Modify store() so that it also stores the alternative translations

associated with the transcript.

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -745,9 +745,9 @@ sub store {
   }
 
   my $original_translation = $transcript->translation();
-  my $original = $transcript;
+  my $original             = $transcript;
   my $seq_region_id;
-  ($transcript, $seq_region_id) = $self->_pre_store($transcript);
+  ( $transcript, $seq_region_id ) = $self->_pre_store($transcript);
 
   # first store the transcript w/o a display xref
   # the display xref needs to be set after xrefs are stored which needs to
@@ -855,6 +855,53 @@ 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
   #