Update get_all_DBEntries() and get_all_DBLinks().

Add the following proxy methods:

* get_all_object_xrefs()    alias for get_all_DBEntries()
* get_all_xrefs()           alias for get_all_DBLinks()

These have no documentation as of yet.

modules/Bio/EnsEMBL/Gene.pm

@@ -635,17 +635,23 @@ sub add_DBEntry {
 
 =head2 get_all_DBEntries
 
-  Arg [1]    : (optional) string external database name
-  Arg [2]    : (optional) string external_db type
-  Example    : @dbentries = @{ $gene->get_all_DBEntries };
-  Description: Retrieves DBEntries (xrefs) for this gene. This does _not_ 
-               include DBEntries that are associated with the transcripts and
-               corresponding translations of this gene (see get_all_DBLinks).
-
-               This method will attempt to lazy-load DBEntries from a
-               database if an adaptor is available and no DBEntries are present
-               on the gene (i.e. they have not already been added or loaded).
-  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
+  Arg [1]    : (optional) String, external database name
+
+  Arg [2]    : (optional) String, external_db type
+
+  Example    : @dbentries = @{ $gene->get_all_DBEntries() };
+
+  Description: Retrieves DBEntries (xrefs) for this gene.  This does
+               *not* include DBEntries that are associated with the
+               transcripts and corresponding translations of this
+               gene (see get_all_DBLinks()).
+
+               This method will attempt to lazy-load DBEntries
+               from a database if an adaptor is available and no
+               DBEntries are present on the gene (i.e. they have not
+               already been added or loaded).
+
+  Return type: Listref of Bio::EnsEMBL::DBEntry objects
   Exceptions : none
   Caller     : get_all_DBLinks, GeneAdaptor::store
   Status     : Stable
@@ -655,7 +661,7 @@ sub add_DBEntry {
 sub get_all_DBEntries {
   my ( $self, $db_name_exp, $ex_db_type ) = @_;
 
-  my $cache_name = "dbentries";
+  my $cache_name = 'dbentries';
 
   if ( defined($db_name_exp) ) {
     $cache_name .= $db_name_exp;
@@ -669,8 +675,8 @@ sub get_all_DBEntries {
   if ( !defined( $self->{$cache_name} ) && defined( $self->adaptor() ) )
   {
     $self->{$cache_name} =
-      $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Gene( $self,
-                                            $db_name_exp, $ex_db_type );
+      $self->adaptor()->db()->get_DBEntryAdaptor()
+      ->fetch_all_by_Gene( $self, $db_name_exp, $ex_db_type );
   }
 
   $self->{$cache_name} ||= [];
@@ -678,26 +684,37 @@ sub get_all_DBEntries {
   return $self->{$cache_name};
 } ## end sub get_all_DBEntries
 
+sub get_all_object_xrefs {
+  my $self = shift;
+  return $self->get_all_DBEntries(@_);
+}
 
 =head2 get_all_DBLinks
 
-  Example    : @dblinks = @{ $gene->get_all_DBLinks };
-             : @dblinks = @{ $gene->get_all_DBLinks("Uniprot%") };
-  Arg [1]    : <optional> database name. SQL wildcard characters (_ and %) can be used to
+  Arg [1]    : String database name (optional)
+               SQL wildcard characters (_ and %) can be used to
                specify patterns.
-  Description: Retrieves _all_ related DBEntries for this gene. This includes
-               all DBEntries that are associated with the transcripts and
-               corresponding translations of this gene.
-
-               If you only want to retrieve the DBEntries associated with the
-               gene (and not the transcript and translations) then you should
-               use the get_all_DBEntries call instead.
-         
-               Note: Each entry may be listed more than once. No uniqueness checks are done.
-                     Also if you put in an incorrect external database name no checks are done
-                     to see if this exists, you will just get an empty list.
-
-  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
+
+  Example    : @dblinks = @{ $gene->get_all_DBLinks() };
+               @dblinks = @{ $gene->get_all_DBLinks('Uniprot%') };
+
+  Description: Retrieves *all* related DBEntries for this gene. This
+               includes all DBEntries that are associated with the
+               transcripts and corresponding translations of this
+               gene.
+
+               If you only want to retrieve the DBEntries
+               associated with the gene (and not the transcript
+               and translations) then you should use the
+               get_all_DBEntries() call instead.
+
+               Note: Each entry may be listed more than once.  No
+               uniqueness checks are done.  Also if you put in an
+               incorrect external database name no checks are done
+               to see if this exists, you will just get an empty
+               list.
+
+  Return type: Listref of Bio::EnsEMBL::DBEntry objects
   Exceptions : none
   Caller     : general
   Status     : Stable
@@ -705,23 +722,25 @@ sub get_all_DBEntries {
 =cut
 
 sub get_all_DBLinks {
-   my $self = shift;
-   my $db_name_exp = shift;
-   my $ex_db_type = shift;
-
-   my @links = @{$self->get_all_DBEntries($db_name_exp, $ex_db_type)};
+  my ( $self, $db_name_exp, $ex_db_type ) = @_;
 
-   # add all of the transcript and translation xrefs to the return list
-   foreach my $transc (@{$self->get_all_Transcripts}) {
-     push @links, @{$transc->get_all_DBEntries($db_name_exp, $ex_db_type)};
+  my @links =
+    @{ $self->get_all_DBEntries( $db_name_exp, $ex_db_type ) };
 
-     my $transl = $transc->translation();
-     push @links, @{$transl->get_all_DBEntries($db_name_exp, $ex_db_type)} if($transl);
-   }
+  # Add all of the transcript and translation xrefs to the return list.
+  foreach my $transcript ( @{ $self->get_all_Transcripts() } ) {
+    push( @links,
+          @{$transcript->get_all_DBLinks( $db_name_exp, $ex_db_type ) }
+    );
+  }
 
-   return \@links;
+  return \@links;
 }
 
+sub get_all_xrefs {
+  my $self = shift;
+  return $self->get_all_DBLinks(@_);
+}
 
 =head2 get_all_Exons
 

modules/Bio/EnsEMBL/Transcript.pm

@@ -181,18 +181,28 @@ sub new {
 
 =head2 get_all_DBLinks
 
-  Arg [1]    : (optional) String, external database name
-  Arg [2]    : (optional) String, external database type
+  Arg [1]    : String database name (optional)
+               SQL wildcard characters (_ and %) can be used to
+               specify patterns.
+
   Example    : my @dblinks = @{ $transcript->get_all_DBLinks() };
-  Description: Retrieves _all_ related DBEntries for this transcript.  
-               This includes all DBEntries that are associated with the
-               corresponding translation.
-
-               If you only want to retrieve the DBEntries associated with the
-               transcript then you should use the get_all_DBEntries call 
-               instead.
-  Returntype : Listref of Bio::EnsEMBL::DBEntry objects, sorted by
-               priority (desc), external db name (asc), display_id (asc)
+               my @dblinks = @{ $transcript->get_all_DBLinks('Uniprot%') };
+
+  Description: Retrieves *all* related DBEntries for this
+               transcript.  This includes all DBEntries that are
+               associated with the corresponding translation.
+
+               If you only want to retrieve the DBEntries associated
+               with the transcript (and not the translation) then
+               you should use the get_all_DBEntries() call instead.
+
+               Note: Each entry may be listed more than once.  No
+               uniqueness checks are done.  Also if you put in an
+               incorrect external database name no checks are done
+               to see if this exists, you will just get an empty
+               list.
+
+  Return type: Listref of Bio::EnsEMBL::DBEntry objects
   Exceptions : none
   Caller     : general
   Status     : Stable
@@ -200,17 +210,16 @@ sub new {
 =cut
 
 sub get_all_DBLinks {
-  my ( $self, $ex_db_exp, $ex_db_type ) = @_;
-
-  my @links;
+  my ( $self, $db_name_exp, $ex_db_type ) = @_;
 
-  push( @links,
-        @{ $self->get_all_DBEntries( $ex_db_exp, $ex_db_type ) } );
+  my @links =
+    @{ $self->get_all_DBEntries( $db_name_exp, $ex_db_type ) };
 
+  # Add all of the transcript and translation xrefs to the return list.
   my $translation = $self->translation();
   if ( defined($translation) ) {
     push( @links,
-          @{$translation->get_all_DBEntries( $ex_db_exp, $ex_db_type ) }
+          @{$translation->get_all_DBEntries( $db_name_exp, $ex_db_type ) }
     );
   }
 
@@ -219,20 +228,28 @@ sub get_all_DBLinks {
   return \@links;
 }
 
+sub get_all_xrefs {
+  my $self = shift;
+  return $self->get_all_DBLinks(@_);
+}
 
 =head2 get_all_DBEntries
 
   Arg [1]    : (optional) String, external database name
+
   Arg [2]    : (optional) String, external database type
+
   Example    : my @dbentries = @{ $gene->get_all_DBEntries() };
-  Description: Retrieves DBEntries (xrefs) for this transcript.  
-               This does _not_ include the corresponding translations 
-               DBEntries (see get_all_DBLinks).
-
-               This method will attempt to lazy-load DBEntries from a
-               database if an adaptor is available and no DBEntries are present
-               on the transcript (i.e. they have not already been added or 
-               loaded).
+
+  Description: Retrieves DBEntries (xrefs) for this transcript.
+               This does *not* include the corresponding
+               translations DBEntries (see get_all_DBLinks()).
+
+               This method will attempt to lazy-load DBEntries
+               from a database if an adaptor is available and no
+               DBEntries are present on the transcript (i.e. they
+               have not already been added or loaded).
+
   Returntype : Listref of Bio::EnsEMBL::DBEntry objects
   Exceptions : none
   Caller     : get_all_DBLinks, TranscriptAdaptor::store
@@ -243,27 +260,33 @@ sub get_all_DBLinks {
 sub get_all_DBEntries {
   my ( $self, $ex_db_exp, $ex_db_type ) = @_;
 
-  my $cache_name = "dbentries";
+  my $cache_name = 'dbentries';
 
   if ( defined($ex_db_exp) ) {
     $cache_name .= $ex_db_exp;
   }
+
   if ( defined($ex_db_type) ) {
     $cache_name .= $ex_db_type;
   }
 
-  # if not cached, retrieve all of the xrefs for this gene
-  if ( !defined $self->{$cache_name} && $self->adaptor() ) {
+  # if not cached, retrieve all of the xrefs for this transcript
+  if ( !defined( $self->{$cache_name} ) && defined( $self->adaptor() ) )
+  {
     $self->{$cache_name} =
-      $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Transcript(
-                                       $self, $ex_db_exp, $ex_db_type );
+      $self->adaptor()->db()->get_DBEntryAdaptor()
+      ->fetch_all_by_Transcript( $self, $ex_db_exp, $ex_db_type );
   }
 
   $self->{$cache_name} ||= [];
 
   return $self->{$cache_name};
-}
+} ## end sub get_all_DBEntries
 
+sub get_all_object_xrefs {
+  my $self = shift;
+  return $self->get_all_DBEntries(@_);
+}
 
 =head2 add_DBEntry
 
@@ -2448,19 +2471,21 @@ sub get_all_DAS_Features {
 
 =head2 _compare_xrefs
 
-  Description: compare xrefs based on priority (descending), then name (ascending),
-               then display_label (ascending)
+  Description: compare xrefs based on priority (descending), then
+               name (ascending), then display_label (ascending)
 
 =cut
 
 sub _compare_xrefs {
   # compare on priority first (descending)
-  if ($a->priority() != $b->priority()) {
+  if ( $a->priority() != $b->priority() ) {
     return $b->priority() <=> $a->priority();
-  } else { # equal priorities, compare on external_db name
-    if ($a->dbname() ne $b->dbname()) {
+  } else {
+    # equal priorities, compare on external_db name
+    if ( $a->dbname() ne $b->dbname() ) {
       return $a->dbname() cmp $b->dbname();
-    } else { # equal priorities and names, compare on display_label
+    } else {
+      # equal priorities and names, compare on display_label
       return $a->display_id() cmp $b->display_id();
     }
   }

modules/Bio/EnsEMBL/Translation.pm

@@ -556,50 +556,56 @@ sub transform {
 
 =head2 get_all_DBEntries
 
-  Arg [1]    : (optional) $ex_db_exp - external db name
-  Example    : @dbentries = @{$translation->get_all_DBEntries()};
-  Description: Retrieves DBEntries (xrefs) for this translation.  
-
-               This method will attempt to lazy-load DBEntries from a
-               database if an adaptor is available and no DBEntries are present
-               on the translation (i.e. they have not already been added or 
-               loaded).
-  Returntype : list reference to Bio::EnsEMBL::DBEntry objects
+  Arg [1]    : (optional) String, external database name
+
+  Arg [2]    : (optional) String, external_db type
+
+  Example    : @dbentries = @{ $translation->get_all_DBEntries() };
+
+  Description: Retrieves DBEntries (xrefs) for this translation.
+
+               This method will attempt to lazy-load DBEntries
+               from a database if an adaptor is available and no
+               DBEntries are present on the translation (i.e. they
+               have not already been added or loaded).
+
+  Returntype : Listref to Bio::EnsEMBL::DBEntry objects
   Exceptions : none
-  Caller     : get_all_DBLinks, TranslationAdaptor::store
+  Caller     : TranslationAdaptor::store
   Status     : Stable
 
 =cut
 
 sub get_all_DBEntries {
-  my $self = shift;
-  my $ex_db_exp = shift;
-  my $ex_db_type = shift;
+  my ( $self, $ex_db_exp, $ex_db_type ) = @_;
 
-  my $cache_name = "dbentries";
+  my $cache_name = 'dbentries';
 
-  if(defined($ex_db_exp)){
+  if ( defined($ex_db_exp) ) {
     $cache_name .= $ex_db_exp;
   }
-  if(defined($ex_db_type)){
+
+  if ( defined($ex_db_type) ) {
     $cache_name .= $ex_db_type;
   }
 
-  # if not cached, retrieve all of the xrefs for this gene
-  if(!defined $self->{$cache_name}) {
-    my $adaptor = $self->adaptor();
-    my $dbID    = $self->dbID();
-
-    return [] if(!$adaptor || !$dbID);
+  # if not cached, retrieve all of the xrefs for this translation
+  if ( !defined( $self->{$cache_name} ) && defined( $self->adaptor() ) )
+  {
     $self->{$cache_name} =
-      $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self, $ex_db_exp, $ex_db_type);
+      $self->adaptor()->db()->get_DBEntryAdaptor()
+      ->fetch_all_by_Translation( $self, $ex_db_exp, $ex_db_type );
   }
 
   $self->{$cache_name} ||= [];
 
   return $self->{$cache_name};
-}
+} ## end sub get_all_DBEntries
 
+sub get_all_object_xrefs {
+      my $self = shift;
+            return $self->get_all_DBEntries(@_);
+}
 
 =head2 add_DBEntry
 
@@ -631,11 +637,18 @@ sub add_DBEntry {
 
 =head2 get_all_DBLinks
 
-  Arg [1]    : see get_all_DBEntries
-  Example    : see get_all_DBEntries
-  Description: This is here for consistancy with the Transcript and Gene 
-               classes. It is a synonym for the get_all_DBEntries method.
-  Returntype : see get_all_DBEntries
+  Arg [1]    : String database name (optional)
+               SQL wildcard characters (_ and %) can be used to
+               specify patterns.
+
+  Example    :  my @dblinks = @{ $translation->get_all_DBLinks() };
+                my @dblinks = @{ $translation->get_all_DBLinks('Uniprot%') };
+
+  Description: This is here for consistancy with the Transcript
+               and Gene classes.  It is a synonym for the
+               get_all_DBEntries() method.
+
+  Return type: Listref to Bio::EnsEMBL::DBEntry objects
   Exceptions : none
   Caller     : general
   Status     : Stable
@@ -647,6 +660,10 @@ sub get_all_DBLinks {
   return $self->get_all_DBEntries(@_);
 }
 
+sub get_all_xrefs {
+  my $self = shift;
+  return $self->get_all_DBLinks(@_);
+}
 
 =head2 get_all_ProteinFeatures