Bio::EnsEMBL::ExternalData::CDSTrack GroupVersion
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Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::GroupVersionAdaptor
Bio::EnsEMBL::Storable
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw )
Inherit
Bio::EnsEMBL::Storable
Synopsis
No synopsis!
Description
No description!
Methods
ccds_status_val_id
No description
Code
ccds_version
No description
Code
chromosome
No description
Code
current_version
No description
Code
first_ncbi_build_version
No description
Code
get_all_Accessions
No description
Code
get_all_Locations
No description
Code
get_ccds_id
No description
Code
get_status
No description
Code
group_id
No description
Code
group_version
No description
Code
last_ncbi_build_version
No description
Code
location_count
No description
Code
ncbi_build_number
No description
Code
ncbi_gene_id
No description
Code
new
No description
Code
strand
No description
Code
tax_id
No description
Code
was_public
No description
Code
Methods description
None available.
Methods code
ccds_status_val_iddescriptionprevnextTop
sub ccds_status_val_id {
  my $self = shift;
  $self->{'ccds_status_val_uid'} = shift if ( @_ );
  return $self->{'ccds_status_val_uid'};
}
ccds_versiondescriptionprevnextTop
sub ccds_version {
  my $self = shift;
  $self->{'ccds_version'} = shift if ( @_ );
  return $self->{'ccds_version'};
}
chromosomedescriptionprevnextTop
sub chromosome {
  my $self = shift;
  $self->{'chromosome'} = shift if ( @_ );
  return $self->{'chromosome'};
}
current_versiondescriptionprevnextTop
sub current_version {
  my $self = shift;
  $self->{'current_version'} = shift if ( @_ );
  return $self->{'current_version'};
}
first_ncbi_build_versiondescriptionprevnextTop
sub first_ncbi_build_version {
  my $self = shift;
  $self->{'first_ncbi_build_version'} = shift if ( @_ );
  return $self->{'first_ncbi_build_version'};
}
get_all_AccessionsdescriptionprevnextTop
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'};
}
get_all_LocationsdescriptionprevnextTop
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'};
}
get_ccds_iddescriptionprevnextTop
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'};
}
get_statusdescriptionprevnextTop
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'};
}
group_iddescriptionprevnextTop
sub group_id {
  my $self = shift;
  $self->{'group_uid'} = shift if ( @_ );
  return $self->{'group_uid'};
}
group_versiondescriptionprevnextTop
sub group_version {
  my $self = shift;
  $self->{'version'} = shift if ( @_ );
  return $self->{'version'};
}
last_ncbi_build_versiondescriptionprevnextTop
sub last_ncbi_build_version {
  my $self = shift;
  $self->{'last_ncbi_build_version'} = shift if ( @_ );
  return $self->{'last_ncbi_build_version'};
}
location_countdescriptionprevnextTop
sub location_count {
  my $self = shift;
  $self->{'location_count'} = shift if ( @_ );
  return $self->{'location_count'};
}
ncbi_build_numberdescriptionprevnextTop
sub ncbi_build_number {
  my $self = shift;
  $self->{'ncbi_build_number'} = shift if ( @_ );
  return $self->{'ncbi_build_number'};
}
ncbi_gene_iddescriptionprevnextTop
sub ncbi_gene_id {
  my $self = shift;
  $self->{'gene_id'} = shift if ( @_ );
  return $self->{'gene_id'};
}
newdescriptionprevnextTop
sub new {
  my($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;
}
stranddescriptionprevnextTop
sub strand {
  my $self = shift;
  $self->{'strand'} = shift if ( @_ );
  return $self->{'strand'};
}



1;
}
tax_iddescriptionprevnextTop
sub tax_id {
  my $self = shift;
  $self->{'tax_id'} = shift if ( @_ );
  return $self->{'tax_id'};
}
was_publicdescriptionprevnextTop
sub was_public {
  my $self = shift;
  $self->{'was_public'} = shift if ( @_ );
  return $self->{'was_public'};
}
General documentation
No general documentation available.