Raw content of Bio::EnsEMBL::StableIdEvent
<![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::StableIdEvent- object representing a stable ID mapping event
=head1 SYNOPSIS
my $old_id = Bio::EnsEMBL::ArchiveStableId->new(
-stable_id => 'ENSG001',
-version => 1,
-type => 'Gene',
);
my $new_id = Bio::EnsEMBL::ArchiveStableId->new(
-stable_id => 'ENSG001',
-version => 2,
-type => 'Gene',
);
my $event = Bio::EnsEMBL::StableIdEvent->new(
-old_id => $old_id,
-new_id => $new_id,
-score => 0.997
);
# directly access attributes in old and new ArchiveStableId
my $old_stable_id = $event->get_attribute( 'old', 'stable_id' );
=head1 DESCRIPTION
This object represents a stable ID mapping event. Such an event links two
ArchiveStableIds with a mapping score.
=head1 METHODS
new
old_ArchiveStableId
new_ArchiveStableId
score
get_attribute
ident_string
=head1 RELATED MODULES
Bio::EnsEMBL::ArchiveStableId
Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Bio::EnsEMBL::StableIdHistoryTree
=cut
package Bio::EnsEMBL::StableIdEvent;
use strict;
use warnings;
no warnings 'uninitialized';
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
=head2 new
Arg[1] : Bio::EnsEMBL::ArchiveStableId $old_id
The old ArchiveStableId in the mapping event
Arg[2] : Bio::EnsEMBL::ArchiveStableId $new_id
The new ArchiveStableId in the mapping event
Arg[3] : (optional) float $score - score of this mapping event
Example : my $event = Bio::EnsEMBL::StableIdEvent->new(
$arch_id1, $arch_id2, 0.977);
Description : object constructor
Return type : Bio::EnsEMBL::StableIdEvent
Exceptions : thrown on wrong argument types
Caller : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_history_tree_by_stable_id, general
Status : At Risk
: under development
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my ($old_id, $new_id, $score) = rearrange([qw(OLD_ID NEW_ID SCORE)], @_);
throw("Need old or new Bio::EnsEMBL::ArchiveStableId to create StableIdEvent")
unless ($old_id || $new_id);
my $self = {};
bless $self, $class;
# initialise object
$self->old_ArchiveStableId($old_id);
$self->new_ArchiveStableId($new_id);
$self->score($score);
return $self;
}
=head2 old_ArchiveStableId
Arg[1] : (optional) Bio::EnsEMBL::ArchiveStableId $archive_id, or undef
The old ArchiveStableId to set for this mapping event
Example : # getter
my $archive_id = $event->old_ArchiveStableId;
# setter
$event->old_ArchiveStableId($archive_id);
Description : Getter/setter for old ArchiveStableId in this mapping event.
Return type : Bio::EnsEMBL::ArchiveStableId
Exceptions : thrown on wrong argument type
Caller : general
Status : At Risk
: under development
=cut
sub old_ArchiveStableId {
my $self = shift;
# setter
if (@_) {
my $archive_id = shift;
# if argument is defined, check type. undef is also legal as an argument.
if (defined($archive_id)) {
throw("Need a Bio::EnsEMBL::ArchiveStableId.") unless
(ref($archive_id) && $archive_id->isa('Bio::EnsEMBL::ArchiveStableId'));
}
$self->{'old_id'} = $archive_id;
}
# getter
return $self->{'old_id'};
}
=head2 new_ArchiveStableId
Arg[1] : (optional) Bio::EnsEMBL::ArchiveStableId $archive_id, or undef
The new ArchiveStableId to set for this mapping event
Example : # getter
my $archive_id = $event->new_ArchiveStableId;
# setter
$event->new_ArchiveStableId($archive_id);
Description : Getter/setter for new ArchiveStableId in this mapping event.
Return type : Bio::EnsEMBL::ArchiveStableId
Exceptions : thrown on wrong argument type
Caller : general
Status : At Risk
: under development
=cut
sub new_ArchiveStableId {
my $self = shift;
# setter
if (@_) {
my $archive_id = shift;
# if argument is defined, check type. undef is also legal as an argument.
if (defined($archive_id)) {
throw("Need a Bio::EnsEMBL::ArchiveStableId.") unless
(ref($archive_id) && $archive_id->isa('Bio::EnsEMBL::ArchiveStableId'));
}
$self->{'new_id'} = $archive_id;
}
# getter
return $self->{'new_id'};
}
=head2 score
Arg[1] : (optional) float $score - the score to set
Example : my $score = $event->score;
Description : Getter/setter for mapping event score.
Return type : float or undef
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub score {
my $self = shift;
$self->{'score'} = shift if (@_);
return $self->{'score'};
}
=head2 get_attribute
Arg[1] : String $type - determines whether to get attribute from 'old'
or 'new' ArchiveStableId
Arg[2] : String $attr - ArchiveStableId attribute to fetch
Example : my $old_stable_id = $event->get_attribute('old', 'stable_id');
Description : Accessor to attributes of the ArchiveStableIds attached to this
event. Convenience method that does the check for undef old
and/or new ArchiveStableId for you.
Return type : same as respective method in Bio::EnsEMBL::ArchiveStableId, or
undef
Exceptions : thrown on wrong arguments
Caller : general
Status : At Risk
: under development
=cut
sub get_attribute {
my ($self, $type, $attr) = @_;
throw("First argument passed to this function has to be 'old' or 'new'.")
unless ($type eq 'old' or $type eq 'new');
my %allowed_attribs = map { $_ => 1 }
qw(stable_id version db_name release assembly);
throw("Attribute $attr not allowed.") unless $allowed_attribs{$attr};
my $call = $type.'_ArchiveStableId';
if (my $id = $self->$call) {
return $id->$attr;
} else {
return undef;
}
}
=head2 ident_string
Example : print $event->ident_string, "\n";
Description : Returns a string that can be used to identify your StableIdEvent.
Useful in debug warnings.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub ident_string {
my $self = shift;
my $old_id = $self->old_ArchiveStableId;
my $new_id = $self->new_ArchiveStableId;
my $str;
if ($old_id) {
$str = $old_id->stable_id.'.'.$old_id->version.' ('.
$old_id->release.')';
} else {
$str = 'null';
}
$str .= ' -> ';
if ($new_id) {
$str .= $new_id->stable_id.'.'.$new_id->version.' ('.
$new_id->release.')';
} else {
$str .= 'null';
}
$str .= ' ['.$self->score.']';
return $str;
}
1;
]]>