species and group deprecatied. As these should not be used now that dbc is not...

species and group deprecatied. As these should not be used now that dbc is not part of the dbadaptor anymore.

modules/Bio/EnsEMBL/DBSQL/DBConnection.pm

@@ -7,8 +7,6 @@
         -dbname  => 'homo_sapiens_core_20_34c',
         -host    => 'ensembldb.ensembl.org',
         -driver  => 'mysql',
-        -species => 'Homo Sapiens',
-        -group   => 'core'
         );
 
 
@@ -56,7 +54,7 @@ use DBI;
 
 use Bio::EnsEMBL::DBSQL::StatementHandle;
 
-use Bio::EnsEMBL::Utils::Exception qw(throw info warning);
+use Bio::EnsEMBL::Utils::Exception qw(deprecate throw info warning);
 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
 
 @ISA = qw(Bio::EnsEMBL::Root); # for backwards compatibility
@@ -397,52 +395,6 @@ sub password {
   $self->{_password};
 }
 
-=head2 species
-
-  Arg [1]    : (optional) string $arg
-               The new value of the species used by this connection. 
-  Example    : $host = $db_connection->species()
-  Description: Getter/Setter for the species of to use for 
-               this connection.  There is currently no point in setting 
-               this value after the connection has already been established 
-               by the constructor.
-  Returntype : string
-  Exceptions : none
-  Caller     : new
-
-=cut
-
-sub species {
-  my ($self, $arg ) = @_;
-  ( defined $arg ) &&
-    ( $self->{_species} = $arg );
-  return $self->{_species};
-}
-
-
-=head2 group
-
-  Arg [1]    : (optional) string $arg
-               The new value of the group used by this connection. 
-  Example    : $host = $db_connection->group()
-  Description: Getter/Setter for the group of to use for 
-               this connection.  There is currently no point in setting 
-               this value after the connection has already been established 
-               by the constructor.
-  Returntype : string
-  Exceptions : none
-  Caller     : new
-
-=cut
-
-sub group {
-  my ($self, $arg ) = @_;
-  ( defined $arg ) &&
-    ( $self->{_group} = $arg );
-  return $self->{_group};
-}
-
-
 
 
 =head2 disconnect_when_inactive
@@ -651,5 +603,38 @@ sub disconnect_if_idle {
   return 0;
 }
 
+####
+#deprecated functions
+####
+
+=head2
+
+   group is no longer available in DBConnection and should be accessed if needed
+   from an adaptor.
+
+=cut
+
+sub group {
+  my ($self, $arg ) = @_;
+  ( defined $arg ) &&
+    ( $self->{_group} = $arg );
+  deprecate "group should not be called from DBConnection but from an adaptor\n";
+  return $self->{_group};
+}
+
+=head2 species
+
+   species is no longer available in DBConnection and should be accessed if needed
+   from an adaptor.
+
+=cut
+
+sub species {
+  my ($self, $arg ) = @_;
+  ( defined $arg ) &&
+    ( $self->{_species} = $arg );
+  deprecate "species should not be called from DBConnection but from an adaptor\n";
+  return $self->{_species};
+}
 
 1;