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1 # BioPerl module for Bio::Map::LinkagePosition
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2 #
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3 # Cared for by Chad Matsalla <bioinformatics1@dieselwurks.com>
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4 #
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5 # Copyright Chad Matsalla
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed
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14 on a Bio::Map::LinkageMap
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15
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16 =head1 SYNOPSIS
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17
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18 use Bio::Map::Position;
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19 my $position = new Bio::Map::LinkagePosition(-positions => 1,
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20 -distance => 22.1 );
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21
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22 # can get listing of positions
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23 my @positions = $position->each_position;
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24
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25
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26 =head1 DESCRIPTION
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27
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28 Position for a Bio::Map::MarkerI compliant object that will be
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29 placed on a Bio::Map::LinkageMap. See L<Bio::Map::MarkerI> and
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30 L<Bio::Map::LinkageMap> for details
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31
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32 =head1 FEEDBACK
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33
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34 =head2 Mailing Lists
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35
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36 User feedback is an integral part of the evolution of this and other
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37 Bioperl modules. Send your comments and suggestions preferably to
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38 the Bioperl mailing list. Your participation is much appreciated.
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39
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40 bioperl-l@bioperl.org - General discussion
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41 http://bioperl.org/MailList.shtml - About the mailing lists
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42
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43 =head2 Reporting Bugs
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44
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45 Report bugs to the Bioperl bug tracking system to help us keep track
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46 of the bugs and their resolution. Bug reports can be submitted via
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47 email or the web:
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48
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49 bioperl-bugs@bioperl.org
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50 http://bugzilla.bioperl.org/
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51
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52 =head1 AUTHOR - Chad Matsalla
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53
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54 Email bioinformatics1@dieselwurks.com
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55
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56 =head1 CONTRIBUTORS
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57
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58 Lincoln Stein, lstein@cshl.org
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59 Heikki Lehvaslaiho, heikki@ebi.ac.uk
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60 Jason Stajich jason@bioperl.org
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61
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62 =head1 APPENDIX
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63
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64 The rest of the documentation details each of the object methods.
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65 Internal methods are usually preceded with a _
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66
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67 =cut
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68
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69
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70 # Let the code begin...
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71
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72
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73 package Bio::Map::LinkagePosition;
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74 use vars qw(@ISA);
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75 use strict;
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76 require 'dumpvar.pl';
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77
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78 use Bio::Map::OrderedPosition;
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79
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80 @ISA = qw(Bio::Map::OrderedPosition);
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81
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82 =head2 new
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83
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84 Title : new
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85 Usage : my $obj = new Bio::Map::LinkagePosition(-positions => $position,
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86 -distance => $distance );
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87 Function: Builds a new Bio::Map::LinkagePosition object
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88 Returns : Bio::Map::LinkagePosition
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89 Args : -order => the relative order of this marker on a linkage map
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90 -positions => positions on a map
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91 =cut
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92
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93 =head2 Bio::Map::PositionI methods
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94
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95 =cut
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96
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97 =head2 order
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98
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99 Title : order
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100 Usage : $o_position->order($new_position) _or_
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101 $o_position->order()
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102 Function: get/set the order position of this position in a map
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103 Returns :
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104 Args : If $new_position is provided, the current position of this Position
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105 will be set to $new_position.
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106
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107 =cut
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108
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109
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110 1;
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