Public Member Functions
public	new ()

public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor	build_adaptor ()

public	store ()

public void	update ()

public void	update_compara ()

public void	store_compara ()

protected void	_store_aliases ()

protected void	_store_sequences ()

protected void	_store_features ()

protected void	_store_annotations ()

protected void	_store_variations ()

protected void	_store_alignments ()

public	taxonomy_adaptor ()

public Arrayref	list_divisions ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_all ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_by_dbID ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_by_dbIDs ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_all_by_sequence_accession ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_all_by_sequence_accession_unversioned ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_all_by_sequence_accession_versioned ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_by_assembly_id ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_by_assembly_id_versioned ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_by_assembly_id_unversioned ()

public	fetch_all_by_taxonomy_id ()

public	fetch_all_by_taxonomy_ids ()

public Arrayref	fetch_all_by_taxonomy_branch ()

public Arrayref	fetch_all_by_division ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_by_species ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_by_name ()

public	fetch_by_any_name ()

public Arrayref	fetch_all_by_dbname ()

public Arrayref	fetch_all_by_name_pattern ()

public Bio::EnsEMBL::Utils::MetaData::GenomeInfo	fetch_by_alias ()

public Arrayref	fetch_all_with_variation ()

public Arrayref	fetch_all_with_peptide_compara ()

public Arrayref	fetch_all_with_pan_compara ()

public Arrayref	fetch_all_with_genome_alignments ()

public Arrayref	fetch_all_with_compara ()

public	fetch_all_with_other_alignments ()

protected void	_fetch_variations ()

protected void	_fetch_other_alignments ()

protected void	_fetch_annotations ()

protected void	_fetch_features ()

protected void	_fetch_publications ()

protected void	_fetch_aliases ()

protected void	_fetch_sequences ()

protected void	_fetch_comparas ()

public Array	fetch_all_comparas ()

public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo	fetch_compara_by_dbID ()

public Array	fetch_all_compara_by_division ()

public Array	fetch_all_compara_by_method ()

public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo	fetch_compara_by_dbname_method_set ()

protected Arrayref	_fetch_compara_with_args ()

protected Arrayref	_fetch_compara_generic ()

protected void	_fetch_children ()

protected Arrayref	_fetch_generic_with_args ()

protected Arrayref	_fetch_generic ()

protected void	_cache ()

protected void	_clear_cache ()

protected Object	_get_cached_obj ()

protected void	_store_cached_obj ()

protected Arrayref	_first_element ()

Detailed Description

Synopsis

my $gdba = Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor->build_adaptor();

my $md = $gdba->fetch_by_species("arabidopsis_thaliana");

Description

Adaptor for storing and retrieving GenomeInfo objects from MySQL genome_info database

To start working with an adaptor:

# getting an adaptor
## adaptor for latest public EG release
my $gdba = Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor->build_adaptor();
## adaptor for specified public EG release
my $gdba = Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor->build_adaptor(21);
## manually specify a given database
my $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new(
-USER=>'anonymous',
-PORT=>4157,
-HOST=>'mysql-eg-publicsql.ebi.ac.uk',
-DBNAME=>'genome_info_21');
my $gdba = Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor->new(-DBC=>$dbc);

To find genomes, use the fetch methods e.g.

# find a genome by name
my $genome = $gdba->fetch_by_species('arabidopsis_thaliana');

# find and iterate over all genomes
for my $genome (\@{$gdba->fetch_all()}) {
    print $genome->name()."\n";
}

# find and iterate over all genomes from plants
for my $genome (\@{$gdba->fetch_all_by_division('EnsemblPlants')}) {
    print $genome->name()."\n";
}

# find and iterate over all genomes with variation
for my $genome (\@{$gdba->fetch_all_with_variation()}) {
    print $genome->name()."\n";
}

# find all comparas for the division of interest
my $comparas = $gdba->fetch_all_compara_by_division('EnsemblPlants');

# find the peptide compara
my ($compara) = grep {$_->is_peptide_compara()} \@$comparas;
print $compara->division()." ".$compara->method()."(".$compara->dbname().")\n";

# print out all the genomes in this compara
for my $genome (\@{$compara->genomes()}) {
    print $genome->name()."\n";
}

Member Function Documentation

protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_cache ( )

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

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_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

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_aliases ( )

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

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_annotations ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo 
  Description: Add annotations to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_children ( )

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

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protected Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_compara_generic ( )

  Arg       : SQL
  Arg        : array ref of bind params
  Description: Fetch compara analyses using supplied SQL
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_compara_with_args ( )

  Arg       : hashref of arguments by column
  Description: Fetch compara analyses by column value pairs
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_comparas ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo 
  Description: Add compara info to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_features ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo 
  Description: Add features to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_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::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_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::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_other_alignments ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo 
  Description: Add other_alignments to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_publications ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo 
  Description: Add publications to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_sequences ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo 
  Description: Add sequences to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_variations ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo 
  Description: Add variations to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_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

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protected Object Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_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

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_store_aliases ( )

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

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_store_alignments ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Description: Stores the alignments for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_store_annotations ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Description: Stores the annotations for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_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

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_store_features ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Description: Stores the features for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_store_sequences ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Description: Stores the sequences for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::_store_variations ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Description: Stores the variations for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::build_adaptor ( )

  Arg  : (optional) Ensembl Genomes release (e.g. 21)
  Example    :

$info = Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo->build_adaptor();

  Description: Creates a new adaptor using the Ensembl Genomes public MySQL instance (using the latest release if specified)
  Returntype : Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor
  Exceptions : croaks if suitable database cannot be found
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info
  Returntype : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_dbname ( )

  Arg       : Name of database
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified database
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_division ( )

  Arg       : Name of division
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome infos for specified division
  Returntype : Arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_name_pattern ( )

  Arg       : Regular expression matching of genome
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified species
  Returntype : Arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_sequence_accession ( )

  Arg       : INSDC sequence accession e.g. U00096.1 or U00096
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified sequence accession
  Returntype : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_sequence_accession_unversioned ( )

  Arg       : INSDC sequence accession e.g. U00096
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified sequence accession
  Returntype : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_sequence_accession_versioned ( )

  Arg       : INSDC sequence accession e.g. U00096.1
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified sequence accession
  Returntype : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_taxonomy_branch ( )

  Arg       : Bio::EnsEMBL::TaxonomyNode
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified taxonomy node and its children
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_taxonomy_id ( )

Undocumented method

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public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_taxonomy_ids ( )

Undocumented method

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public Array Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_compara_by_division ( )

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

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public Array Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_compara_by_method ( )

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

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public Array Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_comparas ( )

  Description: Fetch all compara analyses
  Returntype : array ref of Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_compara ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have any compara or whole genome alignment data
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_genome_alignments ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have whole genome alignment data
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_other_alignments ( )

Undocumented method

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_pan_compara ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have pan comapra data
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_peptide_compara ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have peptide compara data
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_variation ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have variation data
  Returntype : arrayref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_alias ( )

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

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public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_any_name ( )

Undocumented method

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_assembly_id ( )

  Arg       : INSDC assembly accession
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified assembly ID (versioned or unversioned)
  Returntype : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_assembly_id_unversioned ( )

  Arg       : INSDC assembly set chain (unversioned accession)
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified assembly set chain
  Returntype : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_assembly_id_versioned ( )

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

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::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::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::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::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_name ( )

  Arg       : Display name of genome 
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified species
  Returntype : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_species ( )

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

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public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_compara_by_dbID ( )

  Arg       : ID of compara analysis to retrieve
  Description: Fetch compara specified compara analysis
  Returntype : Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::fetch_compara_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::Utils::MetaData::GenomeComparaInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::list_divisions ( )

  Description: Get list of all Ensembl Genomes divisions for which information is available
  Returntype : Arrayref of strings
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::new ( )

Undocumented method

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public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::store ( )

Undocumented method

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public void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::store_compara ( )

  Arg       : Bio::EnsEMBL::Utils::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 Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::taxonomy_adaptor ( )

Undocumented method

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public void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::update ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
  Description: Updates the supplied object and all associated child objects (includes other genomes attached by compara if not already stored)
  Returntype : None
  Exceptions : none
  Caller     : general
  Status     : Stable

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public void Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor::update_compara ( )

  Arg       : Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo
  Description: Updates the supplied object and all associated  genomes
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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

modules/Bio/EnsEMBL/Utils/MetaData/DBSQL/GenomeInfoAdaptor.pm

Public Member Functions

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