diff variant_effect_predictor/Bio/EnsEMBL/IdMapping/Entry.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/IdMapping/Entry.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,178 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 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
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=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;
+