changed display_id() to be more inventive to give the object a name

modules/Bio/EnsEMBL/Exon.pm

@@ -793,7 +793,7 @@ sub peptide {
   return Bio::Seq->new(-seq => $pep_str, 
 		       -moltype => 'protein',
 		       -alphabet => 'protein',
-                       -id => $self->stable_id);
+                       -id => $self->display_id);
 }
 
 
@@ -841,7 +841,7 @@ sub seq {
   }
 
   return Bio::Seq->new(-seq     => $self->{'_seq_cache'},
-                       -id      => $self->stable_id,
+                       -id      => $self->display_id,
                        -moltype => 'dna');
 }
 
@@ -910,8 +910,9 @@ sub hashkey {
   Arg [1]    : none
   Example    : print $exons->display_id();
   Description: This method returns a string that is considered to be
-               the 'display' identifier.  For exons this is the stable id if
-               it is available otherwise it is an empty string.
+               the 'display' identifier. For exons this is (depending on
+               availability and in this order) the stable Id, the dbID or an
+               empty string.
   Returntype : string
   Exceptions : none
   Caller     : web drawing code
@@ -921,7 +922,7 @@ sub hashkey {
 
 sub display_id {
   my $self = shift;
-  return $self->{'stable_id'} || '';
+  return $self->{'stable_id'} || $self->dbID || '';
 }
 
 

modules/Bio/EnsEMBL/Gene.pm

@@ -949,8 +949,9 @@ sub recalculate_coordinates {
   Arg [1]    : none
   Example    : print $gene->display_id();
   Description: This method returns a string that is considered to be
-               the 'display' identifier.  For genes this is the stable id if
-               it is available otherwise it is an empty string.
+               the 'display' identifier. For genes this is (depending on
+               availability and in this order) the stable Id, the dbID or an
+               empty string.
   Returntype : string
   Exceptions : none
   Caller     : web drawing code
@@ -960,7 +961,7 @@ sub recalculate_coordinates {
 
 sub display_id {
   my $self = shift;
-  return $self->{'stable_id'} || '';
+  return $self->{'stable_id'} || $self->dbID || '';
 }
 
 

modules/Bio/EnsEMBL/PredictionTranscript.pm

@@ -456,9 +456,9 @@ sub get_all_Exons {
   Arg [1]    : none
   Example    : print $rf->display_id();
   Description: This method returns a string that is considered to be
-               the 'display' identifier.  For prediction transcripts this is 
-               the stable_id if it is available otherwise it is an empty 
-               string.
+               the 'display' identifier. For prediction transcripts this is
+               (depending on availability and in this order) the stable Id, the
+               dbID or an empty string.
   Returntype : string
   Exceptions : none
   Caller     : web drawing code
@@ -468,7 +468,7 @@ sub get_all_Exons {
 
 sub display_id {
   my $self = shift;
-  return $self->stable_id() || '';
+  return $self->stable_id || $self->dbID || '';
 }
 
 

modules/Bio/EnsEMBL/Transcript.pm

@@ -1276,7 +1276,7 @@ sub five_prime_utr {
   return undef if(!$seq);
 
   return Bio::Seq->new(
-	       -DISPLAY_ID => $self->stable_id,
+	       -DISPLAY_ID => $self->display_id,
 	       -MOLTYPE    => 'dna',
 	       -SEQ        => $seq);
 }
@@ -1311,7 +1311,7 @@ sub three_prime_utr {
   return undef if(!$seq);
 
   return Bio::Seq->new(
-	       -DISPLAY_ID => $self->stable_id,
+	       -DISPLAY_ID => $self->display_id,
 	       -MOLTYPE    => 'dna',
 	       -SEQ        => $seq);
 }
@@ -1419,15 +1419,7 @@ sub translate {
   }
 
   my $mrna = $self->translateable_seq();
-  my $display_id;
-  if( defined $self->translation->stable_id ) {
-    $display_id = $self->translation->stable_id;
-  } elsif ( defined $self->translation->dbID ) {
-    $display_id = $self->translation->dbID();
-  } else {
-    #use memory location as temp id
-    $display_id = scalar($self->translation());
-  }
+  my $display_id = $self->translation->display_id || scalar($self->translation);
 
   # remove final stop codon from the mrna if it is present
   # produced peptides will not have '*' at end
@@ -1488,7 +1480,7 @@ sub translate {
 sub seq {
   my( $self ) = @_;
   return Bio::Seq->new
-    (-DISPLAY_ID => $self->stable_id,
+    (-DISPLAY_ID => $self->display_id,
      -MOLTYPE    => 'dna',
      -SEQ        => $self->spliced_seq);
 }
@@ -2030,8 +2022,9 @@ sub recalculate_coordinates {
   Arg [1]    : none
   Example    : print $transcript->display_id();
   Description: This method returns a string that is considered to be
-               the 'display' identifier.  For transcripts this is the 
-               stable id if it is available otherwise it is an empty string.
+               the 'display' identifier. For transcripts this is (depending on
+               availability and in this order) the stable Id, the dbID or an
+               empty string.
   Returntype : string
   Exceptions : none
   Caller     : web drawing code
@@ -2041,7 +2034,7 @@ sub recalculate_coordinates {
 
 sub display_id {
   my $self = shift;
-  return $self->{'stable_id'} || '';
+  return $self->{'stable_id'} || $self->dbID || '';
 }
 
 

modules/Bio/EnsEMBL/Translation.pm

@@ -511,8 +511,9 @@ sub get_all_DomainFeatures{
   Arg [1]    : none
   Example    : print $translation->display_id();
   Description: This method returns a string that is considered to be
-               the 'display' identifier.  For translations this is the 
-               stable id if it is available otherwise it is an empty string.
+               the 'display' identifier. For translations this is (depending on
+               availability and in this order) the stable Id, the dbID or an
+               empty string.
   Returntype : string
   Exceptions : none
   Caller     : web drawing code
@@ -522,7 +523,7 @@ sub get_all_DomainFeatures{
 
 sub display_id {
   my $self = shift;
-  return $self->{'stable_id'} || '';
+  return $self->{'stable_id'} || $self->dbID || '';
 }