Store the alternative translations later in store().

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -855,53 +855,6 @@ sub store {
     $original_translation->adaptor( $translation->adaptor() );
   } ## end if ( defined($translation...))
 
-  # Do the eqivalent of the above for all alternative translations, if
-  # there are any.
-  my $alt_translations =
-    $transcript->get_all_alternative_translations();
-
-  if ( defined($alt_translations)
-       && scalar( @{$alt_translations} ) > 0 )
-  {
-    foreach my $alt_translation ( @{$alt_translations} ) {
-      my $start_exon = $alt_translation->start_Exon();
-      my $end_exon   = $alt_translation->end_Exon();
-
-      if ( !defined($start_exon) ) {
-        throw("Translation does not define a start exon.");
-      } elsif ( !defined($end_exon) ) {
-        throw("Translation does not defined an end exon.");
-      }
-
-      if ( !defined( $start_exon->dbID() ) ) {
-        my $key = $start_exon->hashkey();
-        ($start_exon) = grep { $_->hashkey() eq $key } @{$exons};
-
-        if ( defined($start_exon) ) {
-          $alt_translation->start_Exon($start_exon);
-        } else {
-          throw(
-            "Translation's start_Exon does not appear to be one of the "
-              . "exons in its associated Transcript" );
-        }
-      } elsif ( !defined( $end_exon->dbID() ) ) {
-        my $key = $end_exon->hashkey();
-        ($end_exon) = grep { $_->hashkey() eq $key } @$exons;
-
-        if ( defined($end_exon) ) {
-          $translation->end_Exon($end_exon);
-        } else {
-          throw(
-              "Translation's end_Exon does not appear to be one of the "
-                . "exons in its associated Transcript." );
-        }
-      }
-
-      $db->get_TranslationAdaptor()
-        ->store( $alt_translation, $transc_dbID );
-    } ## end foreach my $alt_translation...
-  } ## end if ( defined($alt_translations...))
-
   #
   # store the xrefs/object xref mapping
   #
@@ -999,6 +952,56 @@ sub store {
   $attr_adaptor->store_on_Transcript($transc_dbID,
                                      $transcript->get_all_Attributes);
 
+
+  #
+  # Store the alternative translations, if there are any.
+  #
+
+  my $alt_translations =
+    $transcript->get_all_alternative_translations();
+
+  if ( defined($alt_translations)
+       && scalar( @{$alt_translations} ) > 0 )
+  {
+    foreach my $alt_translation ( @{$alt_translations} ) {
+      my $start_exon = $alt_translation->start_Exon();
+      my $end_exon   = $alt_translation->end_Exon();
+
+      if ( !defined($start_exon) ) {
+        throw("Translation does not define a start exon.");
+      } elsif ( !defined($end_exon) ) {
+        throw("Translation does not defined an end exon.");
+      }
+
+      if ( !defined( $start_exon->dbID() ) ) {
+        my $key = $start_exon->hashkey();
+        ($start_exon) = grep { $_->hashkey() eq $key } @{$exons};
+
+        if ( defined($start_exon) ) {
+          $alt_translation->start_Exon($start_exon);
+        } else {
+          throw(
+            "Translation's start_Exon does not appear to be one of the "
+              . "exons in its associated Transcript" );
+        }
+      } elsif ( !defined( $end_exon->dbID() ) ) {
+        my $key = $end_exon->hashkey();
+        ($end_exon) = grep { $_->hashkey() eq $key } @$exons;
+
+        if ( defined($end_exon) ) {
+          $translation->end_Exon($end_exon);
+        } else {
+          throw(
+              "Translation's end_Exon does not appear to be one of the "
+                . "exons in its associated Transcript." );
+        }
+      }
+
+      $db->get_TranslationAdaptor()
+        ->store( $alt_translation, $transc_dbID );
+    } ## end foreach my $alt_translation...
+  } ## end if ( defined($alt_translations...))
+
   #update the original transcript object - not the transfered copy that
   #we might have created
   $original->dbID($transc_dbID);