[Biojava-dev] Feature filtering changes?

[Matthew Pocock]

Sounds good to me. The recursive vs flat filtering is
a bit of a mess right now, and this is at least not a
step backwards. I like the SequenceDB.filter() method,
but wish we could be doing queries like this propperly
over any objects. Ah well. Are you able to write the
JUnit tests & roll over the biojava objects to the new
API, or would you like some help?

Matthew

 --- Thomas Down <td2@sanger.ac.uk> wrote:
> Hi...
> 
> I'm considering making a few changes and additions
> to the
> way features are queried.  The main changes are:
> 
> 1. Add a method on SequenceDB:
> 
>      public FeatureHolder filter(FeatureFilter ff);
> 
> This is equivalent to applying ff to all sequence in
> the database
> and merging the results.  It's already implemented
> for
> BioSQLSequenceDB.  I'll add a naive implementation
> (using
> sequenceIterator) on AbstractSequenceDB.
> 
> This is really useful for cases like finding a gene
> by ID in
> a whole genome database.  It's a small step in
> moving us
> away from an entirely sequence-centric view of
> annotation.
> 
> 
> 2. Add a new single argument filter method on
> FeatureHolder,
>    without the `recurse' flag.  This flag was a
> first attempt
>    at providing an interface for searching
> hierarchical features,
>    but it's not been entirely successful.  In
> particular, if you
>    call `filter' again on a FeatureHolder which was
> created by
>    a filter operation, you're likely to end up with
> duplicated
>    features.  I'd prefer to see filter operations
> constrained
>    using the FeatureFilter grammer itself.
> 
>    The filter(FeatureFilter, boolean) method won't
> be removed
>    (since it's widely used), but will eventually be
> deprecated.
> 
> 3. Add an extra standard FeatureFilter
> implementation.
> 
>        public static class FeatureFilter.IsTopLevel;
> 
>    Non-recursive searches can then be emulated with:
> 
>         myseq.filter(new FeatureFilter.And(
>                             
> FeatureFilter.ByType("foo"),
>                             
> FeatureFilter.IsTopLevel()
>                                           )
>                     );
> 
> 
> Any objections to these?  They should have minimal
> impact on
> existing code, but should prop up the current query
> system
> until BioJava2 is ready.
> 
>      Thomas.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@biojava.org
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