Changes to the way in which external_name and external_db calls are made.

 - These method calls in Gene.pm are delegated to Transcript.pm
 - The calls are species specific, removing the need to query the priority
   column the external_db table.

modules/Bio/EnsEMBL/Gene.pm

@@ -380,12 +380,14 @@ sub dbID {
 
   Arg [1]    : string $external_name
   Example    : none
-  Description: get/set for attribute external_name. It could be calculated
-               from dblinks in a species dependent way. Well introduce 
-               that later.
+  Description: get/set for attribute external_name. It initially calculates
+               the longest transcript for the gene in question and then 
+               delegates the call to the external_name method on Transcript.
+               Species dependant searching is handled by this method on
+               Transcript.
   Returntype : string
   Exceptions : none
-  Caller     : Lite::GeneAdaptor knows how to set it correct
+  Caller     : general
 
 =cut
 
@@ -395,36 +397,92 @@ sub external_name {
   if( defined $arg ) {
     $self->{'_external_name'} = $arg;
   }
+  else { 
+    # find the transcript with the longest length which is 
+    # attached to this gene.  Use the longest length as the
+    # determining factor when having to select between transcripts
+    # and their external references
+    my $transcript = $self->_get_longest_Transcript;
+
+    $self->{'_external_name'} = $transcript->external_name;
+  }
 
-  return $self->{'_external_name'};
+  return $self->{'_external_name'};  
 }
 
 
-
 =head2 external_db	
 
   Arg [1]    : string $external_db
   Example    : none
   Description: get/set for attribute external_db. The db is the one that 
-               belongs to the external_name
+               belongs to the external_name.  It initially calculates
+               the longest transcript for the gene in question and then 
+               delegates the call to the external_db method on Transcript.
+               Species dependant searching is handled by this method on
+               Transcript.
   Returntype : string
   Exceptions : none
   Caller     : general
 
 =cut
 
-
 sub external_db {
   my ($self, $arg ) = @_;
 
   if( defined $arg ) {
     $self->{'_external_db'} = $arg;
   }
+  else {
+    # find the transcript with the longest length which is 
+    # attached to this gene.  Use the longest length as the
+    # determining factor when having to select between transcripts
+    # and their external references
+    my $transcript = $self->_get_longest_Transcript;
+
+    $self->{'_external_db'} = $transcript->external_db;
+  }
 
   return $self->{'_external_db'};
 }
 
 
+=head2 _get_longest_Transcript	
+
+  Args       : none
+  Example    : none
+  Description: An INTERNAL method which determines the longest transcript
+               for the given gene.get/set for attribute external_db. The db is the one that 
+               belongs to the external_name.  It initially calculates
+               the longest transcript for the gene in question and then 
+               delegates the call to the external_db method on Transcript.
+               Species dependant searching is handled by this method on
+               Transcript.
+  Returntype : a single Bio::EnsEMBL::Transcript
+  Exceptions : none
+  Caller     : external_name and external_db methods on Gene.pm
+
+=cut
+
+sub _get_longest_Transcript {
+  my $self = shift;
+
+  my $transcripts = $self->get_all_Transcripts;
+
+  my $longest_index = 0;
+  my $longest_length = 0;
+  my $tran_count = 0;
+
+  foreach my $trans ( @{$transcripts} ) {
+    if ( $trans->length > $longest_length ) {
+      $longest_length = $trans->length;
+      $longest_index = $tran_count;
+    }
+    $tran_count++;
+  }
+  
+  return $transcripts->[$longest_index];
+}
 
 
 =head2 description
@@ -883,7 +941,7 @@ sub temporary_id {
   Description: You can set the species for this gene if you want to use species 
                specific behaviour. Otherwise species is retrieved from attached 
                database.
-  Returntype : Bio::EnsEMBL::Species
+  Returntype : Bio::Species
   Exceptions : none
   Caller     : external_name, external_db, general for setting
 

modules/Bio/EnsEMBL/Transcript.pm

@@ -167,6 +167,9 @@ sub external_db {
   if( defined $arg ) {
     $self->{'_external_db'} = $arg;
   }
+  else { 
+    $self->{'_external_db'} = $self->_get_external_info("db");
+  }
 
   return $self->{'_external_db'};
 }
@@ -184,16 +187,108 @@ sub external_db {
 =cut
 
 sub external_name {
-  my ($self, $arg ) = @_;
+  my ($self, $arg) = @_;
 
   if( defined $arg ) {
     $self->{'_external_name'} = $arg;
   }
+  else {
+    $self->{'_external_name'} = $self->_get_external_info("name");
+  }
 
   return $self->{'_external_name'};
 }
 
 
+=head2 _get_external_info
+
+ Title   : _get_external_info
+ Usage   : $ext_name = $obj->_get_external_info();
+ Function: external_name if available
+ Example : 
+ Returns : the external name of this transcript
+ Args    : string. Switch on whether to return a name or dbname.
+
+=cut
+
+sub _get_external_info {
+  my ($self, $required) = @_;
+
+  # find out from which species this translation comes from
+  my $species = $self->species->species;
+
+  # go and grab the list of DBLinks
+  my $dblinks = $self->get_all_DBLinks;
+
+  # set the priority of the order in which the external dbs are searched
+  # based on the species
+  # the actual order of dbs was determined by the deprecated priority column
+  # in the external_db table
+
+  my @priority_order = [];
+
+  # the kind of case statment switching is performed on the first records
+  # from the meta table of the relevant species.
+
+  # human
+  if ( $species eq 'sapiens' ) {
+    @priority_order = qw{ HUGO SWISSPROT SPTREMBL RefSeq LocusLink };
+  }
+  # anopheles
+  elsif ( $species eq 'gambiae' ) {
+    @priority_order = qw{ ANOSUB SWISSPROT SPTREMBL };
+  }
+  # zebra fish
+  elsif ( $species eq 'rerio' ) {
+    @priority_order = qw{ SWISSPROT SPTREMBL };
+  }
+  # fugu
+  elsif ( $species eq 'rubripes' ) {
+    @priority_order = qw{ SWISSPROT SPTREMBL RefSeq LocusLink HUGO };
+  }
+  # mouse
+  elsif ( $species eq 'musculus' ) {
+    @priority_order = qw{ MarkerSymbol SWISSPROT RefSeq LocusLink };
+  }
+  # default list if species is not set
+  else {
+    $self->warn("Transcript::external_name - No species set. Using default DB order.");
+    @priority_order = qw{ HUGO SWISSPROT SPTREMBL RefSeq LocusLink };
+  }
+
+  # find a match (first one) for the db with the highest available priority
+  my $name = undef;
+  my $db = undef;
+
+  # we would hope that each transcript has only a single DBLink per db but
+  # implement as a loop just in case, taking the first relevant record found
+  foreach my $curr_db ( @priority_order ) { 
+    foreach my $dbl ( @{$dblinks} ) {
+      if ( $curr_db eq $dbl->dbname ) {
+	$name = $dbl->primary_id;
+	$db = $dbl->dbname;
+	last;
+      }
+    }
+    if ( defined $name ) {
+      last;
+    }
+  }
+
+  if ( $required eq 'name' ) {
+    return $name;
+  }
+  elsif ( $required eq 'db' ) {
+    return $db;
+  }
+  else {
+    $self->warn("Transcript::_get_external_info - no xref data could be retrieved.");
+    return undef;
+  }
+    
+}
+
+
 sub is_known {
   my $self = shift;
   if( defined $self->external_name() && $self->external_name() ne '' ) {
@@ -1467,6 +1562,36 @@ sub species {
 
 
 
+=head2 species
+
+  Arg [1]    : optional Bio::Species $species
+  Example    : none
+  Description: You can set the species for this gene if you want to use species 
+               specific behaviour. Otherwise species is retrieved from attached 
+               database.
+  Returntype : Bio::Species
+  Exceptions : none
+  Caller     : external_name, external_db, general for setting
+
+=cut
+
+
+sub species {
+  my ( $self, $species ) = @_;
+
+  if( defined $species ) {
+    $self->{species} = $species;
+  } else {
+    if( ! exists $self->{species} ) {
+      if( defined $self->adaptor() ) {
+	$self->{species} = $self->adaptor()->db->get_MetaContainer()
+	  ->get_Species();
+      }
+    }
+  }
+  
+  return $self->{species};
+}
 
 
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