ensembl-hive
2.6
|
Public Member Functions | |
public Bio::EnsEMBL::Feature | new () |
public String | display_label () |
public String | display_id () |
public String | score () |
public Hash | summary_as_hash () |
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 () |
This is a simple feature which extends the Feature class to add display_label and score attributes.
Definition at line 31 of file SimpleFeature.pm.
public String Bio::EnsEMBL::SimpleFeature::display_id | ( | ) |
Arg [1] : none Example :
Description: This method returns a string that is considered to be the 'display' identifier. For simple features this is the display_label if it is available otherwise it is an empty string. Returntype : string Exceptions : none Caller : web drawing code Status : Stable
public String Bio::EnsEMBL::SimpleFeature::display_label | ( | ) |
Arg [1] : (optional) string $value Example :
Description: Getter/Setter for the display label associated with this feature. Returntype : string Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Feature Bio::EnsEMBL::SimpleFeature::new | ( | ) |
Arg [DISPLAY_LABEL]: The label assigned to this simple feature 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, -ANALYSIS, -STRAND arguments Caller : general, subclass constructors Status : Stable
public String Bio::EnsEMBL::SimpleFeature::score | ( | ) |
Arg [1] : (optional) string $value Example :
Description: Getter/Setter for the score associated with this feature. Returntype : string Exceptions : none Caller : general Status : Stable
public Hash Bio::EnsEMBL::SimpleFeature::summary_as_hash | ( | ) |
Example :
Description: Generates a HashRef compatible with GFFSerializer. Adds score, external_name and logic_name to the basic Feature hash Returntype : Hash Exceptions : none Caller : general Status : Stable