Raw content of Bio::EnsEMBL::ExternalData::CDSTrack::Accession
<![CDATA[package Bio::EnsEMBL::ExternalData::CDSTrack::Accession;
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::AccessionAdaptor;
@ISA = qw(Bio::EnsEMBL::Storable);
sub new {
my($class,@args) = @_;
my $self = bless {},$class;
my ($dbid, $transcript_stable_id, $transcript_version,
$transcript_ncbi_id, $translation_stable_id, $translation_version, $translation_ncbi_id,
$organization_id, $alive, $organization, $approval_authority, $adaptor) =
rearrange([qw(DBID
TRANSCRIPT_STABLE_ID
TRANSCRIPT_VERSION
TRANSCRIPT_NCBI_ID
TRANSLATION_STABLE_ID
TRANSLATION_VERSION
TRANSLATION_NCBI_ID
ORGANIZATION_ID
ALIVE
ORGANIZATION
APPROVAL_AUTHORITY
ADAPTOR
)],@args);
$self->dbID ( $dbid );
$self->transcript_stable_id ( $transcript_stable_id );
$self->transcript_version ( $transcript_version );
$self->transcript_ncbi_id ( $transcript_ncbi_id );
$self->translation_stable_id ( $translation_stable_id );
$self->translation_version ( $translation_version );
$self->translation_ncbi_id ( $translation_ncbi_id );
$self->organization_id ( $organization_id );
$self->alive ( $alive );
$self->organization ( $organization );
$self->approval_authority ( $approval_authority );
$self->adaptor ( $adaptor );
return $self;
}
sub get_all_ccds_ids {
my $self = shift;
if( ! exists $self->{'_ccds_id'} ) {
if( defined $self->adaptor() ) {
my $gva = $self->adaptor()->db()->get_GroupVersionAdaptor();
my @gv = @{$gva->fetch_all_by_accession($self->transcript_stable_id, $self->transcript_version)};
my @ccds_id;
foreach my $gv (@gv){
push @ccds_id, $gv->get_ccds_id;
}
$self->{'_ccds_id'} = \@ccds_id;
}
}
return $self->{'_ccds_id'};
}
sub get_all_GroupVersions {
my $self = shift;
if( ! exists $self->{'_groupversion_array'} ) {
if( defined $self->adaptor() ) {
my $gva = $self->adaptor()->db()->get_GroupVersionAdaptor();
my $groupversions = $gva->fetch_all_by_accession( $self->transcript_stable_id, $self->transcript_version );
$self->{'_groupversion_array'} = $groupversions;
}
}
return $self->{'_groupversion_array'};
}
sub get_current_GroupVersion {
my $self = shift;
my $build_number = shift;
throw("Require ncbi_build_number for get_current_GroupVersion")
unless ($build_number);
#need build number as an accession can have >1 current gv if it is on multiple builds
if( ! exists $self->{'_groupversion_array'} ) {
if( defined $self->adaptor() ) {
my $gva = $self->adaptor()->db()->get_GroupVersionAdaptor();
my $groupversions = $gva->fetch_all_current_by_accession( $self->transcript_stable_id, $self->transcript_version, $build_number );
$self->{'_groupversion_array'} = $groupversions;
}
}
return $self->{'_groupversion_array'};
}
#sub get_all_statuses { #do we only want current status? or status on a certain build?
# my $self = shift;
# if( ! exists $self->{'_status'} ) {
#
# my @status;
# my @status_id = @{$self->adaptor->fetch_all_status_id($self->transcript_stable_id, $self->transcript_version)};
#
# if( defined $self->adaptor() ) {
# my $csa = $self->adaptor()->db()->get_CcdsStatusAdaptor();
#
# foreach my $stat_id (@status_id){
# push @status, $csa->fetch_by_status_id($stat_id)->ccds_status;
# }
# }
# $self->{'_status'} = \@status;
# }
# return $self->{'_status'};
#}
#
#
#sub get_all_Locations { #could bring back multiple sets of locations...
# my $self = shift;
# if( ! exists $self->{'_locations'} ) {
#
# print "in here\n";
#
# if( defined $self->adaptor() ) {
# my $gva = $self->adaptor()->db()->get_GroupVersionAdaptor();
# my @gv = @{$gva->fetch_all_by_accession($self->transcript_stable_id, $self->transcript_version)};
# my @locations;
# foreach my $gv (@gv){
# print $gv->dbID."\n";
# my @loc = @{$gv->get_all_Locations};
# foreach my $l (@loc){
# print $l->exon_start." - ".$l->exon_end."\n";
# }
# push @locations, [@{$gv->get_all_Locations}];
# }
# $self->{'_locations'} = \@locations;
# }
# }
# return $self->{'_locations'};
#
#
#
#}
sub transcript_stable_id {
my $self = shift;
$self->{'nuc_acc'} = shift if ( @_ );
return $self->{'nuc_acc'};
}
sub transcript_version {
my $self = shift;
$self->{'nuc_version'} = shift if ( @_ );
return $self->{'nuc_version'};
}
sub transcript_ncbi_id {
my $self = shift;
$self->{'nuc_gi'} = shift if ( @_ );
return $self->{'nuc_gi'};
}
sub translation_stable_id {
my $self = shift;
$self->{'prot_acc'} = shift if ( @_ );
return $self->{'prot_acc'};
}
sub translation_version {
my $self = shift;
$self->{'prot_version'} = shift if ( @_ );
return $self->{'prot_version'};
}
sub translation_ncbi_id {
my $self = shift;
$self->{'prot_gi'} = shift if ( @_ );
return $self->{'prot_gi'};
}
sub organization_id {
my $self = shift;
$self->{'organization_uid'} = shift if ( @_ );
return $self->{'organization_uid'};
}
sub alive {
my $self = shift;
$self->{'alive'} = shift if ( @_ );
return $self->{'alive'};
}
sub organization {
my $self = shift;
$self->{'name'} = shift if ( @_ );
return $self->{'name'};
}
sub approval_authority {
my $self = shift;
$self->{'approval_authority'} = shift if ( @_ );
return $self->{'approval_authority'};
}
1;
]]>