File Coverage

Bio/Map/LinkagePosition.pm
Criterion Covered Total %
statement 6 6 100.0
branch n/a
condition n/a
subroutine 2 2 100.0
pod n/a
total 8 8 100.0


line stmt bran cond sub pod time code
1             # BioPerl module for Bio::Map::LinkagePosition
2             #
3             # Please direct questions and support issues to
4             #
5             # Cared for by Sendu Bala
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 and
32             L 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
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://github.com/bioperl/bioperl-live/issues
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 2     2   430 use strict;
  2         3  
  2         50  
86              
87              
88 2     2   7 use base qw(Bio::Map::OrderedPosition);
  2         2  
  2         559  
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;