Bio/Map/LinkagePosition.pm

   1 # BioPerl module for Bio::Map::LinkagePosition
   2 #
   3 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   4 #
   5 # Cared for by Sendu Bala <bix@sendu.me.uk>
   6 #
   7 # Copyright Chad Matsalla
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed
  16                                 on a Bio::Map::LinkageMap
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Map::Position;
  21     my $position = Bio::Map::LinkagePosition->new(-positions => 1,
  22                                                  -distance => 22.1 );
  23
  24         # can get listing of positions
  25     my @positions = $position->each_position;
  26
  27
  28 =head1 DESCRIPTION
  29
  30 Position for a Bio::Map::MarkerI compliant object that will be
  31 placed on a Bio::Map::LinkageMap. See L<Bio::Map::MarkerI> and
  32 L<Bio::Map::LinkageMap> for details
  33
  34 =head1 FEEDBACK
  35
  36 =head2 Mailing Lists
  37
  38 User feedback is an integral part of the evolution of this and other
  39 Bioperl modules. Send your comments and suggestions preferably to
  40 the Bioperl mailing list.  Your participation is much appreciated.
  41
  42   bioperl-l@bioperl.org                  - General discussion
  43   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  44
  45 =head2 Support
  46
  47 Please direct usage questions or support issues to the mailing list:
  48
  49 I<bioperl-l@bioperl.org>
  50
  51 rather than to the module maintainer directly. Many experienced and
  52 reponsive experts will be able look at the problem and quickly
  53 address it. Please include a thorough description of the problem
  54 with code and data examples if at all possible.
  55
  56 =head2 Reporting Bugs
  57
  58 Report bugs to the Bioperl bug tracking system to help us keep track
  59 of the bugs and their resolution. Bug reports can be submitted via the
  60 web:
  61
  62   https://redmine.open-bio.org/projects/bioperl/
  63
  64 =head1 AUTHOR - Chad Matsalla
  65
  66 Email bioinformatics1@dieselwurks.com
  67
  68 =head1 CONTRIBUTORS
  69
  70 Lincoln Stein, lstein@cshl.org
  71 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
  72 Jason Stajich jason@bioperl.org
  73 Sendu Bala bix@sendu.me.uk
  74
  75 =head1 APPENDIX
  76
  77 The rest of the documentation details each of the object methods.
  78 Internal methods are usually preceded with a _
  79
  80 =cut
  81
  82 # Let the code begin...
  83
  84 package Bio::Map::LinkagePosition;
  85 use strict;
  86
  87
  88 use base qw(Bio::Map::OrderedPosition);
  89
  90 =head2 new
  91
  92  Title   : new
  93  Usage   : my $obj = Bio::Map::LinkagePosition->new(-positions => $position,
  94                                                                    -distance => $distance);
  95  Function: Builds a new Bio::Map::LinkagePosition object
  96  Returns : Bio::Map::LinkagePosition
  97  Args    : -order => the relative order of this marker on a linkage map
  98                -positions => positions on a map
  99
 100 =cut
 101
 102 =head2 Bio::Map::PositionI methods
 103
 104 =cut
 105
 106 =head2 order
 107
 108  Title   : order
 109  Usage   : $o_position->order($order)
 110            my $order = $o_position->order()
 111  Function: get/set the order position of this position in a map
 112  Returns : int
 113  Args    : none to get, int to set
 114
 115 =cut
 116
 117
 118 1;