Raw content of Bio::EnsEMBL::IdMapping::TinyExon
<![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::TinyExon - lightweight exon object
=head1 SYNOPSIS
# fetch an exon from the db and create a lightweight exon object
# from it
my $exon = $exon_adaptor->fetch_by_stable_id('ENSE000345437');
my $lightweight_exon = Bio::EnsEMBL::IdMapping::TinyExon->new_fast( [
$exon->dbID,
$exon->stable_id,
$exon->version,
$exon->created_date,
$exon->modified_date,
$exon->start,
$exon->end,
$exon->strand,
$exon->slice->seq_region_name,
$exon->slice->coord_system_name,
$exon->slice->coord_system->version,
$exon->slice->subseq( $exon->start, $exon->end, $exon->strand ),
$exon->phase,
$need_project,
] );
=head1 DESCRIPTION
This is a lightweight exon 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
coord_system_name
coord_system_version
seq
phase
need_project
common_start
common_end
common_strand
common_sr_name
length
is_known
=cut
package Bio::EnsEMBL::IdMapping::TinyExon;
# internal data structure (array indices):
#
# 0-4 see TinyFeature
# 5 start
# 6 end
# 7 strand
# 8 seq_region_name
# 9 coord_system_name
# 10 coord_system_version
# 11 seq
# 12 phase
# 13 need_project
# 14 common_start
# 15 common_end
# 16 common_strand
# 17 common_sr_name
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 exon's start coordinate
Description : Getter/setter for the exon'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 exon's end coordinate
Description : Getter/setter for the exon'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 exon's strand
Description : Getter/setter for the exon'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 exon 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 coord_system_name
Arg[1] : (optional) String - coord_system name
Description : Getter/setter for the coord_system name of the slice the exon is
on.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub coord_system_name {
my $self = shift;
$self->[9] = shift if (@_);
return $self->[9];
}
=head2 coord_system_version
Arg[1] : (optional) String - coord_system version
Description : Getter/setter for the coord_system version of the slice the
exon is on.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub coord_system_version {
my $self = shift;
$self->[10] = shift if (@_);
return $self->[10];
}
=head2 seq
Arg[1] : (optional) String - the exon's sequence
Description : Getter/setter for the exon's sequence.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub seq {
my $self = shift;
$self->[11] = shift if (@_);
return $self->[11];
}
=head2 phase
Arg[1] : (optional) Int - the exon's phase
Description : Getter/setter for the exon's phase.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub phase {
my $self = shift;
$self->[12] = shift if (@_);
return $self->[12];
}
=head2 need_project
Arg[1] : (optional) Boolean - attribute to set
Description : Getter/setter for the attribute determining whether an exon
needs to be projected onto a common coord_system. You don't need
to do so if the native coord_system is common to the source and
target assemblies, or if no common coord_system is found (the
Cache object has methods to determine this).
Return type : Boolean
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub need_project {
my $self = shift;
$self->[13] = shift if (@_);
return $self->[13];
}
=head2 common_start
Arg[1] : (optional) Int - the exon's start in common coord_system
coordinates
Description : Getter/setter for the exon's start in common coord_system
coordinates. Will return $self->start if no projection to a
common coord_system is required.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub common_start {
my $self = shift;
# when used as a setter, always set a value
$self->[14] = shift if (@_);
# when used as a getter
if (scalar(@$self) > 14) {
# return value for common coord_system if available (but avoid
# autovivification gotcha!)
return $self->[14];
} elsif ($self->need_project) {
# return undef if common value expected but not there (e.g. no projection
# found
return undef;
} else {
# return native value
return $self->start;
}
}
=head2 common_end
Arg[1] : (optional) Int - the exon's end in common coord_system
coordinates
Description : Getter/setter for the exon's end in common coord_system
coordinates. Will return $self->end if no projection to a
common coord_system is required.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub common_end {
my $self = shift;
# when used as a setter, always set a value
$self->[15] = shift if (@_);
# when used as a getter
if (scalar(@$self) > 14) {
# return value for common coord_system if available (but avoid
# autovivification gotcha!)
return $self->[15];
} elsif ($self->need_project) {
# return undef if common value expected but not there (e.g. no projection
# found
return undef;
} else {
# return native value
return $self->end;
}
}
=head2 common_strand
Arg[1] : (optional) Int - the exon's strand in common coord_system
coordinates
Description : Getter/setter for the exon's strand in common coord_system
coordinates. Will return $self->strand if no projection to a
common coord_system is required.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub common_strand {
my $self = shift;
# when used as a setter, always set a value
$self->[16] = shift if (@_);
# when used as a getter
if (scalar(@$self) > 14) {
# return value for common coord_system if available (but avoid
# autovivification gotcha!)
return $self->[16];
} elsif ($self->need_project) {
# return undef if common value expected but not there (e.g. no projection
# found
return undef;
} else {
# return native value
return $self->strand;
}
}
=head2 common_sr_name
Arg[1] : (optional) String - seq_region name of the exon's slice on the
common coord_system
Description : Getter/setter for the seq_region name of the exon's slice on the
common coord_system coordinates. Will return
$self->seq_region_name if no projection to a common coord_system
is required.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub common_sr_name {
my $self = shift;
# when used as a setter, always set a value
$self->[17] = shift if (@_);
# when used as a getter
if (scalar(@$self) > 14) {
# return value for common coord_system if available (but avoid
# autovivification gotcha!)
return $self->[17];
} elsif ($self->need_project) {
# return undef if common value expected but not there (e.g. no projection
# found
return undef;
} else {
# return native value
return $self->seq_region_name;
}
}
=head2 length
Description : Returns the exon 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);
}
=head2 is_known
Description : Determine whether an exon is known. In the context of stable Id
mapping, this is true for all exons.
Return type : Boolean
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub is_known {
return 1;
}
1;
]]>