ensembl-hive
2.6
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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 () |
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.
public Bio::EnsEMBL::Slice Bio::EnsEMBL::AssemblyExceptionFeature::alternate_slice | ( | ) |
Arg [1] : (optional) string $value Example :
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
public String Bio::EnsEMBL::AssemblyExceptionFeature::display_id | ( | ) |
Arg [1] : none Example :
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
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 :
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
public String Bio::EnsEMBL::AssemblyExceptionFeature::type | ( | ) |
Arg [1] : (optional) string $value Example :
Description: Getter/Setter for the type associated with this feature. Returntype : string Exceptions : none Caller : general Status : Stable