diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index a50cfd74015a666d605bee184a7028c692fbdb29..23d5f92627c3d90664e76dad3a392a12e017954c 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/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);
// }
}
}
diff --git a/uk/ac/sanger/artemis/chado/Feature.java b/uk/ac/sanger/artemis/chado/Feature.java
index 259c72f070945a0fd07949c6d224c60bf168e5ec..9abf44d8b260456775a5813c08a5f1e7c3cd70b6 100644
--- a/uk/ac/sanger/artemis/chado/Feature.java
+++ b/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
- */
- public void addQualifier(long prop_type_id, FeatureProp featprop)
- {
- if(qualifiers == null)
- qualifiers = new Hashtable();
-
- 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);
- }
- }
-
/**
- * 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>
+ * Used in merging the qualifiers to store them as a <code>List</code> of
+ * <code>FeatureProp</code>.
+ * @param the FeatureProp
*/
- public Hashtable getQualifiers()
+ public void addFeatureProp(final FeatureProp featureprop)
{
- return qualifiers;
+ if(featureProps == null)
+ featureProps = new Vector();
+
+ featureProps.add(featureprop);
}
+
/**
* Utility for finding a feature location from a List that corresponds
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 6b17a2764f4b82e48d4c32330bcd21ac69942435..49b2be4d5b3fa0f5333d992f658c89d5fab3b88e 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/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;
}
/**
@@ -494,52 +495,7 @@ 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
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 90b2f0b0560f28f1a27d3a6946702d6698d38b2a..29bf7cd72f371e64bdb3d05fb1c8b37db3d92a80 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/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;
+ }
}
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index faaa54131f79c336b3c4fef0d55213687265bfa9..6933841273c4f5f06a4497eb23b327fef27012d9 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/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())+";");
- }
+ if(featprop.getValue() != null)
+ this_buff.append(qualifier_name+ "=" +
+ GFFStreamFeature.encode(featprop.getValue())+";");
}
- }
+ }
// append dbxrefs
if(dbxref != null && dbxref.size() > 0)