From 69f13ce0a671255ed13412fe00e0755a1d6b9a99 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 17 Nov 2008 13:50:28 +0000
Subject: [PATCH] add getTopLevelFeatures
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9370 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
artemis_sqlmap/Feature.xml | 43 +++++++++++++++++++++++++-------------
1 file changed, 29 insertions(+), 14 deletions(-)
diff --git a/artemis_sqlmap/Feature.xml b/artemis_sqlmap/Feature.xml
index e6b1caed6..e71d256ef 100644
--- a/artemis_sqlmap/Feature.xml
+++ b/artemis_sqlmap/Feature.xml
@@ -146,14 +146,12 @@
</resultMap>
<resultMap id="map-feature-with-residues-result" class="Feature">
- <result property="name" column="name"/>
<result property="uniqueName" column="uniquename"/>
<result property="featureId" column="feature_id"/>
<result property="cvTerm.cvTermId" column="type_id"/>
<result property="cvTerm.name" column="cvterm_name"/>
<!--<result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />-->
<result property="organism.organismId" column="organism_id"/>
- <result property="organism.abbreviation" column="abbreviation"/>
<result property="organism.genus" column="genus"/>
<result property="organism.species" column="species"/>
<result property="organism.commonName" column="common_name"/>
@@ -440,34 +438,51 @@
residues notnull AND residues NOT LIKE '' ORDER BY common_name
</select>
-->
-
-
+
+ <sql id="source_feature_cvterm_names">
+ cvterm.name LIKE '%chromosome%' OR cvterm.name LIKE '%sequence%' OR
+ cvterm.name IN ('supercontig', 'ultra_scaffold', 'golden_path_region', 'contig')
+ </sql>
<select id="getResidueFeatures" parameterClass="java.lang.Integer"
resultMap="map-feature-with-residues-result">
- SELECT feature.name, uniquename, feature_id, type_id, feature.organism_id,
- abbreviation, genus, species, common_name, cvterm.name AS cvterm_name
+ SELECT uniquename, feature_id, type_id, feature.organism_id,
+ genus, species, common_name, cvterm.name AS cvterm_name
FROM cvterm
LEFT JOIN feature ON cvterm.cvterm_id=feature.type_id
LEFT JOIN organism ON organism.organism_id=feature.organism_id
WHERE <isNotNull> feature.organism_id=$value$ AND </isNotNull>
residues notnull AND residues != '' AND
- ( cvterm.name LIKE '%chromosome%' OR cvterm.name LIKE '%sequence%' OR
- cvterm.name IN ('supercontig', 'ultra_scaffold', 'golden_path_region', 'contig') )
- ORDER BY common_name
+ ( <include refid="source_feature_cvterm_names"/> )
+ ORDER BY common_name, uniquename
+ </select>
+
+
+ <select id="getTopLevelFeatures" parameterClass="java.lang.Integer"
+ resultMap="map-feature-with-residues-result">
+ SELECT feature.name, uniquename, feature_id, feature.type_id, feature.organism_id,
+ genus, species, common_name, cvterm.name AS cvterm_name
+ FROM feature
+ JOIN organism using (organism_id)
+ JOIN cvterm on feature.type_id = cvterm.cvterm_id
+ JOIN featureprop using (feature_id)
+ WHERE <isNotNull> feature.organism_id=$value$ AND </isNotNull>
+ featureprop.type_id in (
+ SELECT cvterm_id FROM cvterm JOIN cv using (cv_id) WHERE cv.name = 'genedb_misc' AND cvterm.name = 'top_level_seq' )
+ ORDER BY common_name, uniquename
</select>
+
<select id="getResidueFeaturesByOrganismCommonName" parameterClass="java.lang.String"
resultMap="map-feature-with-residues-result">
- SELECT feature.name, uniquename, feature_id, type_id,
- feature.organism_id, abbreviation, genus, species, common_name
+ SELECT uniquename, feature_id, type_id,
+ feature.organism_id, genus, species, common_name
FROM cvterm
LEFT JOIN feature ON cvterm.cvterm_id=feature.type_id
LEFT JOIN organism ON organism.organism_id=feature.organism_id
WHERE <isNotNull> organism.common_name=#value# AND </isNotNull>
residues notnull AND residues != '' AND
- ( cvterm.name LIKE '%chromosome%' OR cvterm.name LIKE '%sequence%' OR
- cvterm.name IN ('supercontig', 'ultra_scaffold', 'golden_path_region', 'contig') )
- ORDER BY common_name
+ ( <include refid="source_feature_cvterm_names"/> )
+ ORDER BY common_name, uniquename
</select>
--
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