remove deprecated calls

modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm

@@ -529,7 +529,7 @@ sub remove_from_MiscFeature {
     throw("MiscFeature is not stored in this database.");
   }
 
-  my $sth = $db->prepare("DELETE FROM misc_attrib " .
+  my $sth = $db->db->prepare("DELETE FROM misc_attrib " .
                          "WHERE misc_feature_id = ?");
 
   $sth->execute($mf->dbID());

modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm

@@ -802,7 +802,7 @@ sub store {
   # store the coordinate system in the database
   #
 
-  my $sth = $db->prepare('INSERT INTO coord_system ' .
+  my $sth = $db->db->prepare('INSERT INTO coord_system ' .
                          'SET name    = ?, ' .
                              'version = ?, ' .
                              'attrib  = ?,' .

modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm

@@ -191,7 +191,7 @@ sub store {
   my $seq_region_id;
   ($pexon, $seq_region_id) = $self->_pre_store($pexon);
 
-  my $sth = $db->prepare
+  my $sth = $db->db->prepare
     ("INSERT into prediction_exon (prediction_transcript_id, exon_rank, " .
                        "seq_region_id, seq_region_start, seq_region_end, " .
                        "seq_region_strand, start_phase, score, p_value) " .

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -1224,7 +1224,7 @@ sub store {
 
   #store the seq_region
 
-  my $sth = $db->prepare("INSERT INTO seq_region " .
+  my $sth = $db->db->prepare("INSERT INTO seq_region " .
                          "SET    name = ?, " .
                          "       length = ?, " .
                          "       coord_system_id = ?" );

modules/t/MultiTestDB.t

@@ -17,7 +17,7 @@ my $dba = $ens_test->get_DBAdaptor("core");
 
 ok($dba);
 
-my $sth = $dba->prepare("select * from gene");
+my $sth = $dba->db->prepare("select * from gene");
 $sth->execute;
 
 ok(scalar($sth->rows) == 19);
@@ -42,10 +42,10 @@ ok(scalar($sth->rows) == 19);
 
 
 # delete 9 genes from the db
-$sth = $dba->prepare("delete from gene where gene_id >= 18266");
+$sth = $dba->db->prepare("delete from gene where gene_id >= 18266");
 $sth->execute;
 
-$sth = $dba->prepare("select * from gene");
+$sth = $dba->db->prepare("select * from gene");
 $sth->execute;
 
 ok(scalar($sth->rows) == 10);