Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor Class Reference

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

List of all members.

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Class Summary

Description

Base adaptor for storing and retrieving objects from MySQL genome_metadata database

Provides basic methods for store/fetch

See-also

Bio::EnsEMBL::MetaData::BaseInfo

Definition at line 21 of file BaseInfoAdaptor.pm.

Available Methods
protected String	_args_to_sql ()
protected void	_cache ()
protected void	_clear_cache ()
protected	_fetch_children ()
protected Arrayref	_fetch_generic ()
protected Arrayref	_fetch_generic_with_args ()
protected Arrayref	_first_element ()
protected	_get_base_sql ()
protected Object	_get_cached_obj ()
protected void	_get_division_id ()
protected String	_get_id_field ()
protected String	_get_obj_class ()
protected void	_store_cached_obj ()
public	fetch_all ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_dbID ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_dbIDs ()

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Method Documentation

protected String Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_args_to_sql

(

)

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

Code:

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

protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_cache

(

)

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

Code:

protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_clear_cache

(

)

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

Code:

protected Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_children

(

)

Undocumented method

Code:

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

protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_generic

(

)

  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:

protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_generic_with_args

(

)

  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
 

Code:

protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_first_element

(

)

  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
 

Code:

protected Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_base_sql

(

)

Undocumented method

Code:

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

protected Object Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_cached_obj

(

)

  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:

protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_division_id

(

)

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

Code:

protected String Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_id_field

(

)

  Description: Database column containing dbID - must be implemented 
  Returntype : String
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

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

protected Non Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_obj_class

(

)

  Description: Class of object retrieved - must be implemented 
  Returntype : String
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

  Description: Load children of object - no-op implementation, can be overridden
  Arg        : Object to retrieve children for
  Returntype : non
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

/**

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

protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_store_cached_obj

(

)

  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:

public Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_all

(

)

Undocumented method

Code:

public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_by_dbID

(

)

  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:

public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_by_dbIDs

(

)

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

• Bio/EnsEMBL/MetaData/DBSQL/BaseInfoAdaptor.pm