add getOrganismsContainingSrcFeatures

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9367 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/chado/GmodDAO.java

@@ -49,6 +49,7 @@ public abstract class GmodDAO
        implements SequenceDaoI, SchemaDaoI, OrganismDaoI, CvDaoI, PubDaoI, GeneralDaoI
 {
   
+  public abstract List getOrganismsContainingSrcFeatures();
   public abstract List getSimilarityMatchesByFeatureIds(final List featureIds);
   public abstract List getSimilarityMatches(final Integer srcFeatureId);
   public abstract List getClustersByFeatureIds(final List featureIds);

uk/ac/sanger/artemis/chado/IBatisDAO.java

@@ -118,7 +118,12 @@ public class IBatisDAO extends GmodDAO
   
   public List getResidueFeatures(final Integer organismId)
   {
-    return sqlMap.queryForList("getResidueFeatures",organismId);
+
+    CvTerm cvTerm = getCvTermByNameAndCvName("top_level_seq", "genedb_misc");
+    if(cvTerm  != null)
+      return sqlMap.queryForList("getTopLevelFeatures",organismId);
+    else
+      return sqlMap.queryForList("getResidueFeatures",organismId);
   }
   
   public List getResidueFeaturesByOrganismCommonName(final String commonName)
@@ -492,8 +497,6 @@ public class IBatisDAO extends GmodDAO
   
   /**
    * Return a list of top-level features 
-   * 
-   *  
    * @return a (possibly empty) List<Feature> of children
    */
   public List getTopLevelFeatures()
@@ -570,9 +573,22 @@ public class IBatisDAO extends GmodDAO
    */
   public List getResidueFeatures()
   { 
-    return sqlMap.queryForList("getResidueFeatures",null);
+    CvTerm cvTerm = getCvTermByNameAndCvName("top_level_seq", "genedb_misc");
+    if(cvTerm  != null)
+      return sqlMap.queryForList("getTopLevelFeatures",null);
+    else
+      return sqlMap.queryForList("getResidueFeatures",null);
   }
 
+  public List getOrganismsContainingSrcFeatures()
+  {
+    CvTerm cvTerm = getCvTermByNameAndCvName("top_level_seq", "genedb_misc");
+    if(cvTerm  != null)
+      return sqlMap.queryForList("getTopLevelOrganisms", null);
+    else  
+      return sqlMap.queryForList("getOrganismsContainingSrcFeatures", null);
+  }
+  
   /**
    *
    * For a schema return the type_id's with residues.

uk/ac/sanger/artemis/chado/JdbcDAO.java

@@ -101,6 +101,11 @@ public class JdbcDAO extends GmodDAO
   //////
   //////
   
+  public List getOrganismsContainingSrcFeatures()
+  {
+    return null;
+  }
+  
   public Feature getLazyFeatureNoResiduesById(final Integer featureId)
   {
     return null;