=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2023] 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

     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::AssemblyExceptionFeature - A feature that represents an assembly exception

=head1 SYNOPSIS

  use Bio::EnsEMBL::AssemblyExceptionFeature;

  $feature = Bio::EnsEMBL::AssemblyExceptionFeature->new(
    -start   => 100,
    -end     => 220,
    -type    => 'HAP',
    -slice   => $slice,
    -adaptor => $adaptor
  );

=head1 DESCRIPTION

Certain features, e.g. Haplotypes and PARs, are represented as
"exceptions" to the normal assembly.  This class represents such
features.

=head1 METHODS

=cut

package Bio::EnsEMBL::AssemblyExceptionFeature;

use strict;

use vars qw(@ISA);

use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Scalar::Util qw(weaken isweak);

@ISA = qw(Bio::EnsEMBL::Feature);


=head2 new

  Arg [TYPE] : The type (e.g. HAP for haplotype, PAR for PAR)
  Arg [...]  : Named arguments passed to superclass
  Example    : $feature = Bio::EnsEMBL::AssemblyExceptionFeature->new
                        (-start           => 1,
                         -end             => 100,
                         -slice           => $slice,
                         -alternate_slice => $alt_slice,
                         -adaptor         => $adaptor,
                         -type            => 'HAP')
  Description: Constructs a new Bio::EnsEMBL::Feature.  Generally subclasses
               of this method are instantiated, rather than this class itself.
  Returntype : Bio::EnsEMBL::Feature
  Exceptions : Thrown on invalid -SLICE arguments
  Caller     : general, subclass constructors
  Status     : Stable

=cut

sub new {

  my $caller = shift;

  # allow this to be called as class or object method
  my $class = ref($caller) || $caller;
  my $self = $class->SUPER::new(@_);

  my ($type, $alternate_slice) = rearrange(['TYPE', 'ALTERNATE_SLICE'],@_);
  $self->{'type'} = $type;
  $self->{'alternate_slice'} = $alternate_slice;

  return $self;
}


=head2 type

  Arg [1]    : (optional) string $value
  Example    : $type = $assembly_exception_feature->type();
  Description: Getter/Setter for the type associated with this
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub type {

  my $self = shift;

  $self->{'type'} = shift if(@_);

  return $self->{'type'};
}


=head2 alternate_slice

  Arg [1]    : (optional) string $value
  Example    : $alt_slice = $assembly_exception_feature->alternate_slice();
  Description: Getter/Setter for the alternate slice associated with this feature.
               The alternate slice represents the "other side" of the AssemblyExceptionFeature.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub alternate_slice {

  my $self = shift;

  $self->{'alternate_slice'} = shift if(@_);

  return $self->{'alternate_slice'};
}



=head2 display_id

  Arg [1]    : none
  Example    : print $aef->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier.  For assembly exception features
               this is the name of the alternate seqregion or '' if the 
               alternate slice is not defined.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

=cut

sub display_id {
  my $self = shift;
  my $slice = $self->{'alternate_slice'};
  return '' if(!$slice);
  return $slice->seq_region_name();
}



1;
