AssemblyExceptionFeature.pm

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=head1 LICENSE
 
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Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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     http://www.apache.org/licenses/LICENSE-2.0
 
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
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=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;