ensembl-hive  2.6
Bio::EnsEMBL::Operon Class Reference
+ Inheritance diagram for Bio::EnsEMBL::Operon:

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 ()
 

Detailed Description

Synopsis

my $operon = Bio::EnsEMBL::Operon->new(
-START => 123,
-END => 1045,
-STRAND => 1,
-SLICE => $slice,
-DISPLAY_LABEL => $name
);
# print operon information
print("operon start:end:strand is "
. join( ":", map { $operon->$_ } qw(start end strand) )
. "\n" );

Description

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.

Definition at line 30 of file Operon.pm.

Member Function Documentation

◆ add_DBEntry()

public void Bio::EnsEMBL::Operon::add_DBEntry ( )
  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
               The dbEntry to be added
  Example    :
my $dbe = Bio::EnsEMBL::DBEntery->new(...);
$operon->add_DBEntry($dbe);
  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
 
Code:
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◆ add_OperonTranscript()

public Bio::EnsEMBL::Operon::add_OperonTranscript ( )
  Arg [1]    : Bio::EnsEMBL::OperonTranscript - operon transcript to attach to this operon
  Example    :
$operon->add_OperonTranscript($ot);
  Description: Attach a polycistronic operon transcript to this operon
  Exceptions : if argument is not Bio::EnsEMBL::OperonTranscript
  Caller     : general
  Status     : Stable
 
Code:
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◆ created_date()

public String Bio::EnsEMBL::Operon::created_date ( )
  Arg [1]    : (optional) String - created date to set (as a UNIX time int)
  Example    :
$gene->created_date('1141948800');
  Description: Getter/setter for attribute created_date
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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◆ display_label()

public String Bio::EnsEMBL::Operon::display_label ( )
  Arg [1]    : (optional) String - the name/label to set
  Example    :
$operon->name('accBCD');
  Description: Getter/setter for attribute name.
  Returntype : String or undef
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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◆ get_all_Attributes()

public Listref Bio::EnsEMBL::Operon::get_all_Attributes ( )
  Arg [1]    : (optional) String $attrib_code
               The code of the attribute type to retrieve values for
  Example    :
my ($author) = @{ $operon->get_all_Attributes('author') };
my @operon_attributes = @{ $operon->get_all_Attributes };
  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
 
Code:
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◆ get_all_DBEntries()

public Listref Bio::EnsEMBL::Operon::get_all_DBEntries ( )
  Arg [1]    : (optional) String, external database name
  Arg [2]    : (optional) String, external_db type
  Example    :
@dbentries = @{ $gene->get_all_DBEntries() };
  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
 
Code:
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◆ get_all_OperonTranscripts()

public Arrayref Bio::EnsEMBL::Operon::get_all_OperonTranscripts ( )
  Example    :
my $ots = $operon->get_all_OperonTranscripts();
  Description: Retrieve all operon transcripts belonging to this operon
  Returntype : Arrayref of Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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◆ modified_date()

public String Bio::EnsEMBL::Operon::modified_date ( )
  Arg [1]    : (optional) String - modified date to set (as a UNIX time int)
  Example    :
$gene->modified_date('1141948800');
  Description: Getter/setter for attribute modified_date
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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◆ new()

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    :
$gene = Bio::EnsEMBL::Operon->new(...);
  Description: Creates a new operon object
  Returntype : Bio::EnsEMBL::Operon
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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◆ stable_id()

public String Bio::EnsEMBL::Operon::stable_id ( )
  Arg [1]    : (optional) String - the stable ID to set
  Example    :
$operon->stable_id("accR2");
  Description: Getter/setter for stable id for this operon.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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◆ stable_id_version()

public String Bio::EnsEMBL::Operon::stable_id_version ( )
  Arg [1]    : (optional) String - the stable ID with version to set
  Example    :
$operon->stable_id("accR2.3");
  Description: Getter/setter for stable id with version for this operon.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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◆ version()

public Int Bio::EnsEMBL::Operon::version ( )
  Arg [1]    : (optional) Int - the stable ID version to set
  Example    :
$operon->version(1);
  Description: Getter/setter for stable id version for this operon.
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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The documentation for this class was generated from the following file:
Bio::EnsEMBL::Operon::stable_id_version
public String stable_id_version()
Bio::EnsEMBL::Operon
Definition: Operon.pm:30
Bio::EnsEMBL::Operon::version
public Int version()
map
public map()
Bio::EnsEMBL::Feature::end
public Int end()
Bio::EnsEMBL::Operon::get_all_DBEntries
public Listref get_all_DBEntries()
Bio::EnsEMBL::Operon::get_all_Attributes
public Listref get_all_Attributes()
Bio::EnsEMBL::Operon::created_date
public String created_date()
Bio::EnsEMBL::Operon::add_OperonTranscript
public add_OperonTranscript()
Bio::EnsEMBL::Feature::strand
public Int strand()
Bio::EnsEMBL::Feature::start
public Int start()
Bio::EnsEMBL::Operon::add_DBEntry
public void add_DBEntry()
Bio::EnsEMBL::Operon::modified_date
public String modified_date()
Bio::EnsEMBL::Operon::get_all_OperonTranscripts
public Arrayref get_all_OperonTranscripts()
Bio::EnsEMBL::Operon::new
public Bio::EnsEMBL::Operon new()
Bio::EnsEMBL::Operon::stable_id
public String stable_id()
Bio::EnsEMBL::Operon::display_label
public String display_label()