report warning if regitry call to get_alias is called with an invalid species...

report warning if regitry call to get_alias is called with an invalid species name. Also had to add option to get_DBAdaptor to not look up aliases so that warning are not given the first time we use it

modules/Bio/EnsEMBL/Registry.pm

@@ -554,6 +554,7 @@ sub add_DBAdaptor {
 
   Arg [1]    : name of the species to get the adaptor for in the registry.
   Arg [2]    : name of the group to get the adaptor for in the registry.
+  Arg [3]    : if set will not look for alias.
   Example    : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core");
   Returntype : DBAdaptor
   Exceptions : none
@@ -562,10 +563,11 @@ sub add_DBAdaptor {
 =cut
 
 sub get_DBAdaptor {
-  my ( $class, $species, $group ) = @_;
+  my ( $class, $species, $group , $no_alias_check) = @_;
 throw 'arrggh for '.$species if ! defined $species;
-  $species = $class->get_alias($species);
-
+  if(!defined($no_alias_check) or !$no_alias_check){
+    $species = $class->get_alias($species);
+  }
   return $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'};
 }
 
@@ -1104,7 +1106,13 @@ sub get_alias{
   my ($class, $key) = @_;
 
   if(!defined($registry_register{'_ALIAS'}{lc($key)})){
-    return $key;
+    if(!defined( $registry_register{_SPECIES}{ lc($key) }) and !defined ($registry_register{_ALIAS}{ lc($key) })){
+      warn "$key is not a valid species name for this instance\n";
+      return undef;
+    }
+    else{
+      return $key;
+    }
   }
   return $registry_register{'_ALIAS'}{lc($key)};
 }

modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm

@@ -154,7 +154,7 @@ sub gen_load {
   # return if the connection and species, group are the same
 
   if ( defined( $dba->species ) ) {
-    my $db_reg = $reg->get_DBAdaptor( $dba->species, $dba->group );
+    my $db_reg = $reg->get_DBAdaptor( $dba->species, $dba->group, 1 );
     if ( defined($db_reg) ) {
       if ( $dba->dbc->equals( $db_reg->dbc ) ) { return $db_reg }
       else {
@@ -169,6 +169,7 @@ sub gen_load {
       }
     }
   } else {    # no species
+    
     my @db_reg =
       @{ $reg->get_all_DBAdaptors_by_connection( $dba->dbc ) };