Changes in store() to quieten the unit tests.

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -790,11 +790,9 @@ sub store {
   # store translation
   #
 
-  my @translations =
-    @{ $db->get_TranslationAdaptor()
-      ->fetch_all_by_Transcript($transcript) };
-
-  my $translation = shift(@translations);
+  my $alt_translations =
+    $transcript->get_all_alternative_translations();
+  my $translation = $transcript->translation();
 
   if ( defined($translation) ) {
     #make sure that the start and end exon are set correctly
@@ -865,42 +863,45 @@ sub store {
   # Store the alternative translations, if there are any.
   #
 
-  foreach my $alt_translation (@translations) {
-    my $start_exon = $alt_translation->start_Exon();
-    my $end_exon   = $alt_translation->end_Exon();
+  if ( defined($alt_translations) ) {
+    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($start_exon) ) {
+        throw("Translation does not define a start exon.");
+      } elsif ( !defined($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->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(
+        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;
+        }
+      } 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 "
+        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...
+      $db->get_TranslationAdaptor()
+        ->store( $alt_translation, $transc_dbID );
+    } ## end foreach my $alt_translation...
+  } ## end if ( defined($alt_translations...))
 
   #
   # store the xrefs/object xref mapping