implement way of retrieving information for a srcFeature FeatureLoc range

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6325 ee4ac58c-ac51-4696-9907-e4b3aa274f04

artemis_sqlmap/Feature.xml

@@ -145,6 +145,9 @@
         <dynamic>
          <isGreaterThan property="featureLoc.featureBySrcFeatureId.featureId" compareValue="0"> 
            srcfeature_id=$featureLoc.featureBySrcFeatureId.featureId$ 
+         </isGreaterThan>
+		 <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
+           <![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
          </isGreaterThan>
          <isNotNull property="uniqueName">                        
            uniquename LIKE #uniqueName# 
@@ -196,6 +199,7 @@
      </dynamic>
      f.feature_id > 0 
   </select>
+	
 
   <select id="getLazyFeatureById" resultMap ="map-feature-lazy" >
 	SELECT

artemis_sqlmap/FeatureCvTerm.xml

@@ -42,7 +42,7 @@
  
       <!--  select feature_cvterm -->
 	
-	<select id="getFeatureCvTermsBySrcFeatureId" parameterClass="java.lang.Integer"
+	<select id="getFeatureCvTermsBySrcFeature" parameterClass="org.gmod.schema.sequence.Feature"
              resultMap="select-featurecvterm">
         SELECT
           fc.*, 
@@ -60,7 +60,11 @@
         LEFT JOIN pub ON fc.pub_id=pub.pub_id
         LEFT JOIN dbxref ON cvterm.dbxref_id=dbxref.dbxref_id 
         LEFT JOIN db ON dbxref.db_id=db.db_id
-        WHERE feature_id IN (SELECT feature_id FROM featureloc WHERE srcfeature_id=$value$)
+        WHERE feature_id IN 
+		(SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
+	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
+           <![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
+        </isGreaterThan>)
         ORDER BY fc.feature_cvterm_id, fc.rank, type_id, fcp.rank;
      </select>
 	

artemis_sqlmap/FeatureCvTermDbXRef.xml

@@ -32,14 +32,18 @@
        </dynamic>
     </select>
 	
-	<select id="getFeatureCvTermDbXRefBySrcFeatureId" parameterClass="java.lang.Integer"
+	<select id="getFeatureCvTermDbXRefBySrcFeature" parameterClass="org.gmod.schema.sequence.Feature"
              resultMap="map-featurecvtermdbxref">
        SELECT fcd.feature_cvterm_id, dbx.*, db.name 
        FROM feature_cvterm_dbxref fcd 
        LEFT JOIN dbxref dbx ON dbx.dbxref_id=fcd.dbxref_id 
        LEFT JOIN db ON db.db_id=dbx.db_id
 	   LEFT JOIN feature_cvterm fc ON fcd.feature_cvterm_id=fc.feature_cvterm_id
-	   WHERE feature_id IN (SELECT feature_id FROM featureloc WHERE srcfeature_id=$value$)
+	   WHERE feature_id IN 
+       (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
+	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
+           <![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
+        </isGreaterThan>)
     </select>
      
     <select id="getFeatureCvTermDbXRefByFeatureCvTerm" parameterClass="java.lang.Integer"

artemis_sqlmap/FeatureCvTermPub.xml

@@ -30,13 +30,17 @@
     </select>
 	
 	
-	<select id="getFeatureCvTermPubBySrcFeatureId" parameterClass="java.lang.Integer"
+	<select id="getFeatureCvTermPubBySrcFeature" parameterClass="org.gmod.schema.sequence.Feature"
              resultMap="feature_cvterm_pub">
        SELECT fcp.feature_cvterm_id, pub.* 
        FROM feature_cvterm_pub fcp 
        LEFT JOIN pub ON fcp.pub_id=pub.pub_id
        LEFT JOIN feature_cvterm fc ON fcp.feature_cvterm_id=fc.feature_cvterm_id
-       WHERE feature_id IN (SELECT feature_id FROM featureloc WHERE srcfeature_id=$value$)
+       WHERE feature_id IN 
+       (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
+	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
+           <![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
+        </isGreaterThan>)
     </select>
 	
     

artemis_sqlmap/FeatureDbXRef.xml

@@ -55,8 +55,8 @@
     ORDER BY f.type_id,  uniquename
   </select>
 
-  <select id="getFeatureDbXRefsBySrcFeatureId" 
-          parameterClass="java.lang.Integer"
+  <select id="getFeatureDbXRefsBySrcFeature" 
+          parameterClass="org.gmod.schema.sequence.Feature"
           resultMap="map-feature-dbxref">
    	SELECT db.name, dbx.accession, dbx.version, dbx.description,
    	       dbx_f.feature_id, dbx_f.is_current
@@ -64,7 +64,11 @@
     LEFT JOIN dbxref dbx ON dbx.dbxref_id=dbx_f.dbxref_id
     LEFT JOIN db ON db.db_id=dbx.db_id 
     LEFT JOIN feature f ON dbx_f.feature_id=f.feature_id
-	WHERE dbx_f.feature_id IN (SELECT feature_id FROM featureloc WHERE srcfeature_id=$value$)
+	WHERE dbx_f.feature_id IN 
+	  (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
+	  <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
+           <![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
+      </isGreaterThan>)
     ORDER BY f.type_id,  uniquename
   </select>
   

artemis_sqlmap/FeaturePub.xml

@@ -30,16 +30,18 @@
        <result property="pub.cvTerm.cvTermId" column="type_id" />   
      </resultMap>
     
-     <select id="getFeaturePubsBySrcFeatureId" parameterClass="java.lang.Integer" 
+     <select id="getFeaturePubsBySrcFeature" parameterClass="org.gmod.schema.sequence.Feature" 
              resultMap="map-featurepubs">
         SELECT
           f.feature_id AS id, pub.*
         FROM feature f
-        LEFT JOIN featureloc fl     ON f.feature_id  = fl.feature_id
         INNER JOIN feature_pub fpub ON fpub.feature_id = f.feature_id 
         LEFT JOIN pub               ON fpub.pub_id=pub.pub_id  
-        WHERE
-            srcfeature_id=$featureId$ 
+        WHERE f.feature_id IN
+        (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
+	    <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
+           <![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
+        </isGreaterThan>)
         ORDER BY f.uniquename
      </select>
      

artemis_sqlmap/FeatureSynonym.xml

@@ -70,13 +70,17 @@
       </isNotNull>
     </select>
     
-	<select id="getFeatureSynonymsBySrcFeatureId" resultMap="map-alias"
-            parameterClass="java.lang.Integer">
+	<select id="getFeatureSynonymsBySrcFeature" resultMap="map-alias"
+            parameterClass="Feature">
       SELECT fs.*, s.name, s.synonym_sgml, s.type_id
       FROM feature_synonym fs 
       LEFT JOIN feature f ON f.feature_id=fs.feature_id 
       LEFT JOIN synonym s ON fs.synonym_id=s.synonym_id
-      WHERE f.feature_id IN (SELECT feature_id FROM featureloc WHERE srcfeature_id=$value$)
+      WHERE f.feature_id IN 
+        (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
+	  <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND"> 
+           <![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
+      </isGreaterThan>)
     </select>
 	
     <select id="getLazyFeatureSynonymsByUniquename" resultMap="map-alias-part-lazy"