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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor

SYNOPSIS

my $registry = 'Bio::EnsEMBL::Registry';

$registry->
  load_registry_from_db( ...

my $sfa =
  $registry->get_adaptor('homo sapiens', 'core', 'SimpleFeature');

print ref($sfa), "\n";

my $sf_aref =
  $sfa->fetch_all;

print scalar @$sf_aref, "\n";

DESCRIPTION

Simple Feature Adaptor - database access for simple features

METHODS

store

Arg [1]    : list of Bio::EnsEMBL::SimpleFeatures @sf
             the simple features to store in the database
Example    : $simple_feature_adaptor->store(@simple_feats);
Description: Stores a list of simple feature objects in the database
Returntype : none
Exceptions : thrown if @sf is not defined, if any of the features do not
             have an attached slice.
             or if any elements of @sf are not Bio::EnsEMBL::SimpleFeatures 
Caller     : general
Status     : Stable

_tables

Arg [1]    : none
Example    : none
Description: PROTECTED implementation of superclass abstract method
             returns the names, aliases of the tables to use for queries
Returntype : list of listrefs of strings
Exceptions : none
Caller     : internal
Status     : Stable

_columns

Arg [1]    : none
Example    : none
Description: PROTECTED implementation of superclass abstract method
             returns a list of columns to use for queries
Returntype : list of strings
Exceptions : none
Caller     : internal
Status     : Stable

_objs_from_sth

Arg [1]    : hash reference $hashref
Example    : none
Description: PROTECTED implementation of superclass abstract method.
             creates SimpleFeatures from an executed DBI statement handle.
Returntype : list reference to Bio::EnsEMBL::SimpleFeature objects
Exceptions : none
Caller     : internal
Status     : Stable

list_dbIDs

Arg [1]    : none
Example    : @feature_ids = @{$simple_feature_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all simple features in the current db
Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller     : ?
Status     : Stable