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1 # BioPerl module for Bio::Map::OrderedPosition
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2 #
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3 # Cared for by Chad Matsalla <bioinformatics1@dieselwurks.com>
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4 #
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5 # Copyright Chad Matsalla
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::Map::OrderedPosition - Abstracts the notion of a member
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14 of an ordered list of markers. Each marker is a certain distance
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15 from the one in the ordered list before it.
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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::OrderedPosition;
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20 # the first marker in the sequence
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21 my $position = new Bio::Map::OrderedPosition(-order => 1,
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22 -positions => [ [ $map, 22.3] ] );
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23 # the second marker in the sequence, 15.6 units from the fist one
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24 my $position2 = new Bio::Map::OrderedPosition(-order => 2,
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25 -positions => [ [ $map, 37.9] ] );
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26 # the third marker in the sequence, coincidental with the second
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27 # marker
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28 my $position3 = new Bio::Map::OrderedPosition(-order => 3,
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29 -posititions => [ [ $map, 37.9]] );
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30
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31 =head1 DESCRIPTION
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32
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33 This object is an implementation of the PositionI interface and the
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34 Position object handles the specific values of a position.
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35 OrderedPosition is intended to be slightly more specific then Position
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36 but only specific enough for a parser from the MarkerIO subsystem to
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37 create and then pass to a client application to bless into the proper
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38 type. For an example of how this is intended to work, see the
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39 Mapmaker.pm.
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40
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41 No units are assumed here - units are handled by context of which Map
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42 a position is placed in.
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43
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44 Se Bio::Map::Position for additional information.
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45
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46 =head1 FEEDBACK
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47
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48 =head2 Mailing Lists
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49
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50 User feedback is an integral part of the evolution of this and other
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51 Bioperl modules. Send your comments and suggestions preferably to
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52 the Bioperl mailing list. Your participation is much appreciated.
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53
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54 bioperl-l@bioperl.org - General discussion
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55 http://bioperl.org/MailList.shtml - About the mailing lists
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56
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57 =head2 Reporting Bugs
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58
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59 Report bugs to the Bioperl bug tracking system to help us keep track
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60 of the bugs and their resolution. Bug reports can be submitted via
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61 email or the web:
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62
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63 bioperl-bugs@bioperl.org
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64 http://bugzilla.bioperl.org/
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65
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66 =head1 AUTHOR - Chad Matsalla
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67
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68 Email bioinformatics1@dieselwurks.com
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69
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70 =head1 CONTRIBUTORS
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71
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72 Lincoln Stein, lstein@cshl.org
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73 Heikki Lehvaslaiho, heikki@ebi.ac.uk
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74 Jason Stajich, jason@bioperl.org
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75
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76 =head1 APPENDIX
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77
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78 The rest of the documentation details each of the object methods.
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79 Internal methods are usually preceded with a _
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80
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81 =cut
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82
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83
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84 # Let the code begin...
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85
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86
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87 package Bio::Map::OrderedPosition;
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88 use vars qw(@ISA);
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89 use strict;
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90
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91 use Bio::Map::Position;
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92
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93 @ISA = qw(Bio::Map::Position);
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94
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95 =head2 new
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96
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97 Title : new
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98 Usage : my $obj = new Bio::Map::OrderedPosition();
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99 Function: Builds a new Bio::Map::OrderedPosition object
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100 Returns : Bio::Map::OrderedPosition
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101 Args : -order - The order of this position
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102
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103 =cut
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104
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105 sub new {
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106 my($class,@args) = @_;
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107 my $self = $class->SUPER::new(@args);
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108 # $self->{'_order'} = [];
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109
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110 my ($map, $marker, $value, $order) =
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111 $self->_rearrange([qw( MAP
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112 MARKER
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113 VALUE
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114 ORDER
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115 )], @args);
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116 # print join ("|-|", ($map, $marker, $value, $order)), "\n";
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117 $map && $self->map($map);
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118 $marker && $self->marker($marker);
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119 $value && $self->value($value);
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120 $order && $self->order($order);
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121
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122 return $self;
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123 }
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124
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125 =head2 order
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126
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127 Title : order
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128 Usage : $o_position->order($new_position) _or_
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129 $o_position->order()
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130 Function: get/set the order position of this position in a map
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131 Returns :
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132 Args : If $new_position is provided, the current position of this Position
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133 will be set to $new_position.
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134
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135 =cut
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136
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137 sub order {
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138 my ($self,$order) = @_;
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139 if ($order) {
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140 # no point in keeping the old ones
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141 $self->{'_order'} = $order;
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142 }
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143 return $self->{'_order'};
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144 }
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145
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146 =head2 Bio::Map::Position functions
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147
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148 =cut
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149
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150 =head2 known_maps
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151
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152 Title : known_maps
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153 Usage : my @maps = $position->known_maps
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154 Function: Returns the list of maps that this position has values for
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155 Returns : list of Bio::Map::MapI unique ids
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156 Args : none
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157
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158 =head2 in_map
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159
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160 Title : in_map
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161 Usage : if ( $position->in_map($map) ) {}
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162 Function: Tests if a position has values in a specific map
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163 Returns : boolean
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164 Args : a map unique id OR Bio::Map::MapI
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165
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166 =head2 each_position_value
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167
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168 Title : positions
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169 Usage : my @positions = $position->each_position_value($map);
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170 Function: Retrieve a list of positions coded as strings or ints
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171 Returns : Array of position values for a Map
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172 Args : Bio::Map::MapI object to get positions for
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173
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174 =head2 add_position_value
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175
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176 Title : add_position_value
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177 Usage : $position->add_position_value($map,'100');
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178 Function: Add a numeric or string position to the PositionI container
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179 and assoiciate it with a Bio::Map::MapI
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180 Returns : none
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181 Args : $map - Bio::Map::MapI
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182 String or Numeric coding for a position on a map
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183
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184 =head2 purge_position_values
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185
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186 Title : purge_position_values
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187 Usage : $position->purge_position_values
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188 Function: Remove all the position values stored for a position
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189 Returns : none
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190 Args : [optional] only purge values for a given map
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191
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192 =head2 equals
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193
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194 Title : equals
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195 Usage : if( $mappable->equals($mapable2)) ...
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196 Function: Test if a position is equal to another position.
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197 Returns : boolean
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198 Args : Bio::Map::PositionI
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199
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200 =cut
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201
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202 sub equals{
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203 my ($self,$compare) = @_;
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204 return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
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205 return ( $compare->order == $self->order);
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206 }
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207
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208 # admittedly these are really the best comparisons in the world
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209 # but it is a first pass we'll need to refine the algorithm or not
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210 # provide general comparisions and require these to be implemented
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211 # by objects closer to the specific type of data
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212
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213 =head2 less_than
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214
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215 Title : less_than
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216 Usage : if( $mappable->less_than($m2) ) ...
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217 Function: Tests if a position is less than another position
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218 It is assumed that 2 positions are in the same map.
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219 Returns : boolean
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220 Args : Bio::Map::PositionI
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221
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222 =cut
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223
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224
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225 sub less_than{
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226 my ($self,$compare) = @_;
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227 return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
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228 return ( $compare->order < $self->order);
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229 }
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230
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231 =head2 greater_than
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232
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233 Title : greater_than
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234 Usage : if( $mappable->greater_than($m2) ) ...
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235 Function: Tests if position is greater than another position.
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236 It is assumed that 2 positions are in the same map.
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237 Returns : boolean
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238 Args : Bio::Map::PositionI
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239
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240 =cut
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241
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242 sub greater_than{
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243 my ($self,$compare) = @_;
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244 return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
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245 return ( $compare->order > $self->order);
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246 }
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247
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248 1;
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