ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::Operon | new () |
public String | created_date () |
public String | modified_date () |
public String | display_label () |
public String | stable_id () |
public Int | version () |
public String | stable_id_version () |
public Arrayref | get_all_OperonTranscripts () |
public | add_OperonTranscript () |
public void | add_DBEntry () |
public Listref | get_all_Attributes () |
public Listref | get_all_DBEntries () |
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 () |
A representation of an Operon within the Ensembl system. An operon is a collection of one or more polycistronic transcripts which contain one or more genes.
public void Bio::EnsEMBL::Operon::add_DBEntry | ( | ) |
Arg [1] : Bio::EnsEMBL::DBEntry $dbe The dbEntry to be added Example :
Description: Associates a DBEntry with this operon. Note that adding DBEntries will prevent future lazy-loading of DBEntries for this operon (see get_all_DBEntries). Returntype : none Exceptions : thrown on incorrect argument type Caller : general Status : Stable
public Bio::EnsEMBL::Operon::add_OperonTranscript | ( | ) |
Arg [1] : Bio::EnsEMBL::OperonTranscript - operon transcript to attach to this operon Example :
Description: Attach a polycistronic operon transcript to this operon Exceptions : if argument is not Bio::EnsEMBL::OperonTranscript Caller : general Status : Stable
public String Bio::EnsEMBL::Operon::created_date | ( | ) |
Arg [1] : (optional) String - created date to set (as a UNIX time int) Example :
Description: Getter/setter for attribute created_date Returntype : String Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::Operon::display_label | ( | ) |
Arg [1] : (optional) String - the name/label to set Example :
Description: Getter/setter for attribute name. Returntype : String or undef Exceptions : none Caller : general Status : Stable
public Listref Bio::EnsEMBL::Operon::get_all_Attributes | ( | ) |
Arg [1] : (optional) String $attrib_code The code of the attribute type to retrieve values for Example :
Description: Gets a list of Attributes of this operon. Optionally just get Attributes for given code. Returntype : Listref of Bio::EnsEMBL::Attribute Exceptions : warning if gene does not have attached adaptor and attempts lazy load. Caller : general Status : Stable
public Listref Bio::EnsEMBL::Operon::get_all_DBEntries | ( | ) |
Arg [1] : (optional) String, external database name
Arg [2] : (optional) String, external_db type
Example :
Description: Retrieves DBEntries (xrefs) for this operon. This does not* include DBEntries that are associated with the transcripts and corresponding translations of this gene (see get_all_DBLinks()).
This method will attempt to lazy-load DBEntries from a database if an adaptor is available and no DBEntries are present on the gene (i.e. they have not already been added or loaded).
Return type: Listref of Bio::EnsEMBL::DBEntry objects Exceptions : none Caller : get_all_DBLinks, OperonAdaptor::store Status : Stable
public Arrayref Bio::EnsEMBL::Operon::get_all_OperonTranscripts | ( | ) |
Example :
Description: Retrieve all operon transcripts belonging to this operon Returntype : Arrayref of Bio::EnsEMBL::OperonTranscript Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::Operon::modified_date | ( | ) |
Arg [1] : (optional) String - modified date to set (as a UNIX time int) Example :
Description: Getter/setter for attribute modified_date Returntype : String Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Operon Bio::EnsEMBL::Operon::new | ( | ) |
Arg [-START] : int - start postion of the operon Arg [-END] : int - end position of the operon Arg [-STRAND] : int - 1,-1 the strand the operon is on Arg [-SLICE] : Bio::EnsEMBL::Slice - the slice the operon is on Arg [-STABLE_ID] : string - the stable identifier of this operon Arg [-VERSION] : int - the version of the stable identifier of this operon Arg [-DISPLAY_LABEL]: A name/label for this operon Arg [-CREATED_DATE]: string - the date the operon was created Arg [-MODIFIED_DATE]: string - the date the operon was last modified
Example :
Description: Creates a new operon object Returntype : Bio::EnsEMBL::Operon Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::Operon::stable_id | ( | ) |
Arg [1] : (optional) String - the stable ID to set Example :
Description: Getter/setter for stable id for this operon. Returntype : String Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::Operon::stable_id_version | ( | ) |
Arg [1] : (optional) String - the stable ID with version to set Example :
Description: Getter/setter for stable id with version for this operon. Returntype : String Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::Operon::version | ( | ) |
Arg [1] : (optional) Int - the stable ID version to set Example :
Description: Getter/setter for stable id version for this operon. Returntype : Int Exceptions : none Caller : general Status : Stable