Raw content of Bio::EnsEMBL::IdMapping::TinyTranslation
<![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::TinyTranslation - lightweight translation object
=head1 SYNOPSIS
if ( my $tl = $tr->translation ) {
my $lightweight_tl =
Bio::EnsEMBL::IdMapping::TinyTranslation->new_fast( [
$tl->dbID, $tl->stable_id,
$tl->version, $tl->created_date,
$tl->modified_date, $tr->dbID,
$tr->translate->seq, ( $tr->is_known ? 1 : 0 ),
] );
}
=head1 DESCRIPTION
This is a lightweight translation object for the stable Id mapping. See
the documentation in TinyFeature for general considerations about its
design.
=head1 METHODS
transcript_id
seq
is_known
=cut
package Bio::EnsEMBL::IdMapping::TinyTranslation;
# internal data structure (array indices):
#
# 0-4 see TinyFeature
# 5 transcript_id
# 6 seq
# 7 is_known
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 transcript_id
Arg[1] : (optional) Int - the transcript internal Id ("dbID")
Description : Getter/setter for the transcript internal Id this translation is
attached to.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub transcript_id {
my $self = shift;
$self->[5] = shift if (@_);
return $self->[5];
}
=head2 seq
Arg[1] : (optional) String - the translation's sequence
Description : Getter/setter for the translation's sequence.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub seq {
my $self = shift;
$self->[6] = shift if (@_);
return $self->[6];
}
=head2 is_known
Arg[1] : (optional) Boolean - the translation's "known" status
Description : Getter/setter for the translation's "known" status.
Return type : Boolean
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub is_known {
my $self = shift;
$self->[7] = shift if (@_);
return $self->[7];
}
1;
]]>