my ($self, $db) = @_;

  #Have to explicitly pass self->db to this method if required, this highlights which db is being tested 
  throw("Need to define a DBAdaptor to retrieve the schema_build from") if (! $db);
  #avoided using dnadb by default to avoid obfuscation of behaviour
  
  my @dbname = split/_/, $db->dbc->dbname();



  my $schema_build = pop @dbname;
  $schema_build = pop(@dbname).'_'.$schema_build;
  return $schema_build;

  my $self = shift;

  return '-h'.$self->dbc->host().' -u'.$self->dbc->username().' -p'.$self->dbc->password()
	.' -P'.$self->dbc->port().' '.$self->dbc->dbname();
}

1;

   my ($self, $dnadb, $cs_name) = @_; 

  #super dnadb automatically sets the current DBAdaptor as the dnadb
  #this is the only way of checking whether it has been defined properly.
 

  #This needs to use the same host as the registry, which may differ from the efg host!
  #What if we pass a reg config file? with multiple hosts?
  #We probably always want to use the host of the current dnadb?

  #Automatically selects the current core DB from the reg and may be wrong!!
  #How do we want to deal with this?
  
  #So we want a method in DBAdaptor to reset efg DB and dna DB in registry?
  #Or do we just let this happen

  if($dnadb || $self->SUPER::dnadb->group() ne 'core'){

	if(! $dnadb){#Guess dnadb
	  #We are only guessing the dnadb if we have not already defined one
	  #Either by attaching to the efg db
	  #Or by loading the reg
	  #The Importer will automatically check if the dnadb matches and set_by_assembly_version
	  #Do we want this functionality in the efg db->new?
	  #The problem is redefining the db in the registry will not take the extra params required?
	  #Maybe the method will take this. Then we can implement this check and set_dnadb_by_assembly_version
	  #in new.
	  
	  return $self->set_dnadb_by_assembly_version($self->dnadb_assembly);
	}
	
	$self->SUPER::dnadb($dnadb); 

	#set default coordsystem here, do we need to handle non-chromosome here
	$cs_name ||= 'chromosome';

	my $cs;
	eval { $cs = $dnadb->get_CoordSystemAdaptor->fetch_by_name($cs_name)};
	my $error = $@;

	if($error){
	  my ($schema, $build) = split/_/, $self->_get_schema_build($dnadb);
	  $build =~ s/[a-z]//;
	  throw("It appears that the schema of ".$dnadb->dbc->dbname.
			' is incompatible with your current core API version('.$reg->software_version.
			").  You could try using the $schema version of the core API, or alternatively try specifying ".
			"different -dnadb/registry_host parameters to point to a make recent version containing build $build\n");

	}


    #this will only add the default assembly for this DB, if we're generating on another we need to add it separately.
    #or shall we fetch/add all by name?
   
	#This is a non-obious store behaviour!!!!!!!!!!!!!!!!!
	#This can result in coord_system entries being written
	#unknowingly if you are using the efg DB with a write user/pass
    $self->get_FGCoordSystemAdaptor->validate_and_store_coord_system($cs);
  }

  return $self->SUPER::dnadb();#never pass @_ here!

  my ($self, $assm) = @_;
  $self->{'dnadb_assm'} = $assm if $assm;
  return $self->{'dnadb_assm'};
}

#Redefine dbadb here to add coordsystem

  my ($self, $host) = @_;
  $self->{'dnadb_host'} = $host if $host;
  return $self->{'dnadb_host'};

 my ($self, $pass) = @_;
 $self->{'dnadb_pass'} = $pass if $pass;
 return $self->{'dnadb_pass'};

  my ($self, $port) = @_;
  $self->{'dnadb_port'} = $port if $port;
  return $self->{'dnadb_port'};

  my ($self, $user) = @_;
  $self->{'dnadb_user'} = $user if $user;
  return $self->{'dnadb_user'};

	my ($self, $table, $id) = @_;


	throw("DBAdaptor::fetch_all_states is deprecated");


	throw("Need to specifiy a table and an id to retrieve status") if (! $table || ! $id);


	my $sql = "SELECT state FROM status WHERE table_name=\"$table\" AND table_id=\"$id\"";

	my @states = map{ $_ = "@$_"} @{$self->dbc->db_handle->selectall_arrayref($sql)};

	return\@ states;

	my ($self, $gname) = @_;

	throw("Need to specify a group name") if ! $gname;
	my $sql = "SELECT * from experimental_group where name=\"$gname\"";
	return $self->dbc->db_handle->selectrow_array($sql);

	my ($self, $table, $id, $state) = @_;

	throw("DBAdaptor::fetch_status_by_name is deprecated");

	throw("Need to specify a table and an id to retrieve status") if (! $table || ! $id || ! $state);

	#should we enum the state?


	my $sql = "SELECT state FROM status WHERE table_name=\"$table\" AND table_id=\"$id\" AND state=\"$state\"";
	return $self->dbc->db_handle->selectrow_array($sql);

  my ($self) = shift;
  
  my %pairs = (
			   'Channel'            => 'Bio::EnsEMBL::Funcgen::DBSQL::ChannelAdaptor',
			   'ExperimentalChip'   => 'Bio::EnsEMBL::Funcgen::DBSQL::ExperimentalChipAdaptor',
			   'ArrayChip'          => 'Bio::EnsEMBL::Funcgen::DBSQL::ArrayChipAdaptor',
			   'Array'              => 'Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor',
			   'ProbeSet'           => 'Bio::EnsEMBL::Funcgen::DBSQL::ProbeSetAdaptor',
			   'Probe'              => 'Bio::EnsEMBL::Funcgen::DBSQL::ProbeAdaptor',
			   'ProbeFeature'       => 'Bio::EnsEMBL::Funcgen::DBSQL::ProbeFeatureAdaptor',
			   'AnnotatedFeature'   => 'Bio::EnsEMBL::Funcgen::DBSQL::AnnotatedFeatureAdaptor',
			   'RegulatoryFeature'  => 'Bio::EnsEMBL::Funcgen::DBSQL::RegulatoryFeatureAdaptor',
			   'Experiment'         => 'Bio::EnsEMBL::Funcgen::DBSQL::ExperimentAdaptor',
			   'DataSet'            => 'Bio::EnsEMBL::Funcgen::DBSQL::DataSetAdaptor',
			   'FeatureType'        => 'Bio::EnsEMBL::Funcgen::DBSQL::FeatureTypeAdaptor',
			   'FGCoordSystem'      => 'Bio::EnsEMBL::Funcgen::DBSQL::CoordSystemAdaptor',#prepended FG o override core  adaptor
			   'MetaCoordContainer' => 'Bio::EnsEMBL::Funcgen::DBSQL::MetaCoordContainer',
			   'FeatureSet'         => 'Bio::EnsEMBL::Funcgen::DBSQL::FeatureSetAdaptor',
			   'ResultSet'          => 'Bio::EnsEMBL::Funcgen::DBSQL::ResultSetAdaptor',
			   'DataSet'            => 'Bio::EnsEMBL::Funcgen::DBSQL::DataSetAdaptor',
			   'ExperimentalSet'    => 'Bio::EnsEMBL::Funcgen::DBSQL::ExperimentalSetAdaptor',
			   'ExternalFeature'    => 'Bio::EnsEMBL::Funcgen::DBSQL::ExternalFeatureAdaptor',
			   'CellType'           => 'Bio::EnsEMBL::Funcgen::DBSQL::CellTypeAdaptor',
			   'DBEntry'            => 'Bio::EnsEMBL::Funcgen::DBSQL::DBEntryAdaptor',
			   'Slice'              => 'Bio::EnsEMBL::Funcgen::DBSQL::SliceAdaptor',
			   'ResultFeature'      => 'Bio::EnsEMBL::Funcgen::DBSQL::ResultFeatureAdaptor',
			   
			   #New collections
			   'ResultFeatureCollection' => 'Bio::EnsEMBL::Funcgen::Collection::ResultFeature',

	 	       
	       #add required EnsEMBL(core) adaptors here
	       #Should write/retrieve from efg not dna db
			   'UnmappedObject'     => 'Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor',
			   'Analysis'           => 'Bio::EnsEMBL::DBSQL::AnalysisAdaptor',
			   "MetaContainer"      => 'Bio::EnsEMBL::DBSQL::MetaContainer',
	      );
  
  return (\%pairs);

	my ($self, $gname, $loc, $contact) = @_;

	throw("Need to supply a group name, location and contact") if (!($gname && $loc && $contact));

	my $sql = "INSERT INTO experimental_group(name, location, contact) VALUES(\"$gname\",\" $loc\",\" $contact\")";
	$self->dbc->do($sql);

	#$self->dbc->db_handle->last_insert_id(undef, undef, undef, undef);	
	return;#return last insert id here?
}


#General Status methods
#will Move to Bio::EnsEMBL::Funcgen::DBSQL::Status

  my ($self, $class, $obj) = @_;

  if(! (ref($obj) && $obj->isa($class) && $obj->is_stored($self))){
	#throw or warn and return boolean?
	throw('Must provide a valid stored '.$class."\nParameter provided was:\t$obj");
  }

  return;
}





#Move these to Helper.pm! Check method dependencies first!

  my ($self, $table, $file, $ssh) = @_;

  chmod 0755, $file;

  #  warn("Importing $table data from $file");
  #if this gives an Errcode: 2, then your mysql instance cannot see the file.
  #This could be due to a soft link on a visible directory to an unmounted filesystem
  #change this to use the mysqlimport?



  #This is failing as ssh is not set up to login silently without password prompt
  #Need to defined ssh keys?

  #(my $tmp_file = $file) =~ s/.*\///;
  #$tmp_file = '/tmp/'.$tmp_file;

  #my $scp = 'scp $(hostname):'.$file." ".$self->dbc->host().":${tmp_file}";
  #my $sql = "load data infile '$tmp_file' into table $table";
  #$self->dbc->do($sql);
  #remove tmp file via ssh if load successful

  my $cmd = 'mysqlimport -L '.$self->connect_string().' '.$file;
  system($cmd) == 0 || throw("Failed to load data from $file\nExit code:\t".($?>>8)."\n$!");
  
  return;

  my ( $class, @args ) = @_;

  my $self = $class->SUPER::new(@args);
  #Currently only uses dnadb params to auto select
  #If attached dnadb or default reg dnadb does not match 
  #given assembly version.

  my ( $dnadb_host, $dnadb_user, $dnadb_port, $dnadb_pass, $dnadb_assm)
    = rearrange( [ 'DNADB_HOST', 'DNADB_USER',
                   'DNADB_PORT', 'DNADB_PASS',
				   'DNADB_ASSEMBLY',
                 ],
                 @args );

  my $default_dnadb = $self->SUPER::dnadb;
  my ($default_host, $default_port, $default_user, $default_pass, $default_assm, $efg_assm, $dnadb_defined);

  if($default_dnadb->group eq 'core'){
	#This means you have loaded a registry or pass a dnadb to the efg DBAdaptor
	
	$default_host = $default_dnadb->dbc->host;
	$default_port = $default_dnadb->dbc->port;
	$default_user = $default_dnadb->dbc->username;
	$default_pass = $default_dnadb->dbc->password;
	($default_assm = (split/_/, $self->_get_schema_build($default_dnadb))[1]) =~ s/[a-z]//;
	$dnadb_defined = 1;
  }


  #Defaults now set in dnadb as we want to test registry first;
  #These will pick default_dnadb values if params not explicitly set
  $self->{'dnadb_host'} = $dnadb_host || $default_host || 'ensembldb.ensembl.org';
  #Do we need this to be dnadb_ports 3306 5306 for different mysqls?
  #This is not correct for ensembldb, but we over-ride this in set_dnadb_by_assembly_version.
  $self->{'dnadb_port'} = $dnadb_port || $default_port || 3306;
  $self->{'dnadb_user'} = $dnadb_user || $default_user || 'anonymous';
  $self->{'dnadb_pass'} = $dnadb_pass || $default_pass || undef;
  ($efg_assm = (split/_/, $self->_get_schema_build($self))[1]) =~ s/[a-z]//;
  $dnadb_assm ||= $default_assm || $efg_assm;
  $self->{'dnadb_assm'} = $dnadb_assm;


  #Now we only want to reset the dnadb if it does not match the dnadb_assm
  #Use dnadb method here as this will either return a predefined dnadb(attached or reg) or auto select
  #Can we change this so that it only does this when we call dnadb?
  #This resulted in circular reference, so we need to be careful about changing this

  if($self->_get_schema_build($self->dnadb()) !~ /[0-9]+_${dnadb_assm}[a-z]*$/){
	#Do we need to consider reg_config here?
	#We could potentially have two version of the core DB in the config
	#But we would expect the user to handle predefining the dnadb correctly in this case
	warn ':: WARNING: dnadb('.$self->dnadb->dbc->dbname.') does not match required -dnadb_assm '.$self->dnadb_assembly;

	if($dnadb_defined && $dnadb_host){
	  warn ":: Over-riding pre-defined dnadb host values(reg/-dnadb arg) with dnadb params:\t".
		$self->dnadb_user.'@'.$self->dnadb_host.':'.$self->dnadb_port;
	}
	$self->set_dnadb_by_assembly_version($self->dnadb_assembly);
  }

  return $self;

  my ($self, $assm_ver) = @_;

  throw('Must provide and assembly version to set the dnadb') if ! defined $assm_ver;
  my $lspecies = $reg->get_alias($self->species());

  throw('Must provide a species to automatically set dnadb') if $lspecies eq 'default';
	

  #So we use params first
  #else registry params
  #else ensembldb
  #Can we set these in new?

  my @ports = ($self->dnadb_port);

  #Start with lastest MySQL instances
  #WE ARE OVER-RIDING specified port here!
  #we should really account for this and make it nr
  if($self->dnadb_host eq 'ensdb-archive'){#
	@ports = (5304, 3304);
  } 
  elsif($self->dnadb_host eq 'ensembldb.ensembl.org'){
	@ports = (5306, 3306);
  }

  
  #We should probably allow for non-ensembldb core DBs here too
  #Do we need to account for other ports, staging etc for release?
  #These should run fine on 3306.
  #my $current_port = $self->dnadb->dbc->port;
  #This is assuming dnadb port will only ever be one or the other
  #This assumption is restricted to ensembldb in the port loop
  #my $tmp_port = ($current_port == 3306) ? 5306 : 3306;
  
  #Do we need to get species from reg here?
  #And test the species has been set?

  my $sql = 'show databases like "'.$lspecies.'_core_%_'.$assm_ver.'%"';
  my ($dbh, @dbnames, $port, $host_port);

  foreach $port(@ports){	
	#This is probably duplicating connections and over-riding any connection 
	#pooling going on in the base DBConnection if we are using the same host port
	#as the registry connection

	$dbh = DBI->connect('DBI:mysql:host='.$self->dnadb_host.";port=${port}",
						$self->dnadb_user, 
						$self->dnadb_pass, 
						{'RaiseError' => 1});
	#should we eval this?
	#}
	

	@dbnames = map {$_ = "@$_"} @{$dbh->selectall_arrayref($sql)};

	#sort and filter out non-core DBs
	#This will always take the latest release, not the latest genebuild version
	#Which is probably what we want anyway
	@dbnames = grep(/core_[0-9]/, sort @dbnames);
  
	if(scalar(@dbnames)==0){
	  warn(':: Failed to find '.$self->species.' core DB for assembly version '.$assm_ver.' using '
		   .$self->dnadb_user.'@'.$self->dnadb_host.':'.$port);
	}
	else{
	  $host_port = $port;
	  last;
	}
  }

  throw("Failed to find dnadb with assembly version $assm_ver") if(scalar(@dbnames)==0);


  warn ":: Auto-selecting build $assm_ver core DB as:\t".
	$self->dnadb_user.'@'.$dbnames[$#dbnames].':'.$self->dnadb_host.':'.$host_port."\n";


  my $db = $reg->reset_DBAdaptor($lspecies, 'core', $dbnames[$#dbnames], $self->dnadb_host, $host_port, $self->dnadb_user, $self->dnadb_pass);
  
  $self->dnadb($db);

  
  return $db;
}


#Group methods, as not adaptor/class for Group(used in ExperimentAdaptor at present)
#will disppear when Group and GroupAdaptor written

	my ($self, $table, $id, $state) = @_;

	throw("DBAdaptor::set_status is deprecated");

	throw("Need to supply a table, dbid and a valid status") if (!($table && $id && $state));

	my $sql = "INSERT INTO status(table_id, table_name, state) VALUES(\"$id\",\" $table\",\" $state\")";
	$self->dbc->do($sql);

	return;

  Arg [1]    : (optional) int - coord_system_id
  Example    : my $slice_adaptor = $db->get_SliceAdaptor($cs->dbID());
  DESCRIPTION: Retrieves a slice adaptor from the dnadb corresponding 
               to the coord_system_id, or retrieves from the default dnadb
  Returntype : Bio::EnsEMBL::DBSQL::SLiceAdaptor
  Exceptions : Throws if arguments not supplied
  Caller     : general
  Status     : At risk - remove and add this to BaseFeatureAdaptor->fetch_all_by_Slice_constraint