Raw content of Bio::EnsEMBL::AssemblyExceptionFeature
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=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);
@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 new_fast
Arg [1] : hashref to be blessed
Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
Exceptions : none
Returntype : Bio::EnsEMBL::Feature
Caller : general, subclass constructors
Status : Stable
=cut
sub new_fast {
my $class = shift;
my $hashref = shift;
return bless $hashref, $class;
}
=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;
]]>