fix so that PredictionTranscript->translation->seq() works like normal Transcript

modules/Bio/EnsEMBL/PredictionTranscript.pm

@@ -222,11 +222,22 @@ sub translation {
     $end_exon = $exons[0];
   }
 
-  return
-    Bio::EnsEMBL::Translation->new(-START_EXON => $start_exon,
-                                   -END_EXON   => $end_exon,
-                                   -SEQ_START  => 1,
-                                   -SEQ_END    => $end_exon->length());
+  my $pta;
+
+  if($self->adaptor()) {
+    $pta = $self->adaptor()->db()->get_TranslationAdaptor();
+  } else {
+    warning("PredictionTranscript has no adaptor, may not be able to obtain " .
+            "translation");
+  }
+
+  return Bio::EnsEMBL::Translation->new
+    (-ADAPTOR    => $pta,
+     -START_EXON => $start_exon,
+     -END_EXON   => $end_exon,
+     -SEQ_START  => 1,
+     -SEQ_END    => $end_exon->length(),
+     -SEQ        => $self->translate()->seq());
 }
 
 

modules/Bio/EnsEMBL/Translation.pm

@@ -478,6 +478,11 @@ sub length {
 sub seq {
   my $self = shift;
 
+  if(@_) {
+    $self->{'seq'} = shift;
+    return $self->{'seq'};
+  }
+
   return $self->{'seq'} if($self->{'seq'});
 
   my $adaptor = $self->{'adaptor'};
@@ -487,7 +492,7 @@ sub seq {
 
   my $dbID = $self->{'dbID'};
   if(!$dbID) {
-    warning("Cannot retrieve sequence from Translation - adaptor is not set.");
+    warning("Cannot retrieve sequence from Translation - dbID is not set.");
   }
   
   my $tr_adaptor = $self->{'adaptor'}->db()->get_TranscriptAdaptor;