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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Operon.pm