[Biojava-dev] Errors versus Exceptions

[LAW Andrew]

On 20 May 2010, at 05:11, Mark Schreiber wrote:

> If you are using BioJava objects as fake DTO's or EntityBean
> look-a-likes you should really question why you are using BioJava
> objects in the first place. Not sure what BioJava3 objects will look
> like but BJ1.X objects are definitely not good at this.
> 
> It also raises and interesting point which I haven't seen discussed
> much on the list; what will BJ3 be for (or not for). One of the
> painful lessons (for me) from working on BioJava is you can't make an
> API do everything. The more modular approach to BJ3 should help avoid
> this. I see nothing wrong with having a module that is more suitable
> for the kind of work sequence-data-binding you are proposing. This
> modules objects should definitely have public constructors and public
> setters. Why not make use of Entity Beans (Post EJB 3) while your at
> it. If it is in it's own module it will not corrupt the other parts of
> BioJava with "unsafe" beany objects.
> 
> In this case making your own objects (and sharing them) would actually
> be a whole lot better than trying to shoe horn an API that wasn't made
> for this. Some IDEs will even auto-generate databinding objects for
> you; although, I understand there is some strange cases in Ensembl
> that might not make this a good idea).


I think this is really the point that we have been picking at all along. The current way that BJ3 objects seem to be set up makes them difficult to use in any manner other than that intended by the core BJ3 developers. We were hoping that there would be all the generic sequence and coordinate transformation "goodness" available for us in a bean format and then all we would have to do (!!) would be to define the data access methods necessary to populate those objects. That seems to be not the way that things are set up and mapping our ideas and thought processes to BJ3 has not been as easy as we would have liked.



Later,

Andy
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Yada, yada, yada...

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