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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::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