Ensembl Genomes API
Auxillary Perl API for Ensembl Genomes
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Bio::EnsEMBL::LookUp::RemoteLookUp Class Reference

Public Member Functions

public new ()
 
protected _cache ()
 
protected _adaptor ()
 
public
Bio::EnsEMBL::DBSQL::DBAdaptor 		genome_to_dba ()
 
public Array genomes_to_dbas ()
 
public Arrayref compara_to_dba ()
 
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 ()
 

Detailed Description

Synopsis

# creation of default implementation
my $lookup = Bio::EnsEMBL::RemoteLookUp->new();
my $dbas = $lookup->registry()->get_all();
$dbas = $lookup->get_all_by_taxon_id(388919);
$dbas = $lookup->get_by_name_pattern("Escherichia.*");

Description

This module is an implementation of Bio::EnsEMBL::LookUp that uses Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor to
access a MySQL database containing information about Ensembl Genomes contents.

The default constructor uses the public MySQL server and creates an info adaptor using the latest Ensembl Genomes release

    my $lookup = Bio::EnsEMBL::LookUp::RemoteLookUp->new();
    
Alternatively, a different server and adaptor can be specified:

    my $lookup = Bio::EnsEMBL::LookUp::RemoteLookUp->new(-USER=>$user, -HOST=>$host, -PORT=>$port, -ADAPTOR=>$adaptor);

Once constructed, the LookUp instance can be used as documented in Bio::EnsEMBL::LookUp.

Member Function Documentation

protected Bio::EnsEMBL::LookUp::RemoteLookUp::_adaptor ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::LookUp::RemoteLookUp::_cache ( )

Undocumented method

Code:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::compara_to_dba ( ) 
   Description : Build a Bio::EnsEMBL::Compara::DBSQL::DBAdaptor instance with the supplied info object
    Argument    : Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo
    Exceptions  : None
    Return type : Arrayref of strings
Code:
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public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::LookUp::RemoteLookUp::genome_to_dba ( ) 
   Description : Build a Bio::EnsEMBL::DBSQL::DBAdaptor instance with the supplied info object
    Argument    : Bio::EnsEMBL::Utils::MetaData::GenomeInfo
    Exceptions  : None
    Return type : Bio::EnsEMBL::DBSQL::DBAdaptor
Code:
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public Array Bio::EnsEMBL::LookUp::RemoteLookUp::genomes_to_dbas ( ) 
   Description : Build a set of Bio::EnsEMBL::DBSQL::DBAdaptor instances with the supplied info objects
    Argument    : array ref of Bio::EnsEMBL::Utils::MetaData::GenomeInfo
    Exceptions  : None
    Return type : array ref of Bio::EnsEMBL::DBSQL::DBAdaptor
Code:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_assemblies ( ) 
   Description : Return list of all INSDC assembly accessions registered with the helper
    Exceptions  : None
    Return type : Arrayref of strings
Code:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_by_taxon_branch ( )

Undocumented method

Code:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_names ( ) 
   Description : Return list of all species names registered with the helper
    Exceptions  : None
    Return type : Arrayref of strings
Code:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_taxon_ids ( ) 
   Description : Return list of all taxon IDs registered with the helper
    Exceptions  : None
    Return type : Arrayref of integers
Code:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Bio::EnsEMBL::DBSQL::DatabaseAdaptor Bio::EnsEMBL::LookUp::RemoteLookUp::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:
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public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_by_name_exact ( ) 
   Description : Return database adaptor that has the supplied string as an alias/name
    Argument    : String
    Exceptions  : None
    Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
Code:
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public Bio::EnsEMBL::LookUp::RemoteLookUp::new ( )

Undocumented method

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