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
Inherit
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
Methods description
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 |
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 |
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 |
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 |
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
sub alternate_slice
{
my $self = shift;
$self->{'alternate_slice'} = shift if(@_);
return $self->{'alternate_slice'};} | sub display_id
{ my $self = shift;
my $slice = $self->{'alternate_slice'};
return '' if(!$slice);
return $slice->seq_region_name();
}
1;} | sub new
{
my $caller = shift;
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; } | sub new_fast
{ my $class = shift;
my $hashref = shift;
return bless $hashref, $class; } | sub type
{
my $self = shift;
$self->{'type'} = shift if(@_);
return $self->{'type'};} | General documentation
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