Inheritance diagram for Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor:

Class Summary

Synopsis

# metadata_db is an instance of MetaDataDBAdaptor
my $adaptor = $metadata_db->get_GenomeOrganismInfoAdaptor();
my $assembly = $adaptor->fetch_by_name('homo_sapiens');

Description

Adaptor for storing and retrieving GenomeOrganismInfo objects from MySQL ensembl_metadata database

See-also

Bio::EnsEMBL::MetaData::GenomeOrganismInfo

Definition at line 28 of file GenomeOrganismInfoAdaptor.pm.

Available Methods
protected String	_args_to_sql ()
protected void	_cache ()
protected void	_clear_cache ()
protected void	_fetch_aliases ()
protected void	_fetch_children ()
protected Arrayref	_fetch_generic ()
protected Arrayref	_fetch_generic_with_args ()
protected	_fetch_publications ()
protected Arrayref	_first_element ()
protected	_get_base_sql ()
protected Object	_get_cached_obj ()
protected void	_get_division_id ()
protected	_get_id_field ()
protected	_get_obj_class ()
protected void	_store_aliases ()
protected void	_store_cached_obj ()
protected void	_store_publications ()
public	fetch_all ()
public Arrayref	fetch_all_by_name_pattern ()
public Arrayref	fetch_all_by_taxonomy_branch ()
public	fetch_all_by_taxonomy_id ()
public	fetch_all_by_taxonomy_ids ()
public Bio::EnsEMBL::MetaData::GenomeOrganismInfo	fetch_by_alias ()
public	fetch_by_any_name ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_dbID ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_dbIDs ()
public Bio::EnsEMBL::MetaData::GenomeOrganismInfo	fetch_by_display_name ()
public Bio::EnsEMBL::MetaData::GenomeOrganismInfo	fetch_by_name ()
public void	store ()
public Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyNodeAdaptor	taxonomy_adaptor ()
public void	update ()

Method Documentation

protected String Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_args_to_sql ( ) [inherited]

  Description: Add where clauses to SQL given arguments
  Arg        : String - Base SQL
  Arg        : Hashref - arguments
  Returntype : String
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor, and Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor.

protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_cache ( ) [inherited]

  Arg	     : type of object for cache
  Description: Return internal cache for given type
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_clear_cache ( ) [inherited]

  Arg	     : (optional) type of object to clear
  Description: Clear internal cache (optionally just one type)
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::_fetch_aliases ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeOrganismInfo 
  Description: Add aliases to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::_fetch_children ( )

  Arg	     : Arrayref of Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Description: Fetch all children of specified info object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_generic ( ) [inherited]

  Arg	     : SQL to use to fetch object
  Arg	     : arrayref of bind parameters
  Arg        : (optional) if set to 1, all children will be fetched
  Description: Instantiate a GenomeInfo from the database using the specified SQL
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_generic_with_args ( ) [inherited]

  Arg	     : hashref of arguments by column
  Arg        : (optional) if set to 1, all children will be fetched
  Description: Instantiate a GenomeInfo from the database using a 
               generic method, with the supplied arguments
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::_fetch_publications ( )

Undocumented method

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protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_first_element ( ) [inherited]

  Arg	     : arrayref
  Description: Utility method to return the first element in a list, undef if empty
  Returntype : arrayref element
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::_get_base_sql ( )

Undocumented method

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected Object Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_cached_obj ( ) [inherited]

  Arg	     : type of object to retrieve
  Arg	     : ID of object to retrieve
  Description: Retrieve object from internal cache
  Returntype : object
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_division_id ( ) [inherited]

  Arg	     : division name
  Description: Return ID for division, storing if required
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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protected Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::_get_id_field ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::_get_obj_class ( )

Undocumented method

Code:

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::_store_aliases ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Description: Stores the aliases for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_store_cached_obj ( ) [inherited]

  Arg	     : type of object to store
  Arg	     : object to store
  Description: Store object in internal cache
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::_store_publications ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Description: Stores the publications for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_all ( ) [inherited]

Undocumented method

Code:

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::fetch_all_by_name_pattern ( )

  Arg	     : Regular expression matching of organism
  Description: Fetch info for specified organism
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::fetch_all_by_taxonomy_branch ( )

  Arg	     : Bio::EnsEMBL::TaxonomyNode
  Description: Fetch organism info for specified taxonomy node and its children
  Returntype : arrayref of Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::fetch_all_by_taxonomy_id ( )

Undocumented method

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::fetch_all_by_taxonomy_ids ( )

Undocumented method

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public Bio::EnsEMBL::MetaData::GenomeOrganismInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::fetch_by_alias ( )

  Arg	     : Alias of organism
  Description: Fetch info for specified organism
  Returntype : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::fetch_by_any_name ( )

Undocumented method

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_by_dbID ( ) [inherited]

  Arg	     : ID of genome info
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified ID
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_by_dbIDs ( ) [inherited]

  Arg	     : IDs of genome info
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified ID
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::GenomeOrganismInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::fetch_by_display_name ( )

  Arg	     : Name of organism
  Description: Fetch info for specified organism
  Returntype : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::GenomeOrganismInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::fetch_by_name ( )

  Arg	     : Display name of organism 
  Description: Fetch info for specified organism
  Returntype : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public void Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::store ( )

  Arg        : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Description: Store the supplied object
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyNodeAdaptor Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::taxonomy_adaptor ( )

  Arg	     : Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyNodeAdaptor
  Description: Get/set the taxonomy adaptor
  Returntype : Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyNodeAdaptor
  Exceptions : none
  Caller     : internal
  Status     : Stable

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public void Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor::update ( )

  Arg        : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Description: Update the supplied object (must be previously stored)
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

Bio/EnsEMBL/MetaData/DBSQL/GenomeOrganismInfoAdaptor.pm

Class Summary

Synopsis

Description

See-also

Available Methods

Method Documentation