diff variant_effect_predictor/Bio/EnsEMBL/Map/MapLocation.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Map/MapLocation.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,207 @@
+=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::Map::MapLocation
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+Represents a location on a genetic map, yac map, radition hybrid map,
+etc.
+
+=head1 METHODS
+
+=cut
+
+
+package Bio::EnsEMBL::Map::MapLocation;
+
+use strict;
+use vars qw(@ISA);
+
+use Bio::EnsEMBL::Utils::Exception qw(deprecate);
+
+=head2 new
+
+  Arg [1]    : (optional) string $name
+  Arg [2]    : (optional) string $map_name
+  Arg [3]    : (optional) string $chromosome_name
+  Arg [4]    : (optional) string $position
+  Arg [5]    : (optional) float $lod_score
+  Example    : $map_location = Bio::EnsEMBL::Map::MapLocation('DS1234',
+                                                              'genethon',
+                                                              'X',
+                                                              '12.39',
+                                                              50.12);
+  Description: Creates a new MapLocation
+  Returntype : Bio::EnsEMBL::Map::MapLocation
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub new {
+  my ($caller, $name, $map_name, $chromosome_name, $position, $lod_score) = @_;
+
+  my $class = ref($caller) || $caller;
+
+  return bless( {'map_name'        => $map_name,
+                 'name'            => $name,
+                 'chromosome_name' => $chromosome_name,
+                 'position'        => $position,
+                 'lod_score'       => $lod_score}, $class );
+}
+
+
+
+=head2 map_name
+
+  Arg [1]    : string $map_name
+  Example    : $map_name = $map_location->map_name;
+  Description: Getter/Setter for the map name
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub map_name {
+  my $self = shift;
+  $self->{'map_name'} = shift if(@_);
+  return $self->{'map_name'};
+}
+
+
+
+=head2 name
+
+  Arg [1]    : (optional) string $name
+  Example    : $name = $map_location->name;
+  Description: A name associated with the marker at this position.  For
+               example if this is a genethon map location the name will be
+               the synonym of source genethon.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub name {
+  my $self = shift;
+  $self->{'name'} = shift if(@_);
+  return $self->{'name'};
+}
+
+
+=head2 chromosome_name
+
+  Arg [1]    : (optional) string $chromosome_name
+  Example    : $chr_name = $map_location->chromosome_name;
+               $map_location->chromosome_name('X');
+  Description: The name of the chromosome associated with this map location
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub chromosome_name{
+  my $self = shift;
+  $self->{'chromosome_name'} = shift if(@_);
+  return $self->{'chromosome_name'};
+}
+
+
+
+=head2 position
+
+  Arg [1]    : (optional) string $position
+  Example    : $pos = $map_location->position;
+  Description: Getter/Setter for the position of this map location
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub position {
+  my $self = shift;
+  $self->{'position'} = shift if(@_);
+  return $self->{'position'};
+}
+
+
+
+=head2 lod_score
+
+  Arg [1]    : (optional) float $lod
+  Example    : $lod = $map_location->lod_score;
+  Description: Getter/Setter for lod score of this map location
+  Returntype : float
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub lod_score {
+  my $self = shift;
+  $self->{'lod_score'} = shift if(@_);
+  return $self->{'lod_score'};
+}
+
+
+
+=head2 chromosome
+
+  Description: DEPRECATED use chromosome_name() instead
+
+=cut
+
+sub chromosome {
+  my $self = shift;
+  deprecate('use chromosome_name instead');
+
+  if(@_) {
+    my $chr = shift;
+    if(ref($chr)) {
+      $self->chromosome_name($chr->seq_region_name());
+    } else {
+      $self->chromosome_name($chr);
+    }
+  }
+
+  #this object has no way to talk to db and thus no way to
+  #get a chromosome object
+  return $self->chromosome_name();
+}
+
+
+
+
+1;