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Bio-EnsEMBL-112.0_52
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/ Bio::EnsEMBL::DBEntry

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] 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.

CONTACT

Please email comments or questions to the public Ensembl
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Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::DBEntry - Object representing an external reference (xref)

DESCRIPTION

This object holds information about external references (xrefs) to Ensembl objects.

METHODS

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

type

Arg [1]    : String $type
Example    : none
Description: Getter/setter for attribute 'type'.
             The external database type.
Returntype : String
Exceptions : none
Caller     : general

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

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

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

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

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

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

flush_synonyms

Args       : none
Description: Remove all synonyms from this object.
Returntype : none
Exceptions : none
Caller     : general
Status     : Stable

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