Bio::EnsEMBL AssemblyExceptionFeature
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Summary
Bio::EnsEMBL::AssemblyExceptionFeature - A feature that represents an assembly exception
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Feature
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Inherit
Bio::EnsEMBL::Feature
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
alternate_sliceDescriptionCode
display_idDescriptionCode
newDescriptionCode
new_fastDescriptionCode
typeDescriptionCode
Methods description
alternate_slicecode    nextTop
  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_idcodeprevnextTop
  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
newcodeprevnextTop
  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
new_fastcodeprevnextTop
  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
typecodeprevnextTop
  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
Methods code
alternate_slicedescriptionprevnextTop
sub alternate_slice {
  my $self = shift;

  $self->{'alternate_slice'} = shift if(@_);

  return $self->{'alternate_slice'};
}
display_iddescriptionprevnextTop
sub display_id {
  my $self = shift;
  my $slice = $self->{'alternate_slice'};
  return '' if(!$slice);
  return $slice->seq_region_name();
}



1;
}
newdescriptionprevnextTop
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;
}
new_fastdescriptionprevnextTop
sub new_fast {
  my $class = shift;
  my $hashref = shift;
  return bless $hashref, $class;
}
typedescriptionprevnextTop
sub type {
  my $self = shift;

  $self->{'type'} = shift if(@_);

  return $self->{'type'};
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.