LICENSE

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

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     http://www.apache.org/licenses/LICENSE-2.0

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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