branch-1-6/Bio/Map/RelativeI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Map::RelativeI
   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 Sendu Bala
  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::RelativeI - Interface for describing what a Position's coordiantes are
  18                       relative to.
  19
  20 =head1 SYNOPSIS
  21
  22     # do not use this module directly
  23     # See Bio::Map::Relative for an example of
  24     # implementation.
  25
  26 =head1 DESCRIPTION
  27
  28 A Relative object is used to describe what the co-ordinates (numerical(),
  29 start(), end()) of a Position are relative to. By default they are
  30 implicitly assumed to be relative to the start of the map the Position is on.
  31 But setting the relative() of a Position to one of these objects lets us
  32 define otherwise.
  33
  34 =head1 FEEDBACK
  35
  36 =head2 Mailing Lists
  37
  38 User feedback is an integral part of the evolution of this and other
  39 Bioperl modules. Send your comments and suggestions preferably to
  40 the Bioperl mailing list.  Your participation is much appreciated.
  41
  42   bioperl-l@bioperl.org                  - General discussion
  43   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  44
  45 =head2 Support
  46
  47 Please direct usage questions or support issues to the mailing list:
  48
  49 I<bioperl-l@bioperl.org>
  50
  51 rather than to the module maintainer directly. Many experienced and
  52 reponsive experts will be able look at the problem and quickly
  53 address it. Please include a thorough description of the problem
  54 with code and data examples if at all possible.
  55
  56 =head2 Reporting Bugs
  57
  58 Report bugs to the Bioperl bug tracking system to help us keep track
  59 of the bugs and their resolution. Bug reports can be submitted via the
  60 web:
  61
  62   http://bugzilla.open-bio.org/
  63
  64 =head1 AUTHOR - Sendu Bala
  65
  66 Email bix@sendu.me.uk
  67
  68 =head1 APPENDIX
  69
  70 The rest of the documentation details each of the object methods.
  71 Internal methods are usually preceded with a _
  72
  73 =cut
  74
  75 # Let the code begin...
  76
  77 package Bio::Map::RelativeI;
  78 use strict;
  79
  80 use base qw(Bio::Root::RootI);
  81
  82 =head2 absolute_conversion
  83
  84  Title   : absolute_conversion
  85  Usage   : my $absolute_coord = $relative->absolute_conversion($pos);
  86  Function: Convert the start co-ordinate of the supplied position into a number
  87            relative to the start of its map.
  88  Returns : scalar number
  89  Args    : Bio::Map::PositionI object
  90
  91 =cut
  92
  93 sub absolute_conversion {
  94     my $self = shift;
  95     $self->throw_not_implemented();
  96 }
  97
  98 =head2 type
  99
 100  Title   : type
 101  Usage   : my $type = $relative->type();
 102  Function: Get the type of thing we are relative to. The types correspond
 103            to a method name, so the value of what we are relative to can
 104            subsequently be found by $value = $relative->$type;
 105
 106            Note that type is set by the last method that was set, or during
 107            new().
 108
 109  Returns : the string 'map', 'element' or 'position', or undef
 110  Args    : none
 111
 112 =cut
 113
 114 sub type {
 115     my $self = shift;
 116     $self->throw_not_implemented();
 117 }
 118
 119 =head2 map
 120
 121  Title   : map
 122  Usage   : my $int = $relative->map();
 123            $relative->map($int);
 124  Function: Get/set the distance from the start of the map that the Position's
 125            co-ordiantes are relative to.
 126  Returns : int
 127  Args    : none to get, OR
 128            int to set; a value of 0 means relative to the start of the map.
 129
 130 =cut
 131
 132 sub map {
 133     my $self = shift;
 134     $self->throw_not_implemented();
 135 }
 136
 137 =head2 element
 138
 139  Title   : element
 140  Usage   : my $element = $relative->element();
 141            $relative->element($element);
 142  Function: Get/set the map element (Mappable) the Position is relative to. If
 143            the Mappable has more than one Position on the Position's map, we
 144            will be relative to the Mappable's first Position on the map.
 145  Returns : Bio::Map::MappableI
 146  Args    : none got get, OR
 147            Bio::Map::MappableI to set
 148
 149 =cut
 150
 151 sub element {
 152     my $self = shift;
 153     $self->throw_not_implemented();
 154 }
 155
 156 =head2 position
 157
 158  Title   : position
 159  Usage   : my $position = $relative->position();
 160            $relative->position($position);
 161  Function: Get/set the Position your Position is relative to. Your Position
 162            will be made relative to the start of this supplied Position. It
 163            makes no difference what maps the Positions are on.
 164  Returns : Bio::Map::PositionI
 165  Args    : none got get, OR
 166            Bio::Map::PositionI to set
 167
 168 =cut
 169
 170 sub position {
 171     my $self = shift;
 172     $self->throw_not_implemented();
 173 }
 174
 175 =head2 description
 176
 177  Title   : description
 178  Usage   : my $description = $relative->description();
 179            $relative->description($description);
 180  Function: Get/set a textual description of what this relative describes.
 181  Returns : string
 182  Args    : none to get, OR
 183            string to set
 184
 185 =cut
 186
 187 sub description {
 188     my $self = shift;
 189     $self->throw_not_implemented();
 190 }
 191
 192 1;