sub seq_region_start {
my $self = shift;
$self->{'seq_region_start'} = shift if(@_);
return $self->{'seq_region_start'};
}
ensembl-hive
2.6
|
Public Member Functions | |
public Bio::EnsEMBL::CDS | new () |
public Bio::EnsEMBL::Transcript | transcript () |
public Bio::EnsEMBL::Translation | translation () |
public String | seq_region_start () |
public String | seq_region_end () |
public Bio::EnsEMBL::Gene | get_Gene () |
public String | translation_id () |
public Int | phase () |
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 CDS feature within the Ensembl CDS. It represents the coding regions of a transcript.
public Bio::EnsEMBL::Gene Bio::EnsEMBL::CDS::get_Gene | ( | ) |
Description: Get the gene associated with the ExonTranscript, if a transcript has been set Returntype : Bio::EnsEMBL::Gene or undef Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::CDS Bio::EnsEMBL::CDS::new | ( | ) |
Arg [...] : Named arguments passed to superclass Example :
Description: Constructs a new Bio::EnsEMBL::CDS. Returntype : Bio::EnsEMBL::CDS Exceptions : Thrown on invalid -SLICE, -STRAND arguments Caller : general, subclass constructors Status : Stable
public Int Bio::EnsEMBL::CDS::phase | ( | ) |
Arg [1] : (optional) string $phase Example :
Description: This method returns an integer that describes the phase of the coding feature Returntype : integer Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::CDS::seq_region_end | ( | ) |
Arg [1] : (optional) string $seq_region_end Example :
Description: Getter/Setter for the seq_region_end for this CDS. Overwrite default method from Feature as CDS does not have a table Returntype : String Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::CDS::seq_region_start | ( | ) |
Arg [1] : (optional) string $seq_region_start Example :
Description: Getter/Setter for the seq_region_start for this CDS. Overwrite default method from Feature as CDS does not have a table Returntype : String Exceptions : none Caller : general Status : Stable
public Hash Bio::EnsEMBL::CDS::summary_as_hash | ( | ) |
Example :
Description: Generates a HashRef compatible with GFFSerializer. Adds Parent, source and phase to the basic feature hash Returntype : Hash Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Transcript Bio::EnsEMBL::CDS::transcript | ( | ) |
Arg [1] : (optional) Bio::EnsEMBL::Transcript Example :
Description: Getter/Setter for the transcript associated with this CDS. Returntype : Bio::EnsEMBL::Transcript Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Translation Bio::EnsEMBL::CDS::translation | ( | ) |
Description: Fetch the translation associated with this transcript, if it exists. Return undef if there is no translation, ie. a pseudogene Returntype : Bio::EnsEMBL::Translation or undef Caller : general Status : Stable
public String Bio::EnsEMBL::CDS::translation_id | ( | ) |
Arg [1] : (optional) string $translation_id Example :
Description: Getter/Setter for the stable_id for the translation associated with this CDS. Returntype : String Exceptions : none Caller : general Status : Stable