Bio/Map/MarkerI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Map::MarkerI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Sendu Bala <bix@sendu.me.uk>
   8 #
   9 # Copyright Jason Stajich
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Map::MarkerI - Interface for basic marker functionality
  18
  19 =head1 SYNOPSIS
  20
  21     # do not use this module directly
  22     # See Bio::Map::Marker for an example of
  23     # implementation.
  24
  25 =head1 DESCRIPTION
  26
  27 A Marker is a Bio::Map::Mappable with some properties particular to markers.
  28 It also offers a number of convienience methods to make dealing with map
  29 elements easier.
  30
  31 =head1 FEEDBACK
  32
  33 =head2 Mailing Lists
  34
  35 User feedback is an integral part of the evolution of this and other
  36 Bioperl modules. Send your comments and suggestions preferably to
  37 the Bioperl mailing list.  Your participation is much appreciated.
  38
  39   bioperl-l@bioperl.org                  - General discussion
  40   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  41
  42 =head2 Support
  43
  44 Please direct usage questions or support issues to the mailing list:
  45
  46 L<bioperl-l@bioperl.org>
  47
  48 rather than to the module maintainer directly. Many experienced and
  49 reponsive experts will be able look at the problem and quickly
  50 address it. Please include a thorough description of the problem
  51 with code and data examples if at all possible.
  52
  53 =head2 Reporting Bugs
  54
  55 Report bugs to the Bioperl bug tracking system to help us keep track
  56 of the bugs and their resolution. Bug reports can be submitted via the
  57 web:
  58
  59   http://bugzilla.open-bio.org/
  60
  61 =head1 AUTHOR - Jason Stajich
  62
  63 Email jason@bioperl.org
  64
  65 =head1 CONTRIBUTORS
  66
  67 Heikki Lehvaslaiho heikki-at-bioperl-dot-org
  68 Lincoln Stein      lstein@cshl.org
  69 Jason Stajich      jason@bioperl.org
  70 Chad Matsalla      bioinformatics1@dieselwurks.com
  71 Sendu Bala         bix@sendu.me.uk
  72
  73 =head1 APPENDIX
  74
  75 The rest of the documentation details each of the object methods.
  76 Internal methods are usually preceded with a _
  77
  78 =cut
  79
  80 package Bio::Map::MarkerI;
  81 use strict;
  82
  83 use base qw(Bio::Map::MappableI);
  84
  85 =head2 get_position_object
  86
  87  Title   : get_position_class
  88  Usage   : my $position = $marker->get_position_object();
  89  Function: To get an object of the default Position class
  90            for this Marker. Subclasses should redefine this method.
  91            The Position returned needs to be a L<Bio::Map::PositionI> with
  92                    -element set to self.
  93  Returns : L<Bio::Map::PositionI>
  94  Args    : none for an 'empty' PositionI object, optionally
  95            Bio::Map::MapI and value string to set the Position's -map and -value
  96            attributes.
  97
  98 =cut
  99
 100 sub get_position_object {
 101     my $self = shift;
 102     $self->throw_not_implemented();
 103 }
 104
 105 =head2 position
 106
 107  Title   : position
 108  Usage   : my $position = $mappable->position();
 109                    $mappable->position($position);
 110  Function: Get/Set the Position of this Marker (where it is on which map),
 111            purging all other positions before setting.
 112  Returns : L<Bio::Map::PositionI>
 113  Args    : Bio::Map::PositionI
 114             OR
 115            Bio::Map::MapI AND
 116            scalar
 117             OR
 118            scalar, but only if the marker has a default map
 119
 120 =cut
 121
 122 sub position {
 123     my $self = shift;
 124     $self->throw_not_implemented();
 125 }
 126
 127 =head2 positions
 128
 129  Title   : positions
 130  Usage   : $marker->positions([$pos1, $pos2, $pos3]);
 131  Function: Add multiple Bio::Map::PositionI to this marker
 132  Returns : n/a
 133  Args    : array ref of $map/value tuples or array ref of Bio::Map::PositionI
 134
 135 =cut
 136
 137 sub positions {
 138     my $self = shift;
 139     $self->throw_not_implemented();
 140 }
 141
 142 =head2 default_map
 143
 144  Title   : default_map
 145  Usage   : my $map = $marker->default_map();
 146  Function: Get/Set the default map for the marker.
 147  Returns : L<Bio::Map::MapI>
 148  Args    : [optional] new L<Bio::Map::MapI>
 149
 150 =cut
 151
 152 sub default_map {
 153     my $self = shift;
 154     $self->throw_not_implemented();
 155 }
 156
 157 =head2 in_map
 158
 159  Title   : in_map
 160  Usage   : if ( $marker->in_map($map) ) {}
 161  Function: Tests if this marker is found on a specific map
 162  Returns : boolean
 163  Args    : a map unique id OR Bio::Map::MapI
 164
 165 =cut
 166
 167 1;