PepDnaAlignFeature.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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
 
     http://www.apache.org/licenses/LICENSE-2.0
 
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
  <http://www.ensembl.org/Help/Contact>.
 
=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;