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

Class Summary

Synopsis

# metadata_db is an instance of MetaDataDBAdaptor
my $adaptor = $metadata_db->get_GenomeComparaInfoAdaptor();
my @comparas = $adaptor->fetch_all_by_method('PROTEIN_TREES');
for my $genome (@{@comparas[0]->genomes()}) {
  print $genome->name()."\n";
}

Description

Adaptor for storing and retrieving GenomeComparaInfo objects from MySQL genome_info database

See-also

Bio::EnsEMBL::MetaData::GenomeComparaInfo Bio::EnsEMBL::MetaData::GenomeInfo

Definition at line 31 of file GenomeComparaInfoAdaptor.pm.

Available Methods
protected	_args_to_sql ()
protected void	_cache ()
protected void	_clear_cache ()
protected void	_fetch_children ()
protected	_fetch_compara_genomes ()
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	_get_id_field ()
protected	_get_obj_class ()
protected void	_store_cached_obj ()
protected	_store_compara_genomes ()
public void	data_release ()
public	fetch_all ()
public	fetch_all_by_division ()
public Array	fetch_all_by_method ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_dbID ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_dbIDs ()
public Bio::EnsEMBL::MetaData::GenomeComparaInfo	fetch_by_dbname_method_set ()
public Arrayref	fetch_databases ()
public	fetch_division_databases ()
public void	set_ensembl_genomes_release ()
public	set_ensembl_release ()
public void	store ()
public void	update ()

Method Documentation

protected Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::_args_to_sql ( )

Undocumented method

Code:

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

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::GenomeComparaInfoAdaptor::_fetch_children ( )

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

Code:

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

protected Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::_fetch_compara_genomes ( )

Undocumented method

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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

Code:

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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::GenomeComparaInfoAdaptor::_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

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

Undocumented method

Code:

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

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

Undocumented method

Code:

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

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 Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::_store_compara_genomes ( )

Undocumented method

Code:

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public void Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::data_release ( )

  Arg	     : Bio::EnsEMBL::MetaData::DataReleaseInfo
  Description: Default release to use when querying 
  Returntype : None
  Exceptions : none
  Caller     : general
  Status     : Stable

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

Undocumented method

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::fetch_all_by_division ( )

Undocumented method

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public Array Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::fetch_all_by_method ( )

  Arg	     : Method of compara analyses to retrieve
  Description: Fetch compara specified compara analysis
  Returntype : array ref of  Bio::EnsEMBL::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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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::GenomeComparaInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::fetch_by_dbname_method_set ( )

  Arg	     : DBName of compara analyses to retrieve
  Arg	     : Method of compara analyses to retrieve
  Arg	     : Set of compara analyses to retrieve
  Description: Fetch specified compara analysis
  Returntype : Bio::EnsEMBL::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::fetch_databases ( )

  Arg        : (optional) release
  Description: Fetch all compara-associated databases for the specified release
  Returntype : Arrayref of strings
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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  Arg        : division
  Arg        : (optional) release
  Description: Fetch all compara-associated databases for the specified release
  Returntype : Arrayref of strings
  Exceptions : none
  Caller     : general
  Status     : Stable

/**

public Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::fetch_division_databases ( )

Undocumented method

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public void Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::set_ensembl_genomes_release ( )

  Arg	     : Ensembl Genomes release number
  Description: Set release to use when querying 
  Returntype : None
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor::set_ensembl_release ( )

Undocumented method

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

  Arg	     : Bio::EnsEMBL::MetaData::GenomeComparaInfo
  Description: Stores the supplied object and all associated  genomes (if not already stored)
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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

  Arg	     : Bio::EnsEMBL::MetaData::GenomeComparaInfo
  Description: Updates the supplied object and all associated  genomes
  Returntype : None
  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/GenomeComparaInfoAdaptor.pm

Class Summary

Synopsis

Description

See-also

Available Methods

Method Documentation