LICENSE
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::KaryotypeBandAdaptor
SYNOPSIS
$kary_adaptor = $db_adaptor->get_KaryotypeBandAdaptor();
foreach $band ( @{ $kary_adaptor->fetch_all_by_Slice($slice) } ) {
# do something with band
}
$band = $kary_adaptor->fetch_by_dbID($id);
my @bands = @{ $kary_adaptor->fetch_all_by_chr_name('X') };
my $band = $kary_adaptor->fetch_by_chr_band( '4', 'q23' );
DESCRIPTION
Database adaptor to provide access to KaryotypeBand objects
METHODS
store
Arg [1] : list of Bio::EnsEMBL::KaryotypeBand @k
the karyotype bands to store in the database
Example : $karyotype_adaptor->store(@karyotype_band);
Description: Stores a list of karyotype band objects in the database
Returntype : none
Exceptions : thrown if @k is not defined, if any of the features do not
have an attached slice.
or if any elements of @k are not Bio::EnsEMBL::KaryotypeBand
Caller : general
Status : Stable
fetch_all_by_chr_name
Arg [1] : string $chr_name
Name of the chromosome from which to retrieve band objects
Example : @bands=@{$karyotype_band_adaptor->fetch_all_by_chr_name('X')};
Description: Fetches all the karyotype band objects from the database for the
given chromosome.
Returntype : listref of Bio::EnsEMBL::KaryotypeBand in chromosomal
(assembly) coordinates
Exceptions : none
Caller : general
Status : Stable
list_dbIDs
Arg [1] : none
Example : @kary_ids = @{$karyotype_band_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all karyotype bands in the
current db
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : reference to a list of ints
Exceptions : none
Caller : ?
Status : Stable