Raw content of Bio::EnsEMBL::IdMapping::Entry
<![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::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;
use strict;
use warnings;
no warnings 'uninitialized';
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
=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;
]]>