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<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE sqlMap
PUBLIC "-//ibatis.apache.org//DTD SQL Map 2.0//EN"
"http://ibatis.apache.org/dtd/sql-map-2.dtd">
<sqlMap namespace="FeatureLoc">
<typeAlias alias="FeatureLoc"
type="org.gmod.schema.sequence.FeatureLoc"/>
<resultMap id="map-location-lazy"
class="FeatureLoc">
<result property="featureByFeatureId.featureId" column="feature_id" />
<result property="srcFeatureId" column="srcfeature_id" nullValue="-999" />
<result property="featureBySrcFeatureId" column="{featureId=srcfeature_id}"
select="getLazyFeatureNoResiduesById" />
<result property="fmin" column="fmin" nullValue="-999" />
<result property="fmax" column="fmax" nullValue="-999" />
<result property="strand" column="strand" nullValue="0" />
<result property="phase" column="phase" />
<result property="residueInfo" column="residue_info"/>
<result property="locGroup" column="locgroup"/>
<result property="rank" column="rank"/>
<result property="fminPartial" column="is_fmin_partial"/>
<result property="fmaxPartial" column="is_fmax_partial"/>
</resultMap>
<!-- select featureloc -->
<select id="getFeatureLoc" resultMap="map-location-lazy">
SELECT feature_id, srcfeature_id, fmin, fmax, strand, phase, residue_info, locgroup, rank, is_fmin_partial, is_fmax_partial
FROM featureloc
WHERE featureloc.feature_id=#id#
</select>
<select id="getFeatureLocBySrcFeatureId" resultMap="map-location-lazy">
SELECT feature_id, srcfeature_id, fmin, fmax, strand, phase, residue_info, locgroup, rank, is_fmin_partial, is_fmax_partial
FROM featureloc
WHERE srcfeature_id=#id#
</select>
<select id="getFeatureLocsByListOfIds" resultMap ="map-location-lazy">
SELECT feature_id, srcfeature_id, fmin, fmax, strand, phase, residue_info, locgroup, rank, is_fmin_partial, is_fmax_partial
FROM featureloc
WHERE featureloc.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
</select>
<!-- used to find match feature from the subject and query featureId -->
<select id="getFeatureIdBySrcFeatureId" parameterClass="Feature" resultClass="java.lang.Integer">
<iterate property="featureLocsForFeatureId" conjunction="INTERSECT" >
SELECT feature_id FROM featureloc WHERE srcfeature_id=#featureLocsForFeatureId[].featureBySrcFeatureId.featureId#
</iterate>
</select>
<!-- WRITE BACK METHODS -->
<!-- UPDATE -->
<update id="updateFeatureLoc"
parameterClass="FeatureLoc">
UPDATE featureloc
SET fmin=$fmin$, fmax=$fmax$, strand=$strand$,
is_fmin_partial=#fminPartial#,
is_fmax_partial=#fmaxPartial#
<isNotNull property="phase">
, phase=$phase$
</isNotNull>
<isNull property="phase">
, phase=NULL
</isNull>
WHERE
<isGreaterThan property="featureByFeatureId.featureId" compareValue="0">
feature_id=$featureByFeatureId.featureId$
</isGreaterThan>
<isLessEqual property="featureByFeatureId.featureId" compareValue="0">
<isNotNull property="featureByFeatureId.uniqueName">
feature_id=(SELECT feature_id FROM feature WHERE uniquename=#featureByFeatureId.uniqueName#)
</isNotNull>
</isLessEqual>
<isGreaterThan property="featureBySrcFeatureId.featureId" compareValue="0" prepend="AND">
srcfeature_id=$featureBySrcFeatureId.featureId$
</isGreaterThan>
</update>
<update id="updateFeatureLocByChangingSequence"
parameterClass="uk.ac.sanger.artemis.chado.FeatureForUpdatingResidues">
UPDATE featureloc
SET
<isNotNull property="newSubSequence">
fmin=fmin+$length$, fmax=fmax+$length$
</isNotNull>
<isNull property="newSubSequence">
fmin=fmin-$length$, fmax=fmax-$length$
</isNull>
WHERE fmin >= $startBase$ AND srcfeature_id=$featureId$
</update>
<insert id="insertFeatureLoc"
parameterClass="FeatureLoc">
INSERT INTO featureloc
( featureloc_id, feature_id, srcfeature_id, fmin, fmax, strand, rank
<isNotNull property="phase">
, phase
</isNotNull>
)
VALUES
( nextval('featureloc_featureloc_id_seq'),
$featureByFeatureId.featureId$,
$featureBySrcFeatureId.featureId$,
$fmin$,
$fmax$,
$strand$,
$rank$
<isNotNull property="phase">
, $phase$
</isNotNull>
)
</insert>
</sqlMap>
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