ensembl-hive
2.6
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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 () |
This object holds information about external references (xrefs) to Ensembl objects.
Definition at line 12 of file DBEntry.pm.
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
public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DBEntry::analysis | ( | ) |
Arg [1] : Bio::EnsEMBL::Analysis $analysis Example :
Description: get/set for attribute analysis Returntype : Bio::EnsEMBL::Analysis Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::DBEntry::comment | ( | ) |
Args : none Example :
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
public String Bio::EnsEMBL::DBEntry::database | ( | ) |
Args : none Example :
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
public String Bio::EnsEMBL::DBEntry::db_display_name | ( | ) |
Arg [1] : String $db_display_name Example :
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
public String Bio::EnsEMBL::DBEntry::db_version | ( | ) |
public String Bio::EnsEMBL::DBEntry::dbname | ( | ) |
Arg [1] : (optional) String $arg - value to set Example :
Description: Getter/setter for attribute 'dbname'. The name of the external database. Returntype : String Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::DBEntry::description | ( | ) |
Arg [1] : (optional) String $arg - value to set Example :
Description: Getter/setter for attribute 'description'. The object's description, from the xref table Returntype : String Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::DBEntry::display_id | ( | ) |
Arg [1] : (optional) String $arg - value to set Example :
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
public void Bio::EnsEMBL::DBEntry::flush_synonyms | ( | ) |
Args : none Description: Remove all synonyms from this object. Returntype : none Exceptions : none Caller : general Status : Stable
public Listref Bio::EnsEMBL::DBEntry::get_all_dependents | ( | ) |
Args[1] : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object Example :
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
public Listref Bio::EnsEMBL::DBEntry::get_all_masters | ( | ) |
Args[1] : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object Example :
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
public Listref Bio::EnsEMBL::DBEntry::get_all_synonyms | ( | ) |
Args : none Example :
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
public String Bio::EnsEMBL::DBEntry::info_text | ( | ) |
Arg [1] : String $info_text Example :
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
public String Bio::EnsEMBL::DBEntry::info_type | ( | ) |
Arg [1] : String $info_type Example :
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
public String Bio::EnsEMBL::DBEntry::linkage_annotation | ( | ) |
Arg [1] : String $object_xref_text Example :
Description: Getter/setter for attribute 'linkage_annotation'. The object xref 'linkage annotation'. Returntype : String Exceptions : none Caller : general
public Bio::EnsEMBL::DBEntry Bio::EnsEMBL::DBEntry::new | ( | ) |
Args [...] : list of named parameters Example :
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
public String Bio::EnsEMBL::DBEntry::optional_id | ( | ) |
Args : none Example :
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
public String Bio::EnsEMBL::DBEntry::primary_id | ( | ) |
Arg [1] : (optional) String $arg - value to set Example :
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
public String Bio::EnsEMBL::DBEntry::priority | ( | ) |
Arg [1] : int $priority Example :
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
public String Bio::EnsEMBL::DBEntry::release | ( | ) |
Arg [1] : (optional) String $arg - value to set Example :
Description: Getter/setter for attribute 'release'. The external database release name. Returntype : String Exceptions : none Caller : general Status : Stable
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
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
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
public String Bio::EnsEMBL::DBEntry::type | ( | ) |
Arg [1] : String $type Example :
Description: Getter/setter for attribute 'type'. The external database type. Returntype : String Exceptions : none Caller : general
public String Bio::EnsEMBL::DBEntry::version | ( | ) |
Arg [1] : (optional) String $arg - value to set Example :
Description: Getter/setter for attribute 'version'. The object's version in the external database. Returntype : String Exceptions : none Caller : general Status : Stable