Raw content of Bio::EnsEMBL::PepDnaAlignFeature
<![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::PepDnaAlignFeature - Ensembl specific pep-dna pairwise
alignment feature
=head1 SYNOPSIS
See BaseAlignFeature
=head1 METHODS
=cut
package Bio::EnsEMBL::PepDnaAlignFeature;
use Bio::EnsEMBL::BaseAlignFeature;
use vars qw(@ISA);
use strict;
@ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
=head2 transform
Arg [1] : none
Example : none
Description: Overwrites Bio:EnsEMBL:Feature->transform as
to give error message
Status : Stable
=cut
sub transform {
my $self = shift;
$self->throw( "PepDnaAlignFeatures cant be transformed as".
" they are not on EnsEMBL coord system" );
}
=head2 _hit_unit
Arg [1] : none
Example : none
Description: PRIVATE implementation of abstract superclass method. Returns
3 as the 'unit' used for the hit sequence.
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::BaseAlignFeature
Status : Stable
=cut
sub _hit_unit {
return 3;
}
=head2 _query_unit
Arg [1] : none
Example : none
Description: PRIVATE implementation of abstract superclass method. Returns
1 as the 'unit' used for the query sequence.
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::BaseAlignFeature
Status : Stable
=cut
sub _query_unit {
return 1;
}
1;
]]>