Bio/Map/RelativeI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Map::RelativeI
   4 #
   5 # Cared for by Sendu Bala <bix@sendu.me.uk>
   6 #
   7 # Copyright Sendu Bala
   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::RelativeI - Interface for describing what a Position's coordiantes are
  16                       relative to.
  17
  18 =head1 SYNOPSIS
  19
  20     # do not use this module directly
  21     # See Bio::Map::Relative for an example of
  22     # implementation.
  23
  24 =head1 DESCRIPTION
  25
  26 A Relative object is used to describe what the co-ordinates (numerical(),
  27 start(), end()) of a Position are relative to. By default they are
  28 implicitly assumed to be relative to the start of the map the Position is on.
  29 But setting the relative() of a Position to one of these objects lets us
  30 define otherwise.
  31
  32 =head1 FEEDBACK
  33
  34 =head2 Mailing Lists
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to
  38 the Bioperl mailing list.  Your participation is much appreciated.
  39
  40   bioperl-l@bioperl.org                  - General discussion
  41   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  42
  43 =head2 Reporting Bugs
  44
  45 Report bugs to the Bioperl bug tracking system to help us keep track
  46 of the bugs and their resolution. Bug reports can be submitted via the
  47 web:
  48
  49   http://bugzilla.open-bio.org/
  50
  51 =head1 AUTHOR - Sendu Bala
  52
  53 Email bix@sendu.me.uk
  54
  55 =head1 APPENDIX
  56
  57 The rest of the documentation details each of the object methods.
  58 Internal methods are usually preceded with a _
  59
  60 =cut
  61
  62 # Let the code begin...
  63
  64 package Bio::Map::RelativeI;
  65 use strict;
  66
  67 use base qw(Bio::Root::RootI);
  68
  69 =head2 absolute_conversion
  70
  71  Title   : absolute_conversion
  72  Usage   : my $absolute_coord = $relative->absolute_conversion($pos);
  73  Function: Convert the start co-ordinate of the supplied position into a number
  74            relative to the start of its map.
  75  Returns : scalar number
  76  Args    : Bio::Map::PositionI object
  77
  78 =cut
  79
  80 sub absolute_conversion {
  81     my $self = shift;
  82     $self->throw_not_implemented();
  83 }
  84
  85 =head2 type
  86
  87  Title   : type
  88  Usage   : my $type = $relative->type();
  89  Function: Get the type of thing we are relative to. The types correspond
  90            to a method name, so the value of what we are relative to can
  91            subsequently be found by $value = $relative->$type;
  92
  93            Note that type is set by the last method that was set, or during
  94            new().
  95
  96  Returns : the string 'map', 'element' or 'position', or undef
  97  Args    : none
  98
  99 =cut
 100
 101 sub type {
 102     my $self = shift;
 103     $self->throw_not_implemented();
 104 }
 105
 106 =head2 map
 107
 108  Title   : map
 109  Usage   : my $int = $relative->map();
 110            $relative->map($int);
 111  Function: Get/set the distance from the start of the map that the Position's
 112            co-ordiantes are relative to.
 113  Returns : int
 114  Args    : none to get, OR
 115            int to set; a value of 0 means relative to the start of the map.
 116
 117 =cut
 118
 119 sub map {
 120     my $self = shift;
 121     $self->throw_not_implemented();
 122 }
 123
 124 =head2 element
 125
 126  Title   : element
 127  Usage   : my $element = $relative->element();
 128            $relative->element($element);
 129  Function: Get/set the map element (Mappable) the Position is relative to. If
 130            the Mappable has more than one Position on the Position's map, we
 131            will be relative to the Mappable's first Position on the map.
 132  Returns : Bio::Map::MappableI
 133  Args    : none got get, OR
 134            Bio::Map::MappableI to set
 135
 136 =cut
 137
 138 sub element {
 139     my $self = shift;
 140     $self->throw_not_implemented();
 141 }
 142
 143 =head2 position
 144
 145  Title   : position
 146  Usage   : my $position = $relative->position();
 147            $relative->position($position);
 148  Function: Get/set the Position your Position is relative to. Your Position
 149            will be made relative to the start of this supplied Position. It
 150            makes no difference what maps the Positions are on.
 151  Returns : Bio::Map::PositionI
 152  Args    : none got get, OR
 153            Bio::Map::PositionI to set
 154
 155 =cut
 156
 157 sub position {
 158     my $self = shift;
 159     $self->throw_not_implemented();
 160 }
 161
 162 =head2 description
 163
 164  Title   : description
 165  Usage   : my $description = $relative->description();
 166            $relative->description($description);
 167  Function: Get/set a textual description of what this relative describes.
 168  Returns : string
 169  Args    : none to get, OR
 170            string to set
 171
 172 =cut
 173
 174 sub description {
 175     my $self = shift;
 176     $self->throw_not_implemented();
 177 }
 178
 179 1;