/usr/share/perl5/Bio/Map/LinkagePosition.pm is in libbio-perl-perl 1.6.924-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 | # BioPerl module for Bio::Map::LinkagePosition
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed
on a Bio::Map::LinkageMap
=head1 SYNOPSIS
use Bio::Map::Position;
my $position = Bio::Map::LinkagePosition->new(-positions => 1,
-distance => 22.1 );
# can get listing of positions
my @positions = $position->each_position;
=head1 DESCRIPTION
Position for a Bio::Map::MarkerI compliant object that will be
placed on a Bio::Map::LinkageMap. See L<Bio::Map::MarkerI> and
L<Bio::Map::LinkageMap> for details
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Chad Matsalla
Email bioinformatics1@dieselwurks.com
=head1 CONTRIBUTORS
Lincoln Stein, lstein@cshl.org
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
Jason Stajich jason@bioperl.org
Sendu Bala bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Map::LinkagePosition;
use strict;
use base qw(Bio::Map::OrderedPosition);
=head2 new
Title : new
Usage : my $obj = Bio::Map::LinkagePosition->new(-positions => $position,
-distance => $distance);
Function: Builds a new Bio::Map::LinkagePosition object
Returns : Bio::Map::LinkagePosition
Args : -order => the relative order of this marker on a linkage map
-positions => positions on a map
=cut
=head2 Bio::Map::PositionI methods
=cut
=head2 order
Title : order
Usage : $o_position->order($order)
my $order = $o_position->order()
Function: get/set the order position of this position in a map
Returns : int
Args : none to get, int to set
=cut
1;
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