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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Map::MapLocation
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24
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25 =head1 SYNOPSIS
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26
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27 =head1 DESCRIPTION
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28
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29 Represents a location on a genetic map, yac map, radition hybrid map,
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30 etc.
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31
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32 =head1 METHODS
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33
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34 =cut
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35
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36
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37 package Bio::EnsEMBL::Map::MapLocation;
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38
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39 use strict;
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40 use vars qw(@ISA);
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41
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42 use Bio::EnsEMBL::Utils::Exception qw(deprecate);
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43
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44 =head2 new
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45
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46 Arg [1] : (optional) string $name
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47 Arg [2] : (optional) string $map_name
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48 Arg [3] : (optional) string $chromosome_name
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49 Arg [4] : (optional) string $position
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50 Arg [5] : (optional) float $lod_score
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51 Example : $map_location = Bio::EnsEMBL::Map::MapLocation('DS1234',
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52 'genethon',
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53 'X',
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54 '12.39',
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55 50.12);
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56 Description: Creates a new MapLocation
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57 Returntype : Bio::EnsEMBL::Map::MapLocation
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58 Exceptions : none
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59 Caller : general
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60 Status : stable
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61
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62 =cut
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63
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64 sub new {
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65 my ($caller, $name, $map_name, $chromosome_name, $position, $lod_score) = @_;
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66
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67 my $class = ref($caller) || $caller;
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68
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69 return bless( {'map_name' => $map_name,
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70 'name' => $name,
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71 'chromosome_name' => $chromosome_name,
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72 'position' => $position,
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73 'lod_score' => $lod_score}, $class );
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74 }
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75
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76
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77
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78 =head2 map_name
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79
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80 Arg [1] : string $map_name
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81 Example : $map_name = $map_location->map_name;
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82 Description: Getter/Setter for the map name
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83 Returntype : string
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84 Exceptions : none
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85 Caller : general
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86 Status : stable
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87
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88 =cut
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89
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90 sub map_name {
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91 my $self = shift;
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92 $self->{'map_name'} = shift if(@_);
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93 return $self->{'map_name'};
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94 }
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95
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96
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97
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98 =head2 name
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99
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100 Arg [1] : (optional) string $name
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101 Example : $name = $map_location->name;
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102 Description: A name associated with the marker at this position. For
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103 example if this is a genethon map location the name will be
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104 the synonym of source genethon.
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105 Returntype : string
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106 Exceptions : none
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107 Caller : general
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108 Status : stable
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109
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110 =cut
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111
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112 sub name {
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113 my $self = shift;
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114 $self->{'name'} = shift if(@_);
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115 return $self->{'name'};
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116 }
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117
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118
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119 =head2 chromosome_name
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120
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121 Arg [1] : (optional) string $chromosome_name
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122 Example : $chr_name = $map_location->chromosome_name;
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123 $map_location->chromosome_name('X');
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124 Description: The name of the chromosome associated with this map location
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125 Returntype : string
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126 Exceptions : none
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127 Caller : general
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128 Status : stable
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129
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130 =cut
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131
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132 sub chromosome_name{
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133 my $self = shift;
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134 $self->{'chromosome_name'} = shift if(@_);
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135 return $self->{'chromosome_name'};
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136 }
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137
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138
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139
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140 =head2 position
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141
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142 Arg [1] : (optional) string $position
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143 Example : $pos = $map_location->position;
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144 Description: Getter/Setter for the position of this map location
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145 Returntype : string
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146 Exceptions : none
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147 Caller : general
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148 Status : stable
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149
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150 =cut
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151
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152 sub position {
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153 my $self = shift;
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154 $self->{'position'} = shift if(@_);
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155 return $self->{'position'};
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156 }
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157
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158
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159
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160 =head2 lod_score
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161
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162 Arg [1] : (optional) float $lod
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163 Example : $lod = $map_location->lod_score;
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164 Description: Getter/Setter for lod score of this map location
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165 Returntype : float
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166 Exceptions : none
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167 Caller : general
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168 Status : stable
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169
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170 =cut
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171
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172 sub lod_score {
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173 my $self = shift;
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174 $self->{'lod_score'} = shift if(@_);
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175 return $self->{'lod_score'};
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176 }
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177
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178
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179
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180 =head2 chromosome
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181
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182 Description: DEPRECATED use chromosome_name() instead
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183
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184 =cut
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185
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186 sub chromosome {
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187 my $self = shift;
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188 deprecate('use chromosome_name instead');
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189
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190 if(@_) {
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191 my $chr = shift;
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192 if(ref($chr)) {
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193 $self->chromosome_name($chr->seq_region_name());
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194 } else {
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195 $self->chromosome_name($chr);
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196 }
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197 }
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198
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199 #this object has no way to talk to db and thus no way to
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200 #get a chromosome object
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201 return $self->chromosome_name();
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202 }
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203
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204
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205
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206
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207 1;
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