=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
Questions may also be sent to the Ensembl help desk at
=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
$Bio::EnsEMBL::AssemblyExceptionFeature::VERSION = '112.0_56'; # TRIAL
$Bio::EnsEMBL::AssemblyExceptionFeature::VERSION = '112.056';
use strict;
use vars qw(@ISA);
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;