Raw content of Bio::EnsEMBL::Map::QtlFeature
<![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::Map::QtlFeature
=head1 SYNOPSIS
=head1 DESCRIPTION
Represents a QtlFeature in the EnsEMBL database. QtlFeatures are
generally very long and its not clear wether a representation in Contig
coordinates actually makes sense. In the database they will have
chromosomal coordinates.
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::QtlFeature;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Feature;
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 new
Arg [1] : Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor $adaptor
Example : none
Description: Create a QtlFeature
Returntype : Bio::EnsEMBL::Map::QtlFeature
Exceptions : none
Caller : general, DBSQL::QtlFeatureAdaptor
Status : Stable
=cut
sub new {
my ( $class, $adaptor, $slice, $start, $end, $qtl, $analysis ) = @_;
$class = ref( $class ) ||$class;
my $self = bless( {
'adaptor' => $adaptor,
'slice' => $slice,
'start' => $start,
'end' => $end,
'qtl' => $qtl,
'analysis' => $analysis,
'strand' => 0
}, $class );
return $self;
}
=head2 qtl
Arg [1] : Bio::EnsEMBL::Map::Qtl $qtl
the qtl object for this feature
Example : none
Description: return the Qtl object associated with this location
Returntype : Bio::EnsEMBL::Map::Qtl
Exceptions : none
Caller : general
Status : Stable
=cut
sub qtl {
my $self = shift;
if(@_) {
$self->{'qtl'} = shift;
}
return $self->{'qtl'};
}
=head2 strand
Arg [1] : none
Example : $strand = $qtl_feat->strand();
Description: Overrides the Feature strand method to always return a
value of 0 for qtl features (they are unstranded features)
Returntype : int (always 0)
Exceptions : none
Caller : general
Status : Stable
=cut
sub strand {
my $self = shift;
return 0;
}
=head2 move
Arg [1] : $start - The new end of this qtl feature
Arg [2] : $end - The new start of this qtl feature
Arg [3] : $strand - ignored always set to 0
Example : $qtl_feat->move(1, 10_000);
Description: Overrides superclass move() method to ensure strand is always 0.
See Bio::EnsEMBL::Feature::move
Returntype : none
Exceptions : none
Caller : general
Status : Stable
=cut
sub move {
my ($self, $start, $end, $strand) = @_;
#maintain a strandedness of 0
return $self->SUPER::move($start,$end,0);
}
1;
]]>