whitespace, remove old Glovar method!

modules/Bio/EnsEMBL/Utils/ConversionSupport.pm

@@ -394,7 +394,6 @@ sub create_commandline_options {
 	$param_hash{$param} = $first;
       }
     }
-
   }
 
   # replace values
@@ -684,10 +683,8 @@ sub get_database {
     "${prefix}host",
     "${prefix}port",
     "${prefix}user",
-        # "${prefix}pass", not required since might be empty
     "${prefix}dbname",
   );
-
   my %adaptors = (
     core    => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
     ensembl => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
@@ -780,60 +777,6 @@ sub get_dbconnection {
 
 }
 
-=head2 get_glovar_database
-
-  Example     : my $dba = $support->get_glovar_database;
-  Description : Connects to the Glovar database.
-  Return type : Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor
-  Exceptions  : thrown if no connection to a core db exists
-  Caller      : general
-
-=cut
-
-sub get_glovar_database {
-    my $self = shift;
-    $self->check_required_params(qw(
-        glovarhost
-        glovarport
-        glovaruser
-        glovarpass
-        glovardbname
-        oracle_home
-        ld_library_path
-        glovar_snp_consequence_exp
-    ));
-
-    # check for core dbadaptor
-    my $core_db = $self->dba;
-    unless ($core_db && (ref($core_db) =~ /Bio::.*::DBSQL::DBAdaptor/)) {
-        $self->log_error("You have to connect to a core db before you can get a glovar dbadaptor.\n");
-        exit;
-    }
-    
-    # setup Oracle environment
-    $ENV{'ORACLE_HOME'} = $self->param('oracle_home');
-    $ENV{'LD_LIBRARY_PATH'} = $self->param('ld_library_path');
-
-    # connect to Glovar db
-    $self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor');
-    my $dba = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
-            -host   => $self->param("glovarhost"),
-            -port   => $self->param("glovarport"),
-            -user   => $self->param("glovaruser"),
-            -pass   => $self->param("glovarpass"),
-            -dbname => $self->param("glovardbname"),
-            -group  => 'glovar',
-    );
-
-    # setup adaptor inter-relationships
-    $dba->dnadb($core_db);
-    $self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::GlovarSNPAdaptor');
-    my $glovar_snp_adaptor = $dba->get_GlovarSNPAdaptor;
-    $glovar_snp_adaptor->consequence_exp($self->param('glovar_snp_consequence_exp'));
-    $core_db->add_ExternalFeatureAdaptor($glovar_snp_adaptor);
-
-    return $dba;
-}
 
 =head2 dba
 
@@ -867,8 +810,7 @@ sub dba {
 
 sub dynamic_use {
   my ($self, $classname) = @_;
-    my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ?
-                                        ($1,$2) : ('::', $classname);
+  my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ? ($1,$2) : ('::', $classname);
 
   no strict 'refs';
   # return if module has already been imported
@@ -1272,9 +1214,7 @@ sub log_error {
 
 sub log_verbose {
   my ($self, $txt, $indent) = @_;
-
   return(0) unless $self->param('verbose');
-
   $self->log($txt, $indent);
   return(1);
 }
@@ -1295,11 +1235,9 @@ sub log_verbose {
 
 sub log_stamped {
   my ($self, $txt, $indent) = @_;
-    
   # append timestamp and memory usage to log text
   $txt =~ s/(\n*)$//;
   $txt .= " ".$self->date_and_mem.$1;
-    
   $self->log($txt, $indent);
   return(1);
 }