use groupBy to merge FeatureProps

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4705 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

@@ -712,7 +712,11 @@ public class ChadoTransactionManager
             // happens when duplicating features 
             FeatureProp featureprop = new FeatureProp();
             featureprop.setValue((String)qualifier_values.elementAt(value_index));
-            chado_feature.addQualifier(type_id, featureprop);
+            CvTerm cvTerm = new CvTerm();
+            cvTerm.setCvTermId(type_id);
+            featureprop.setCvTerm(cvTerm);
+            chado_feature.addFeatureProp(featureprop);
+ //           chado_feature.addQualifier(type_id, featureprop);
  //         }
         }
       }

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

@@ -69,8 +69,6 @@ public class Feature
   private Organism organism;
   /** optional primary public stable identifier */
   private FeatureDbXRef featureDbXRef;
-  /** merged featureprops */
-  private Hashtable qualifiers;
   /** list of FeatureProp */
   private Collection featureProps;
   /** list of FeatureRelationship children */
@@ -403,11 +401,11 @@ public class Feature
   {
     this.featureProps = featureProps;
     
-    for(int i=0; i<featureProps.size(); i++)
+/*    for(int i=0; i<featureProps.size(); i++)
     {
       FeatureProp featureprop = (FeatureProp)(((List)featureProps).get(i));
       addQualifier(featureprop.getCvTerm().getCvTermId(), featureprop);
-    }
+    }*/
   }
   
   /**
@@ -494,44 +492,19 @@ public class Feature
     this.featureSynonymsForFeatureId = featureSynonymsForFeatureId;
   }
   
-  
-  
   /**
-   * Used in merging the qualifiers to store them as a <code>Hashtable</code> of
-   * the cvTerm type_id (of the property name) and the property values as a 
-   * <code>Vector</code>.
-   * @param	the cvTerm type_id of the property name
-   * @param	the property value	
+   * Used in merging the qualifiers to store them as a <code>List</code> of
+   * <code>FeatureProp</code>.
+   * @param the FeatureProp 
    */
-  public void addQualifier(long prop_type_id, FeatureProp featprop)
+  public void addFeatureProp(final FeatureProp featureprop)
   {
-    if(qualifiers == null)
-      qualifiers = new Hashtable();
+    if(featureProps == null) 
+      featureProps = new Vector();
     
-    final Long type_id = new Long(prop_type_id);
-    if(qualifiers.containsKey(type_id))
-    {
-      Vector v = (Vector)qualifiers.get(type_id);
-      v.add(featprop);
-      qualifiers.put(type_id, v);
-    }
-    else
-    {
-      Vector v = new Vector();
-      v.add(featprop);
-      qualifiers.put(type_id, v);
-    }
+    featureProps.add(featureprop);
   }
   
-  /**
-   * Get the qualifiers which are stored as a <code>Hashtable</code> of cvTerm
-   * type_id (of the property name) and the property values as a <code>Vector</code>.
-   * @return	the qualifiers as a <code>Hashtable</code>
-   */
-  public Hashtable getQualifiers()
-  {
-    return qualifiers;
-  }
 
   /**
    * Utility for finding a feature location from a List that corresponds

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

@@ -92,7 +92,8 @@ public class IBatisDAO implements ChadoDAO
     List feature_list = sqlMap.queryForList("getFeature", feature);
 
     // merge same features in the list
-    return mergeList(feature_list);
+    //return mergeList(feature_list);
+    return feature_list;
   }
 
   /**
@@ -495,51 +496,6 @@ public class IBatisDAO implements ChadoDAO
     sqlMap.commitTransaction();
   }
 
-  /**
-   * Takes a list and creates a new one merging all feature objects
-   * within it with the same feature and stores the qualifiers/attributes
-   *  as a hash
-   * @param list of feature objects
-   * @return list of flattened/merged feature objects
-   */
-  protected static List mergeList(final List list)
-  {
-    // merge same features in the list
-    int feature_size  = list.size();
-    final List flatten_list = new Vector();
-    Feature featNext  = null;
-
-    for(int i = 0; i < feature_size; i++)
-    {
-      Feature feat = (Feature)list.get(i);
-      String name  = feat.getUniqueName();
-
-      feat.addQualifier(feat.getFeatureprop().getCvTerm().getCvTermId(),
-                        feat.getFeatureprop());
-
-      if(i < feature_size - 1)
-        featNext = (Feature)list.get(i + 1);
-      else
-        featNext = null;
-      
-      // merge next line if part of the same feature
-      while(featNext != null && featNext.getUniqueName().equals(name))
-      {
-        feat.addQualifier(featNext.getFeatureprop().getCvTerm().getCvTermId(),
-                          featNext.getFeatureprop());
-        i++;
-
-        if(i < feature_size - 1)
-          featNext = (Feature)list.get(i + 1);
-        else
-          break;
-      }
-
-      flatten_list.add(feat);
-    }
-
-    return flatten_list;
-  }
 
   /**
    * Takes a list and creates a <code>Hashtable</code> with the keys

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

@@ -251,7 +251,7 @@ public class JdbcDAO
       throw new RuntimeException(sqle);
     }
     // merge same features in the list
-    return IBatisDAO.mergeList(list);
+    return mergeList(list);
   }
   
 
@@ -1183,4 +1183,51 @@ public class JdbcDAO
     }
   }
 
+  /**
+   * Takes a list and creates a new one merging all feature objects
+   * within it with the same feature and stores the qualifiers/attributes
+   *  as a hash
+   * @param list of feature objects
+   * @return list of flattened/merged feature objects
+   */
+  private static List mergeList(final List list)
+  {
+    // merge same features in the list
+    int feature_size  = list.size();
+    final List flatten_list = new Vector();
+    Feature featNext  = null;
+
+    for(int i = 0; i < feature_size; i++)
+    {
+      Feature feat = (Feature)list.get(i);
+      String name  = feat.getUniqueName();
+
+      feat.addFeatureProp(feat.getFeatureprop());
+      //feat.addQualifier(feat.getFeatureprop().getCvTerm().getCvTermId(),
+      //                  feat.getFeatureprop());
+
+      if(i < feature_size - 1)
+        featNext = (Feature)list.get(i + 1);
+      else
+        featNext = null;
+      
+      // merge next line if part of the same feature
+      while(featNext != null && featNext.getUniqueName().equals(name))
+      {
+        //feat.addQualifier(featNext.getFeatureprop().getCvTerm().getCvTermId(),
+        //                  featNext.getFeatureprop());
+        feat.addFeatureProp(featNext.getFeatureprop());
+        i++;
+
+        if(i < feature_size - 1)
+          featNext = (Feature)list.get(i + 1);
+        else
+          break;
+      }
+
+      flatten_list.add(feat);
+    }
+
+    return flatten_list;
+  }
 }

uk/ac/sanger/artemis/util/DatabaseDocument.java

@@ -740,29 +740,20 @@ public class DatabaseDocument extends Document
     //this_buff.append("feature_id="+feature_id+";");
     
     // attributes
-    Hashtable qualifiers = feat.getQualifiers();
-    
-    if(qualifiers != null && qualifiers.size() > 0)
+    if(feat.getFeatureProps() != null)
     {
-      Enumeration e_qualifiers = qualifiers.keys();
-      while(e_qualifiers.hasMoreElements())
+      List featureprops = (List)feat.getFeatureProps();
+      for(int j=0; j<featureprops.size(); j++)
       {
-        Long qualifier_type_id = (Long)e_qualifiers.nextElement();
-        String qualifier_name = getCvtermName(qualifier_type_id.longValue(), dao);
+        FeatureProp featprop = (FeatureProp)featureprops.get(j);
+        String qualifier_name = getCvtermName(featprop.getCvTerm().getCvTermId(), dao);
         if(qualifier_name == null)
           continue;
-        
-        Vector qualifier_value = (Vector)qualifiers.get(qualifier_type_id);
-        for(int j=0; j<qualifier_value.size(); j++)
-        {
-          FeatureProp featprop = (FeatureProp)qualifier_value.get(j);
-         
         if(featprop.getValue() != null)
           this_buff.append(qualifier_name+ "=" +
                            GFFStreamFeature.encode(featprop.getValue())+";");
       }
     }
-    } 
 
     // append dbxrefs
     if(dbxref != null && dbxref.size() > 0)