Bio/Map/MarkerI.pm

   1 #
   2 # BioPerl module for Bio::Map::MarkerI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Sendu Bala <bix@sendu.me.uk>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Map::MarkerI - Interface for basic marker functionality
  17
  18 =head1 SYNOPSIS
  19
  20     # do not use this module directly
  21     # See Bio::Map::Marker for an example of
  22     # implementation.
  23
  24 =head1 DESCRIPTION
  25
  26 A Marker is a Bio::Map::Mappable with some properties particular to markers.
  27 It also offers a number of convienience methods to make dealing with map
  28 elements easier.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this and other
  35 Bioperl modules. Send your comments and suggestions preferably to
  36 the Bioperl mailing list.  Your participation is much appreciated.
  37
  38   bioperl-l@bioperl.org                  - General discussion
  39   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  40
  41 =head2 Support
  42
  43 Please direct usage questions or support issues to the mailing list:
  44
  45 I<bioperl-l@bioperl.org>
  46
  47 rather than to the module maintainer directly. Many experienced and
  48 reponsive experts will be able look at the problem and quickly
  49 address it. Please include a thorough description of the problem
  50 with code and data examples if at all possible.
  51
  52 =head2 Reporting Bugs
  53
  54 Report bugs to the Bioperl bug tracking system to help us keep track
  55 of the bugs and their resolution. Bug reports can be submitted via the
  56 web:
  57
  58   https://github.com/bioperl/bioperl-live/issues
  59
  60 =head1 AUTHOR - Jason Stajich
  61
  62 Email jason@bioperl.org
  63
  64 =head1 CONTRIBUTORS
  65
  66 Heikki Lehvaslaiho heikki-at-bioperl-dot-org
  67 Lincoln Stein      lstein@cshl.org
  68 Jason Stajich      jason@bioperl.org
  69 Chad Matsalla      bioinformatics1@dieselwurks.com
  70 Sendu Bala         bix@sendu.me.uk
  71
  72 =head1 APPENDIX
  73
  74 The rest of the documentation details each of the object methods.
  75 Internal methods are usually preceded with a _
  76
  77 =cut
  78
  79 package Bio::Map::MarkerI;
  80 use strict;
  81
  82 use base qw(Bio::Map::MappableI);
  83
  84 =head2 get_position_object
  85
  86  Title   : get_position_class
  87  Usage   : my $position = $marker->get_position_object();
  88  Function: To get an object of the default Position class
  89            for this Marker. Subclasses should redefine this method.
  90            The Position returned needs to be a L<Bio::Map::PositionI> with
  91                    -element set to self.
  92  Returns : L<Bio::Map::PositionI>
  93  Args    : none for an 'empty' PositionI object, optionally
  94            Bio::Map::MapI and value string to set the Position's -map and -value
  95            attributes.
  96
  97 =cut
  98
  99 sub get_position_object {
 100     my $self = shift;
 101     $self->throw_not_implemented();
 102 }
 103
 104 =head2 position
 105
 106  Title   : position
 107  Usage   : my $position = $mappable->position();
 108                    $mappable->position($position);
 109  Function: Get/Set the Position of this Marker (where it is on which map),
 110            purging all other positions before setting.
 111  Returns : L<Bio::Map::PositionI>
 112  Args    : Bio::Map::PositionI
 113             OR
 114            Bio::Map::MapI AND
 115            scalar
 116             OR
 117            scalar, but only if the marker has a default map
 118
 119 =cut
 120
 121 sub position {
 122     my $self = shift;
 123     $self->throw_not_implemented();
 124 }
 125
 126 =head2 positions
 127
 128  Title   : positions
 129  Usage   : $marker->positions([$pos1, $pos2, $pos3]);
 130  Function: Add multiple Bio::Map::PositionI to this marker
 131  Returns : n/a
 132  Args    : array ref of $map/value tuples or array ref of Bio::Map::PositionI
 133
 134 =cut
 135
 136 sub positions {
 137     my $self = shift;
 138     $self->throw_not_implemented();
 139 }
 140
 141 =head2 default_map
 142
 143  Title   : default_map
 144  Usage   : my $map = $marker->default_map();
 145  Function: Get/Set the default map for the marker.
 146  Returns : L<Bio::Map::MapI>
 147  Args    : [optional] new L<Bio::Map::MapI>
 148
 149 =cut
 150
 151 sub default_map {
 152     my $self = shift;
 153     $self->throw_not_implemented();
 154 }
 155
 156 =head2 in_map
 157
 158  Title   : in_map
 159  Usage   : if ( $marker->in_map($map) ) {}
 160  Function: Tests if this marker is found on a specific map
 161  Returns : boolean
 162  Args    : a map unique id OR Bio::Map::MapI
 163
 164 =cut
 165
 166 1;