view variant_effect_predictor/Bio/EnsEMBL/PepDnaAlignFeature.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 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

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=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;