/ 
Bio-EnsEMBL-112.0_55
River stage zero No dependents
/ Bio::EnsEMBL::Operon

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::Operon - Object representing an operon

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.

METHODS

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

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

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

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

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

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

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

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

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

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

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

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