Raw content of Bio::EnsEMBL::Collection::RepeatFeature
<![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
package Bio::EnsEMBL::Collection::RepeatFeature;
=head1 NAME
Bio::EnsEMBL::Collection::Exon - Feature collection implementation for
repeat features.
=head1 DESCRIPTION
=head2 Extended feature representation
A repeat feature is represented by the basic feature representation (see
documentation of Bio::EnsEMBL::Collection) and by the following extended
feature representation:
=over 4
=item 1.
Repeat start
=item 2.
Repeat end
=item 3.
Repeat consensus internal ID
=item 4.
Analysis internal ID
=item 5.
Score
=back
=cut
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use base( 'Bio::EnsEMBL::Collection',
'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor' );
sub _create_feature {
my ( $this, $feature_type, $args ) = @_;
throw( '_create_feature() '
. 'is not implemented for '
. 'repeat feature collections' );
}
sub _create_feature_fast {
my ( $this, $feature_type, $args ) = @_;
my $feature =
$this->SUPER::_create_feature_fast( $feature_type, $args );
if ( !$this->lightweight() ) {
push( @{$feature},
$args->{'hstart'}, $args->{'hend'},
$args->{'repeat_consensus'}->dbID(),
$args->{'analysis'}->dbID(),
$args->{'score'} );
}
return $feature;
}
sub _tables {
my ($this) = @_;
my @tables = $this->SUPER::_tables();
if ( $this->lightweight() ) { return ( $tables[0] ) }
return @tables;
}
sub _columns {
my ($this) = @_;
my @columns = $this->SUPER::_columns();
if ( $this->lightweight() ) {
@columns[ Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns ] =
map( 1, Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns );
}
return @columns;
}
sub _default_where_clause {
my ($this) = @_;
if ( $this->lightweight() ) { return '' }
return $this->SUPER::_default_where_clause();
}
1;
# $Id: RepeatFeature.pm,v 1.14 2009/03/04 10:58:13 ak4 Exp $
]]>