Bio::EnsEMBL::LookUp::LocalLookUp Class Reference

Public Member Functions
public	new ()
public Registry	registry ()
public File	cache_file ()
public	update_from_registry ()
public	taxonomy_adaptor ()
protected void	_register_dba ()
protected	_dba_id ()
protected	_get_dbc_meta ()
protected	_hash_dba ()
protected	_hash_dba_from_values ()
protected	_invert_dba_hash ()
protected Arrayref	_registry_to_hash ()
protected	_registry_to_json ()
public void	write_registry_to_file ()
public	clear_cache ()
protected	_load_registry_from_json ()
public	load_registry_from_file ()
public	load_registry_from_url ()
public Arrayref	dba_to_args ()
protected	_dba_to_locator ()
protected	_dbc_to_locator ()
protected	_intern_db_connections ()
public Arrayref	get_all_DBConnections ()
public Arrayref	get_all_dbnames ()
public Arrayref	get_all ()
public	get_all_by_taxon_branch ()
public Arrayref	get_all_by_taxon_id ()
public Arrayref	get_by_name_exact ()
public Arrayref	get_all_by_accession ()
public Bio::EnsEMBL::DBSQL::DatabaseAdaptor	get_by_assembly_accession ()
public Arrayref	get_all_by_name_pattern ()
public Arrayref	get_all_by_dbname ()
public Arrayref	get_all_taxon_ids ()
public Arrayref	get_all_names ()
public Arrayref	get_all_accessions ()
public Arrayref	get_all_versioned_accessions ()
public Arrayref	get_all_assemblies ()
public Arrayref	get_all_versioned_assemblies ()
public void	register_all_dbs ()
protected	_register_singlespecies_core ()
protected	_register_multispecies_core ()
protected	_register_multispecies_x ()
protected	_query_multispecies_db ()
protected	_add_aliases ()
protected	_runtime_include ()
protected	_check_name ()
protected	_login_hash ()

Detailed Description

Synopsis

# creation from a database server
Bio::EnsEMBL::LookUp::LocalLookUp->register_all_dbs( $conf->{host},
       $conf->{port}, $conf->{user}, $conf->{pass}, $conf->{db});
my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new();
my $dbas = $lookup->registry()->get_all();
$dbas = $lookup->get_all_by_taxon_id(388919);
$dbas = $lookup->get_by_name_pattern("Escherichia.*");

# creation from a URL
my $lookup = Bio::EnsEMBL::LookUp::::LocalLookUp->new(-URL=>'http://bacteria.ensembl.org/registry.json');

Description

This module is an implementation of Bio::EnsEMBL::LookUp that uses a local hash to store information about available Ensembl Genomes data. 
It can be constructed in a number of different ways:

A remote cache file containing a JSON representation of the hash can be supplied:

    my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new(-URL=>'http://bacteria.ensembl.org/registry.json');

Alternatively, a local file containing the required JSON can be specified instead:

    my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new(-FILE=>"/path/to/reg.json");

Finally, a Registry already loaded with core databases can be supplied:

    my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new(-REGISTRY=>'Bio::EnsEMBL::Registry');

If the standard Registry is used, the argument can be omitted completely:

    my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new();

To populate the registry with just the Ensembl Genomes databases for the current software 
release on a specified server, the following method can be used:

    Bio::EnsEMBL::LookUp::LocalLookUp->register_all_dbs( $host,
       $port, $user, $pass);

Once a lookup has been created, it can be used as specified in Bio::EnsEMBL::LookUp

Member Function Documentation

protected Bio::EnsEMBL::LookUp::LocalLookUp::_add_aliases

(

)

   Description : Registry all aliases
    Argument    : Species name
    Argument    : Arrayref of alias strings
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_check_name

(

)

   Description : Check that the name is not longer than 64 characters
    Argument    : Name to check
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_dba_id

(

)

Undocumented method

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_dba_to_locator

(

)

   Description : return a hash key for a DBAdaptor
    Argument    : Bio::EnsEMBL::DBAdaptor
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_dbc_to_locator

(

)

   Description : return a hash key for a DBConnection
    Argument    : Bio::EnsEMBL::DBConnection
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_get_dbc_meta

(

)

Undocumented method

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_hash_dba

(

)

   Description : Add details from a DBAdaptor to the internal hashes of details
    Argument    : Bio::EnsEMBL::DBAdaptor
    Argument    : (optional) If set to 1, do not update from a DBAdaptor if already processed (allows updates of an existing LookUp instance)
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_hash_dba_from_values

(

)

   Description : Add supplied details to the internal hashes of details
    Argument    : Bio::EnsEMBL::DBAdaptor to hash
    Argument    : Arrayref of taxonomy IDs to use as keys
    Argument    : Arrayref of aliases to use as keys
    Argument    : Arrayref of ENA accessions to use as keys
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_intern_db_connections

(

)

  Description : Go through all available DBAdaptors of registry and ensure they use the same
                DBConnection instance.
  Exceptions  : None
  Status      : At Risk
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_invert_dba_hash

(

)

Undocumented method

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_load_registry_from_json

(

)

   Description : load the registry from the supplied JSON string
    Argument    : JSON string
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_login_hash

(

)

   Description : Generate dbadaptor login hash from supplied arguments
    Argument    : Host
    Argument    : Port
    Argument    : User
    Argument    : Password
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_query_multispecies_db

(

)

   Description : Find all species in the multispecies database
 

Code:

protected void Bio::EnsEMBL::LookUp::LocalLookUp::_register_dba

(

)

   Description : Add a single DBAdaptor to the registry and the internal hashes of details
    Argument    : Bio::EnsEMBL::DBAdaptor
    Return      : None
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_register_multispecies_core

(

)

   Description : Register core dbas for all species in the supplied database
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_register_multispecies_x

(

)

   Description : Register specified dba type for all species in the supplied database
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_register_singlespecies_core

(

)

   Description : Register core dbas for all species in the supplied database
 

Code:

protected Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::_registry_to_hash

(

)

   Description : Generate a hash array structure for the current registry and species details for turning to JSON
    Returns     : Arrayref of hashes
 

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_registry_to_json

(

)

Undocumented method

Code:

protected Bio::EnsEMBL::LookUp::LocalLookUp::_runtime_include

(

)

   Description : Load the specified module (usually a DatabaseAdaptor)
    Argument    : Module name
 

Code:

public File Bio::EnsEMBL::LookUp::LocalLookUp::cache_file

(

)

  Arg [1]     : File to use for local caching
  Description : Sets and retrieves the local cache file 
  Returntype  : File name if set; otherwise undef
  Status      : Stable
 

Code:

public Bio::EnsEMBL::LookUp::LocalLookUp::clear_cache

(

)

Undocumented method

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::dba_to_args

(

)

   Description : Dump the arguments needed for contructing a DBA
    Argument    : Bio::EnsEMBL::DBAdaptor
    Return      : Arrayref of args
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all

(

)

   Description : Return all database adaptors that have been retrieved from registry
    Argument    : None
    Exceptions  : None
    Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_accessions

(

)

   Description : Return list of all INSDC sequence accessions (or other seq_region names) registered with the helper
    Exceptions  : None
    Return type : Arrayref of strings
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_assemblies

(

)

   Description : Return list of all INSDC assembly accessions registered with the helper
    Exceptions  : None
    Return type : Arrayref of strings
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_accession

(

)

   Description : Returns the database adaptor(s) that contains a seq_region with the supplied INSDC accession (or other seq_region name)
    Argument    : Int
    Exceptions  : None
    Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_dbname

(

)

   Description : Returns all database adaptors that have the supplied dbname
    Argument    : String
    Exceptions  : None
    Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_name_pattern

(

)

   Description : Return all database adaptors that have an alias/name that match the supplied regexp
    Argument    : String
    Exceptions  : None
    Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
 

Code:

public Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_taxon_branch

(

)

Undocumented method

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_taxon_id

(

)

   Description : Returns all database adaptors that have the supplied taxonomy ID
    Argument    : Int
    Exceptions  : None
    Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_DBConnections

(

)

   Description : Return all database connections used by the DBAs retrieved from the registry
    Argument    : None
    Exceptions  : None
    Return type : Arrayref of Bio::EnsEMBL::DBSQL::DBConnection
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_dbnames

(

)

   Description : Return all database names used by the DBAs retrieved from the registry
    Argument    : None
    Exceptions  : None
    Return type : Arrayref of strings
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_names

(

)

   Description : Return list of all species names registered with the helper
    Exceptions  : None
    Return type : Arrayref of strings
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_taxon_ids

(

)

   Description : Return list of all taxon IDs registered with the helper
    Exceptions  : None
    Return type : Arrayref of integers
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_versioned_accessions

(

)

   Description : Return list of all versioned INSDC sequence accessions (or other seq_region names) registered with the helper
    Exceptions  : None
    Return type : Arrayref of strings
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_versioned_assemblies

(

)

   Description : Return list of all versioned INSDC assembly accessions registered with the helper
    Exceptions  : None
    Return type : Arrayref of strings
 

Code:

public Bio::EnsEMBL::DBSQL::DatabaseAdaptor Bio::EnsEMBL::LookUp::LocalLookUp::get_by_assembly_accession

(

)

   Description : Returns the database adaptor that contains the assembly with the supplied INSDC assembly accession
    Argument    : Int
    Exceptions  : None
    Return type : Bio::EnsEMBL::DBSQL::DatabaseAdaptor
 

Code:

public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_by_name_exact

(

)

   Description : Return all database adaptors that have the supplied string as an alias/name
    Argument    : String
    Exceptions  : None
    Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
 

Code:

public Bio::EnsEMBL::LookUp::LocalLookUp::load_registry_from_file

(

)

Undocumented method

Code:

public Bio::EnsEMBL::LookUp::LocalLookUp::load_registry_from_url

(

)

Undocumented method

Code:

public Bio::EnsEMBL::LookUp::LocalLookUp::new

(

)

Undocumented method

Code:

public void Bio::EnsEMBL::LookUp::LocalLookUp::register_all_dbs

(

)

   Description : Helper method to load the registry with all multispecies core databases on the supplied server
    Argument    : Host
    Argument    : Port
    Argument    : User
    Argument    : Password
    Argument    : (optional) String with database regexp (default is _collection_core_[0-9]_eVersion_[0-9]+)
    Exceptions  : None
    Return type : None
 

Code:

public Registry Bio::EnsEMBL::LookUp::LocalLookUp::registry

(

)

  Arg [1]     : Registry module to use (default is Bio::EnsEMBL::Registry)
  Description : Sets and retrieves the Registry 
  Returntype  : Registry if set; otherwise undef
  Exceptions  : if an attempt is made to set the value more than once
  Status      : Stable
 

Code:

public Bio::EnsEMBL::LookUp::LocalLookUp::taxonomy_adaptor

(

)

Undocumented method

Code:

public Bio::EnsEMBL::LookUp::LocalLookUp::update_from_registry

(

)

   Description : Update internal hashes of database adaptors by name/taxids from the registry. Invoke when registry has been updated independently.
    Argument    : (optional) If set to 1, do not update from a DBAdaptor if already processed (allows updates of an existing LookUp instance)
    Exceptions  : None
 

Code:

public void Bio::EnsEMBL::LookUp::LocalLookUp::write_registry_to_file

(

)

   Description : Write the contents of the registry and species lists to a JSON file
    Argument    : File name
    Return      : None
 

Code:

---

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

• modules/Bio/EnsEMBL/LookUp/LocalLookUp.pm