check for primary dbxref in addLazyQualifiers()

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10750 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java

@@ -43,6 +43,7 @@ import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 
+import org.gmod.schema.general.DbXRef;
 import org.gmod.schema.sequence.FeatureCvTerm;
 import org.gmod.schema.sequence.FeatureDbXRef;
 import org.gmod.schema.sequence.FeaturePub;
@@ -136,6 +137,17 @@ public class GeneUtils
     }
     
     // dbxrefs
+    if(feature.getQualifierByName("Dbxref") == null)
+    {
+      DbXRef dbxref = feature.getChadoLazyFeature().getDbXRef();
+      if(dbxref != null)
+      {
+        String value = dbxref.getDb().getName() + ":" + 
+                       dbxref.getAccession();
+        feature.getQualifiers().setQualifier(new Qualifier("Dbxref", value));
+      }
+    }
+    
     final Collection featureDbXRefs = feature.getChadoLazyFeature().getFeatureDbXRefs();
     final Iterator it2 = featureDbXRefs.iterator();
     while(it2.hasNext())
@@ -155,39 +167,40 @@ public class GeneUtils
     
     // feature cvterms (GO, product....)
     final Collection featureCvTerms = feature.getChadoLazyFeature().getFeatureCvTerms();
-    final Iterator it3 = featureCvTerms.iterator();
-    
-    while(it3.hasNext())
+    if(featureCvTerms != null)
     {
-      FeatureCvTerm featureCvTerm = (FeatureCvTerm)it3.next();
-      List featureCvTermDbXRefList = null;
-      
-      if(featureCvTerm.getFeatureCvTermDbXRefs() != null)
-        featureCvTermDbXRefList = new Vector(featureCvTerm.getFeatureCvTermDbXRefs());
+      final Iterator it3 = featureCvTerms.iterator();
+      while(it3.hasNext())
+      {
+        FeatureCvTerm featureCvTerm = (FeatureCvTerm)it3.next();
+        List featureCvTermDbXRefList = null;
+       
+        if(featureCvTerm.getFeatureCvTermDbXRefs() != null)
+          featureCvTermDbXRefList = new Vector(featureCvTerm.getFeatureCvTermDbXRefs());
       
-      List featureCvTermPubList = null;
+        List featureCvTermPubList = null;
       
-      if(featureCvTerm.getFeatureCvTermPubs() != null)
-        featureCvTermPubList = new Vector(featureCvTerm.getFeatureCvTermPubs());
+        if(featureCvTerm.getFeatureCvTermPubs() != null)
+          featureCvTermPubList = new Vector(featureCvTerm.getFeatureCvTermPubs());
        
-      ByteBuffer this_buff = new ByteBuffer();
-      DatabaseDocument.appendControlledVocabulary(this_buff, null, featureCvTerm,
+        ByteBuffer this_buff = new ByteBuffer();
+        DatabaseDocument.appendControlledVocabulary(this_buff, null, featureCvTerm,
                                  featureCvTermDbXRefList,featureCvTermPubList, null, false);
       
-      final String qualifierString = new String(this_buff.getBytes());
-      int ind = qualifierString.indexOf('=');
-      final String name  = qualifierString.substring(0, ind);
-      final String value = GFFStreamFeature.decode(
+        final String qualifierString = new String(this_buff.getBytes());
+        int ind = qualifierString.indexOf('=');
+        final String name  = qualifierString.substring(0, ind);
+        final String value = GFFStreamFeature.decode(
           qualifierString.substring(ind+1, qualifierString.length()-1));
       
-      Qualifier qualifier = feature.getQualifiers().getQualifierByName(name);
-      if(qualifier == null)
-        qualifier = new Qualifier(name, value);
-      else
-        qualifier.addValue(value);
-      feature.getQualifiers().setQualifier(qualifier);
+        Qualifier qualifier = feature.getQualifiers().getQualifierByName(name);
+        if(qualifier == null)
+          qualifier = new Qualifier(name, value);
+        else
+          qualifier.addValue(value);
+        feature.getQualifiers().setQualifier(qualifier);
+      }
     }
-    
     // feature pubs - literature
     final Collection featurePubs = feature.getChadoLazyFeature().getFeaturePubs();