Bio::EnsEMBL::Compara::GenomeDB Class Reference
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
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

click to view
The documentation for this class was generated from the following file:
- Bio/EnsEMBL/Compara/GenomeDB.pm