Raw content of Bio::EnsEMBL::ExternalData::CancerGenomeProject::DBSQL::DBAdaptor #$Id: DBAdaptor.pm,v 1.1 2002/10/14 13:32:26 w3adm Exp $ # =head1 NAME Bio::EnsEMBL::ExternalData::CancerGenomeProject::DBSQL::DBAdaptor - Class for a sequence variation database providing external features for EnsEMBL =head1 SYNOPSIS $oncodb = Bio::EnsEMBL::ExternalData::CancerGenomeProject::DBSQL::DBAdaptor->new( -dbname => 'onco' -user => 'root' ); # accessing sequence variations by id # $onco is a Bio::EnsEMBL::ExternalData::Variation object # the method call returns an array of Variation objects; # one for each location my @oncos = $oncodb->get_LocusAdaptor->fetch_by_refonco_id("578"); my $onco = pop @oncos; =head1 DESCRIPTION This object is an abstraction over the EnsEMBL SNP database. Adaptors can be obtained for the database to allow for the storage or retrival of objects stored within the database. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Ensebl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: ensembl-dev@ebi.ac.uk - General discussion =head1 AUTHOR - Heikki Lehvaslaiho Email heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::EnsEMBL::ExternalData::CancerGenomeProject::DBSQL::DBAdaptor; use strict; use vars qw(@ISA); @ISA = qw(Bio::EnsEMBL::DBSQL::DBConnection); #use the DBConnection superclass constructor =head2 get_LocusAdaptor Function : Retrieves a LocusAdaptor from this database Returntype: Bio::EnsEMBL::ExternalData::CancerGenomeProject::DBSQL::LocusAdaptor Exceptions: none Caller : perl/default/oncoview Bio::EnsEMBL::DBSQL::ProxyLocusAdaptor =cut sub get_LocusAdaptor { my $self = shift; return $self->_get_adaptor("Bio::EnsEMBL::ExternalData::CancerGenomeProject::DBSQL::LocusAdaptor"); } 1;