view variant_effect_predictor/Bio/EnsEMBL/OperonTranscript.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::OperonTranscript - Object representing a polycistronic transcript that is part of an operon

=head1 SYNOPSIS

my $operon_transcript =
  Bio::EnsEMBL::OperonTranscript->new( -START  => $start,
									   -END    => $end,
									   -STRAND => $strand,
									   -SLICE  => $slice );
$operon->add_OperonTranscript($operon_transcript);

=head1 DESCRIPTION

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.

=head1 METHODS

=cut

package Bio::EnsEMBL::OperonTranscript;

use strict;
use warnings;

use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);

use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature);

=head2 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    : $gene = Bio::EnsEMBL::OperonTranscript->new(...);
  Description: Creates a new operon transcript object
  Returntype : Bio::EnsEMBL::OperonTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub new {
	my $caller = shift;

	my $class = ref($caller) || $caller;
	my $self = $class->SUPER::new(@_);
	my ( $stable_id, $version, $created_date, $modified_date, $display_label ) =
	  rearrange( [  'STABLE_ID',    'VERSION',
					'CREATED_DATE', 'MODIFIED_DATE', 'DISPLAY_LABEL' ],
				 @_ );

	$self->stable_id($stable_id);
	$self->version($version);
	$self->{'created_date'}  = $created_date;
	$self->{'modified_date'} = $modified_date;
	$self->display_label($display_label);
	return $self;
}

=head2 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

=cut

sub created_date {
  my $self = shift;
  $self->{'created_date'} = shift if ( @_ );
  return $self->{'created_date'};
}


=head2 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

=cut

sub modified_date {
  my $self = shift;
  $self->{'modified_date'} = shift if ( @_ );
  return $self->{'modified_date'};
}


=head2 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

=cut

sub display_label {
	my $self = shift;
	$self->{'display_label'} = shift if (@_);
	return $self->{'display_label'};
}

=head2 stable_id

  Arg [1]    : (optional) String - the stable ID to set
  Example    : $operon->stable_id("accR2A");
  Description: Getter/setter for stable id for this operon transcript.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub stable_id {
	my $self = shift;
	$self->{'stable_id'} = shift if (@_);
	return $self->{'stable_id'};
}

=head2 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 transcript.
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut
sub version {
  my $self = shift;
  $self->{'version'} = shift if(@_);
  return $self->{'version'};
}

=head2 operon

  Example    : $operon = $ot->operon();
  Description: getter for the operon to which this transcript belongs
  Returntype : Bio::EnsEMBL::Operon
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut
sub operon {
	my $self = shift;
	if ( !exists $self->{'operon'} ) {
		if ( defined $self->adaptor() ) {
			my $ta = $self->adaptor()->db()->get_OperonAdaptor();
			my $operon = $ta->fetch_by_operon_transcript($self);
			$self->{'operon'} = $operon;
		}
	}
	return $self->{'operon'};
}

=head2 get_all_Genes

  Example    : $genes = $ot->get_all_Genes();
  Description: get all the genes that are attached to this operon transcript
  Returntype : Arrayref of Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut
sub get_all_Genes {
	my $self = shift;
	if(! defined $self->{_gene_array}) {
	  if(defined $self->dbID() && defined $self->adaptor()) {
	    my $ta = $self->adaptor()->db()->get_OperonTranscriptAdaptor();
      my $transcripts = $ta->fetch_genes_by_operon_transcript($self);
      $self->{_gene_array} = $transcripts;
	  }
	  else {
	    $self->{_gene_array} = [];
	  }
	}
	return $self->{_gene_array};
}
=head2 add_gene

  Arg [1]    : Bio::EnsEMBL::Gene - gene to attach to this polycistronic transcript
  Example    : $operon->add_gene($gene);
  Description: Attach a gene to this polycistronic transcript
  Exceptions : if argument is not Bio::EnsEMBL::Gene
  Caller     : general
  Status     : Stable

=cut
sub add_gene {
	my ($self,$gene) = @_;
	assert_ref($gene,'Bio::EnsEMBL::Gene');
	push @{$self->get_all_Genes()},$gene;
	return;
}

=head2 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

=cut

sub add_DBEntry {
  my $self = shift;
  my $dbe = shift;

  unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
    throw('Expected DBEntry argument');
  }

  $self->{'dbentries'} ||= [];
  push @{$self->{'dbentries'}}, $dbe;
}


=head2 get_all_Attributes

  Arg [1]    : (optional) String $attrib_code
               The code of the attribute type to retrieve values for
  Example    : my ($author) = @{ $ot->get_all_Attributes('author') };
               my @ot_attributes = @{ $ot->get_all_Attributes };
  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

=cut

sub get_all_Attributes {
	my $self        = shift;
	my $attrib_code = shift;

	if ( !exists $self->{'attributes'} ) {
		if ( !$self->adaptor() ) {
			return [];
		}

		my $attribute_adaptor = $self->adaptor->db->get_AttributeAdaptor();
		$self->{'attributes'} = $attribute_adaptor->fetch_all_by_OperonTranscript($self);
	}

	if ( defined $attrib_code ) {
		my @results =
		  grep { uc( $_->code() ) eq uc($attrib_code) }
		  @{ $self->{'attributes'} };
		return \@results;
	} else {
		return $self->{'attributes'};
	}
}

=head2 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 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

=cut

sub get_all_DBEntries {
	my ( $self, $db_name_exp, $ex_db_type ) = @_;

	my $cache_name = 'dbentries';

	if ( defined($db_name_exp) ) {
		$cache_name .= $db_name_exp;
	}

	if ( defined($ex_db_type) ) {
		$cache_name .= $ex_db_type;
	}

	# if not cached, retrieve all of the xrefs for this gene
	if ( !defined( $self->{$cache_name} ) && defined( $self->adaptor() ) ) {
		$self->{$cache_name} =
		  $self->adaptor()->db()->get_DBEntryAdaptor()
		  ->fetch_all_by_Operon( $self->operon(), $db_name_exp, $ex_db_type );
	}

	$self->{$cache_name} ||= [];

	return $self->{$cache_name};
}

1;