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CREATE SCHEMA frange;
SET search_path = frange,public,pg_catalog;
CREATE TABLE featuregroup (
featuregroup_id serial not null,
primary key (featuregroup_id),
subject_id int not null,
foreign key (subject_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
object_id int not null,
foreign key (object_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
group_id int not null,
foreign key (group_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
srcfeature_id int null,
foreign key (srcfeature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
fmin int null,
fmax int null,
strand int null,
is_root int not null default 0,
constraint featuregroup_c1 unique (subject_id,object_id,group_id,srcfeature_id,fmin,fmax,strand)
);
CREATE INDEX featuregroup_idx1 ON featuregroup (subject_id);
CREATE INDEX featuregroup_idx2 ON featuregroup (object_id);
CREATE INDEX featuregroup_idx3 ON featuregroup (group_id);
CREATE INDEX featuregroup_idx4 ON featuregroup (srcfeature_id);
CREATE INDEX featuregroup_idx5 ON featuregroup (strand);
CREATE INDEX featuregroup_idx6 ON featuregroup (is_root);
CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4, varchar) RETURNS setof featuregroup AS '
SELECT g2.*
FROM featuregroup g1,
featuregroup g2
WHERE g1.is_root = 1
AND ( g1.srcfeature_id = g2.srcfeature_id OR g2.srcfeature_id IS NULL )
AND g1.group_id = g2.group_id
AND g1.srcfeature_id = (SELECT feature_id FROM feature WHERE uniquename = $3)
AND boxquery($1, $2) @ boxrange(g1.fmin,g2.fmax)
' LANGUAGE 'sql';
CREATE OR REPLACE FUNCTION groupcontains(int4, int4, varchar) RETURNS setof featuregroup AS '
SELECT *
FROM groupoverlaps($1,$2,$3)
WHERE fmin <= $1 AND fmax >= $2
' LANGUAGE 'sql';
CREATE OR REPLACE FUNCTION groupinside(int4, int4, varchar) RETURNS setof featuregroup AS '
SELECT *
FROM groupoverlaps($1,$2,$3)
WHERE fmin >= $1 AND fmax <= $2
' LANGUAGE 'sql';
CREATE OR REPLACE FUNCTION groupidentical(int4, int4, varchar) RETURNS setof featuregroup AS '
SELECT *
FROM groupoverlaps($1,$2,$3)
WHERE fmin = $1 AND fmax = $2
' LANGUAGE 'sql';
CREATE OR REPLACE FUNCTION groupoverlaps(int4, int4) RETURNS setof featuregroup AS '
SELECT *
FROM featuregroup
WHERE is_root = 1
AND boxquery($1, $2) @ boxrange(fmin,fmax)
' LANGUAGE 'sql';
CREATE OR REPLACE FUNCTION groupoverlaps(_int4, _int4, _varchar) RETURNS setof featuregroup AS '
DECLARE
mins alias for $1;
maxs alias for $2;
srcs alias for $3;
f featuregroup%ROWTYPE;
i int;
s int;
BEGIN
i := 1;
FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP
SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i];
FOR f IN
SELECT *
FROM featuregroup WHERE group_id IN (
SELECT group_id FROM featuregroup
WHERE (srcfeature_id = s OR srcfeature_id IS NULL)
AND group_id IN (
SELECT group_id FROM groupoverlaps( mins[i], maxs[i] )
WHERE srcfeature_id = s
)
)
LOOP
RETURN NEXT f;
END LOOP;
END LOOP;
RETURN;
END;
' LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION groupcontains(_int4, _int4, _varchar) RETURNS setof featuregroup AS '
DECLARE
mins alias for $1;
maxs alias for $2;
srcs alias for $3;
f featuregroup%ROWTYPE;
i int;
s int;
BEGIN
i := 1;
FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP
SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i];
FOR f IN
SELECT *
FROM featuregroup WHERE group_id IN (
SELECT group_id FROM featuregroup
WHERE (srcfeature_id = s OR srcfeature_id IS NULL)
AND fmin <= mins[i]
AND fmax >= maxs[i]
AND group_id IN (
SELECT group_id FROM groupoverlaps( mins[i], maxs[i] )
WHERE srcfeature_id = s
)
)
LOOP
RETURN NEXT f;
END LOOP;
END LOOP;
RETURN;
END;
' LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION groupinside(_int4, _int4, _varchar) RETURNS setof featuregroup AS '
DECLARE
mins alias for $1;
maxs alias for $2;
srcs alias for $3;
f featuregroup%ROWTYPE;
i int;
s int;
BEGIN
i := 1;
FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP
SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i];
FOR f IN
SELECT *
FROM featuregroup WHERE group_id IN (
SELECT group_id FROM featuregroup
WHERE (srcfeature_id = s OR srcfeature_id IS NULL)
AND fmin >= mins[i]
AND fmax <= maxs[i]
AND group_id IN (
SELECT group_id FROM groupoverlaps( mins[i], maxs[i] )
WHERE srcfeature_id = s
)
)
LOOP
RETURN NEXT f;
END LOOP;
END LOOP;
RETURN;
END;
' LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION groupidentical(_int4, _int4, _varchar) RETURNS setof featuregroup AS '
DECLARE
mins alias for $1;
maxs alias for $2;
srcs alias for $3;
f featuregroup%ROWTYPE;
i int;
s int;
BEGIN
i := 1;
FOR i in array_lower( mins, 1 ) .. array_upper( mins, 1 ) LOOP
SELECT INTO s feature_id FROM feature WHERE uniquename = srcs[i];
FOR f IN
SELECT *
FROM featuregroup WHERE group_id IN (
SELECT group_id FROM featuregroup
WHERE (srcfeature_id = s OR srcfeature_id IS NULL)
AND fmin = mins[i]
AND fmax = maxs[i]
AND group_id IN (
SELECT group_id FROM groupoverlaps( mins[i], maxs[i] )
WHERE srcfeature_id = s
)
)
LOOP
RETURN NEXT f;
END LOOP;
END LOOP;
RETURN;
END;
' LANGUAGE 'plpgsql';
--functional index that depends on the above functions
CREATE INDEX bingroup_boxrange ON featuregroup USING RTREE (boxrange(fmin, fmax)) WHERE is_root = 1;
CREATE OR REPLACE FUNCTION _fill_featuregroup(INTEGER, INTEGER) RETURNS INTEGER AS '
DECLARE
groupid alias for $1;
parentid alias for $2;
g featuregroup%ROWTYPE;
BEGIN
FOR g IN
SELECT DISTINCT 0, fr.subject_id, fr.object_id, groupid, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, 0
FROM feature_relationship AS fr,
featureloc AS fl
WHERE fr.object_id = parentid
AND fr.subject_id = fl.feature_id
LOOP
INSERT INTO featuregroup
(subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root)
VALUES
(g.subject_id, g.object_id, g.group_id, g.srcfeature_id, g.fmin, g.fmax, g.strand, 0);
PERFORM _fill_featuregroup(groupid,g.subject_id);
END LOOP;
RETURN 1;
END;
' LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION fill_featuregroup() RETURNS INTEGER AS '
DECLARE
p featuregroup%ROWTYPE;
l featureloc%ROWTYPE;
isa int;
c int;
BEGIN
TRUNCATE featuregroup;
SELECT INTO isa cvterm_id FROM cvterm WHERE (name = ''isa'' OR name = ''is_a'');
-- Recursion is the biggest performance killer for this function.
-- We can dodge the first round of recursion using the "fr1 / GROUP BY" approach.
-- Luckily, most feature graphs are only 2 levels deep, so most recursion is
-- avoidable.
RAISE NOTICE ''Loading root and singleton features.'';
FOR p IN
SELECT DISTINCT 0, f.feature_id, f.feature_id, f.feature_id, srcfeature_id, fmin, fmax, strand, 1
FROM feature AS f
LEFT JOIN feature_relationship ON (f.feature_id = object_id)
LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id)
WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship )
AND srcfeature_id IS NOT NULL
LOOP
INSERT INTO featuregroup
(subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root)
VALUES
(p.object_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 1);
END LOOP;
RAISE NOTICE ''Loading child features. If your database contains grandchild'';
RAISE NOTICE ''features, they will be loaded recursively and may take a long time.'';
FOR p IN
SELECT DISTINCT 0, fr0.subject_id, fr0.object_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand, count(fr1.subject_id)
FROM feature_relationship AS fr0
LEFT JOIN feature_relationship AS fr1 ON ( fr0.subject_id = fr1.object_id),
featureloc AS fl
WHERE fr0.subject_id = fl.feature_id
AND fr0.object_id IN (
SELECT f.feature_id
FROM feature AS f
LEFT JOIN feature_relationship ON (f.feature_id = object_id)
LEFT JOIN featureloc ON (f.feature_id = featureloc.feature_id)
WHERE f.feature_id NOT IN ( SELECT subject_id FROM feature_relationship )
AND f.feature_id IN ( SELECT object_id FROM feature_relationship )
AND srcfeature_id IS NOT NULL
)
GROUP BY fr0.subject_id, fr0.object_id, fl.srcfeature_id, fl.fmin, fl.fmax, fl.strand
LOOP
INSERT INTO featuregroup
(subject_id, object_id, group_id, srcfeature_id, fmin, fmax, strand, is_root)
VALUES
(p.subject_id, p.object_id, p.object_id, p.srcfeature_id, p.fmin, p.fmax, p.strand, 0);
IF ( p.is_root > 0 ) THEN
PERFORM _fill_featuregroup(p.subject_id,p.subject_id);
END IF;
END LOOP;
RETURN 1;
END;
' LANGUAGE 'plpgsql';
SET search_path = public,pg_catalog;
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