Raw content of Bio::EnsEMBL::OligoFeature
<![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::OligoFeature - A module to represent an oligonucleotide probe's
genomic mapping.
=head1 SYNOPSIS
use Bio::EnsEMBL::OligoFeature;
my $feature = Bio::EnsEMBL::OligoFeature->new(
-PROBE => $probe,
-MISMATCHCOUNT => 0,
-SLICE => $chr_1_slice,
-START => 1_000_000,
-END => 1_000_024,
-STRAND => -1,
);
=head1 DESCRIPTION
An OligoFeature object represents the genomic placement of an OligoProbe
object. The data are stored in the oligo_feature table.
=head1 METHODS
=cut
package Bio::EnsEMBL::OligoFeature;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Feature;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 new
Arg [-PROBE] : Bio::EnsEMBL::OligoProbe - probe
An OligoFeature must have a probe. This probe must already be stored if
you plan to store the feature.
Arg [-MISMATCHCOUNT]: int
Number of mismatches over the length of the probe.
Arg [-SLICE] : Bio::EnsEMBL::Slice
The slice on which this feature is.
Arg [-START] : int
The start coordinate of this feature relative to the start of the slice
it is sitting on. Coordinates start at 1 and are inclusive.
Arg [-END] : int
The end coordinate of this feature relative to the start of the slice
it is sitting on. Coordinates start at 1 and are inclusive.
Arg [-STRAND] : int
The orientation of this feature. Valid values are 1, -1 and 0.
Arg [-dbID] : (optional) int
Internal database ID.
Arg [-ADAPTOR] : (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
Database adaptor.
Example : my $feature = Bio::EnsEMBL::OligoFeature->new(
-PROBE => $probe,
-MISMATCHCOUNT => 0,
-SLICE => $chr_1_slice,
-START => 1_000_000,
-END => 1_000_024,
-STRAND => -1,
);
Description: Constructor for OligoFeature objects.
Returntype : Bio::EnsEMBL::OligoFeature
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($probe, $mismatchcount )
= rearrange(['PROBE', 'MISMATCHCOUNT'], @_);
$self->probe($probe);
$self->mismatchcount($mismatchcount);
return $self;
}
=head2 new_fast
Args : Hashref with all internal attributes set
Example : none
Description: Quick and dirty version of new. Only works if the code is very
disciplined.
Returntype : Bio::EnsEMBL::OligoFeature
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub new_fast {
my ($class, $hashref) = @_;
return bless ($hashref, $class);
}
=head2 probeset
Arg [1] : (optional) string - probeset
Example : my $probeset = $feature->probeset();
Description: Getter and setter for the probeset for this feature. Shortcut
for $feature->probe->probeset(), which should be used instead.
Probeset is not persisted if set with this method.
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
: Use $feature->probe->probeset() because this may be removed
=cut
sub probeset {
my $self = shift;
$self->{'probeset'} = shift if @_;
if ($self->{'probe'}) {
$self->{'probeset'} = $self->probe()->probeset();
}
return $self->{'probeset'};
}
=head2 mismatchcount
Arg [1] : int - number of mismatches
Example : my $mismatches = $feature->mismatchcount();
Description: Getter and setter for number of mismatches for this feature.
Returntype : int
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub mismatchcount {
my $self = shift;
$self->{'mismatchcount'} = shift if @_;
return $self->{'mismatchcount'};
}
=head2 probelength
Args : None
Example : my $probelength = $feature->probelength();
Description: Getter for the length of the probe. Shortcut for
$feature->probe->probelength(), which should be used instead.
Originally, this method returned the length of the feature,
which was often, but not always, the same as the length of the
probe.
Returntype : int
Exceptions : None
Caller : General
Status : Medium Risk
: Use $feature->probe->probelength() because this may be removed
=cut
sub probelength {
my $self = shift;
return $self->probe->probelength();
}
=head2 probe
Arg [1] : Bio::EnsEMBL::AffyProbe - probe
Example : my $probe = $feature->probe();
Description: Getter, setter and lazy loader of probe attribute for
OligoFeature objects. Features are retrieved from the database
without attached probes, so retrieving probe information for a
feature will involve another query.
Returntype : Bio::EnsEMBL::OligoProbe
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub probe {
my $self = shift;
my $probe = shift;
if ($probe) {
if ( !ref $probe || !$probe->isa('Bio::EnsEMBL::OligoProbe') ) {
throw('Probe must be a Bio::EnsEMBL::OligoProbe object');
}
$self->{'probe'} = $probe;
}
if ( !defined $self->{'probe'} && $self->dbID() && $self->adaptor() ) {
$self->{'probe'} = $self->adaptor()->db()->get_OligoProbeAdaptor()->fetch_by_OligoFeature($self);
}
return $self->{'probe'};
}
1;
]]>