Available Methods
Bio::EnsEMBL::MetaData::DatabaseInfo Class Reference
Inheritance diagram for Bio::EnsEMBL::MetaData::DatabaseInfo:

List of all members.

Class Summary

Synopsis

my $info = Bio::EnsEMBL::MetaData::DatabaseInfo->new(-DBNAME=>"homo_sapiens_core_84_38", -SUBJECT=>$human_genome);
print $info->dbname();

Description

Object encapsulating information about a database that can be associated with genomes or releases.

See-also

Bio::EnsEMBL::MetaData::BaseInfo Bio::EnsEMBL::MetaData::DBSQLDatabaseInfoAdaptor

Definition at line 23 of file DatabaseInfo.pm.

Available Methods

protected void _load_child ()
protected String _parse_type ()
protected void _preload ()
protected _unload ()
public
Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor 		adaptor ()
public Int count_hash_lengths ()
public count_hash_values ()
public DbID dbID ()
public String dbname ()
public division ()
public new ()
public String species_id ()
public
Bio::EnsEMBL::MetaData::GenomeInfo 		subject ()
public Hashref to_hash ()
public to_string ()
public String type ()

Method Documentation

protected void Bio::EnsEMBL::MetaData::BaseInfo::_load_child ( ) [inherited] 
  Description: Lazy load method for loading children from database if not initialised
  Arg        : Key to find child data in object hash
  Arg        : Method for loading child data from adaptor()
  Returntype : none
  Exceptions : none
  Caller     : Internal
  Status     : Stable
Code:
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protected String Bio::EnsEMBL::MetaData::DatabaseInfo::_parse_type ( ) 
  Description: Derive type from database name
  Returntype : String
  Exceptions : none
  Caller     : internal
  Status     : Stable
Code:
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protected void Bio::EnsEMBL::MetaData::BaseInfo::_preload ( ) [inherited] 
  Description: Ensure all children are loaded (used for hash transformation)
  Returntype : none
  Exceptions : none
  Caller     : Internal
  Status     : Stable
Code:
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  Description: Remove all children (used after hash transformation to ensure object is minimised)
  Returntype : none
  Exceptions : none
  Caller     : dump_metadata.pl
  Status     : Stable

/**

Reimplemented in Bio::EnsEMBL::MetaData::GenomeAssemblyInfo, and Bio::EnsEMBL::MetaData::GenomeInfo.

protected Bio::EnsEMBL::MetaData::BaseInfo::_unload ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::MetaData::GenomeAssemblyInfo, and Bio::EnsEMBL::MetaData::GenomeInfo.

public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor Bio::EnsEMBL::MetaData::BaseInfo::adaptor ( ) [inherited] 
  Arg        : (optional) adaptor to set set
  Description: Gets/sets GenomeInfoAdaptor
  Returntype : Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor
  Exceptions : none
  Caller     : Internal
  Status     : Stable
Code:
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Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public Int Bio::EnsEMBL::MetaData::BaseInfo::count_hash_lengths ( ) [inherited] 
  Description: Sums sizes of arrays found in hash as values
  Arg		 : hashref
  Returntype : integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
Code:
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Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public Bio::EnsEMBL::MetaData::BaseInfo::count_hash_values ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public DbID Bio::EnsEMBL::MetaData::BaseInfo::dbID ( ) [inherited] 
  Arg        : (optional) dbID to set set
  Description: Gets/sets internal genome_id used as database primary key
  Returntype : dbID string
  Exceptions : none
  Caller     : Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor
  Status     : Stable
Code:
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Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public String Bio::EnsEMBL::MetaData::DatabaseInfo::dbname ( ) 
  Arg        : (optional) dbname to set
  Description: Gets/sets dbname
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bio::EnsEMBL::MetaData::DatabaseInfo::division ( )

Undocumented method

Code:
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public Bio::EnsEMBL::MetaData::DatabaseInfo::new ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public String Bio::EnsEMBL::MetaData::DatabaseInfo::species_id ( ) 
  Arg        : (optional) species_id to set
  Description: Gets/sets species_id
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DatabaseInfo::subject ( ) 
  Arg        : (optional) subject
  Description: Gets/sets subject that database is associated with
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo or Bio::EnsEMBL::MetaData::DataReleaseInfo
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::MetaData::DatabaseInfo::to_hash ( ) 
  Description: Render as plain hash suitable for export as JSON/XML
  Returntype : Hashref
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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  Description: Render as string for display
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

/**

Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public Bio::EnsEMBL::MetaData::DatabaseInfo::to_string ( )

Undocumented method

Code:
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public String Bio::EnsEMBL::MetaData::DatabaseInfo::type ( ) 
  Arg        : (optional) database type to set
  Description: Gets/sets database type
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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The documentation for this class was generated from the following file: