ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::Intron | new () |
public Int | length () |
public Bio::EnsEMBL::Exon | prev_Exon () |
public Bio::EnsEMBL::Exon | next_Exon () |
public Int | rank () |
public Boolean | is_splice_canonical () |
public ArrayRef | splice_seq () |
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 () |
public Boolean Bio::EnsEMBL::Intron::is_splice_canonical | ( | ) |
Example :
Description : Indicates if the splice site is considered normal. This means splice site variants equal to (D == donor, A == acceptor) GT (D) => AG (A) AT (D) => AC (A) GC (D) => AG (A) Returntype : Boolean indicating if the splice was as expected Exceptions : See splice_seq
public Int Bio::EnsEMBL::Intron::length | ( | ) |
Args : none Example :
Description: Returns the length of this intron Returntype : Integer Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Intron Bio::EnsEMBL::Intron::new | ( | ) |
Arg [1] : Bio::EnsEMBL::Exon The 5' exon for the intron; required Arg [2] : Bio::EnsEMBL::Exon The 3' exon for the intron; required Arg [3] : Bio::EnsEMBL::Analysis Analysis to link to this Intron Example :
Description: Create an Intron object from two exons and an optional analysis Returntype : Bio::EnsEMBL::Intron Exceptions : exons not on the same strand or slice. Caller : general Status : Stable
public Bio::EnsEMBL::Exon Bio::EnsEMBL::Intron::next_Exon | ( | ) |
Args : none Example :
Description: Returns the exon after this Intron Returntype : Bio::EnsEMBL::Exon Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Exon Bio::EnsEMBL::Intron::prev_Exon | ( | ) |
Args : none Example :
Description: Returns the exon before this Intron Returntype : Bio::EnsEMBL::Exon Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::Intron::rank | ( | ) |
Args : none Example :
Description: Returns the rank of this Intron Returntype : Integer Exceptions : none Caller : general Status : Stable
public ArrayRef Bio::EnsEMBL::Intron::splice_seq | ( | ) |
Example :
Description : Get the donor and acceptor splice sites for this intron Returntype : ArrayRef[String] The donor and acceptor sequences as Strings Exceptions : Thrown if a feature Slice cannot be found