[Biojava-l] Is there a way to determine the query within a FeatureFilter?

Thomas Down thomas at derkholm.net
Wed Jan 7 08:45:08 EST 2004

Once upon a time, Benjamin Schuster-Boeckler wrote:
> Benjamin Schuster-Boeckler wrote:
> >As I understood the principle, a FeatureFilter will be used to test 
> >one Feature after the other through it's accept(Feature f) method. Now 
> >my problem is that this is _far_ too slow. I need to check millions of 
> >Features of which only a few will be selected. So what I want to do is 
> >to get the "rule" that the FeatureFilter uses and translate it into a 
> >SQL query so I can get the right Features from the database straight 
> >away. Unfortunately, I don't see a way how this could be possible. 
> Ah, toString() could do it, am I right? I think it returns a neat 
> pattern that I could parse token for token...

You certainly could do this if you wanted to.  However, I would
generally advise against it.  If you look at all the FeatureFilter
implementations in BioJava, you'll find that they all have accessor
methods for getting at their parameters.  So while it's possible
to convert a filter to text then parse it again, you'd do better
by looking at filters as parse-trees, ready to analyse directly.

You'll find code which manipulates FeatureFilters in this way
throughout the BioJava code base.  One bit which might be
particularly relevant to you is the (private) method sqlizeFilter
in BioSQLSequenceDB.  It's pretty simplistic, but might give you
some ideas.

One thing to remember is that you don't have to translate
every part of a complex filter to SQL -- just do the easy/
important bits, then use the FeatureFilter.accept methods
to apply the parts of the filter your translater doesn't
understand, and you should still get correct results with
good performance.

In the past, David Huen has talked about some more general
solutions for FeatureFilter -> SQL translation, so he might
want to add something here,


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