ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::RepeatFeature | new () |
public Bio::EnsEMBL::RepeatConsensus | repeat_consensus () |
public Int | hstart () |
public Int | score () |
public Int | hend () |
public Int | hstrand () |
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 () |
This a feature representing a repeat region on a sequence
Definition at line 45 of file RepeatFeature.pm.
public String Bio::EnsEMBL::RepeatFeature::display_id | ( | ) |
Arg [1] : none Example :
Description: This method returns a string that is considered to be the 'display' identifier. For repeat_features this is the name of the repeat consensus if it is available otherwise it is an empty string. Returntype : string Exceptions : none Caller : web drawing code Status : Stable
public Int Bio::EnsEMBL::RepeatFeature::hend | ( | ) |
Arg [1] : (optional) int $hend Example :
Description: Getter/Setter for the end bp of this repeat match on the consensus sequence. Returntype : int Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::RepeatFeature::hstart | ( | ) |
Arg [1] : (optional) int $hstart Example :
Description: Getter/Setter for the start bp of this repeat match on the consensus sequence. Returntype : int Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::RepeatFeature::hstrand | ( | ) |
Arg [1] : none Example :
Description: always returns 1. method exists for consistancy with other features. Returntype : int Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::RepeatFeature Bio::EnsEMBL::RepeatFeature::new | ( | ) |
Arg [REPEAT_CONSENSUS] : Bio::EnsEMBL::RepeatConsensus (optional) The repeat consensus for this repeat feature Arg [HSTART] : int (optional) The hit start on the consensus sequence Arg [HEND] : int (optional) The hit end on the consensus sequence Arg [SCORE] : float (optional) The score Arg [...] : Named arguments to superclass constructor (see Bio::EnsEMBL::Feaure) Example :
Description: Creates a new Bio::EnsEMBL::RepeatFeature object Returntype : Bio::EnsEMBL::RepeatFeature Exceptions : none Caller : RepeatFeatureAdaptors Status : Stable
public Bio::EnsEMBL::RepeatConsensus Bio::EnsEMBL::RepeatFeature::repeat_consensus | ( | ) |
Arg [1] : (optional) Bio::EnsEMBL::RepeatConsensus Example :
Description: Getter/Setter for the repeat consensus of this repeat Returntype : Bio::EnsEMBL::RepeatConsensus Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::RepeatFeature::score | ( | ) |
Arg [1] : (optional) float $score Example :
Description: Getter/Setter for the score of this repeat feature Returntype : int Exceptions : none Caller : general Status : Stable
public Hashref Bio::EnsEMBL::RepeatFeature::summary_as_hash | ( | ) |
Example :
Description : Retrieves a textual summary of this Repeat feature. Not inherited from Feature. Returns : hashref of arrays of descriptive strings Status : Intended for internal use