Bio/Map/RelativeI.pm

   1 #
   2 # BioPerl module for Bio::Map::RelativeI
   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 Sendu Bala
   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::RelativeI - Interface for describing what a Position's coordiantes are
  17                       relative to.
  18
  19 =head1 SYNOPSIS
  20
  21     # do not use this module directly
  22     # See Bio::Map::Relative for an example of
  23     # implementation.
  24
  25 =head1 DESCRIPTION
  26
  27 A Relative object is used to describe what the co-ordinates (numerical(),
  28 start(), end()) of a Position are relative to. By default they are
  29 implicitly assumed to be relative to the start of the map the Position is on.
  30 But setting the relative() of a Position to one of these objects lets us
  31 define otherwise.
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to
  39 the Bioperl mailing list.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org                  - General discussion
  42   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  43
  44 =head2 Support
  45
  46 Please direct usage questions or support issues to the mailing list:
  47
  48 I<bioperl-l@bioperl.org>
  49
  50 rather than to the module maintainer directly. Many experienced and
  51 reponsive experts will be able look at the problem and quickly
  52 address it. Please include a thorough description of the problem
  53 with code and data examples if at all possible.
  54
  55 =head2 Reporting Bugs
  56
  57 Report bugs to the Bioperl bug tracking system to help us keep track
  58 of the bugs and their resolution. Bug reports can be submitted via the
  59 web:
  60
  61   https://redmine.open-bio.org/projects/bioperl/
  62
  63 =head1 AUTHOR - Sendu Bala
  64
  65 Email bix@sendu.me.uk
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74 # Let the code begin...
  75
  76 package Bio::Map::RelativeI;
  77 use strict;
  78
  79 use base qw(Bio::Root::RootI);
  80
  81 =head2 absolute_conversion
  82
  83  Title   : absolute_conversion
  84  Usage   : my $absolute_coord = $relative->absolute_conversion($pos);
  85  Function: Convert the start co-ordinate of the supplied position into a number
  86            relative to the start of its map.
  87  Returns : scalar number
  88  Args    : Bio::Map::PositionI object
  89
  90 =cut
  91
  92 sub absolute_conversion {
  93     my $self = shift;
  94     $self->throw_not_implemented();
  95 }
  96
  97 =head2 type
  98
  99  Title   : type
 100  Usage   : my $type = $relative->type();
 101  Function: Get the type of thing we are relative to. The types correspond
 102            to a method name, so the value of what we are relative to can
 103            subsequently be found by $value = $relative->$type;
 104
 105            Note that type is set by the last method that was set, or during
 106            new().
 107
 108  Returns : the string 'map', 'element' or 'position', or undef
 109  Args    : none
 110
 111 =cut
 112
 113 sub type {
 114     my $self = shift;
 115     $self->throw_not_implemented();
 116 }
 117
 118 =head2 map
 119
 120  Title   : map
 121  Usage   : my $int = $relative->map();
 122            $relative->map($int);
 123  Function: Get/set the distance from the start of the map that the Position's
 124            co-ordiantes are relative to.
 125  Returns : int
 126  Args    : none to get, OR
 127            int to set; a value of 0 means relative to the start of the map.
 128
 129 =cut
 130
 131 sub map {
 132     my $self = shift;
 133     $self->throw_not_implemented();
 134 }
 135
 136 =head2 element
 137
 138  Title   : element
 139  Usage   : my $element = $relative->element();
 140            $relative->element($element);
 141  Function: Get/set the map element (Mappable) the Position is relative to. If
 142            the Mappable has more than one Position on the Position's map, we
 143            will be relative to the Mappable's first Position on the map.
 144  Returns : Bio::Map::MappableI
 145  Args    : none got get, OR
 146            Bio::Map::MappableI to set
 147
 148 =cut
 149
 150 sub element {
 151     my $self = shift;
 152     $self->throw_not_implemented();
 153 }
 154
 155 =head2 position
 156
 157  Title   : position
 158  Usage   : my $position = $relative->position();
 159            $relative->position($position);
 160  Function: Get/set the Position your Position is relative to. Your Position
 161            will be made relative to the start of this supplied Position. It
 162            makes no difference what maps the Positions are on.
 163  Returns : Bio::Map::PositionI
 164  Args    : none got get, OR
 165            Bio::Map::PositionI to set
 166
 167 =cut
 168
 169 sub position {
 170     my $self = shift;
 171     $self->throw_not_implemented();
 172 }
 173
 174 =head2 description
 175
 176  Title   : description
 177  Usage   : my $description = $relative->description();
 178            $relative->description($description);
 179  Function: Get/set a textual description of what this relative describes.
 180  Returns : string
 181  Args    : none to get, OR
 182            string to set
 183
 184 =cut
 185
 186 sub description {
 187     my $self = shift;
 188     $self->throw_not_implemented();
 189 }
 190
 191 1;