1 # BioPerl module for Bio::Map::LinkagePosition
3 # Please direct questions and support issues to <bioperl-l@bioperl.org>
5 # Cared for by Sendu Bala <bix@sendu.me.uk>
7 # Copyright Chad Matsalla
9 # You may distribute this module under the same terms as perl itself
11 # POD documentation - main docs before the code
15 Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed
16 on a Bio::Map::LinkageMap
20 use Bio::Map::Position;
21 my $position = Bio::Map::LinkagePosition->new(-positions => 1,
24 # can get listing of positions
25 my @positions = $position->each_position;
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
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.
42 bioperl-l@bioperl.org - General discussion
43 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
47 Please direct usage questions or support issues to the mailing list:
49 I<bioperl-l@bioperl.org>
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.
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
62 https://github.com/bioperl/bioperl-live/issues
64 =head1 AUTHOR - Chad Matsalla
66 Email bioinformatics1@dieselwurks.com
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
77 The rest of the documentation details each of the object methods.
78 Internal methods are usually preceded with a _
82 # Let the code begin...
84 package Bio
::Map
::LinkagePosition
;
88 use base
qw(Bio::Map::OrderedPosition);
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
102 =head2 Bio::Map::PositionI methods
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
113 Args : none to get, int to set