Raw content of Bio::EnsEMBL::DBEntry
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::DBEntry -
Object representing an external reference (xref)
=head1 SYNOPSIS
=head1 DESCRIPTION
This object holds information about external references (xrefs) to
Ensembl objects.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBEntry;
use strict;
use warnings;
no warnings qw(uninitialized);
use Bio::EnsEMBL::Storable;
use Bio::Annotation::DBLink;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(deprecate);
our @ISA = qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink);
=head2 new_fast
Arg [1] : Hashref $hashref - hash reference to bless as new DBEntry object
Description: A very quick constructor that requires internal knowledge of
the class. This is used in speed critical sections of the code
where many objects need to be created quickly.
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : general
Status : Stable
=cut
sub new_fast {
my $class = shift;
my $hashref = shift;
bless $hashref, $class;
return $hashref;
}
=head2 new
Args [...] : list of named parameters
Example : my $dbentry = new Bio::EnsEMBL::DBEntry(
-adaptor => $adaptor,
-primary_id => $pid,
-version => $version,
-dbname => $dbname,
-release => $release,
-display_id => $did,
-description => $description,
-primary_id_linkable =>$primary_id_linkable,
-display_id_linkable =>$display_id_linkable,
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
-info_text => $info_text,
-type => $type,
-secondary_db_name => $secondary_db_name,
-secondary_db_table => $secondary_db_table
-linkage_annotation => $object_xref_text);
Description: Creates a new DBEntry object
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : Bio::EnsEMBL::DBEntryAdaptor
Status : At Risk
Due to 'PRIMARY_ID_LINKABLE','DISPLAY_ID_LINKABLE','PRIORITY',
'INFO_TYPE', 'INFO_TEXT', ''DB_DISPLAY_NAME', 'TYPE',
'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE'
being under development - if you don't use any of these the
method can be considered Stable
=cut
sub new {
my ($class, @args) = @_;
my $self = bless {},$class;
my ( $adaptor, $dbID, $primary_id, $version,
$dbname, $release, $display_id, $description,
$primary_id_linkable, $display_id_linkable, $priority,
$db_display_name, $info_type, $info_text, $type,
$secondary_db_name, $secondary_db_table, $link_annotation, $analysis) =
rearrange ( ['ADAPTOR','DBID','PRIMARY_ID','VERSION',
'DBNAME','RELEASE','DISPLAY_ID','DESCRIPTION',
'PRIMARY_ID_LINKABLE','DISPLAY_ID_LINKABLE','PRIORITY',
'DB_DISPLAY_NAME', 'INFO_TYPE', 'INFO_TEXT', 'TYPE',
'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE', 'LINKAGE_ANNOTATION', 'ANALYSIS'], @args );
$self->{'adaptor'} = $adaptor;
$self->{'dbID'} = $dbID;
if( defined $primary_id ) { $self->primary_id( $primary_id ) }
if( defined $version ) { $self->version( $version ) } else
{ $self->version( "" ); }
if( defined $dbname ) { $self->dbname( $dbname ) }
if( defined $release) { $self->release( $release ) }
if( defined $display_id) { $self->display_id( $display_id ) }
if( defined $description) { $self->description($description) }
if( defined $primary_id_linkable) { $self->primary_id_linkable($primary_id_linkable) }
if( defined $display_id_linkable) { $self->display_id_linkable($display_id_linkable) }
if( defined $priority) { $self->priority($priority) }
if( defined $db_display_name) { $self->db_display_name($db_display_name) }
if( defined $info_type) { $self->info_type($info_type) }
if( defined $info_text) { $self->info_text($info_text) }
if( defined $type) { $self->type($type) }
if( defined $secondary_db_name) { $self->secondary_db_name($secondary_db_name) }
if( defined $secondary_db_table) { $self->secondary_db_table($secondary_db_table) }
$self->linkage_annotation($link_annotation) if defined $link_annotation;
$self->analysis($analysis) if defined $analysis;
return $self;
}
=head2 primary_id
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'primary_id'.
This is the object's primary id in the external database.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub primary_id {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{primary_id} = $arg;
}
return $self->{primary_id};
}
=head2 display_id
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'display_id'.
The object's preferred display name. This can be the same
as primary_id or ensembl-specific.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub display_id{
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{display_id} = $arg;
}
return $self->{display_id};
}
=head2 optional_id
Args : none
Example : none
Description: Additional getter for attribute 'display_id'.
The object's preferred display name.
Only include for BioPerl interface compliance, please use
$self->display_id().
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub optional_id {
my $self = shift;
return $self->display_id;
}
=head2 dbname
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'dbname'.
The name of the external database.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub dbname {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{dbname} = $arg;
}
return $self->{dbname};
}
=head2 database
Args : none
Example : none
Description: Additional getter for attribute 'dbname'.
The name of the external database.
Only include for BioPerl interface compliance, please use
$self->dbname().
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub database {
my $self = shift;
return $self->dbname();
}
=head2 release
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'release'.
The external database release name.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub release {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{release} = $arg;
}
return $self->{release};
}
=head2 version
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'version'.
The object's version in the external database.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub version {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{version} = $arg;
}
return $self->{version};
}
=head2 description
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'description'.
The object's description, from the external_db table
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub description {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{description} = $arg;
}
return $self->{description};
}
=head2 analysis
Arg [1] : Bio::EnsEMBL::Analysis $analysis
Example : none
Description: get/set for attribute analysis
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
Status : Stable
=cut
sub analysis {
my $self = shift;
$self->{analysis} = shift if( @_ );
return $self->{analysis};
}
=head2 comment
Args : none
Example : none
Description: Additional getter for attribute 'description'.
The object's description.
Only include for BioPerl interface compliance, please use
$self->description().
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub comment {
my $self = shift;
return $self->description();
}
=head2 primary_id_linkable
Arg [1] : (optional) Boolean $arg - value to set
Example : none
Description: Getter/setter for attribute 'primary_id_linkable'.
Returntype : String
Exceptions : none
Caller : general
Status : At Risk
: due to it being under development
=cut
sub primary_id_linkable {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{primary_id_linkable} = $arg;
}
return $self->{primary_id_linkable};
}
=head2 display_id_linkable
Arg [1] : (optional) Boolean $arg - value to set
Example : none
Description: Getter/setter for attribute 'display_id_linkable'.
Returntype : String
Exceptions : none
Caller : general
Status : At Risk
: due to it being under development
=cut
sub display_id_linkable {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{display_id_linkable} = $arg;
}
return $self->{display_id_linkable};
}
=head2 priority
Arg [1] : int $priority
Example : none
Priority : Getter/setter for attribute 'priority'. Note this
is the priority from the external_db table.
Returntype : String
Exceptions : none
Caller : general
Status : At Risk
: due to it being under development
=cut
sub priority {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{priority} = $arg;
}
return $self->{priority};
}
=head2 db_display_name
Arg [1] : String $db_display_name
Example : none
Description: Getter/setter for attribute 'db_display_name'.
The preferred display name for the external database. Has
"Projected " prepended if info_type='PROJECTION'.
Returntype : String
Exceptions : none
Caller : general
=cut
sub db_display_name {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{db_display_name} = $arg;
}
my $name;
if ($self->{info_type} && $self->{info_type} eq "PROJECTION") {
$name = "Projected " . $self->{db_display_name};
} else {
$name = $self->{db_display_name};
}
return $name;
}
=head2 info_type
Arg [1] : String $info_type
Example : none
Description: Getter/setter for attribute 'info_type'.
Returntype : String
Exceptions : none
Caller : general
=cut
sub info_type {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{info_type} = $arg;
}
return $self->{info_type};
}
=head2 info_text
Arg [1] : String $info_text
Example : none
Description: Getter/setter for attribute 'info_text'.
Returntype : String
Exceptions : none
Caller : general
=cut
sub info_text {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{info_text} = $arg;
}
return $self->{info_text};
}
=head2 linkage_annotation
Arg [1] : String $object_xref_text
Example : none
Description: Getter/setter for attribute 'linkage_annotation'.
Returntype : String
Exceptions : none
Caller : general
=cut
sub linkage_annotation {
my ( $self, $arg ) = @_;
$self->{linkage_annotation} = $arg if defined $arg;
return $self->{linkage_annotation};
}
=head2 type
Arg [1] : String $type
Example : none
Description: Getter/setter for attribute 'type'.
Returntype : String
Exceptions : none
Caller : general
=cut
sub type {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{type} = $arg;
}
return $self->{type};
}
=head2 secondary_db_name
Arg [1] : String $secondary_db_name
Example : none
Description: Getter/setter for attribute 'secondary_db_name'.
Returnsecondary_db_name : String
Exceptions : none
Caller : general
=cut
sub secondary_db_name {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{secondary_db_name} = $arg;
}
return $self->{secondary_db_name};
}
=head2 secondary_db_table
Arg [1] : String $secondary_db_table
Example : none
Description: Getter/setter for attribute 'secondary_db_table'.
Returnsecondary_db_table : String
Exceptions : none
Caller : general
=cut
sub secondary_db_table {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{secondary_db_table} = $arg;
}
return $self->{secondary_db_table};
}
=head2 add_synonym
Arg [1] : String $arg - synonym to add
Example : none
Description: Add a synonym for the external object.
Returntype : none
Exceptions : none
Caller : general
Status : Stable
=cut
sub add_synonym {
my ( $self, $arg ) = @_;
if( defined $arg ) {
push( @{$self->{synonyms}}, $arg );
}
}
=head2 get_all_synonyms
Args : none
Example : my @synonyms = @{ $db_entry->get_all_synonyms };
Description: Get a list of synonyms known for this object.
Synonyms are lazy-loaded if required.
Returntype : listref of strings. May be empty.
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_synonyms {
my $self = shift;
# lazy-load synonyms if required
if (!$self->{synonyms} && $self->{adaptor}) {
$self->{synonyms} = $self->{adaptor}->fetch_all_synonyms($self->dbID());
}
return $self->{synonyms};
}
=head2 flush_synonyms
Args : none
Example : none
Description: Remove all synonyms from this object.
Returntype : none
Exceptions : none
Caller : general
Status : Stable
=cut
sub flush_synonyms {
my $self = shift;
$self->{synonyms} = [];
}
=head2 status
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'status'.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub status{
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{status} = $arg;
}
return $self->{status};
}
=head1 DEPRECATED METHODS
=cut
=head2 get_synonyms
Description: DEPRECATED use get_all_synonyms instead
=cut
sub get_synonyms {
my $self = shift;
deprecate("get_synonyms has been renamed get_all_synonyms.");
return $self->get_all_synonyms;
}
1;
]]>