Raw content of Bio::EnsEMBL::ExternalData::CDSTrack::GroupVersion
<![CDATA[package Bio::EnsEMBL::ExternalData::CDSTrack::GroupVersion;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::GroupVersionAdaptor;
@ISA = qw(Bio::EnsEMBL::Storable);
sub new {
my($class,@args) = @_;
my $self = bless {},$class;
my ($dbid, $group_id, $group_version, $ncbi_build_number,
$first_ncbi_build_version, $last_ncbi_build_version, $ncbi_gene_id,
$location_count, $ccds_status_val_id, $ccds_version, $was_public,
$current_version, $tax_id, $chromosome, $strand, $adaptor) =
rearrange([qw(DBID
GROUP_ID
GROUP_VERSION
NCBI_BUILD_NUMBER
FIRST_NCBI_BUILD_VERSION
LAST_NCBI_BUILD_VERSION
NCBI_GENE_ID
LOCATION_COUNT
CCDS_STATUS_VAL_ID
CCDS_VERSION
WAS_PUBLIC
CURRENT_VERSION
TAX_ID
CHROMOSOME
STRAND
ADAPTOR
)],@args);
$self->dbID ( $dbid );
$self->group_id ( $group_id );
$self->group_version ( $group_version );
$self->ncbi_build_number ( $ncbi_build_number );
$self->first_ncbi_build_version ( $first_ncbi_build_version );
$self->last_ncbi_build_version ( $last_ncbi_build_version );
$self->ncbi_gene_id ( $ncbi_gene_id );
$self->location_count ( $location_count );
$self->ccds_status_val_id ( $ccds_status_val_id );
$self->ccds_version ( $ccds_version );
$self->was_public ( $was_public );
$self->current_version ( $current_version );
$self->tax_id ( $tax_id );
$self->chromosome ( $chromosome );
$self->strand ( $strand );
$self->adaptor ( $adaptor );
return $self;
}
sub get_all_Accessions {
my $self = shift;
if( ! exists $self->{'_accession_array'} ) {
if( defined $self->adaptor() ) {
my $aa = $self->adaptor()->db()->get_AccessionAdaptor();
my $accessions = $aa->fetch_all_by_GroupVersion( $self );
$self->{'_accession_array'} = $accessions;
}
}
return $self->{'_accession_array'};
}
sub get_all_Locations { #for XY will only return X coords
my $self = shift;
if( ! exists $self->{'_location_array'} ) {
if( defined $self->adaptor() ) {
my $la = $self->adaptor()->db()->get_LocationAdaptor();
my $locations = $la->fetch_all_by_GroupVersion( $self );
$self->{'_location_array'} = $locations;
}
}
return $self->{'_location_array'};
}
sub get_ccds_id {
my $self = shift;
if( ! exists $self->{'_ccds_id'} ) {
if( defined $self->adaptor() ) {
my $ca = $self->adaptor()->db()->get_CcdsAdaptor();
if (defined $ca->fetch_by_GroupVersion($self)){
my ($ccds_id) = $ca->fetch_by_GroupVersion($self)->ccds_id;
$ccds_id = join "", 'CCDS', $ccds_id, '.', $self->ccds_version;
$self->{'_ccds_id'} = $ccds_id;
}
}
}
return $self->{'_ccds_id'};
}
sub get_status {
my $self = shift;
if( ! exists $self->{'_status'} ) {
if( defined $self->adaptor() ) {
my $csa = $self->adaptor()->db()->get_CcdsStatusAdaptor();
my ($status) = $csa->fetch_by_status_id($self->ccds_status_val_id)->ccds_status;
$self->{'_status'} = $status;
}
}
return $self->{'_status'};
}
sub group_id {
my $self = shift;
$self->{'group_uid'} = shift if ( @_ );
return $self->{'group_uid'};
}
sub group_version {
my $self = shift;
$self->{'version'} = shift if ( @_ );
return $self->{'version'};
}
sub ncbi_build_number {
my $self = shift;
$self->{'ncbi_build_number'} = shift if ( @_ );
return $self->{'ncbi_build_number'};
}
sub first_ncbi_build_version {
my $self = shift;
$self->{'first_ncbi_build_version'} = shift if ( @_ );
return $self->{'first_ncbi_build_version'};
}
sub last_ncbi_build_version {
my $self = shift;
$self->{'last_ncbi_build_version'} = shift if ( @_ );
return $self->{'last_ncbi_build_version'};
}
sub ncbi_gene_id {
my $self = shift;
$self->{'gene_id'} = shift if ( @_ );
return $self->{'gene_id'};
}
sub location_count {
my $self = shift;
$self->{'location_count'} = shift if ( @_ );
return $self->{'location_count'};
}
sub ccds_status_val_id {
my $self = shift;
$self->{'ccds_status_val_uid'} = shift if ( @_ );
return $self->{'ccds_status_val_uid'};
}
sub ccds_version {
my $self = shift;
$self->{'ccds_version'} = shift if ( @_ );
return $self->{'ccds_version'};
}
sub was_public {
my $self = shift;
$self->{'was_public'} = shift if ( @_ );
return $self->{'was_public'};
}
sub current_version {
my $self = shift;
$self->{'current_version'} = shift if ( @_ );
return $self->{'current_version'};
}
sub tax_id {
my $self = shift;
$self->{'tax_id'} = shift if ( @_ );
return $self->{'tax_id'};
}
sub chromosome {
my $self = shift;
$self->{'chromosome'} = shift if ( @_ );
return $self->{'chromosome'};
}
sub strand {
my $self = shift;
$self->{'strand'} = shift if ( @_ );
return $self->{'strand'};
}
1;
]]>