Inheritance diagram for Bio::EnsEMBL::DBEntry:

Public Member Functions
public Bio::EnsEMBL::DBEntry	new ()

public String	primary_id ()

public String	display_id ()

public String	optional_id ()

public String	dbname ()

public String	database ()

public String	release ()

public String	version ()

public String	db_version ()

public String	description ()

public Bio::EnsEMBL::Analysis	analysis ()

public String	comment ()

public String	priority ()

public String	db_display_name ()

public String	info_type ()

public String	info_text ()

public String	linkage_annotation ()

public String	type ()

public String	secondary_db_name ()

public String	secondary_db_table ()

public void	add_synonym ()

public Listref	get_all_synonyms ()

public Listref	get_all_dependents ()

public Listref	get_all_masters ()

public void	flush_synonyms ()

public String	status ()

Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()

public Instance	new_fast ()

public Int	dbID ()

public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()

public Boolean	is_stored ()

public	get_all_DAS_Features ()

Detailed Description

Description

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

Definition at line 12 of file DBEntry.pm.

Member Function Documentation

◆ add_synonym()

public void Bio::EnsEMBL::DBEntry::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

Code:

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◆ analysis()

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DBEntry::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

Code:

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◆ comment()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ database()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ db_display_name()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ db_version()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ dbname()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ description()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ display_id()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ flush_synonyms()

public void Bio::EnsEMBL::DBEntry::flush_synonyms ( )

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

Code:

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◆ get_all_dependents()

public Listref Bio::EnsEMBL::DBEntry::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

Code:

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◆ get_all_masters()

public Listref Bio::EnsEMBL::DBEntry::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

Code:

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◆ get_all_synonyms()

public Listref Bio::EnsEMBL::DBEntry::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

Code:

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◆ info_text()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ info_type()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ linkage_annotation()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ new()

public Bio::EnsEMBL::DBEntry Bio::EnsEMBL::DBEntry::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

Code:

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◆ optional_id()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ primary_id()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ priority()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ release()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ secondary_db_name()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ secondary_db_table()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ status()

public String Bio::EnsEMBL::DBEntry::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

Code:

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◆ type()

public String Bio::EnsEMBL::DBEntry::type ( )

  Arg [1]    : String $type
  Example    :

none

  Description: Getter/setter for attribute 'type'.
               The external database type.
  Returntype : String
  Exceptions : none
  Caller     : general

Code:

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◆ version()

public String Bio::EnsEMBL::DBEntry::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

Code:

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The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/DBEntry.pm

Public Member Functions

Detailed Description

Description

Member Function Documentation

◆ add_synonym()

◆ analysis()

◆ comment()

◆ database()

◆ db_display_name()

◆ db_version()

◆ dbname()

◆ description()

◆ display_id()

◆ flush_synonyms()

◆ get_all_dependents()

◆ get_all_masters()

◆ get_all_synonyms()

◆ info_text()

◆ info_type()

◆ linkage_annotation()

◆ new()

◆ optional_id()

◆ primary_id()

◆ priority()

◆ release()

◆ secondary_db_name()

◆ secondary_db_table()

◆ status()

◆ type()

◆ version()