sub downstart {
my $self = shift;
if (@_) {
$self->{_downstart} = shift @_;
return
}
if (! defined $self->{_downstart}) {
$self->_derive_coords('down');
}
return $self->{_downstart}
}
ensembl-hive
2.6
|
Public Member Functions | |
public Bio::EnsEMBL::Upstream | new () |
public Bio::EnsEMBL::Transcript | transcript () |
public Int | length () |
protected void | _flush_cache () |
public Int | upstart () |
public Int | upend () |
public Int | downstart () |
public Int | downend () |
public | transform () |
public Arrayref | derive_upstream_coords () |
public Arrayref | derive_downstream_coords () |
protected void | _derive_coords () |
protected In | _bases_to_trim () |
protected Bio::EnsEMBL::Exon | _first_coding_Exon () |
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 () |
An object that determines the upstream region of a transcript. Such a region is non-coding and ensures that other genes or transcripts are not present. Ultimately, these objects can be used to looking for promoter elements. To this end, it is also possible to derive a region downstream of the first exon, within the first intron and where promoter elements sometimes are found.
Definition at line 45 of file Upstream.pm.
protected In Bio::EnsEMBL::Upstream::_bases_to_trim | ( | ) |
Arg : string $end_to_trim (either 'right_end' or 'left_end'). Arg : Bio::EnsEMBL::Slice Example :
Description: Finds exons from other genes/transcripts that invade our upstream/downstream slice and returns the number of bases that should be truncated from the appropriate end of the upstream/downstream region. Returntype : in Exceptions : Throws if argument is not either 'right_end' or 'left_end' Caller : $self->_derive_coords Status : Stable
protected void Bio::EnsEMBL::Upstream::_derive_coords | ( | ) |
Arg : string $direction (either 'up' or 'down'). Example :
Description: Determines the coordinates of either upstream or downstream region. Returntype : none Exceptions : Throws if argument is not either 'up' or 'down' Caller : $self->upstart, $self->upend, $self->downstart, $self->downend Status : Stable
protected Bio::EnsEMBL::Exon Bio::EnsEMBL::Upstream::_first_coding_Exon | ( | ) |
Arg : none Example :
Description: Finds the first exon of our transcript that contains coding bases. Returntype : Bio::EnsEMBL::Exon Exceptions : none Caller : $self->_derive_coords, $self->_bases_to_trim Status : Stable
protected void Bio::EnsEMBL::Upstream::_flush_cache | ( | ) |
Arg : none Example :
Description: Empties cached coordinates (called when coordinate scheme or region length has changed). Returntype : none Exceptions : none Caller : $self->length, $self->transform Status : Stable
public Arrayref Bio::EnsEMBL::Upstream::derive_downstream_coords | ( | ) |
Arg : none Example :
Description: Derives downstream coordinates (for compatability with older scripts). Returntype : arrayref Exceptions : none Caller : general Status : Stable
public Arrayref Bio::EnsEMBL::Upstream::derive_upstream_coords | ( | ) |
Arg : none Example :
Description: Derives upstream coordinates (for compatability with older scripts). Returntype : arrayref Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::Upstream::downend | ( | ) |
Arg : none Example :
Description: Returns the end coordinate of the region in the first intron of the transcript. This coordinate is always furthest from the first exon (irregardless of strand). Returntype : int Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::Upstream::downstart | ( | ) |
Arg : none Example :
Description: Returns the start coordinate of the region in the first intron of the transcript. This coordinate is always closest to the first exon (irregardless of strand). Returntype : int Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::Upstream::length | ( | ) |
Arg : (optional) int $length Example :
Description: Getter/setter for upstream region length. Returntype : int Exceptions : Throws if length is requested before it has been set. Caller : $self->new, $self->_derive_coords Status : Stable
public Bio::EnsEMBL::Upstream Bio::EnsEMBL::Upstream::new | ( | ) |
Arg [transcript] : (optional) Bio::EnsEMBL::Transcript Arg [length] : (optional) int $length Example :
Description: Creates a new upstream object Returntype : Bio::EnsEMBL::Upstream Exceptions : none Caller : Bio::EnsEMBL::Transcript, general Status : Stable
public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Upstream::transcript | ( | ) |
Arg : (optional) Bio::EnsEMBL::Transcript Example :
Description: Getter/setter for transcript object Returntype : Bio::EnsEMBL::Transcript Exceptions : Throws if argument is not undefined or a Bio::EnsEMBL::Transcript Caller : $self->new, $self->_derive_coords, $self->_first_coding_Exon Status : Stable
public Bio::EnsEMBL::Upstream::transform | ( | ) |
Arg : Example :
Description: Not yet implemented Returntype : Exceptions : Caller : Status : At Risk
public Int Bio::EnsEMBL::Upstream::upend | ( | ) |
Arg : none Example :
Description: Returns the end coordinate of the region upstream of the transcript. This coordinate always always abutts the translation initiation codon, whereas upstart always returns the coorindate furthest from the translation initiation codon. Returntype : int Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::Upstream::upstart | ( | ) |
Arg : none Example :
Description: Returns the start coordinate of the region upstream of the transcript. This coordinate is always the furthest from the translation initiation codon, whereas upend always abutts the translation initiation codon. Returntype : int Exceptions : none Caller : general Status : Stable