Raw content of Bio::EnsEMBL::IdMapping::TinyFeature
<![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::TinyFeature - lightweight feature object
=head1 SYNOPSIS
This object isn't instantiated. See objects which inherit from it
(TinyGene, TinyTranscript, etc.) for examples.
=head1 DESCRIPTION
This is the base class for the lightweight feature objects used by the
stable Id maping application. For performance reasons, these objects
are instantiated using a new_fast() method. The internal implementation
is an arrayref (rather than the more common hashref), which optimises
memory usage.
There are no adaptors to fetch TinyFeatures from the database. You
rather use the normal feature adaptors and then create the TinyFeatures
from the heavy objects you get. The memory saving will therefore mainly
take effect when serialising and reloading these objects.
Also note that TinyFeatures don't have a slice attached to them - all
location information (where required) is stored on the feature object
directly.
=head1 METHODS
new_fast
id
stable_id
version
created_date
modified_date
to_string
=cut
package Bio::EnsEMBL::IdMapping::TinyFeature;
# internal data structure (array indices):
#
# 0 dbID
# 1 stable_id
# 2 version
# 3 created_date
# 4 modified_date
#
# other instance variables differ by subclass implementation, so look there.
use strict;
use warnings;
no warnings 'uninitialized';
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
=head2 new_fast
Arg[1] : Arrayref $array_ref - the arrayref to bless into the new object
Description : Constructor.
Return type : Bio::EnsEMBL::IdMapping::TinyFeature implementing class
Exceptions : none
Caller : Bio::EnsEMBL::IdMapping::Cache
Status : At Risk
: under development
=cut
sub new_fast {
my $class = shift;
my $array_ref = shift;
return bless $array_ref, $class;
}
=head2 id
Arg[1] : (optional) Int - the feature's internal Id ("dbID")
Description : Getter/setter for the feature's internal Id.
Return type : Int
Exceptions : none
Caller : Bio::EnsEMBL::IdMapping::Cache
Status : At Risk
: under development
=cut
sub id {
my $self = shift;
$self->[0] = shift if (@_);
return $self->[0];
}
=head2 stable_id
Arg[1] : (optional) String - the feature's stable Id
Description : Getter/setter for the feature's stable Id.
Return type : String
Exceptions : none
Caller : Bio::EnsEMBL::IdMapping::Cache
Status : At Risk
: under development
=cut
sub stable_id {
my $self = shift;
$self->[1] = shift if (@_);
return $self->[1];
}
=head2 version
Arg[1] : (optional) Int - the feature's stable Id version
Description : Getter/setter for the feature's stable Id version.
Return type : Int
Exceptions : none
Caller : Bio::EnsEMBL::IdMapping::Cache
Status : At Risk
: under development
=cut
sub version {
my $self = shift;
$self->[2] = shift if (@_);
return $self->[2];
}
=head2 created_date
Arg[1] : (optional) String - the feature's stable Id creation date
Description : Getter/setter for the feature's stable Id creation date.
Return type : String
Exceptions : none
Caller : Bio::EnsEMBL::IdMapping::Cache
Status : At Risk
: under development
=cut
sub created_date {
my $self = shift;
$self->[3] = shift if (@_);
return $self->[3];
}
=head2 modified_date
Arg[1] : (optional) String - the feature's stable Id modification date
Description : Getter/setter for the feature's stable Id modification date.
Return type : String
Exceptions : none
Caller : Bio::EnsEMBL::IdMapping::Cache
Status : At Risk
: under development
=cut
sub modified_date {
my $self = shift;
$self->[4] = shift if (@_);
return $self->[4];
}
=head2 to_string
Example : print LOG "Created ", $f->to_string, "\n";
Description : Prints a string representation of the feature for debug
purposes.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub to_string {
my $self = shift;
return $self->id.':'.$self->stable_id.'.'.$self->version;
}
1;
]]>