diff variant_effect_predictor/Bio/EnsEMBL/Mapper/Pair.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Mapper/Pair.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,118 @@
+=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::Mapper::Pair
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+Two regions mapped between different coordinate systems are each
+represented by a Bio::EnsEMBL::Mapper::Unit and joined together as a
+Bio::EnsEMBL::Mapper::Pair.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::Mapper::Pair;
+
+use strict;
+
+sub new {
+  my ( $proto, $from, $to, $ori ) = @_;
+
+  my $class = ref($proto) || $proto;
+
+  return
+    bless( { 'from' => $from, 'to' => $to, 'ori' => $ori }, $class );
+}
+
+=head2 to
+
+  Arg  1      Bio::EnsEMBL::Mapper::Unit $seqobj
+	      from and to represent the two regions
+	      which are mapped to each other
+  Function    accessor method
+  Returntype  Bio::EnsEMBL::Mapper::Unit
+  Exceptions  none
+  Caller      Bio::EnsEMBL::Mapper::Pair
+  Status     : Stable
+
+=cut
+
+sub to {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'to'} = $value;
+  }
+
+  return $self->{'to'};
+}
+
+=head2 from
+
+  Arg  1      Bio::EnsEMBL::Mapper::Unit $seqobj
+	      from and to represent the two regions
+	      which are mapped to each other
+  Function    accessor method
+  Returntype  Bio::EnsEMBL::Mapper::Unit
+  Exceptions  none
+  Caller      Bio::EnsEMBL::Mapper::Pair
+  Status     : Stable
+
+=cut
+sub from {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'from'} = $value;
+  }
+
+  return $self->{'from'};
+}
+
+=head2 ori
+
+  Arg  1      Bio::EnsEMBL::Mapper::Unit $ori
+  Function    accessor method
+	      relative orientation of the the
+	      two mapped regions
+  Returntype  Bio::EnsEMBL::Mapper::Unit
+  Exceptions  none
+  Caller      Bio::EnsEMBL::Mapper::Pair
+  Status     : Stable
+
+=cut
+
+sub ori {
+  my ( $self, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'ori'} = $value;
+  }
+
+  return $self->{'ori'};
+}
+
+1;