DBAdaptor method db renamed dbc to stop confusion so all references to this have been changed

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->db->prepare("DELETE FROM misc_attrib " .
+  my $sth = $db->dbc->prepare("DELETE FROM misc_attrib " .
                          "WHERE misc_feature_id = ?");
 
   $sth->execute($mf->dbID());

modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm

@@ -126,7 +126,7 @@ sub new {
 
   if( ref($dbobj) =~ /DBAdaptor$/){
     $self->db($dbobj);
-    $self->dbc($dbobj->db);
+    $self->dbc($dbobj->dbc);
   }
   else{
     throw("Don't have a DBAdaptor [$dbobj] for new adaptor");

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -170,7 +170,7 @@ sub generic_fetch {
   #append additional clauses which may have been defined
   $sql .= "\n$final_clause";
 
-  my $sth = $db->db->prepare($sql);
+  my $sth = $db->dbc->prepare($sql);
      $sth->execute;
 
   my $res = $self->_objs_from_sth($sth, $mapper, $slice);

modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm

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

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -203,7 +203,7 @@ sub new_fast{
 	 $con->isa('Bio::EnsEMBL::DBSQL::DBConnection')) {
     throw("$con passed is not of type Bio::EnsEMBL::DBSQL::DBConnection");
   }
-  $self->db($con);
+  $self->dbc($con);
   $self->species($con->species());
   $self->group($con->group());
 
@@ -225,11 +225,11 @@ sub new_merged{
 
 
 
-=head2 db
+=head2 dbc
 
   Arg[1]    : (optional) Bio::EnsEMBL::DBSQL::DBConnection
 
-  Exmaple    : $dbc = $dba->db();
+  Exmaple    : $dbc = $dba->dbc();
   Description: Getter/Setter for DBConnection.
   Returntype : Bio::EnsEMBL::DBSQL::DBConnection
   Exceptions : none
@@ -237,11 +237,22 @@ sub new_merged{
 
 =cut
 
-sub db{
+sub dbc{
   my ($self, $arg ) = @_;
   ( defined $arg ) &&
-    ( $self->{_db} = $arg );
-  $self->{_db};
+    ( $self->{_dbc} = $arg );
+  $self->{_dbc};
+}
+
+=head2 db
+
+
+=cut
+
+sub db{
+  my ($self, $arg ) = @_;
+ deprecate("db Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ return $self->dbc($arg);
 }
 
 

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->db->prepare
+  my $sth = $db->dbc->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->db->prepare("INSERT INTO seq_region " .
+  my $sth = $db->dbc->prepare("INSERT INTO seq_region " .
                          "SET    name = ?, " .
                          "       length = ?, " .
                          "       coord_system_id = ?" );
@@ -1267,7 +1267,7 @@ sub prepare {
   my $self = shift;
   my $sql = shift;
 
-  return $self->db()->dnadb()->db->prepare( $sql );
+  return $self->db()->dnadb()->dbc->prepare( $sql );
 }
 
 sub _build_exception_cache {

modules/Bio/EnsEMBL/Storable.pm

@@ -130,7 +130,7 @@ sub is_stored {
   my $db = shift;
 
   if($db and $db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')) {
-    $db = $db->db();
+    $db = $db->dbc();
   }
   if(!$db || !ref($db) || !$db->isa('Bio::EnsEMBL::DBSQL::DBConnection')) {
     throw('db argument must be a Bio::EnsEMBL::DBSQL::DBConnection');

modules/t/MultiTestDB.t

@@ -17,7 +17,7 @@ my $dba = $ens_test->get_DBAdaptor("core");
 
 ok($dba);
 
-my $sth = $dba->db->prepare("select * from gene");
+my $sth = $dba->dbc->prepare("select * from gene");
 $sth->execute;
 
 ok(scalar($sth->rows) == 20);
@@ -42,10 +42,10 @@ ok(scalar($sth->rows) == 20);
 
 
 # delete 9 genes from the db
-$sth = $dba->db->prepare("delete from gene where gene_id >= 18266");
+$sth = $dba->dbc->prepare("delete from gene where gene_id >= 18266");
 $sth->execute;
 
-$sth = $dba->db->prepare("select * from gene");
+$sth = $dba->dbc->prepare("select * from gene");
 $sth->execute;
 
 ok(scalar($sth->rows) == 10);

modules/t/attributeAdaptor.t

@@ -50,7 +50,7 @@ $aa->store_on_MiscFeature($mf, [$attrib]);
 #
 # make sure the misc_attrib table was updated
 #
-my $count = $db->db->db_handle->selectall_arrayref
+my $count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT count(*) FROM misc_attrib " .
    "WHERE misc_feature_id = 1")->[0]->[0];
 
@@ -59,7 +59,7 @@ ok($count == 1);
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->db->db_handle->selectall_arrayref
+$count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT count(*) FROM attrib_type " .
    "WHERE code = 'test_code'")->[0]->[0];
 ok($count == 1);
@@ -87,7 +87,7 @@ $aa->remove_from_MiscFeature($mf);
 #
 # make sure the misc_attrib table was updated
 #
-$count = $db->db->db_handle->selectall_arrayref
+$count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT count(*) FROM misc_attrib " .
    "WHERE misc_feature_id = 1")->[0]->[0];
 
@@ -119,7 +119,7 @@ $aa->store_on_Slice($slice, [$attrib]);
 #
 # make sure the seq_region_attrib table was updated
 #
-$count = $db->db->db_handle->selectall_arrayref
+$count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
 
@@ -128,7 +128,7 @@ ok($count == 1);
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->db->db_handle->selectall_arrayref
+$count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT count(*) FROM attrib_type " .
    "WHERE code = 'test_code2'")->[0]->[0];
 ok($count == 1);
@@ -156,7 +156,7 @@ $aa->remove_from_Slice($slice);
 #
 # make sure the seq_region_attrib table was updated
 #
-$count = $db->db->db_handle->selectall_arrayref
+$count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
 
@@ -178,7 +178,7 @@ $aa->store_on_Slice($slice, [$attrib]);
 #
 # make sure the seq_region_attrib table was updated
 #
-$count = $db->db->db_handle->selectall_arrayref
+$count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
 
@@ -187,7 +187,7 @@ ok($count == 1);
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->db->db_handle->selectall_arrayref
+$count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT count(*) FROM attrib_type " .
    "WHERE code = 'test_code2'")->[0]->[0];
 ok($count == 1);

modules/t/compressedSequenceAdaptor.t

@@ -36,7 +36,7 @@ $multi_db->save('core', 'dnac', 'seq_region');
 #we can get weird padding at the end due to the last byte being not
 #fully packed but still labelled as non-gap 
 my $sth = 
-  $db->db->prepare('INSERT INTO seq_region (name, length, coord_system_id) ' .
+  $db->dbc->prepare('INSERT INTO seq_region (name, length, coord_system_id) ' .
                'VALUES (?,?,?)');
 $sth->execute('testfrag', $len,$contig_cs->dbID);
 

modules/t/coordSystemAdaptor.t

@@ -155,7 +155,7 @@ ok(!$cs->is_sequence_level);
 ok(!$cs->is_top_level);
 ok($cs->rank() == 10);
 
-my $sth = $db->db->prepare('SELECT attrib FROM coord_system ' .
+my $sth = $db->dbc->prepare('SELECT attrib FROM coord_system ' .
                        'WHERE  name = ? and version = ?');
 $sth->execute('newsystem', 'NCBI35');
 

modules/t/dbConnection.t

@@ -30,12 +30,12 @@ my $db    = $multi->get_DBAdaptor('core');
 #
 my $dbc;
 {
-  my $db_name = $db->db->dbname;
-  my $port    = $db->db->port;
-  my $user    = $db->db->username;
-  my $pass    = $db->db->password;
-  my $host    = $db->db->host;
-  my $driver  = $db->db->driver;
+  my $db_name = $db->dbc->dbname;
+  my $port    = $db->dbc->port;
+  my $user    = $db->dbc->username;
+  my $pass    = $db->dbc->password;
+  my $host    = $db->dbc->host;
+  my $driver  = $db->dbc->driver;
 
   $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new(-dbname => $db_name,
 						-user   => $user,

modules/t/dbEntries.t

@@ -37,7 +37,7 @@ ok( $db );
 my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
 
 
-my $sth = $db->db->prepare( 'select count(*) from object_xref where ensembl_object_type = "Translation"' );
+my $sth = $db->dbc->prepare( 'select count(*) from object_xref where ensembl_object_type = "Translation"' );
 $sth->execute();
 
 my ( $xref_count )  = $sth->fetchrow_array();

modules/t/gene.t

@@ -603,7 +603,7 @@ debug( "Storing gene" );
 $gene_ad->store($gene);
 
 
-my $dbe_id = $db->db->db_handle->selectall_arrayref("SELECT display_xref_id FROM gene")->[0]->[0];
+my $dbe_id = $db->dbc->db_handle->selectall_arrayref("SELECT display_xref_id FROM gene")->[0]->[0];
 
 ok($dbe_id && $dbe_id == $dbe->dbID());
 

modules/t/markerFeatureAdaptor.t

@@ -109,7 +109,7 @@ ok($marker_feature->dbID &&
    $marker_feature->adaptor == $mfa);
 
 
-my $sth = $db->db->prepare('SELECT count(*) from marker_feature');
+my $sth = $db->dbc->prepare('SELECT count(*) from marker_feature');
 $sth->execute;
 my ($count) = $sth->fetchrow_array;
 $sth->finish();

modules/t/miscSetAdaptor.t

@@ -73,7 +73,7 @@ $msa->store($misc_set);
 ok($misc_set->dbID());
 ok($misc_set->adaptor() == $msa);
 
-my $count = $db->db->db_handle->selectall_arrayref
+my $count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT COUNT(*) FROM misc_set WHERE code = 'code'")->[0]->[0];
 
 ok($count == 1);
@@ -99,7 +99,7 @@ $msa->store($misc_set);
 
 ok($misc_set->dbID && $misc_set->adaptor);
 
-$count = $db->db->db_handle->selectall_arrayref
+$count = $db->dbc->db_handle->selectall_arrayref
   ("SELECT COUNT(*) FROM misc_set WHERE code = 'code'")->[0]->[0];
 ok($count == 1);
 

modules/t/sliceAdaptor.t

@@ -406,7 +406,7 @@ ok($slice->seq_region_name =~ /$clone_name\.\d+/);
 # highest (lowest-numbered) ranked comes out first
 $multi->hide('core', 'seq_region');
 
-my $sth = $db->db->prepare(qq{INSERT INTO seq_region (coord_system_id, name,
+my $sth = $db->dbc->prepare(qq{INSERT INTO seq_region (coord_system_id, name,
                                                   length)
                 SELECT cs.coord_system_id, 'TESTREGION', 1000000
                 FROM coord_system cs