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1 # $Id: Position.pm,v 1.9 2002/10/22 07:45:16 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Map::Position
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Map::Position - A single position of a Marker in a Map
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Map::Position;
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20 my $position = new Bio::Map::Position(-map => $map,
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21 -marker => $marker
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22 -value => 100
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23 );
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24
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25 =head1 DESCRIPTION
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26
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27 This object is an implementation of the PositionI interface that
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28 handles the specific values of a position. This allows an element
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29 (e.g. Marker) to have multiple positions within a map and still be
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30 treated as a single entity.
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31
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32 This does not directly handle the concept of a relative map in which
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33 no known exact positions exist but markers are just ordered relative
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34 to one another - in that case arbitrary values must be assigned for
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35 position values.
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36
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37 No units are assumed here - units are handled by context of which Map
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38 a position is placed in or the subclass of this Position.
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39
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40 =head1 FEEDBACK
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41
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42 =head2 Mailing Lists
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43
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44 User feedback is an integral part of the evolution of this and other
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45 Bioperl modules. Send your comments and suggestions preferably to
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46 the Bioperl mailing list. Your participation is much appreciated.
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47
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48 bioperl-l@bioperl.org - General discussion
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49 http://bioperl.org/MailList.shtml - About the mailing lists
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50
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51 =head2 Reporting Bugs
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52
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53 Report bugs to the Bioperl bug tracking system to help us keep track
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54 of the bugs and their resolution. Bug reports can be submitted via
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55 email or the web:
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56
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57 bioperl-bugs@bioperl.org
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58 http://bugzilla.bioperl.org/
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59
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60 =head1 AUTHOR - Jason Stajich
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61
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62 Email jason@bioperl.org
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63
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64 Describe contact details here
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65
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66 =head1 CONTRIBUTORS
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67
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68 Lincoln Stein, lstein@cshl.org
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69 Heikki Lehvaslaiho, heikki@ebi.ac.uk
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70 Chad Matsalla, bioinformatics1@dieselwurks.com
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71
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72 =head1 APPENDIX
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73
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74 The rest of the documentation details each of the object methods.
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75 Internal methods are usually preceded with a _
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76
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77 =cut
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78
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79
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80 # Let the code begin...
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81
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82
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83 package Bio::Map::Position;
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84 use vars qw(@ISA);
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85 use strict;
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86
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87 # Object preamble - inherits from Bio::Root::Root
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88
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89 use Bio::Root::Root;
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90 use Bio::Map::PositionI;
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91
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92 @ISA = qw(Bio::Root::Root Bio::Map::PositionI );
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93
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94 =head2 new
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95
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96 Title : new
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97 Usage : my $obj = new Bio::Map::Position();
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98 Function: Builds a new Bio::Map::Position object
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99 Returns : Bio::Map::Position
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100 Args : -map a <Bio::Map::MapI> object
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101 -marker a <Bio::Map::MarkerI> object
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102 -value string or number
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103
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104 =cut
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105
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106 sub new {
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107 my($class,@args) = @_;
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108 my $self = $class->SUPER::new(@args);
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109
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110 my ($map, $marker, $value) =
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111 $self->_rearrange([qw( MAP
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112 MARKER
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113 VALUE
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114 )], @args);
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115
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116 $map && $self->map($map);
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117 $marker && $self->marker($marker);
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118 $value && $self->value($value);
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119
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120 return $self;
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121 }
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122
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123 =head2 map
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124
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125 Title : map
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126 Usage : my $id = map->$map;
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127 Function: Get/Set the map the position is in.
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128 Returns : L<Bio::Map::MapI>
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129 Args : [optional] new L<Bio::Map::MapI>
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130
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131 =cut
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132
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133 sub map {
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134 my ($self,$map) = @_;
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135 if( defined $map ) {
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136 $self->throw("This is [$map], not a Bio::Map::MapI object")
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137 unless $map->isa('Bio::Map::MapI');
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138 $self->{'_map'} = $map;
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139 }
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140 return $self->{'_map'};
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141 }
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142
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143 =head2 marker
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144
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145 Title : marker
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146 Usage : my $id = marker->$marker;
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147 Function: Get/Set the marker the position is in.
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148 Returns : L<Bio::Map::MarkerI>
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149 Args : [optional] new L<Bio::Map::MarkerI>
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150
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151 =cut
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152
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153 sub marker {
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154 my ($self,$marker) = @_;
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155 if( defined $marker ) {
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156 $self->thow("This is [$marker], not a Bio::Map::MarkerI object")
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157 unless $marker->isa('Bio::Map::MarkerI');
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158 $self->{'_marker'} = $marker;
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159 }
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160 return $self->{'_marker'};
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161 }
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162
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163 =head2 value
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164
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165 Title : value
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166 Usage : my $pos = $position->value;
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167 Function: Get/Set the value for this postion
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168 Returns : scalar, value
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169 Args : [optional] new value to set
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170
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171 =cut
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172
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173 sub value {
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174 my ($self,$value) = @_;
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175 if( defined $value ) {
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176 $self->{'_value'} = $value;
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177 }
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178 return $self->{'_value'};
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179 }
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180
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181 =head2 numeric
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182
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183 Title : numeric
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184 Usage : my $num = $position->numeric;
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185 Function: Read-only method that is guarantied to return a numeric
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186 representation for this position.
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187 Returns : numeric (int or real)
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188 Args : none
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189
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190 =cut
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191
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192 sub numeric {
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193 my ($self) = @_;
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194 my $num = $self->{'_value'} || 0;
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195
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196 # expand this to cover scientific notation, too!
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197 $self->throw("This value [$num] is not numeric!")
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198 unless $num && $num =~ /^[+-]?[\d.]+$/;
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199 return $num;
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200 }
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201
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202 1;
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