lib/Bio/Map/OrderedPositionWithDistance.pm

   1 ### TO BE DELETED ###
   2
   3 # BioPerl module for Bio::Map::OrderedPositionWithDistance
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Chad Matsalla <bioinformatics1@dieselwurks.com>
   8 #
   9 # Copyright Chad Matsalla
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Map::OrderedPositionWithDistance - Abstracts the notion of a member
  18         of an ordered list of markers. Each marker is a certain distance
  19         from the one in the ordered list before it.
  20
  21 =head1 SYNOPSIS
  22
  23     use Bio::Map::OrderedPositionWithDistance;
  24         # the first marker in the sequence
  25     my $position = Bio::Map::OrderedPositionWithDistance->new(-positions => 1,
  26                         -distance => 22.3 );
  27         # the second marker in the sequence, 15.6 units from the fist one
  28     my $position2 = Bio::Map::OrderedPositionWithDistance->new(-positions => 2,
  29                         -distance => 15.6 );
  30         # the third marker in the sequence, coincidental with the second
  31         # marker
  32     my $position3 = Bio::Map::OrderedPositionWithDistance->new(-positions => 3,
  33                         -distance => 0 );
  34
  35
  36 =head1 DESCRIPTION
  37
  38 This object is an implementation of the PositionI interface and the
  39 Position object handles the specific values of a position.
  40 OrderedPositionWithDistance is intended to be slightly more specific
  41 then Position but only specific enough for a parser from the MarkerIO
  42 subsystem to create and then pass to a client application to bless into
  43 the proper type. For an example of how this is intended to work, see the
  44 Mapmaker.pm.
  45
  46 No units are assumed here - units are handled by context of which Map
  47 a position is placed in.
  48
  49 Se Bio::Map::Position for additional information.
  50
  51 =head1 FEEDBACK
  52
  53 =head2 Mailing Lists
  54
  55 User feedback is an integral part of the evolution of this and other
  56 Bioperl modules. Send your comments and suggestions preferably to
  57 the Bioperl mailing list.  Your participation is much appreciated.
  58
  59   bioperl-l@bioperl.org                  - General discussion
  60   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  61
  62 =head2 Support
  63
  64 Please direct usage questions or support issues to the mailing list:
  65
  66 I<bioperl-l@bioperl.org>
  67
  68 rather than to the module maintainer directly. Many experienced and
  69 reponsive experts will be able look at the problem and quickly
  70 address it. Please include a thorough description of the problem
  71 with code and data examples if at all possible.
  72
  73 =head2 Reporting Bugs
  74
  75 Report bugs to the Bioperl bug tracking system to help us keep track
  76 of the bugs and their resolution. Bug reports can be submitted via the
  77 web:
  78
  79   https://github.com/bioperl/bioperl-live/issues
  80
  81 =head1 AUTHOR - Chad Matsalla
  82
  83 Email bioinformatics1@dieselwurks.com
  84
  85 =head1 CONTRIBUTORS
  86
  87 Lincoln Stein, lstein@cshl.org
  88 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
  89
  90 =head1 APPENDIX
  91
  92 The rest of the documentation details each of the object methods.
  93 Internal methods are usually preceded with a _
  94
  95 =cut
  96
  97
  98 # Let the code begin...
  99
 100
 101 package Bio::Map::OrderedPositionWithDistance;
 102 use strict;
 103
 104
 105 use base qw(Bio::Map::Position);
 106
 107 =head2 new
 108
 109  Title   : new
 110  Usage   : my $obj = Bio::Map::OrderedPositionWithDistance->new();
 111  Function: Builds a new Bio::Map::OrderedPositionWithDistance object
 112  Returns : Bio::Map::OrderedPositionWithDistance
 113  Args    : -positions  - Should be a single value representing the order
 114         of this marker within the list of markers
 115         -distance - The distance this marker is from the marker before it.
 116                 0 reflects coincidentality.
 117
 118 =cut
 119
 120 sub new {
 121   my($class,@args) = @_;
 122   my $self = $class->SUPER::new(@args);
 123   $self->{'_positions'} = [];
 124   my ($positions,$distance) = $self->_rearrange([qw(POSITIONS DISTANCE)], @args);
 125   if( ref($positions) =~ /array/i ) {
 126       foreach my $p ( @$positions ) {
 127           $self->add_position($p);
 128       }
 129   } else {
 130       $self->add_position($positions);
 131   }
 132         $distance && $self->distance($distance);
 133
 134   return $self;
 135
 136 }
 137
 138
 139 =head2 distance($new_distance)
 140
 141  Title   : distance($new_distance)
 142  Usage   : $position->distance(new_distance) _or_
 143         $position->distance()
 144  Function: get/set the distance of this position from the previous marker
 145  Returns : A scalar representing the current distance for this position.
 146  Args    : If $new_distance is provided the distance of this Position will
 147         be set to $new_distance
 148
 149 =cut
 150
 151 sub distance {
 152         my ($self,$distance) = @_;
 153         if ($distance) {
 154            $self->{'_distance'} = $distance;
 155         }
 156         return $self->{'_distance'};
 157 }
 158
 159
 160 1;