Raw content of Bio::EnsEMBL::IdMapping::TinyGene
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::IdMapping::TinyGene - lightweight gene object
=head1 SYNOPSIS
# fetch a gene from the db and create a lightweight gene object from it
my $gene = $gene_adaptor->fetch_by_stable_id('ENSG000345437');
my $lightweight_gene = Bio::EnsEMBL::IdMapping::TinyGene->new_fast( [
$gene->dbID, $gene->stable_id,
$gene->version, $gene->created_date,
$gene->modified_date, $gene->start,
$gene->end, $gene->strand,
$gene->slice->seq_region_name, $gene->biotype,
$gene->status, $gene->analysis->logic_name,
( $gene->is_known ? 1 : 0 ),
] );
=head1 DESCRIPTION
This is a lightweight gene object for the stable Id mapping. See the
documentation in TinyFeature for general considerations about its
design.
=head1 METHODS
start
end
strand
seq_region_name
biotype
status
logic_name
is_known
add_Transcript
get_all_Transcripts
length
=cut
package Bio::EnsEMBL::IdMapping::TinyGene;
# internal data structure (array indices):
#
# 0-4 see TinyFeature
# 5 start
# 6 end
# 7 strand
# 8 seq_region_name
# 9 biotype
# 10 status
# 11 logic_name
# 12 is_known
# 13 [transcripts]
use strict;
use warnings;
no warnings 'uninitialized';
use Bio::EnsEMBL::IdMapping::TinyFeature;
our @ISA = qw(Bio::EnsEMBL::IdMapping::TinyFeature);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
=head2 start
Arg[1] : (optional) Int - the gene's start coordinate
Description : Getter/setter for the gene's start coordinate.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub start {
my $self = shift;
$self->[5] = shift if (@_);
return $self->[5];
}
=head2 end
Arg[1] : (optional) Int - the gene's end coordinate
Description : Getter/setter for the gene's end coordinate.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub end {
my $self = shift;
$self->[6] = shift if (@_);
return $self->[6];
}
=head2 strand
Arg[1] : (optional) Int - the gene's strand
Description : Getter/setter for the gene's strand.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub strand {
my $self = shift;
$self->[7] = shift if (@_);
return $self->[7];
}
=head2 seq_region_name
Arg[1] : (optional) String - seq_region name
Description : Getter/setter for the seq_region name of the slice the gene is
on.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub seq_region_name {
my $self = shift;
$self->[8] = shift if (@_);
return $self->[8];
}
=head2 biotype
Arg[1] : (optional) String - the gene's biotype
Description : Getter/setter for the gene's biotype.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub biotype {
my $self = shift;
$self->[9] = shift if (@_);
return $self->[9];
}
=head2 strand
Arg[1] : (optional) String - the gene's status
Description : Getter/setter for the gene's status.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub status {
my $self = shift;
$self->[10] = shift if (@_);
return $self->[10];
}
=head2 logic_name
Arg[1] : (optional) String - the gene's analysis' logic_name
Description : Getter/setter for the gene's analysis' logic_name.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub logic_name {
my $self = shift;
$self->[11] = shift if (@_);
return $self->[11];
}
=head2 is_known
Arg[1] : (optional) Boolean - the gene's "known" status
Description : Getter/setter for the gene's "known" status.
Return type : Boolean
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub is_known {
my $self = shift;
$self->[12] = shift if (@_);
return $self->[12];
}
=head2 add_Transcript
Arg[1] : Bio::EnsEMBL::IdMapping::TinyTranscript $tr - the transcript to
add
Example : $tiny_gene->add_Transcript($tiny_transcript);
Description : Adds a transcript to a gene.
Return type : none
Exceptions : thrown on wrong or missing argument
Caller : general
Status : At Risk
: under development
=cut
sub add_Transcript {
my $self = shift;
my $tr = shift;
unless ($tr && $tr->isa('Bio::EnsEMBL::IdMapping::TinyTranscript')) {
throw('Need a Bio::EnsEMBL::IdMapping::TinyTranscript.');
}
push @{ $self->[13] }, $tr;
}
=head2 get_all_Transcripts
Example : foreach my $tr (@{ $tiny_gene->get_all_Transcripts }) {
# do something with transcript
}
Description : Returns all transcripts attached to that gene.
Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyTranscript objects
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_all_Transcripts {
return $_[0]->[13] || [];
}
=head2 length
Description : Returns the gene length (distance between start and end).
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub length {
my $self = shift;
return ($self->end - $self->start + 1);
}
1;
]]>