ensembl-hive
2.6
|
Public Member Functions | |
public Bio::EnsEMBL::OperonTranscript | 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 Bio::EnsEMBL::Operon | operon () |
public Arrayref | get_all_Genes () |
public | add_Gene () |
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 a polycistronic transcript from an operon within the Ensembl system. An operon is a collection of one or more polycistronic transcripts, which contain one or more genes.
Definition at line 23 of file OperonTranscript.pm.
public void Bio::EnsEMBL::OperonTranscript::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::OperonTranscript::add_Gene | ( | ) |
Arg [1] : Bio::EnsEMBL::Gene - gene to attach to this polycistronic transcript Example :
Description: Attach a gene to this polycistronic transcript Exceptions : if argument is not Bio::EnsEMBL::Gene Caller : general Status : Stable
public String Bio::EnsEMBL::OperonTranscript::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::OperonTranscript::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::OperonTranscript::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 transcript. 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::OperonTranscript::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 transcript. 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, OperontTranscriptAdaptor::store Status : Stable
public Arrayref Bio::EnsEMBL::OperonTranscript::get_all_Genes | ( | ) |
Example :
Description: get all the genes that are attached to this operon transcript Returntype : Arrayref of Bio::EnsEMBL::Gene Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::OperonTranscript::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::OperonTranscript Bio::EnsEMBL::OperonTranscript::new | ( | ) |
Arg [-START] : int - start postion of the operon transcript Arg [-END] : int - end position of the operon transcript Arg [-STRAND] : int - 1,-1 tehe strand the operon transcript is on Arg [-SLICE] : Bio::EnsEMBL::Slice - the slice the operon transcript is on Arg [-STABLE_ID] : string - the stable identifier of this operon transcript Arg [-VERSION] : int - the version of the stable identifier of this operon transcript Arg [-CREATED_DATE]: string - the date the operon transcript was created Arg [-MODIFIED_DATE]: string - the date the operon transcript was last modified
Example :
Description: Creates a new operon transcript object Returntype : Bio::EnsEMBL::OperonTranscript Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Operon Bio::EnsEMBL::OperonTranscript::operon | ( | ) |
Example :
Description: getter for the operon to which this transcript belongs Returntype : Bio::EnsEMBL::Operon Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::OperonTranscript::stable_id | ( | ) |
Arg [1] : (optional) String - the stable ID to set Example :
Description: Getter/setter for stable id for this operon transcript. Returntype : String Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::OperonTranscript::stable_id_version | ( | ) |
Arg [1] : (optional) String - the stable ID with version to set Example :
Description: Getter/setter for stable id with version. Returntype : String Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::OperonTranscript::version | ( | ) |
Arg [1] : (optional) Int - the stable ID version to set Example :
Description: Getter/setter for stable id version for this operon transcript. Returntype : Int Exceptions : none Caller : general Status : Stable