Raw content of Bio::EnsEMBL::ExternalData::Expression::SeqTag # # EnsEMBL module for Bio::EnsEMBL::ExternalData::Expression::SeqTag # # Cared for by EnsEMBL (www.ensembl.org) # # Copyright GRL and EBI # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::EnsEMBL::ExternalData::Expression::SeqTag =head1 SYNOPSIS @contig = $db->get_Contigs(); $clone = $db->get_Clone(); @genes = $clone->get_all_Genes(); =head1 DESCRIPTION Represents information on one Clone =head1 CONTACT Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::EnsEMBL::ExternalData::Expression::SeqTag; use vars qw(@ISA); use strict; use Bio::DBLinkContainerI; @ISA = qw(Bio::DBLinkContainerI); =head2 new Title : new Usage : Function: Example : Returns : SeqTag object Args : =cut sub new { my ($class,$adaptor,@args) = @_; my $self = {}; bless $self,$class; $self->adaptor($adaptor); $self->_set_from_args(@args); return $self; } =head2 add_DBLink Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args : =cut sub add_DBLink{ my ($self,$com) = @_; if( ! $com->isa('Bio::Annotation::DBLink') ) { $self->throw("Is not a link object but a [$com]"); } push(@{$self->{'link'}},$com); } =head2 each_DBLink Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : Args : =cut sub each_DBLink{ my ($self) = @_; return @{$self->{'link'}} if defined $self->{'link'}; } =head2 id Title : id Usage : $obj->id($newval) Function: Example : Returns : value of tag id Args : newvalue (optional) =cut sub id { my ($obj,$value) = @_; if( defined $value) { $obj->{'_id'} = $value; } return $obj->{'_id'}; } =head2 source Title : source Usage : $obj->source($newval) Function: Example : Returns : value of source Args : newvalue (optional) =cut sub source { my ($obj,$value) = @_; if( defined $value) { $obj->{'_source'} = $value; } return $obj->{'_source'}; } =head2 name Title : name Usage : $obj->name($newval) Function: Example : Returns : value of name Args : newvalue (optional) =cut sub name { my ($obj,$value) = @_; if( defined $value) { $obj->{'_name'} = $value; } return $obj->{'_name'}; } =head2 frequency Title : frequency Usage : $obj->frequency($newval) Function: Example : Returns : value of frequency Args : newvalue (optional) =cut sub frequency { my ($obj,$value) = @_; if( defined $value) { $obj->{'_frequency'} = $value; } return $obj->{'_frequency'}; } =head2 relative_frequency Title : relative_frequency Usage : $obj->realtive_frequency($newval) Function: Example : Returns : value of realtive_frequency Args : newvalue (optional) =cut sub relative_frequency { my ($obj,$value) = @_; if( defined $value) { $obj->{'_relative_frequency'} = $value; } return $obj->{'_relative_frequency'}; } =head2 adaptor Title : adaptor Usage : $obj->adaptor($newval) Function: Example : Returns : value of adaptor Args : newvalue (optional) =cut sub adaptor { my ($obj,$value) = @_; if( defined $value) { $obj->{'adaptor'} = $value; } return $obj->{'adaptor'}; } sub _set_from_args { my ($self,@args)=@_; my ($id,$source,$name,$frequency,$relative_frequency)=@args; $self->id($id); $self->source($source); $self->name($name); $self->frequency($frequency); $self->relative_frequency($relative_frequency); }