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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::AssemblyExceptionFeature - A feature that represents an assembly exception

SYNOPSIS

use Bio::EnsEMBL::AssemblyExceptionFeature;

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

DESCRIPTION

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

METHODS

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

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

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

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