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1 # BioPerl module for Bio::Map::OrderedPositionWithDistance
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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::OrderedPositionWithDistance - 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::OrderedPositionWithDistance;
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20 # the first marker in the sequence
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21 my $position = new Bio::Map::OrderedPositionWithDistance(-positions => 1,
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22 -distance => 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::OrderedPositionWithDistance(-positions => 2,
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25 -distance => 15.6 );
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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::OrderedPositionWithDistance(-positions => 3,
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29 -distance => 0 );
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30
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31
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32 =head1 DESCRIPTION
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33
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34 This object is an implementation of the PositionI interface and the
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35 Position object handles the specific values of a position.
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36 OrderedPositionWithDistance is intended to be slightly more specific
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37 then Position but only specific enough for a parser from the MarkerIO
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38 subsystem to create and then pass to a client application to bless into
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39 the proper type. For an example of how this is intended to work, see the
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40 Mapmaker.pm.
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41
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42 No units are assumed here - units are handled by context of which Map
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43 a position is placed in.
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44
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45 Se Bio::Map::Position for additional information.
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46
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47 =head1 FEEDBACK
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48
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49 =head2 Mailing Lists
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50
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51 User feedback is an integral part of the evolution of this and other
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52 Bioperl modules. Send your comments and suggestions preferably to
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53 the Bioperl mailing list. Your participation is much appreciated.
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54
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55 bioperl-l@bioperl.org - General discussion
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56 http://bioperl.org/MailList.shtml - About the mailing lists
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57
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58 =head2 Reporting Bugs
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59
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60 Report bugs to the Bioperl bug tracking system to help us keep track
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61 of the bugs and their resolution. Bug reports can be submitted via
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62 email or the web:
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63
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64 bioperl-bugs@bioperl.org
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65 http://bugzilla.bioperl.org/
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66
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67 =head1 AUTHOR - Chad Matsalla
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68
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69 Email bioinformatics1@dieselwurks.com
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70
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71 =head1 CONTRIBUTORS
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72
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73 Lincoln Stein, lstein@cshl.org
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74 Heikki Lehvaslaiho, heikki@ebi.ac.uk
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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::OrderedPositionWithDistance;
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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::Root::Root;
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92 use Bio::Map::Position;
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93
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94 @ISA = qw(Bio::Map::Position);
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95
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96 =head2 new
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97
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98 Title : new
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99 Usage : my $obj = new Bio::Map::OrderedPositionWithDistance();
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100 Function: Builds a new Bio::Map::OrderedPositionWithDistance object
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101 Returns : Bio::Map::OrderedPositionWithDistance
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102 Args : -positions - Should be a single value representing the order
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103 of this marker within the list of markers
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104 -distance - The distance this marker is from the marker before it.
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105 0 reflects coincidentality.
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106
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107 =cut
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108
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109 sub new {
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110 my($class,@args) = @_;
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111 my $self = $class->SUPER::new(@args);
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112 $self->{'_positions'} = [];
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113 my ($positions,$distance) = $self->_rearrange([qw(POSITIONS DISTANCE)], @args);
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114 if( ref($positions) =~ /array/i ) {
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115 foreach my $p ( @$positions ) {
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116 $self->add_position($p);
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117 }
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118 } else {
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119 $self->add_position($positions);
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120 }
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121 $distance && $self->distance($distance);
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122
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123 return $self;
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124
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125 }
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126
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127
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128 =head2 distance($new_distance)
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129
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130 Title : distance($new_distance)
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131 Usage : $position->distance(new_distance) _or_
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132 $position->distance()
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133 Function: get/set the distance of this position from the previous marker
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134 Returns : A scalar representing the current distance for this position.
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135 Args : If $new_distance is provided the distance of this Position will
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136 be set to $new_distance
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137
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138 =cut
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139
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140 sub distance {
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141 my ($self,$distance) = @_;
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142 if ($distance) {
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143 $self->{'_distance'} = $distance;
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144 }
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145 return $self->{'_distance'};
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146 }
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147
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148
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149 1;
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