Bio::EnsEMBL
DBEntry
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Summary
Bio::EnsEMBL::DBEntry -
Object representing an external reference (xref)
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
Description
This object holds information about external references (xrefs) to
Ensembl objects.
Methods
Methods description
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 |
Arg [1] : Bio::EnsEMBL::Analysis $analysis
Example : none
Description: get/set for attribute analysis
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
Status : Stable |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Args : none
Example : none
Description: Remove all synonyms from this object.
Returntype : none
Exceptions : none
Caller : general
Status : Stable |
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 |
Description: DEPRECATED use get_all_synonyms instead |
Arg [1] : String $info_text
Example : none
Description: Getter/setter for attribute 'info_text'.
Returntype : String
Exceptions : none
Caller : general |
Arg [1] : String $info_type
Example : none
Description: Getter/setter for attribute 'info_type'.
Returntype : String
Exceptions : none
Caller : general |
Arg [1] : String $object_xref_text
Example : none
Description: Getter/setter for attribute 'linkage_annotation'.
Returntype : String
Exceptions : none
Caller : general |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Arg [1] : String $secondary_db_name
Example : none
Description: Getter/setter for attribute 'secondary_db_name'.
Returnsecondary_db_name : String
Exceptions : none
Caller : general |
Arg [1] : String $secondary_db_table
Example : none
Description: Getter/setter for attribute 'secondary_db_table'.
Returnsecondary_db_table : String
Exceptions : none
Caller : general |
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'status'.
Returntype : String
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : String $type
Example : none
Description: Getter/setter for attribute 'type'.
Returntype : String
Exceptions : none
Caller : general |
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 |
Methods code
sub add_synonym
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
push( @{$self->{synonyms}}, $arg );
}} | sub analysis
{ my $self = shift;
$self->{analysis} = shift if( @_ );
return $self->{analysis};} | sub comment
{ my $self = shift;
return $self->description(); } | sub database
{ my $self = shift;
return $self->dbname(); } | 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;} | sub dbname
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{dbname} = $arg;
}
return $self->{dbname};} | sub description
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{description} = $arg;
}
return $self->{description};} | sub display_id
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{display_id} = $arg;
}
return $self->{display_id};} | sub display_id_linkable
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{display_id_linkable} = $arg;
}
return $self->{display_id_linkable};} | sub flush_synonyms
{ my $self = shift;
$self->{synonyms} = [];} | sub get_all_synonyms
{
my $self = shift;
if (!$self->{synonyms} && $self->{adaptor}) {
$self->{synonyms} = $self->{adaptor}->fetch_all_synonyms($self->dbID());
}
return $self->{synonyms}; } | sub get_synonyms
{ my $self = shift;
deprecate("get_synonyms has been renamed get_all_synonyms.");
return $self->get_all_synonyms;
}
1;} | sub info_text
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{info_text} = $arg;
}
return $self->{info_text};} | sub info_type
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{info_type} = $arg;
}
return $self->{info_type};} | sub linkage_annotation
{ my ( $self, $arg ) = @_;
$self->{linkage_annotation} = $arg if defined $arg;
return $self->{linkage_annotation};} | sub new
{ my ($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;} | sub new_fast
{ my $class = shift;
my $hashref = shift;
bless $hashref, $class;
return $hashref; } | sub optional_id
{ my $self = shift;
return $self->display_id; } | sub primary_id
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{primary_id} = $arg;
}
return $self->{primary_id};} | sub primary_id_linkable
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{primary_id_linkable} = $arg;
}
return $self->{primary_id_linkable};} | sub priority
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{priority} = $arg;
}
return $self->{priority};} | sub release
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{release} = $arg;
}
return $self->{release};} | sub secondary_db_name
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{secondary_db_name} = $arg;
}
return $self->{secondary_db_name};} | sub secondary_db_table
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{secondary_db_table} = $arg;
}
return $self->{secondary_db_table};} | sub status
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{status} = $arg;
}
return $self->{status};} | sub type
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{type} = $arg;
}
return $self->{type};} | sub version
{ my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{version} = $arg;
}
return $self->{version};} | General documentation
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