ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::KarytotypeBand | new () |
public String | name () |
public String | stain () |
public Int | strand () |
public void | move () |
public String | display_id () |
public Hashref | 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 () |
KaryotypeBand objects encapsulate data pertaining to a single karyotype band. Access these objects through a Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor. KarytoypeBand inherits from Bio::EnsEMBL::Feature and can be used just as any other feature can be.
Definition at line 45 of file KaryotypeBand.pm.
public String Bio::EnsEMBL::KaryotypeBand::display_id | ( | ) |
Arg [1] : none Example :
Description: This method returns a string that is considered to be the 'display' identifier. For karyotype bands this is the name of the karyotype band or '' if no name is defined. Returntype : string Exceptions : none Caller : web drawing code Status : Stable
public void Bio::EnsEMBL::KaryotypeBand::move | ( | ) |
Arg [1] : $start - The new end of this band Arg [2] : $end - The new start of this band Arg [3] : $strand - ignored always set to 0 Example :
Description: Overrides superclass move() method to ensure strand is always 0. See Bio::EnsEMBL::Feature::move Returntype : none Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::KaryotypeBand::name | ( | ) |
Arg [1] : (optional) string $value Example :
Description: Getter/Setter for the name of this band Returntype : string Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::KarytotypeBand Bio::EnsEMBL::KaryotypeBand::new | ( | ) |
Arg [NAME] : string (optional) The name of this band Arg [STAIN]: string (optional) The stain of this band Arg [...] : Arguments passed to superclass constructor. See Bio::EnsEMBL::Feature Example :
Description: Constructor. Creates a new KaryotypeBand object, which can be treated as any other feature object. Note that karyotypes bands always have strand = 0. Returntype : Bio::EnsEMBL::KarytotypeBand Exceptions : none Caller : Bio::EnsEMBL::KaryotypeBandAdaptor Status : Stable
public String Bio::EnsEMBL::KaryotypeBand::stain | ( | ) |
Arg [1] : (optional) string $value Example :
Description: get/set for the band stain (e.g. 'gpos50') Returntype : string Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::KaryotypeBand::strand | ( | ) |
Arg [1] : none Example :
Description: Overrides the Feature strand method to always return a value of 0 for karyotype features (they are unstranded features) Returntype : int (always 0) Exceptions : none Caller : general Status : Stable
public Hashref Bio::EnsEMBL::KaryotypeBand::summary_as_hash | ( | ) |
Example :
Description : Extends Feature::summary_as_hash Retrieves a summary of this Karyotype object.
Returns : hashref of arrays of descriptive strings Status : Intended for internal use