=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut =head1 NAME Bio::EnsEMBL::DBEntry - Object representing an external reference (xref) =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); our @ISA = qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink); =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, -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 => $object_xref_text); Description: Creates a new DBEntry object Returntype : Bio::EnsEMBL::DBEntry Exceptions : none Caller : Bio::EnsEMBL::DBEntryAdaptor Status : At Risk Due to 'PRIORITY', 'INFO_TYPE', 'INFO_TEXT', ''DB_DISPLAY_NAME', 'TYPE', 'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE' being under development - if you don't use any of these the method can be considered Stable =cut sub new { my ($class, @args) = @_; my $self = bless {},$class; my ( $adaptor, $dbID, $primary_id, $version, $dbname, $release, $display_id, $description, $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', '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( 0 ); } 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 $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 db_version Arg [1] : (optional) String $arg - value to set Example : none Description: Alias for release(). The release/version of the external DB Returntype : String Exceptions : none Caller : general Status : Stable =cut sub db_version { my ( $self, $arg ) = @_; return $self->release($arg); } =head2 description Arg [1] : (optional) String $arg - value to set Example : none Description: Getter/setter for attribute 'description'. The object's description, from the xref 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 priority Arg [1] : int $priority Example : none Priority : Getter/setter for attribute 'priority'. The external database priority. 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'. Defines the method by which the linked object was connected to this xref. Available types are: 'CHECKSUM', 'COORDINATE_OVERLAP', 'DEPENDENT', 'DIRECT', 'INFERRED_PAIR', 'MISC', 'NONE', 'PROBE', 'PROJECTION', 'SEQUENCE_MATCH' AND 'UNMAPPED'. 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'. Additional information recorded during the xref association. Intended to be used as metadata. 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'. The object xref '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'. The external database 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 Description: Getter/setter for attribute 'secondary_db_name'. The external database 'secondary' database name. Returntype : 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 Description: Getter/setter for attribute 'secondary_db_table'. The external database 'secondary' database table. Returns : 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 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 get_all_dependents Args[1] : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object Example : my @dependents = @{ $db_entry->get_all_dependents }; Description: Get a list of DBEntrys that are depenednet on the DBEntry. if an ensembl gene transcript or translation is given then only the ones on that object will be given Returntype : listref of DBEntrys. May be empty. Exceptions : none Caller : general Status : UnStable =cut sub get_all_dependents { my $self = shift; my $ensembl_object = shift; return $self->adaptor()->get_all_dependents($self->dbID(), $ensembl_object); } =head2 get_all_masters Args[1] : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object Example : my @masters = @{ $db_entry->get_all_masters }; Description: Get a list of DBEntrys that are the masters of the DBEntry. if an ensembl gene transcript or translation is given then only the ones on that object will be given. Returntype : listref of DBEntrys. May be empty. Exceptions : none Caller : general Status : UnStable =cut sub get_all_masters { my $self = shift; my $ensembl_object = shift; return $self->adaptor()->get_all_masters($self->dbID(), $ensembl_object); } =head2 flush_synonyms Args : 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 Description: Getter/setter for attribute 'status'. The external database status. Returntype : String Exceptions : none Caller : general Status : Stable =cut sub status{ my ( $self, $arg ) = @_; if( defined $arg ) { $self->{status} = $arg; } return $self->{status}; } 1;