Bio/Map/MarkerI.pm

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