————————=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
Bio::EnsEMBL::IdMapping::Entry - object representing a ScoredMappingMatrix entry
=head1 SYNOPSIS
=head1 DESCRIPTION
This object represents a ScoredMappingMatrix entry. It is defined by a
pair of a source and target object's internal Id and a score for this
mapping.
=head1 METHODS
new
new_fast
source
target
score
to_string
=cut
package
Bio::EnsEMBL::IdMapping::Entry;
$Bio::EnsEMBL::IdMapping::Entry::VERSION
=
'112.0_54'
;
# TRIAL
$Bio::EnsEMBL::IdMapping::Entry::VERSION
=
'112.054'
;
use
strict;
use
warnings;
no
warnings
'uninitialized'
;
=head2 new
Example : my $entry = Bio::EnsEMBL::IdMapping::Entry->new();
Description : Constructor. This is a no-argument constructor, so you need to
populate the object manually. Rarely used since in most cases
new_fast() is preferred.
Return type : a Bio::EnsEMBL::IdMapping::Entry object
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub
new {
my
$caller
=
shift
;
my
$class
=
ref
(
$caller
) ||
$caller
;
my
$self
= [];
bless
(
$self
,
$class
);
return
$self
;
}
=head2 new_fast
Arg[1] : Arrayref $array_ref - the arrayref to bless into the Entry
object
Example : my $entry = Bio::EnsEMBL::IdMapping::Entry->new_fast([
$source_gene->id, $target_gene->id, 0.9]);
Description : Fast constructor.
Return type : a Bio::EnsEMBL::IdMapping::Entry object
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub
new_fast {
my
$class
=
shift
;
my
$array_ref
=
shift
;
return
bless
$array_ref
,
$class
;
}
=head2 source
Arg[1] : (optional) Int - source object's internal Id
Description : Getter/setter for source object's internal Id.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub
source {
my
$self
=
shift
;
$self
->[0] =
shift
if
(
@_
);
return
$self
->[0];
}
=head2 target
Arg[1] : (optional) Int - target object's internal Id
Description : Getter/setter for target object's internal Id.
Return type : Int
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub
target {
my
$self
=
shift
;
$self
->[1] =
shift
if
(
@_
);
return
$self
->[1];
}
=head2 score
Arg[1] : (optional) Float - a score
Description : Getter/setter for score for the mapping between source and
target object.
Return type : Float
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub
score {
my
$self
=
shift
;
$self
->[2] =
shift
if
(
@_
);
return
$self
->[2];
}
=head2 to_string
Example : print LOG $entry->to_string, "\n";
Description : Returns a string representation of the Entry object. Useful for
debugging and logging.
Return type : String
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub
to_string {
my
$self
=
shift
;
return
sprintf
(
'%-10s%-10s%-5.6f'
,
$self
->source,
$self
->target,
$self
->score);
}
1;