Bio/Map/LinkagePosition.pm

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