Raw content of Bio::EnsEMBL::ExternalData::Mole::Entry
<![CDATA[package Bio::EnsEMBL::ExternalData::Mole::Entry;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::ExternalData::Mole::DBSQL::EntryAdaptor;
@ISA = qw(Bio::EnsEMBL::Storable);
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($dbid, $accession_version,
$name, $topology, $molecule_type,
$data_class, $tax_division, $sequence_length,
$accession_obj, $dbxref_objs, $comment_objs,
$description_obj,$sequence_obj, $taxonomy_obj) =
rearrange([qw(DBID
ACCESSION_VERSION
NAME
TOPOLOGY
MOLECULE_TYPE
DATA_CLASS
TAX_DIVISION
SEQUENCE_LENGTH
ACCESSION_OBJ
DBXREF_OBJS
COMMENT_OBJS
DESCRIPTION_OBJ
SEQUENCE_OBJ
TAXONOMY_OBJ
)],@_);
$self->dbID ( $dbid );
$self->accession_version ( $accession_version );
$self->name ( $name );
$self->topology ( $topology );
$self->molecule_type ( $molecule_type );
$self->data_class ( $data_class );
$self->tax_division ( $tax_division );
$self->sequence_length ( $sequence_length ) if (defined $sequence_length);
if(!ref($accession_obj) || !$accession_obj->isa('Bio::EnsEMBL::ExternalData::Mole::Accession')) {
throw('-ACCESSION_OBJ argument must be a Bio::EnsEMBL::ExternalData::Mole::Accession not '.
$accession_obj);
}
$self->accession_obj($accession_obj);
if ($dbxref_objs) {
$self->{'dbxref_objs'} = $dbxref_objs;
} else {
$self->{'dbxref_objs'} = [];
}
if ($comment_objs) {
$self->{'comment_objs'} = $comment_objs;
} else {
$self->{'comment_objs'} = [];
}
if (defined $description_obj) {
if(!ref($description_obj) || !$description_obj->isa('Bio::EnsEMBL::ExternalData::Mole::Description')) {
throw('-DESCRIPTION_OBJ argument must be a Bio::EnsEMBL::ExternalData::Mole::Description not '.
$description_obj);
}
$self->description_obj($description_obj);
} else {
warning("No description object for Entry ".$self->accession_version);
}
if (defined $sequence_obj) {
if(!ref($sequence_obj) || !$sequence_obj->isa('Bio::EnsEMBL::ExternalData::Mole::Sequence')) {
throw('-SEQUENCE_OBJ argument must be a Bio::EnsEMBL::ExternalData::Mole::Sequence not '.
$sequence_obj);
}
$self->sequence_obj($sequence_obj);
} else {
warning("No sequence object for Entry ".$self->accession_version);
}
if (defined $taxonomy_obj) {
if(!ref($taxonomy_obj) || !$taxonomy_obj->isa('Bio::EnsEMBL::ExternalData::Mole::Taxonomy')) {
throw('-DESCRIPTION_OBJ argument must be a Bio::EnsEMBL::ExternalData::Mole::Taxonomy not '.
$taxonomy_obj);
}
$self->taxonomy_obj($taxonomy_obj);
} else {
warning("No taxonomy object for Entry ".$self->accession_version);
}
return $self; # success - we hope!
}
sub accession_version {
my $self = shift;
$self->{'accession_version'} = shift if ( @_ );
return $self->{'accession_version'};
}
sub name {
my $self = shift;
$self->{'name'} = shift if ( @_ );
return $self->{'name'};
}
sub topology {
my $self = shift;
$self->{'topology'} = shift if ( @_ );
return $self->{'topology'};
}
sub molecule_type {
my $self = shift;
$self->{'molecule_type'} = shift if ( @_ );
return $self->{'molecule_type'};
}
sub data_class {
my $self = shift;
$self->{'data_class'} = shift if ( @_ );
return $self->{'data_class'};
}
sub tax_division {
my $self = shift;
$self->{'tax_division'} = shift if ( @_ );
return $self->{'tax_division'};
}
sub sequence_length {
my $self = shift;
$self->{'sequence_length'} = shift if ( @_ );
return $self->{'sequence_length'};
}
sub accession_obj {
my $self = shift;
if(@_) {
my $acc = shift;
if(defined($acc) && (!ref($acc) || !$acc->isa('Bio::EnsEMBL::ExternalData::Mole::Accession'))) {
throw('accession_obj argument must be a Bio::EnsEMBL::ExternalData::Mole::Accession');
}
$self->{'accession_obj'} = $acc;
}
return $self->{'accession_obj'};
}
sub get_all_DBXrefs {
my ($self) = @_;
if (!defined $self->{'dbxref_objs'} && defined $self->adaptor()) {
$self->{'dbxref_objs'} = $self->adaptor()->db()->get_DBXrefAdaptor()->fetch_all_by_Entry($self);
}
return $self->{'dbxref_objs'};
}
sub comment_objs {
my $self = shift;
my $comments = shift;
if( ! exists $self->{'comment_objs'} ) {
$self->{'comment_objs'} = [];
}
foreach my $comment ( @$comments ) {
if( ! $comment->isa( "Bio::EnsEMBL::ExternalData::Mole::Comment" )) {
throw( "Argument to add_Comments has to be a Bio::EnsEMBL::ExternalData::Mole::Comment" );
}
push( @{$self->{'comment_objs'}}, $comment );
}
return $self->{'comment_objs'};
}
sub description_obj {
my $self = shift;
if(@_) {
my $desc = shift;
if(defined($desc) && (!ref($desc) || !$desc->isa('Bio::EnsEMBL::ExternalData::Mole::Description'))) {
throw('description_obj argument must be a Bio::EnsEMBL::ExternalData::Mole::Description');
}
$self->{'description_obj'} = $desc;
}
return $self->{'description_obj'};
}
sub sequence_obj {
my $self = shift;
if(@_) {
my $seq = shift;
if(defined($seq) && (!ref($seq) || !$seq->isa('Bio::EnsEMBL::ExternalData::Mole::Sequence'))) {
throw('sequence_obj argument must be a Bio::EnsEMBL::ExternalData::Mole::Sequence');
}
$self->{'sequence_obj'} = $seq;
}
return $self->{'sequence_obj'};
}
sub taxonomy_obj {
my $self = shift;
if(@_) {
my $taxonomy = shift;
if(defined($taxonomy) && (!ref($taxonomy) || !$taxonomy->isa('Bio::EnsEMBL::ExternalData::Mole::Taxonomy'))) {
throw('taxonomy_obj argument must be a Bio::EnsEMBL::ExternalData::Mole::Taxonomy');
}
$self->{'taxonomy_obj'} = $taxonomy;
}
return $self->{'taxonomy_obj'};
}
1;
]]>