all implementations (outside the
> BioJava distribution) of this interface to break in the sense that they
> will all have to add an implementation of the getName() method...
>

     Yes indeed, and it does break for instance a lot of my code.

     A comment from a practical point of view, and from someone working in an
     industrial environment where it does really matter whether or not software
     deliberately breaks once you upgrade your (class-)libraries, and the person
     who coded it is currently not available. To this end, OO adds a significant
     improvement, because essentially you DO NOT have to fiddle around in
     library code, but instead you can derive your own things if you're
     unsatisfied with what the library offers. Of course, that's theory, and
     practice is different, but still, I think it's not a bad idea to at least
     aim at it.

     To make a long story short, what I wanted to suggest is, why not have an
     interface NamedSequenceDB which inherits from SequenceDB, and everyone is
     fine to have his SequenceDB implementation be a named one. There are a lot
     of cases where you simply don't need a name, and the fact that it hasn't
     been there until now at least doesn't disprove this.

     What do you think?

          Hilmar