—————=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
Bio::EnsEMBL::PepDnaAlignFeature - Ensembl specific pep-dna pairwise
alignment feature
=head1 SYNOPSIS
See BaseAlignFeature
=head1 METHODS
=cut
package
Bio::EnsEMBL::PepDnaAlignFeature;
$Bio::EnsEMBL::PepDnaAlignFeature::VERSION
=
'112.0_52'
;
# TRIAL
$Bio::EnsEMBL::PepDnaAlignFeature::VERSION
=
'112.052'
;
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;