fixes for cluster/ortho/paralog

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6342 ee4ac58c-ac51-4696-9907-e4b3aa274f04

artemis_sqlmap/Feature.xml

@@ -66,6 +66,15 @@
                                 select="getOrganism" />
   </resultMap>
 	
+	
+  <resultMap id="map-feature-name-lazy" class="Feature">
+	 <result property="uniqueName" column="uniquename"/>
+	 <result property="cvTerm.name" column="name" />
+	 <result property="featureRelationshipsForSubjectId" column="{subject_id=id}" 
+                                       select="getParentFeatureRelationship" /> 
+  </resultMap>
+	  	
+	
   <resultMap id="map-feature-withprop" class="Feature" 
 	         groupBy="featureId" extends="map-basicfeature">
     <result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
@@ -95,10 +104,13 @@
 	
 
   <resultMap id="map-clusterfeature" class="Feature" 
-	         groupBy="featureId" extends="map-basicfeature">       
-    <result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
+	         groupBy="featureId">
+	<result property="featureId" column="id"/>
+    <result property="uniqueName" column="cluster_name"/>       
+    <result property="cvTerm.name" column="cluster_cvterm"/>
 	<result property="featureProps" column="{feature_id=id}" 
                                        select="getFeaturePropByFeatureId" />
+	  
 	<result property="featureRelationshipsForSubjectId" 
    	            resultMap="FeatureRelationship.map-feature-relationship-for-subjectId"  />  
     <result property="analysisFeatures" resultMap="AnalysisFeature.map-analysisfeature" />                                                
@@ -216,6 +228,15 @@
     WHERE f.feature_id=$featureId$
   </select>
 	
+  <select id="getLazyFeatureNameAndTypeById" resultMap ="map-feature-name-lazy" >
+	SELECT
+	  uniquename, cvTerm.name, feature_id AS id
+	FROM feature f
+	LEFT JOIN cvterm ON cvterm.cvterm_id=type_id
+    WHERE f.feature_id=$featureId$
+  </select>
+	
+	
   <select id="getFeatureById" resultMap ="map-feature-withprop" 
 		cacheModel="feature-cache">
 	SELECT
@@ -308,23 +329,25 @@
   <select id="getLazyClustersByFeatureIds" parameterClass="java.util.List" 
                              resultMap="map-clusterfeature">
 	SELECT
-	  timelastmodified, 
 	  f.feature_id AS id,
-	  fr.feature_relationship_id, 
+	  f.uniquename AS cluster_name,
+	  cv_f.name AS cluster_cvterm,
+	  f1.uniquename AS subject_name,
 	  fr.subject_id,
-	  fr.type_id AS relation_type_id,
-	  fr.value AS relation_value,
-	  fr.rank,
-	  f.uniquename, 
-	  f.type_id, 
-	  f.name AS feature_name,    
-	  f.seqlen,
+	  cv_fr.name AS fr_name,
+	  common_name AS subject_common_name,
+	  cv_f1.name AS subject_cvterm,
 	  rawscore, normscore, significance, identity, a.analysis_id,
 	  a.name, description, program, programversion, algorithm, sourcename, sourceversion,sourceuri, timeexecuted     
 	FROM feature f
 	LEFT JOIN feature_relationship fr ON  f.feature_id=fr.object_id 
 	LEFT JOIN analysisfeature af ON f.feature_id=af.feature_id
 	LEFT JOIN analysis a ON af.analysis_id=a.analysis_id
+	LEFT JOIN feature f1 ON f1.feature_id=subject_id 
+	LEFT JOIN organism ON f1.organism_id=organism.organism_id
+    LEFT JOIN cvterm AS cv_f1 ON cv_f1.cvterm_id=f1.type_id
+	LEFT JOIN cvterm AS cv_fr ON cv_fr.cvterm_id=fr.type_id
+	LEFT JOIN cvterm AS cv_f  ON cv_f.cvterm_id=f.type_id
 	WHERE f.feature_id IN <iterate open="(" close=")" conjunction=","> #[]# </iterate>
   </select>
 

artemis_sqlmap/FeatureRelationship.xml

@@ -23,10 +23,15 @@
 		<result property="featureByObjectId.featureId" column="object_id"/>
      </resultMap>
 
-	 <resultMap id="map-feature-relationship-for-subjectId" class="FeatureRelationship"
-		        extends="map-basic-feature-relationship">
-		<result property="featureBySubjectId" column="subject_id" 
-			                                  select="getLazyFeatureById"/>
+	<resultMap id="map-feature-relationship-for-subjectId" class="FeatureRelationship">
+		<result property="cvTerm.name" column="fr_name"/>
+		<result property="featureBySubjectId.featureId" column="subject_id"/>
+		<result property="featureBySubjectId.uniqueName" column="subject_name"/>
+		<result property="featureBySubjectId.organism.commonName" column="subject_common_name"/>
+		<result property="featureBySubjectId.cvTerm.name" column="subject_cvterm" />
+		<result property="featureBySubjectId.featureRelationshipsForSubjectId" 
+			                           column="{{subject_id=subject_id}}" 
+                                       select="getParentFeatureRelationship" /> 
     </resultMap>
 	
     <resultMap id="select-relationship" class="FeatureRelationship">
@@ -40,6 +45,17 @@
         <result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
      </resultMap>
 
+    <resultMap id="map-parent-relationship" class="FeatureRelationship">
+		<result property="featureRelationshipId" column="feature_relationship_id"/>
+        <result property="featureBySubjectId" column="subject_id" 
+			                                  select="getLazyFeatureById" />
+        <result property="featureByObjectId"  column="object_id"
+			                                  select="getLazyFeatureNameAndTypeById" />
+        <result property="value" column="value" />
+        <result property="rank" column="rank" />
+        <result property="cvTerm.name" column="name" />
+     </resultMap>	
+	     
      <!--  select feature_relationship -->
      <select id="getFeatureRelationship" resultMap="select-relationship">
        SELECT feature_relationship_id, subject_id, object_id, type_id, value, rank 
@@ -55,6 +71,13 @@
          </dynamic>
      </select>
 
+	<select id="getParentFeatureRelationship" resultMap="map-parent-relationship">
+       SELECT feature_relationship_id, subject_id, object_id, type_id, value, rank, cvterm.name
+       FROM feature_relationship
+	   LEFT JOIN cvterm ON cvterm_id=type_id
+       WHERE subject_id=#subject_id# AND 
+		( cvterm.name='derives_from' OR cvterm.name='part_of' OR cvterm.name='proper_part_of' )
+     </select>
 	
     <update id="updateFeatureRelationshipsForSubjectId" 
            parameterClass="FeatureRelationship">