Bio::EnsEMBL::DBSQL::GenomeContainer Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::GenomeContainer:

Public Member Functions
public Bio::EnsEMBL::GenomeContainer	new ()
public The	store ()
public void	update ()
protected Bio::EnsEMBL::DBSQL::MetaContainer	_meta_container ()
public String	get_version ()
public String	get_accession ()
public String	get_assembly_name ()
public String	get_assembly_date ()
public String	get_genebuild_start_date ()
public String	get_genebuild_method ()
public String	get_genebuild_initial_release_date ()
public String	get_genebuild_last_geneset_update ()
protected Int	_get_length ()
public Int	get_ref_length ()
public ListRef	get_toplevel ()
public ListRef	get_karyotype ()
public ListRef	get_coord_systems ()
protected Int	_get_count ()
public Int	get_count ()
public ArrayRef	fetch_all_statistics ()
public Bio::EnsEMBL::Genome	fetch_by_statistic ()
public Boolean	is_empty ()
public Bio::EnsEMBL::Attrib	get_attrib ()
public Int	get_coding_count ()
public Int	get_rcoding_count ()
public Int	get_snoncoding_count ()
public Int	get_rsnoncoding_count ()
public Int	get_mnoncoding_count ()
public Int	get_rmnoncoding_count ()
public Int	get_lnoncoding_count ()
public Int	get_rlnoncoding_count ()
public Int	get_pseudogene_count ()
public Int	get_rpseudogene_count ()
public Int	get_alt_coding_count ()
public Int	get_alt_rcoding_count ()
public Int	get_alt_snoncoding_count ()
public Int	get_alt_rsnoncoding_count ()
public Int	get_alt_mnoncoding_count ()
public Int	get_alt_rmnoncoding_count ()
public Int	get_alt_lnoncoding_count ()
public Int	get_alt_rlnoncoding_count ()
public Int	get_alt_pseudogene_count ()
public Int	get_alt_rpseudogene_count ()
public Int	get_short_variation_count ()
public Int	get_prediction_count ()
public Int	get_structural_variation_count ()
public Int	get_transcript_count ()
public Int	get_alt_transcript_count ()
public Int	has_karyotype ()
public Int	is_high_coverage ()
public Int	is_polyploid ()
public Arrayref	get_genome_components ()
protected	_obj_from_sth ()
Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()
public DBI::StatementHandle	prepare ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public Boolean	is_multispecies ()
public Int	species_id ()
protected	_list_dbIDs ()
protected	_straight_join ()
protected	_can_straight_join ()
public Listref	bind_param_generic_fetch ()
protected	_bind_param_generic_fetch ()
public String	generate_in_constraint ()
public Listref	generic_fetch ()
public Int	generic_count ()
protected	_generate_sql ()
public Bio::EnsEMBL::Feature	fetch_by_dbID ()
protected	_uncached_fetch_by_dbID ()
public Listref	fetch_all_by_dbID_list ()
protected	_uncached_fetch_all_by_dbID_list ()
protected ArrayRef	_uncached_fetch_all_by_id_list ()
public	fetch_all ()
public Scalar	last_insert_id ()
public	insert_ignore_clause ()
protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()
protected Boolean	_no_id_cache ()
public Boolean	ignore_cache_override ()
public Int	schema_version ()
protected	_tables ()
protected	_columns ()
protected	_default_where_clause ()
protected	_left_join ()
protected	_final_clause ()
protected	_objs_from_sth ()
protected	_build_id_cache ()
protected	_logic_name_to_constraint ()

Detailed Description

Synopsis

use Bio::EnsEMBL::Registry;
 
Bio::EnsEMBL::Registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous'
);
 
$genome =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "GenomeContainer" );
 
my $version = $genome->get_version;
 
my $ref_length = $genome->get_ref_length;
 
my $coord_systems = $genome->get_coord_systems;

Description

This module is responsible for fetching and storing genome-wide information.
Genome is an abstract object which contains information linking the species, the assembly and the ensembl annotation.

Definition at line 37 of file GenomeContainer.pm.

Member Function Documentation

_get_count()

protected Int Bio::EnsEMBL::DBSQL::GenomeContainer::_get_count

(

)

  Arg [1]    : none
  Example    :

$count = $genome->_get_count('coding_cnt');

  Description: Internal method to return a count for a given attribute code
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

_get_length()

protected Int Bio::EnsEMBL::DBSQL::GenomeContainer::_get_length

(

)

  Arg [1]    : none
  Example    :

$length = $genome->_get_length('toplevel');

  Description: Internal method to return the length for a type of slices
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

_meta_container()

protected Bio::EnsEMBL::DBSQL::MetaContainer Bio::EnsEMBL::DBSQL::GenomeContainer::_meta_container

(

)

  Arg [1]    : none
  Example    :

$meta_container = $genome->_meta_container();

  Description: Internal method to return a MetaContainer object for the genome
  Returntype : Bio::EnsEMBL::DBSQL::MetaContainer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

_obj_from_sth()

protected Bio::EnsEMBL::DBSQL::GenomeContainer::_obj_from_sth

(

)

Undocumented method

Code:

fetch_all_statistics()

public ArrayRef Bio::EnsEMBL::DBSQL::GenomeContainer::fetch_all_statistics

(

)

  Arg [1]    : none
  Example    :

$list = $genome->fetch_all_statistics();

  Description: Retrieve all entries stored in the genome_statistics table
  Returntype : ArrayRef of Bio::EnsEMBL::Genome
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

fetch_by_statistic()

public Bio::EnsEMBL::Genome Bio::EnsEMBL::DBSQL::GenomeContainer::fetch_by_statistic

(

)

  Arg [1]    : string $statistic
  Example    :

$results = $genome->fetch_by_statistic('coding_cnt');

  Description: Returns a Genome object for a given statistic
  Returntype : Bio::EnsEMBL::Genome
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_accession()

public String Bio::EnsEMBL::DBSQL::GenomeContainer::get_accession

(

)

  Arg [1]    : (optional) assembly accession
  Example    :

$accession = $genome->get_accession();

  Description: Getter/setter for the accession of the assembly currently used

  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_coding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_coding_count

(

)

  Arg [1]    : (optional) alt coding count
  Example    :

$alt_coding_count = $genome->get_alt_coding_count();

  Description: Getter/setter for the number of coding genes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_lnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_lnoncoding_count

(

)

  Arg [1]    : (optional) alt long non coding count
  Example    :

$alt_lnoncoding_count = $genome->get_alt_lnoncoding_count();

  Description: Getter/setter for the number of long non coding genes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_mnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_mnoncoding_count

(

)

  Arg [1]    : (optional) alt miscellaneous non coding count
  Example    :

$alt_mnoncoding_count = $genome->get_alt_mnoncoding_count();

  Description: Getter/setter for the number of miscellaneous non coding genes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_pseudogene_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_pseudogene_count

(

)

  Arg [1]    : (optional) alt pseudogene count
  Example    :

$alt_pseudogene_count = $genome->get_alt_pseudogene_count();

  Description: Getter/setter for the number of pseudogenes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_rcoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_rcoding_count

(

)

  Arg [1]    : (optional) alt readthrough coding count
  Example    :

$alt_rcoding_count = $genome->get_alt_rcoding_count();

  Description: Getter/setter for the number of readthrough coding genes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_rlnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_rlnoncoding_count

(

)

  Arg [1]    : (optional) alt readthrough long non coding count
  Example    :

$alt_lnoncoding_count = $genome->get_alt_lnoncoding_count();

  Description: Getter/setter for the number of readthrough long non coding genes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_rmnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_rmnoncoding_count

(

)

  Arg [1]    : (optional) alt readthrough miscellaneous non coding count
  Example    :

$alt_rmnoncoding_count = $genome->get_alt_rmnoncoding_count();

  Description: Getter/setter for the number of readthrough miscellaneous non coding genes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_rpseudogene_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_rpseudogene_count

(

)

  Arg [1]    : (optional) alt readthrough pseudogene count
  Example    :

$alt_rpseudogene_count = $genome->get_alt_pseudogene_count();

  Description: Getter/setter for the number of readthrough pseudogenes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_rsnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_rsnoncoding_count

(

)

  Arg [1]    : (optional) alt readthrough short non coding count
  Example    :

$alt_rsnoncoding_count = $genome->get_alt_rsnoncoding_count();

  Description: Getter/setter for the number of readthrough short non coding genes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_snoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_snoncoding_count

(

)

  Arg [1]    : (optional) alt short non coding count
  Example    :

$alt_snoncoding_count = $genome->get_alt_snoncoding_count();

  Description: Getter/setter for the number of short non coding genes on alternate sequences

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_alt_transcript_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_alt_transcript_count

(

)

  Arg [1]    : (optional) alt transcript count
  Example    :

$alt_transcript_count = $genome->get_alt_transcript_count();

  Description: Getter/setter for the number of transcripts on alternate sequences in the current build
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_assembly_date()

public String Bio::EnsEMBL::DBSQL::GenomeContainer::get_assembly_date

(

)

  Arg [1]    : (optional) assembly date
  Example    :

$assembly_date = $genome->get_assembly_date();

  Description: Getter/setter for the date of the assembly currently used

  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_assembly_name()

public String Bio::EnsEMBL::DBSQL::GenomeContainer::get_assembly_name

(

)

  Arg [1]    : (optional) assembly name
  Example    :

$assembly_name = $genome->get_assembly_name();

  Description: Getter/setter for the name of the assembly currently used

  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_attrib()

public Bio::EnsEMBL::Attrib Bio::EnsEMBL::DBSQL::GenomeContainer::get_attrib

(

)

  Arg [1]    : statistic
  Example    :

$results = $genome->_get_attrib('coding_cnt');

  Description: Returns the attribute object for a given statistic
  Returntype : Bio::EnsEMBL::Attrib
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_coding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_coding_count

(

)

  Arg [1]    : (optional) coding count
  Example    :

$coding_count = $genome->get_coding_count();

  Description: Getter/setter for the number of coding genes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_coord_systems()

public ListRef Bio::EnsEMBL::DBSQL::GenomeContainer::get_coord_systems

(

)

  Arg [1]    : none
  Example    :

$coord_systems = $genome->get_coord_systems();

  Description: Returns the coord_systems for the assembly currently used

  Returntype : ListRef of Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_count

(

)

  Arg [1]    : none
  Example    :

$count = $genome->get_count('coding_cnt');

  Description: Retrieve a count for a given attribute code
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_genebuild_initial_release_date()

public String Bio::EnsEMBL::DBSQL::GenomeContainer::get_genebuild_initial_release_date

(

)

  Arg [1]    : (optional) genebuild initial release date
  Example    :

$genebuild_initial_release_date = $genome->get_initial_release_date();

  Description: Getter/setter for the initial release date of the genebuild currently used

  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_genebuild_last_geneset_update()

public String Bio::EnsEMBL::DBSQL::GenomeContainer::get_genebuild_last_geneset_update

(

)

  Arg [1]    : (optional) genebuild last geneset update
  Example    :

$genebuild_last_geneset_update = $genome->get_last_geneset_update();

  Description: Getter/setter for the last geneset update of the genebuild currently used

  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_genebuild_method()

public String Bio::EnsEMBL::DBSQL::GenomeContainer::get_genebuild_method

(

)

  Arg [1]    : (optional) genebuild start date
  Example    :

$genebuild_method = $genome->get_genebuild_method();

  Description: Getter/setter for the method of the genebuild currently used

  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_genebuild_start_date()

public String Bio::EnsEMBL::DBSQL::GenomeContainer::get_genebuild_start_date

(

)

  Arg [1]    : (optional) genebuild start date
  Example    :

$genebuild_start_date = $genome->get_genebuild_start_date();

  Description: Getter/setter for the start date of the genebuild currently used

  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_genome_components()

public Arrayref Bio::EnsEMBL::DBSQL::GenomeContainer::get_genome_components

(

)

  Arg        : None
  Example    :

$components = $genome->get_genome_components();

  Description: Returns the list of (diploid) components, for a
               polyploid genome
  Returntype : Arrayref
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_karyotype()

public ListRef Bio::EnsEMBL::DBSQL::GenomeContainer::get_karyotype

(

)

  Arg [1]    : none
  Example    :

$karyotype = $genome->get_karyotype();

  Description: Returns the karyotype for the assembly currently used

  Returntype : ListRef of Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_lnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_lnoncoding_count

(

)

  Arg [1]    : (optional) long non coding count
  Example    :

$lnoncoding_count = $genome->get_lnoncoding_count();

  Description: Getter/setter for the number of long non coding genes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_mnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_mnoncoding_count

(

)

  Arg [1]    : (optional) miscellaneous non coding count
  Example    :

$mnoncoding_count = $genome->get_mnoncoding_count();

  Description: Getter/setter for the number of miscellaneous non coding genes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_prediction_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_prediction_count

(

)

  Arg [1]    : (optional) logic_name
  Example    :

$prediction_count = $genome->get_prediction_count();

  Description: Getter for the number of predicted genes in the current build
               Can be restricted to a given analysis

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_pseudogene_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_pseudogene_count

(

)

  Arg [1]    : (optional) pseudogene count
  Example    :

$pseudogene_count = $genome->get_pseudogene_count();

  Description: Getter/setter for the number of pseudogenes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_rcoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_rcoding_count

(

)

  Arg [1]    : (optional) readthrough coding count
  Example    :

$rcoding_count = $genome->get_rcoding_count();

  Description: Getter/setter for the number of readthrough coding genes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_ref_length()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_ref_length

(

)

  Arg [1]    : (optional) golden path length
  Example    :

$ref_length = $genome->get_ref_length();

  Description: Getter/setter for the golden path of the assembly currently used
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_rlnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_rlnoncoding_count

(

)

  Arg [1]    : (optional) readthrough long non coding count
  Example    :

$rlnoncoding_count = $genome->get_rlnoncoding_count();

  Description: Getter/setter for the number of readthrough long non coding genes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_rmnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_rmnoncoding_count

(

)

  Arg [1]    : (optional) readthrough miscellaneous non coding count
  Example    :

$rmnoncoding_count = $genome->get_rmnoncoding_count();

  Description: Getter/setter for the number of readthrough miscellaneous non coding genes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_rpseudogene_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_rpseudogene_count

(

)

  Arg [1]    : (optional) readthrough pseudogene count
  Example    :

$rpseudogene_count = $genome->get_rpseudogene_count();

  Description: Getter/setter for the number of readthrough pseudogenes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_rsnoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_rsnoncoding_count

(

)

  Arg [1]    : (optional) readthrough short non coding count
  Example    :

$rsnoncoding_count = $genome->get_rsnoncoding_count();

  Description: Getter/setter for the number of readthrough short non coding genes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_short_variation_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_short_variation_count

(

)

  Arg [1]    : (optional) short variation count
  Example    :

$short_variation_count = $genome->get_short_variation_count();

  Description: Getter/setter for the number of short variants in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_snoncoding_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_snoncoding_count

(

)

  Arg [1]    : (optional) short non coding count
  Example    :

$snoncoding_count = $genome->get_snoncoding_count();

  Description: Getter/setter for the number of short non coding genes in the current build

  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_structural_variation_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_structural_variation_count

(

)

  Arg [1]    : none
  Example    :

$structural_variation_count = $genome->get_structural_variation_count();

  Description: Return the number of structural variations in the current build
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_toplevel()

public ListRef Bio::EnsEMBL::DBSQL::GenomeContainer::get_toplevel

(

)

  Arg [1]    : none
  Example    :

$toplevel = $genome->get_toplevel();

  Description: Returns the toplevel for the assembly currently used

  Returntype : ListRef of Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_transcript_count()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::get_transcript_count

(

)

  Arg [1]    : (optional) transcript count
  Example    :

$transcript_count = $genome->get_transcript_count();

  Description: Getter/setter for the number of transcripts in the current build
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_version()

public String Bio::EnsEMBL::DBSQL::GenomeContainer::get_version

(

)

  Arg [1]    : (optional) assembly version
  Example    :

$version = $genome->get_version();

  Description: Getter/Setter for the assembly version

  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

has_karyotype()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::has_karyotype

(

)

  Arg        : None
  Example    :

$has_karyotype = $genome->has_karyotype();

  Description: Boolean indicating whether a genome has a karyotype (ie chromosomes)
               or not
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

is_empty()

public Boolean Bio::EnsEMBL::DBSQL::GenomeContainer::is_empty

(

)

  Arg [1]    : none
  Example    :

$results = $genome->is_empty;

  Description: Boolean to check if there is data in the genome container
  Returntype : Boolean
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

is_high_coverage()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::is_high_coverage

(

)

  Arg        : None
  Example    :

$is_high_coverage = $genome->is_high_coverage();

  Description: Boolean indicating whether an assembly is high coverage
               or not
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

is_polyploid()

public Int Bio::EnsEMBL::DBSQL::GenomeContainer::is_polyploid

(

)

  Arg        : None
  Example    :

$is_polyploid = $genome->is_polyploid();

  Description: Returns whether the genome is or is not polyploid.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::GenomeContainer Bio::EnsEMBL::DBSQL::GenomeContainer::new

(

)

  Arg [...]  : Superclass args.  See Bio::EnsEMBL::DBSQL::BaseAdaptor
  Description: Instantiates a Bio::EnsEMBL::DBSQL::GenomeContainer
  Returntype : Bio::EnsEMBL::GenomeContainer
  Exceptions : none
  Caller     : DBAdaptor
  Status     : Stable

Code:

store()

public The Bio::EnsEMBL::DBSQL::GenomeContainer::store

(

)

  Arg [1]    : Statistic
               The type of statistic to store
  Arg [2]    : Value
               The corresponding value for the statistic
  Arg [3]    : (optional) Attribute
               If more than one value exists for the statistics, it will be distinguished by its attribute
  Example    :

$genome_adaptor->store('coding_cnt', 20769);

  Description: Stores a genome statistic in the database
  Returntype : The database identifier (dbID) of the newly stored genome statistic
  Exceptions :
  Caller     : general
  Status     : Stable

Code:

update()

public void Bio::EnsEMBL::DBSQL::GenomeContainer::update

(

)

  Arg [1]    : Statistic
               The type of statistic to update
  Arg [2]    : Value
               The corresponding value for the statistic
  Arg [3]    : (optional) Attribute
               If more than one value exists for the statistics, it will be distinguished by its attribute
  Example    :

$genome_adaptor->update('coding_cnt', 20769);

  Description: Updates an existing genome statistic in the database
  Returntype : none
  Exceptions :
  Caller     : general
  Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm