Raw content of Bio::EnsEMBL::IdMapping::TinyTranscript
<![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::TinyTranscript - lightweight transcript object
=head1 SYNOPSIS
# fetch a transcript from the db and create a lightweight
# transcript object from it
my $tr = $transcript_adaptor->fetch_by_stable_id('ENST000345437');
my $lightweight_tr =
Bio::EnsEMBL::IdMapping::TinyTranscript->new_fast( [
$tr->dbID, $tr->stable_id,
$tr->version, $tr->created_date,
$tr->modified_date, $tr->start,
$tr->end, $tr->strand,
$tr->length, md5_hex( $tr->spliced_seq ),
( $tr->is_known ? 1 : 0 ),
] );
=head1 DESCRIPTION
This is a lightweight transcript object for the stable Id mapping. See
the documentation in TinyFeature for general considerations about its
design.
=head1 METHODS
start
end
strand
length
seq_md5_sum
is_known
add_Translation
translation
add_Exon
get_all_Exons
=cut
package Bio::EnsEMBL::IdMapping::TinyTranscript;
# internal data structure (array indices):
#
# 0-4 see TinyFeature
# 5 start
# 6 end
# 7 strand
# 8 length
# 9 seq_md5_sum
# 10 is_known
# 11 translation
# 12 [exons]
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 transcript's start coordinate
Description : Getter/setter for the transcript'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 transcript's end coordinate
Description : Getter/setter for the transcript'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 transcript's strand
Description : Getter/setter for the transcript'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 length
Arg[1] : (optional) Int - the transcript's length
Description : Getter/setter for the transcript's length. Note that this is
*not* the distance between start and end, but rather the sum of
the lengths of all exons.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub length {
my $self = shift;
$self->[8] = shift if (@_);
return $self->[8];
}
=head2 seq_md5_sum
Arg[1] : (optional) String - the md5 digest of the transcript's sequence
Description : Getter/setter for the md5 digest of the transcript's sequence.
Note that when used as a setter, you are expected to pass a
digest, not the raw sequence (i.e. the digest is not created for
you).
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub seq_md5_sum {
my $self = shift;
$self->[9] = shift if (@_);
return $self->[9];
}
=head2 is_known
Arg[1] : (optional) Boolean - the transcript's "known" status
Description : Getter/setter for the transcript's "known" status.
Return type : Boolean
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub is_known {
my $self = shift;
$self->[10] = shift if (@_);
return $self->[10];
}
=head2 add_Translation
Arg[1] : Bio::EnsEMBL::IdMapping::TinyTranslation $tl - the translation
to add
Example : $tiny_transcript->add_Translation($tiny_translation);
Description : Adds a translation to this transcript.
Return type : none
Exceptions : thrown on wrong or missing argument
Caller : general
Status : At Risk
: under development
=cut
sub add_Translation {
my $self = shift;
my $tl = shift;
unless ($tl && $tl->isa('Bio::EnsEMBL::IdMapping::TinyTranslation')) {
throw('Need a Bio::EnsEMBL::IdMapping::TinyTranslation.');
}
$self->[11] = $tl;
}
=head2 translation
Description : Getter for the transcript's translation.
Return type : Bio::EnsEMBL::IdMapping::TinyTranslation
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub translation {
return $_[0]->[11];
}
=head2 add_Exon
Arg[1] : Bio::EnsEMBL::IdMapping::TinyExon $exon - the exon to add
Example : $tiny_transcript->add_Exon($tiny_exon);
Description : Adds an exon to this transcript.
Return type : none
Exceptions : thrown on wrong or missing argument
Caller : general
Status : At Risk
: under development
=cut
sub add_Exon {
my $self = shift;
my $exon = shift;
unless ($exon && $exon->isa('Bio::EnsEMBL::IdMapping::TinyExon')) {
throw('Need a Bio::EnsEMBL::IdMapping::TinyExon.');
}
push @{ $self->[12] }, $exon;
}
=head2 get_all_Exons
Example : foreach my $exon (@{ $tiny_transcript->get_all_Exons }) {
# do something with exon
}
Description : Returns all exons attached to that transcript.
Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyExon objects
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_all_Exons {
return $_[0]->[12] || [];
}
1;
]]>