Bio::EnsEMBL AffyFeature
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Summary
Bio::EnsEMBL::AffyFeature - A module to represent an Affy probe's genomic
mapping.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::OligoFeature
Bio::EnsEMBL::Utils::Exception qw ( throw )
Inherit
Bio::EnsEMBL::OligoFeature
Synopsis
  use Bio::EnsEMBL::AffyFeature;
my $feature = Bio::EnsEMBL::AffyFeature->new( -PROBE => $probe, -MISMATCHCOUNT => 0, -SLICE => $chr_1_slice, -START => 1_000_000, -END => 1_000_024, -STRAND => -1, );
Description
An AffyFeature object represents the genomic placement of an AffyProbe
object. The data are stored in the oligo_feature table.
Methods
newDescriptionCode
probeDescriptionCode
Methods description
newcode    nextTop
  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
probecodeprevnextTop
  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
Methods code
newdescriptionprevnextTop
sub new {
	my $caller = shift;

	my $class = ref($caller) || $caller;

	my $self = $class->SUPER::new(@_);
	
	return $self;
}
probedescriptionprevnextTop
sub probe {
    my $self = shift;
	my $probe = shift;
    if ($probe) {
		if ( !ref $probe || !$probe->isa('Bio::EnsEMBL::AffyProbe') ) {
			throw('Probe must be a Bio::EnsEMBL::AffyProbe object');
		}
		$self->{'probe'} = $probe;
    }
	if ( !defined $self->{'probe'} && $self->dbID() && $self->adaptor() ) {
	    $self->{'probe'} = $self->adaptor()->db()->get_AffyProbeAdaptor()->fetch_by_AffyFeature($self);
	}
    return $self->{'probe'};
}

1;
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.