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

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CONTACT

  Please email comments or questions to the public Ensembl
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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

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL