Bio::EnsEMBL::AssemblyExceptionFeature Class Reference

Inheritance diagram for Bio::EnsEMBL::AssemblyExceptionFeature:

Public Member Functions
public Bio::EnsEMBL::Feature	new ()
public String	type ()
public Bio::EnsEMBL::Slice	alternate_slice ()
public String	display_id ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

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.

Definition at line 27 of file AssemblyExceptionFeature.pm.

Member Function Documentation

alternate_slice()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::AssemblyExceptionFeature::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

Code:

display_id()

public String Bio::EnsEMBL::AssemblyExceptionFeature::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

Code:

new()

public Bio::EnsEMBL::Feature Bio::EnsEMBL::AssemblyExceptionFeature::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

Code:

type()

public String Bio::EnsEMBL::AssemblyExceptionFeature::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

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm