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Commit 8bf5bb43 authored by Patrick Meidl's avatar Patrick Meidl
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better pod

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modules/Bio/EnsEMBL/DBEntry.pm
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#
# EnsEMBL module for DBEntry
#
# Cared for by Arne Stabenau <stabenau@ebi.ac.uk>
#
# Copyright EMBL/EBI 2001
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=pod
package Bio::EnsEMBL::DBEntry;
=head1 NAME
=head1 NAME
Bio::EnsEMBL::DBEntry - Module to collect information about an external reference
Bio::EnsEMBL::DBEntry -
Object representing an external reference (xref)
=head1 SYNOPSIS
=head1 DESCRIPTION
This module stores information about external references to EnsEMBL objects
This object holds information about external references (xrefs) to Ensembl
objects.
=head1 CONTACT
=head1 METHODS
Post questions to the EnsEMBL developer mailing list: <ensembl-dev@ebi.ac.uk>
=head1 METHODS
=head1 LICENCE
=cut
This code is distributed under an Apache style licence. Please see
http://www.ensembl.org/info/about/code_licence.html for details.
=head1 AUTHOR
Arne Stabenau <stabenau@ebi.ac.uk>, Ensembl core API team
package Bio::EnsEMBL::DBEntry;
=head1 CONTACT
use Bio::EnsEMBL::Storable;
use Bio::Annotation::DBLink;
Please post comments/questions to the Ensembl development list
<ensembl-dev@ebi.ac.uk>
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(deprecate);
=cut
use vars qw(@ISA $AUTOLOAD);
use strict;
use warnings;
no warnings qw(uninitialized);
@ISA = qw( Bio::EnsEMBL::Storable Bio::Annotation::DBLink );
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] : hash reference $hashref
Example : none
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 : ?
Caller : general
Status : Stable
=cut
......@@ -64,38 +61,40 @@ use warnings;
sub new_fast {
my $class = shift;
my $hashref = shift;
bless $hashref, $class;
$hashref->{synonyms} = [];
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);
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);
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'
: being under development
: If you don't use any of these the sub can be considered Stable
Due to 'PRIMARY_ID_LINKABLE','DISPLAY_ID_LINKABLE','PRIORITY'
being under development - if you don't use any of these the
method can be considered Stable
=cut
......@@ -135,14 +134,13 @@ sub new {
}
=head2 primary_id
Arg [1] : string $primary_id
Arg [1] : (optional) String $arg - value to set
Example : none
Description: get/set for attribute primary_id
its this objects primary id in the external database
Returntype : string
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
......@@ -154,20 +152,18 @@ sub primary_id {
if( defined $arg ) {
$self->{primary_id} = $arg;
}
return $self->{primary_id};
}
=head2 display_id
Arg [1] : string $display_id
Arg [1] : (optional) String $arg - value to set
Example : none
Description: get/set for attribute display_id
This objects preferred display string. That can be the same
as primary id or ensembl specific.
Returntype : string
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
......@@ -180,79 +176,80 @@ sub display_id{
$self->{display_id} = $arg;
}
return $self->{display_id};
}
=head2 optional_id
=head2 dbname
Arg [1] : string $dbname
Args : none
Example : none
Description: get/set for attribute dbname
Returntype : string
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 dbname {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{dbname} = $arg;
}
return $self->{dbname};
sub optional_id {
my $self = shift;
return $self->display_id;
}
=head2 dbname
=head2 database
Args : none
Arg [1] : (optional) String $arg - value to set
Example : none
Description: additional get for the dbname to make it compliant to
some interface
Returntype : string
Description: Getter/setter for attribute 'dbname'.
The name of the external database.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
=cut
sub database {
my $self = shift;
return $self->dbname();
sub dbname {
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{dbname} = $arg;
}
return $self->{dbname};
}
=head2 optional_id
=head2 database
Args : none
Example : none
Description: additional get for the display_id to make it compliant to
some interface
Returntype : string
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 optional_id {
sub database {
my $self = shift;
return $self->display_id;
return $self->dbname();
}
=head2 release
Arg [1] : string $release
Arg [1] : (optional) String $arg - value to set
Example : none
Description: get/set for attribute release
Returntype : string
Description: Getter/setter for attribute 'release'.
The external database release name.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
......@@ -270,10 +267,11 @@ sub release {
=head2 version
Arg [1] : string $version
Arg [1] : (optional) String $arg - value to set
Example : none
Description: get/set for attribute version
Returntype : string
Description: Getter/setter for attribute 'version'.
The object's version in the external database.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
......@@ -289,14 +287,13 @@ sub version {
}
=head2 description
Arg [1] : string $description
Arg [1] : (optional) String $arg - value to set
Example : none
Description: get/set for attribute description
Returntype : string
Description: Getter/setter for attribute 'description'.
The object's description.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
......@@ -312,12 +309,33 @@ sub description {
}
=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] : boolean $primary_id_linkable
Arg [1] : (optional) Boolean $arg - value to set
Example : none
Description: get/set for attribute primary_id_linkable
Returntype : string
Description: Getter/setter for attribute 'primary_id_linkable'.
Returntype : String
Exceptions : none
Caller : general
Status : At Risk
......@@ -333,12 +351,13 @@ sub primary_id_linkable {
return $self->{primary_id_linkable};
}
=head2 display_id_linkable
Arg [1] : boolean $display_id_linkable
Arg [1] : (optional) Boolean $arg - value to set
Example : none
Display_id_linkable: get/set for attribute display_id_linkable
Returntype : string
Description: Getter/setter for attribute 'display_id_linkable'.
Returntype : String
Exceptions : none
Caller : general
Status : At Risk
......@@ -359,8 +378,8 @@ sub display_id_linkable {
Arg [1] : int $priority
Example : none
Priority : get/set for attribute priority
Returntype : string
Priority : Getter/setter for attribute 'priority'.
Returntype : String
Exceptions : none
Caller : general
Status : At Risk
......@@ -381,8 +400,10 @@ sub priority {
Arg [1] : String $db_display_name
Example : none
Db_display_name: get/set for attribute db_display_name
Returntype : string; has "Projected " prepended if info_type='PROJECTION'
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
......@@ -409,8 +430,8 @@ sub db_display_name {
Arg [1] : String $info_type
Example : none
Info_type: get/set for attribute info_type
Returntype : string
Description: Getter/setter for attribute 'info_type'.
Returntype : String
Exceptions : none
Caller : general
......@@ -429,8 +450,8 @@ sub info_type {
Arg [1] : String $info_text
Example : none
Info_text: get/set for attribute info_text
Returntype : string
Description: Getter/setter for attribute 'info_text'.
Returntype : String
Exceptions : none
Caller : general
......@@ -447,10 +468,9 @@ sub info_text {
=head2 add_synonym
Arg 1 : string $synonym
Arg [1] : String $arg - synonym to add
Example : none
Description: adding a synonynm for the external object under which it is
also known
Description: Add a synonym for the external object.
Returntype : none
Exceptions : none
Caller : general
......@@ -470,9 +490,9 @@ sub add_synonym {
=head2 get_all_synonyms
Args : none
Example : @synonyms = @{$db_entry->get_all_synonyms()};
Description: get a list of synonym added to this object
Returntype : list reference of strings
Example : my @synonyms = @{ $db_entry->get_all_synonyms };
Description: Get a list of synonyms known for this object.
Returntype : listref of strings
Exceptions : none
Caller : general
Status : Stable
......@@ -489,7 +509,7 @@ sub get_all_synonyms {
Args : none
Example : none
Description: remove all synonyms from this object
Description: Remove all synonyms from this object.
Returntype : none
Exceptions : none
Caller : general
......@@ -505,10 +525,10 @@ sub flush_synonyms {
=head2 status
Arg [1] : string $status
Arg [1] : (optional) String $arg - value to set
Example : none
Description: get/set for attribute status
Returntype : string
Description: Getter/setter for attribute 'status'.
Returntype : String
Exceptions : none
Caller : general
Status : Stable
......@@ -517,33 +537,11 @@ sub flush_synonyms {
sub status{
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{status} = $arg;
}
return $self->{status};
}
=head2 comment
Args : none
Example : none
Description: additional get for description to comply with bioperl
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
#Cheat to comply with bioperl
sub comment {
my ($self) = @_;
if ($self) {
return $self->description();
}
my ( $self, $arg ) = @_;
if( defined $arg ) {
$self->{status} = $arg;
}
return $self->{status};
}
......@@ -565,3 +563,4 @@ sub get_synonyms {
}
1;
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