[Biojava-dev] FeatureFilter.OverlapsExtent

[Matthew Pocock]

Thomas Down wrote:

> Hi,
>
> I've been trying to tidy up javadoc and stuff in the various 
> FeatureFilter-related classes and spotted a new filter implementation 
> called FeatureFilter.OverlapsExtent.  This seems to be redundant with 
> the existing FeatureFilter.ShadowOverlapsLocation (which was in 
> biojava 1.3) but has a couple of problems:
>
>    - There's no corresponding ContainsExtent
>    - It's missing all the hooks which make FeatureFilter query 
> optimization work.
>
> Right now, there only seems to be one use of this filter, in 
> FeatureBlockSequenceRenderer.  Does anyone object if I kill it off and 
> switch FeatureBlockSequenceRenderer over to ShadowOverlapsLocation?

My bad. I added it to fix some rendering glitches with CDS features 
without an exon in the visible range. As long as it is semantically 
equivalent to ShadowOverlapsLocation, then do the switch. Can you make 
sure there's a factory method on FeatureTools for the shadow ones?

>
>       Thomas.

Matthew