Class Summary

Description

Synopsis

  use Bio::EnsEMBL::Compara::DnaFrag; 
  my $genome_db = new Bio::EnsEMBL::Compara::GenomeDB();

SET VALUES
  $genome_db-\>dbID(22);
  $genome_db-\>dba($dba);
  $genome_db-\>name("Homo sapiens");
  $genome_db-\>assembly("NCBI36");
  $genome_db-\>taxon_id(9606);
  $genome_db-\>taxon($taxon);
  $genome_db-\>genebuild("2006-12-Ensembl");
  $genome_db-\>assembly_default(1);
  $genome_db-\>locator("Bio::EnsEMBL::DBSQL::DBAdaptor/host=???;port=???;user=???;dbname=homo_sapiens_core_51_36m;species=Homo sapiens;disconnect_when_inactive=1");

GET VALUES
  $dbID = $genome_db-\>dbID;
  $genome_db_adaptor = $genome_db-\>adaptor;
  $name = $genome_db-\>name;
  $assembly = $genome_db-\>assembly;
  $taxon_id = $genome_db-\>taxon_id;
  $taxon = $genome_db-\>taxon;
  $genebuild = $genome_db-\>genebuild;
  $assembly_default = $genome_db-\>assembly_default;
  $locator = $genome_db-\>locator;

Description

The GenomeDB object stores information about each species including the taxon_id, species name, assembly, genebuild and the location of the core database.

Definition at line 43 of file GenomeDB.pm.

Available Methods
public Bio::EnsEMBL::Compara::GenomeDBAdaptor	adaptor ()
public String	assembly ()
public Int	assembly_default ()
public DBConnection	connect_to_genome_locator ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db_adaptor ()
public Int	dbID ()
public String	genebuild ()
public String	get_short_name ()
public String	locator ()
public String	name ()
public Bio::EnsEMBL::Compara::GenomeDB	new ()
public Bio::EnsEMBL::Compara::GenomeDB	new_fast ()
public String	short_name ()
public Bio::EnsEMBL::Compara::NCBITaxon	taxon ()
public Int	taxon_id ()

Method Documentation

public Bio::EnsEMBL::Compara::GenomeDBAdaptor Bio::EnsEMBL::Compara::GenomeDB::adaptor ( )

  Arg [1]    : (optional) Bio::EnsEMBL::Compara::GenomeDBAdaptor $adaptor
  Example    : $adaptor = $GenomeDB->adaptor();
  Description: Getter/Setter for the GenomeDB object adaptor used
               by this GenomeDB for database interaction.
  Returntype : Bio::EnsEMBL::Compara::GenomeDBAdaptor
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Compara::GenomeDB::assembly ( )

  Arg [1]    : (optional) string
  Example    : $gdb->assembly('NCBI36');
  Description: Getter/Setter for the assembly type of this genome db.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::Compara::GenomeDB::assembly_default ( )

  Arg [1]    : (optional) int
  Example    : $gdb->assembly_default(1);
  Description: Getter/Setter for the assembly_default of this genome db.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public DBConnection Bio::EnsEMBL::Compara::GenomeDB::connect_to_genome_locator ( )

  Arg [1]    : string
  Description: uses the locator string to connect to the external genome database
  Returntype : DBConnection/DBAdaptor defined in locator string
              (usually a Bio::EnsEMBL::DBSQL::DBAdaptor)
              return undef if locator undefined or unable to connect
  Exceptions : none
  Caller     : internal private method 
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::Compara::GenomeDB::db_adaptor ( )

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $dba
               The DBAdaptor containing sequence information for the genome
               represented by this object.
  Example    : $gdb->db_adaptor($dba);
  Description: Getter/Setter for the DBAdaptor containing sequence 
               information for the genome represented by this object.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : thrown if the argument is not a
               Bio::EnsEMBL::DBSQL::DBAdaptor
  Caller     : general
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::Compara::GenomeDB::dbID ( )

  Arg [1]    : (optional) int $value the new value of this objects database 
               identifier
  Example    : $dbID = $genome_db->dbID;
  Description: Getter/Setter for the internal identifier of this GenomeDB
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Compara::GenomeDB::genebuild ( )

  Arg [1]    : (optional) string
  Example    : $gdb->genebuild('2006-12-Ensembl');
  Description: Getter/Setter for the genebuild type of this genome db.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Compara::GenomeDB::get_short_name ( )

  Example    : $gdb->get_short_name;
  Description: The name of this genome in the Gspe ('G'enera
               'spe'cies) format. Can also handle 'G'enera 's'pecies
               's'ub 's'pecies (Gsss)
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Compara::GenomeDB::locator ( )

  Arg [1]    : string
  Description: Returns a string which describes where the external genome (ensembl core)
               database base is located. Locator format is:
               "Bio::EnsEMBL::DBSQL::DBAdaptor/host=ecs4port=3351;user=ensro;dbname=mus_musculus_core_20_32"
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Compara::GenomeDB::name ( )

  Arg [1]    : (optional) string $value
  Example    : $gdb->name('Homo sapiens');
  Description: Getter setter for the name of this genome database, usually
               just the species name.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Compara::GenomeDB Bio::EnsEMBL::Compara::GenomeDB::new ( )

  Example :
    my $genome_db = new Bio::EnsEMBL::Compara::GenomeDB();
    $genome_db->dba($dba);
    $genome_db->name("Homo sapiens");
    $genome_db->assembly("NCBI36");
    $genome_db->taxon_id(9606);
    $genome_db->dbID(22);
    $genome_db->genebuild("2006-12-Ensembl");

  Description: Creates a new GenomeDB object
  Returntype : Bio::EnsEMBL::Compara::GenomeDB
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Compara::GenomeDB Bio::EnsEMBL::Compara::GenomeDB::new_fast ( )

  Arg [1]    : hash reference $hashref
  Example    : 
  Description: This is an ultra fast constructor which requires knowledge of
               the objects internals to be used.
  Returntype : Bio::EnsEMBL::Compara::GenomeDB
  Exceptions : none
  Caller     : Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Compara::GenomeDB::short_name ( )

  Example    : $gdb->short_name;
  Description: The name of this genome in the Gspe ('G'enera
               'spe'cies) format. Can also handle 'G'enera 's'pecies
               's'ub 's'pecies (Gsss)
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Compara::NCBITaxon Bio::EnsEMBL::Compara::GenomeDB::taxon ( )

  Description: uses taxon_id to fetch the NCBITaxon object
  Returntype : Bio::EnsEMBL::Compara::NCBITaxon object 
  Exceptions : if taxon_id or adaptor not defined
  Caller     : general
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::Compara::GenomeDB::taxon_id ( )

  Arg [1]    : (optional) int
  Example    : $gdb->taxon_id(9606);
  Description: Getter/Setter for the taxon id of the contained genome db
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

Bio/EnsEMBL/Compara/GenomeDB.pm

Class Summary

Description

Synopsis

Description

Available Methods

Method Documentation