Entry.pm

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=head1 LICENSE
 
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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
 
     http://www.apache.org/licenses/LICENSE-2.0
 
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
  <http://www.ensembl.org/Help/Contact>.
 
=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;