Raw content of Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor
=head1 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' );
=head1 DESCRIPTION
Database adaptor to provide access to KaryotypeBand objects
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::KaryotypeBand;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
#_tables
#
# Arg [1] : none
# Example : none
# Description: PROTECTED Implementation of abstract superclass method to
# provide the name of the tables to query
# Returntype : string
# Exceptions : none
# Caller : internal
sub _tables {
my $self = shift;
return (['karyotype','k'])
}
#_columns
# Arg [1] : none
# Example : none
# Description: PROTECTED Implementation of abstract superclass method to
# provide the name of the columns to query
# Returntype : list of strings
# Exceptions : none
# Caller : internal
sub _columns {
my $self = shift;
#warning _objs_from_sth implementation depends on ordering
return qw (
k.karyotype_id
k.seq_region_id
k.seq_region_start
k.seq_region_end
k.band
k.stain );
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my $db = $self->db();
my $slice_adaptor = $db->get_SliceAdaptor();
my @features;
my %slice_cache;
my($karyotype_id,$seq_region_id,$seq_region_start,$seq_region_end,
$band,$stain);
$sth->bind_columns(\$karyotype_id, \$seq_region_id, \$seq_region_start,
\$seq_region_end, \$band, \$stain);
while ( $sth->fetch() ) {
#need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
my $slice = $slice_cache{$seq_region_id} ||=
$slice_adaptor->fetch_by_seq_region_id($seq_region_id);
push( @features,
$self->_create_feature( 'Bio::EnsEMBL::KaryotypeBand', {
-START => $seq_region_start,
-END => $seq_region_end,
-SLICE => $slice,
-ADAPTOR => $self,
-DBID => $karyotype_id,
-NAME => $band,
-STAIN => $stain
} ) );
}
return \@features;
}
=head2 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
=cut
sub fetch_all_by_chr_name {
my ($self,$chr_name) = @_;
throw('Chromosome name argument expected') if(!$chr_name);
my $slice =
$self->db->get_SliceAdaptor->fetch_by_region(undef, $chr_name);
unless ($slice){
warning("Cannot retrieve chromosome $chr_name");
return;
}
return $self->fetch_all_by_Slice($slice);
}
=head2 fetch_by_chr_band
Arg [1] : string $chr_name
Name of the chromosome from which to retrieve the band
Arg [2] : string $band
The name of the band to retrieve from the specified chromosome
Example : @bands = @{$kary_adaptor->fetch_all_by_chr_band('4', 'q23')};
Description: Fetches the karyotype band object from the database
for the given chromosome and band name. If no such band
exists, undef is returned instead. This function uses fuzzy
matching of the band name. For example the bands 'q23.1' and
'q23.4' could be matched by fetch_all_by_chr_band('20', 'q23');
Returntype : Bio::EnsEMBL::KaryotypeBand in chromosomal coordinates.
Exceptions : throws if chr or band is missing in arguments
Caller : general
Status : Stable
=cut
sub fetch_all_by_chr_band {
my ($self, $chr_name, $band) = @_;
throw('Chromosome name argument expected') if(!$chr_name);
throw('Band argument expected') if(!$band);
my $slice = $self->db->get_SliceAdaptor->fetch_by_region(undef,
$chr_name);
my $constraint = "k.band like '$band%'";
return $self->fetch_all_by_Slice_constraint($slice,$constraint);
}
sub fetch_by_chr_band {
my $self = shift;
deprecate('Use fetch_all_by_chr_band instead.');
my ($band) = @{$self->fetch_all_by_chr_band(@_)};
return $band;
}
=head2 list_dbIDs
Arg [1] : none
Example : @kary_ids = @{$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
=cut
sub list_dbIDs {
my ($self, $ordered) = shift;
return $self->_list_dbIDs("karyotype",undef, $ordered);
}
1;
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