Bio::Das::ProServer::SourceAdaptor::Transport efg_transport
SummaryIncluded librariesPackage variablesDescriptionGeneral documentationMethods
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Summary
efg_transport.pm
Package variables
No package variables defined.
Included modules
Bio::Das::ProServer::SourceAdaptor::Transport::generic
Bio::EnsEMBL::DBSQL::DBAdaptor
Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor
Bio::EnsEMBL::Registry
Data::Dumper
Inherit
Bio::Das::ProServer::SourceAdaptor::Transport::generic
Synopsis
No synopsis!
Description
Transport module to retrieve REsult features from efg database
Methods
DESTROY
No description
Code
adaptor
No description
Code
chromosome_by_region
No description
Code
disconnect
No description
Code
Methods description
None available.
Methods code
DESTROYdescriptionprevnextTop
sub DESTROY {
  my $self = shift;
  $self->disconnect();
}

1;
}
adaptordescriptionprevnextTop
sub adaptor {
    my $self = shift;
    unless($self->{'_adaptor'}) {
        
        my $host     = $self->config->{'host'}     || 'localhost';
        my $port     = $self->config->{'port'}     || '3306';
        my $dbname   = $self->config->{'dbname'};
        my $username = $self->config->{'username'} || 'ensro';
        my $password = $self->config->{'password'} || '';
        my $species  = $self->config->{'species'}  || 'homo_sapiens';
        my $data_version  = $self->config->{'data_version'};
        
        $self->{'_adaptor'} ||= Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new
            (
             -host    => $host,
             -user    => $username,
             -dbname  => $dbname,
             -species => $species,
             -pass    => $password,
             -port    => $port,
             );
        print Dumper $self->{'_adaptor'} if ($self->{'debug'});
        return $self->{'_adaptor'};
    }
}
chromosome_by_regiondescriptionprevnextTop
sub chromosome_by_region {
  my ($self, $chr, $start, $end) = @_;
  my $slice = $self->adaptor->get_SliceAdaptor->fetch_by_region
      (
       'chromosome', $chr, $start, $end
       );
  return $slice;
}
disconnectdescriptionprevnextTop
sub disconnect {
  my $self = shift;
  return unless (exists $self->{'_adaptor'});
  $self->{'_adaptor'}->disconnect();
  delete $self->{'_adaptor'};
  $self->{'debug'} and print STDERR "$self PERFORMED DBA DISCONNECT\n";
}
General documentation
LICENCETop
This code is distributed under an Apache style licence. Please see
/info/about/code_licence.html for details.
AUTHORTop
Stefan Graf, Ensembl Functional Genomics
CONTACTTop
Please post comments/questions to the Ensembl development list
<ensembl-dev@ebi.ac.uk>