Re: R-tree and start/end queries

How does the performance of the R-tree searches compare to the Bio::GFF
binning approach?

I've been wondering for a while how well the postgres builtins would do
for this application.

Dmitri

> -----Original Message-----
> From: pgsql-sql-owner@postgresql.org
> [mailto:pgsql-sql-owner@postgresql.org] On Behalf Of Chris Mungall
> Sent: Wednesday, September 21, 2005 3:14 PM
> To: Sean Davis
> Cc: pgsql-sql@postgresql.org; Hilmar Lapp
> Subject: Re: [SQL] R-tree and start/end queries
>
>
>
> On Wed, 21 Sep 2005, Sean Davis wrote:
>
> > I have a table like:
> >
> > Create table gf (
> >     pk    serial,
> >     start int,
> >     end   int,
> >     gf    varchar
> > );
> >
> > I want to do queries along the lines of:
> >
> > "find all gf that overlap with (10000,20000)" or
> > "find all gf that overlap with each other"
> >
> > And others.  I have read over the documentation, but I still remain
> > unclear about how to implement R-tree indexing in this
> situation.  Any
> > suggestions?
>
> Hi Sean
>
> I'm guessing that this is for some kind of genome database, yep?
>
> You may want to look at the chado database which has a
> growing library of functions for this sort of thing;
> www.gmod.org/schema
>
> Here is the code for doing range interval functions; our
> featureloc is equivalent to your "gf" (though we separate the
> entity from the entity being located). Our fmin and fmax may
> be equivalent to your start and end above (unless you
> indicate directionality with start>end in which case the
> intersection functions get a bit trickier). Our feature_id is
> probably equivalent to your gf column.
>
> We use the builtin pg types "point" and "box" and make an
> RTREE index over
> this:
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> --
> -- functions operating on featureloc ranges
> --
>
> -- create a point
> CREATE OR REPLACE FUNCTION create_point (int, int) RETURNS
> point AS  'SELECT point ($1, $2)' LANGUAGE 'sql';
>
> -- create a range box
> -- (make this immutable so we can index it)
> CREATE OR REPLACE FUNCTION boxrange (int, int) RETURNS box AS
>  'SELECT box (create_point(0, $1),
> create_point($2,500000000))' LANGUAGE 'sql' IMMUTABLE;
>
> -- create a query box
> CREATE OR REPLACE FUNCTION boxquery (int, int) RETURNS box AS
>  'SELECT box (create_point($1, $2), create_point($1, $2))'
> LANGUAGE 'sql' IMMUTABLE;
>
> --functional index that depends on the above functions
> CREATE INDEX binloc_boxrange ON featureloc USING RTREE
> (boxrange(fmin, fmax));
>
>
> CREATE OR REPLACE FUNCTION featureloc_slice(int, int) RETURNS
> setof featureloc AS
>   'SELECT * from featureloc where boxquery($1, $2) @
> boxrange(fmin,fmax)' LANGUAGE 'sql';
>
> CREATE OR REPLACE FUNCTION featureloc_slice(varchar, int, int)
>   RETURNS setof featureloc AS
>   'SELECT featureloc.*
>    FROM featureloc
>    INNER JOIN feature AS srcf ON (srcf.feature_id =
> featureloc.srcfeature_id)
>    WHERE boxquery($2, $3) @ boxrange(fmin,fmax)
>    AND srcf.name = $1 '
> LANGUAGE 'sql';
>
> CREATE OR REPLACE FUNCTION featureloc_slice(int, int, int)
>   RETURNS setof featureloc AS
>   'SELECT *
>    FROM featureloc
>    WHERE boxquery($2, $3) @ boxrange(fmin,fmax)
>    AND srcfeature_id = $1 '
> LANGUAGE 'sql';
>
> -- can we not just do these as views?
> CREATE OR REPLACE FUNCTION feature_overlaps(int)
>  RETURNS setof feature AS
>  'SELECT feature.*
>   FROM feature
>    INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id)
>    INNER JOIN featureloc AS y ON (y.feature_id=$1)
>   WHERE
>    x.srcfeature_id = y.srcfeature_id            AND
>    ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) '
> LANGUAGE 'sql';
>
> CREATE OR REPLACE FUNCTION feature_disjoint_from(int)
>  RETURNS setof feature AS
>  'SELECT feature.*
>   FROM feature
>    INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id)
>    INNER JOIN featureloc AS y ON (y.feature_id=$1)
>   WHERE
>    x.srcfeature_id = y.srcfeature_id            AND
>    ( x.fmax < y.fmin OR x.fmin > y.fmax ) '
> LANGUAGE 'sql';
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Cheers
> Chris
>
> > Thanks,
> > Sean
> >
> >
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