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Summary

Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor -
Database adaptor for a Glovar database

Package variables

Included modules

Inherit

Bio::EnsEMBL::DBSQL::DBAdaptor

Synopsis

    $db_adaptor = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
        -user   => 'root',
        -pass   => 'secret',
        -dbname => 'pog',
        -host   => 'caldy',
        -driver => 'Oracle'
        );
    $snp_adaptor = $db_adaptor->get_GlovarSNPAdaptor;

Description

This object represents a Glovar database. Once created you can retrieve object
adaptors that allow you to create objects from data in the Glovar database.
It delegates its connection responsibilities to the DBConnection class (no
longer inherited from) and its object adaptor retrieval to the static
Bio::EnsEMBL::Registry.

Methods

Methods description

  Example     : my %object_adaptors = %{ $dbadaptor->get_available_adaptors };
  Description : returns a lookup hash of object adaptors for this DBAdaptor
  Return type : Hashref
  Exceptions  : none
  Caller      : Bio::EnsEMBL::Utils::ConfigRegistry

  Arg [-DNADB]: (optional) Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor DNADB 
               All sequence, assembly, contig information etc, will be
               retrieved from this database instead.
  Arg [..]   : Other args are passed to
               Bio::EnsEMBL::ExternalData::Glovar::DBConnection
  Exmaple    : $db = new Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor(
                                                    -species => 'Homo_sapiens',
                                                    -group   => 'glovar'
						    -user    => 'root',
						    -dbname  => 'pog',
						    -host    => 'caldy',
						    -driver  => 'Oracle');
  Description: Constructor for DBAdaptor.
  Returntype : Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor
  Exceptions : none
  Caller     : general

Methods code

sub get_available_adaptors {

  my %pairs = (
    "Glovar"        => "Bio::EnsEMBL::ExternalData::Glovar::GlovarAdaptor",
    "GlovarSNP"     => "Bio::EnsEMBL::ExternalData::Glovar::GlovarSNPAdaptor",
    "GlovarSTS"     => "Bio::EnsEMBL::ExternalData::Glovar::GlovarSTSAdaptor",
    #"GlovarTrace"   => "Bio::EnsEMBL::ExternalData::Glovar::GlovarTraceAdaptor",
    "GlovarHaplotype" => "Bio::EnsEMBL::ExternalData::Glovar::GlovarHaplotypeAdaptor",
    "GlovarBaseComposition" => "Bio::EnsEMBL::ExternalData::Glovar::GlovarBaseCompositionAdaptor",
  );
  return (\%pairs);
}

1;

}

sub new {

    my($class, @args) = @_;
    my $self ={};
    bless $self,$class;

    $self->dbc(new Bio::EnsEMBL::ExternalData::Glovar::DBConnection(@args));

    my ($species, $group, $con, $dnadb) =
        rearrange([qw(SPECIES GROUP DBCONN DNADB)], @args);

    if(defined($con)){
        $self->dbc($con);
    }
    else{
        $self->dbc(new Bio::EnsEMBL::ExternalData::Glovar::DBConnection(@args));
    }

    if(defined($species)){
        $self->species($species);
    }
    else{
        $self->species("DEFAULT");
    }
    if(defined($group)){
        $self->group($group);
    }

    $self = Bio::EnsEMBL::Utils::ConfigRegistry::gen_load($self);

    if(defined $dnadb) {
        $self->dnadb($dnadb);
    }

    return $self;

}

General documentation

This code is distributed under an Apache style licence:
Please see /code_licence.html for details

Tony Cox <avc@sanger.ac.uk>
Patrick Meidl <pm2@sanger.ac.uk>

Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk