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CREATE OR REPLACE FUNCTION feature_subalignments(integer) RETURNS SETOF featureloc AS '
DECLARE
return_data featureloc%ROWTYPE;
f_id ALIAS FOR $1;
feature_data feature%rowtype;
featureloc_data featureloc%rowtype;
s text;
fmin integer;
slen integer;
BEGIN
--RAISE NOTICE ''feature_id is %'', featureloc_data.feature_id;
SELECT INTO feature_data * FROM feature WHERE feature_id = f_id;
FOR featureloc_data IN SELECT * FROM featureloc WHERE feature_id = f_id LOOP
--RAISE NOTICE ''fmin is %'', featureloc_data.fmin;
return_data.feature_id = f_id;
return_data.srcfeature_id = featureloc_data.srcfeature_id;
return_data.is_fmin_partial = featureloc_data.is_fmin_partial;
return_data.is_fmax_partial = featureloc_data.is_fmax_partial;
return_data.strand = featureloc_data.strand;
return_data.phase = featureloc_data.phase;
return_data.residue_info = featureloc_data.residue_info;
return_data.locgroup = featureloc_data.locgroup;
return_data.rank = featureloc_data.rank;
s = feature_data.residues;
fmin = featureloc_data.fmin;
slen = char_length(s);
WHILE char_length(s) LOOP
--RAISE NOTICE ''residues is %'', s;
--trim off leading match
s = trim(leading ''|ATCGNatcgn'' from s);
--if leading match detected
IF slen > char_length(s) THEN
return_data.fmin = fmin;
return_data.fmax = featureloc_data.fmin + (slen - char_length(s));
--if the string started with a match, return it,
--otherwise, trim the gaps first (ie do not return this iteration)
RETURN NEXT return_data;
END IF;
--trim off leading gap
s = trim(leading ''-'' from s);
fmin = featureloc_data.fmin + (slen - char_length(s));
END LOOP;
END LOOP;
RETURN;
END;
' LANGUAGE 'plpgsql';
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