File Coverage

Bio/Map/RelativeI.pm
Criterion Covered Total %
statement 6 18 33.3
branch n/a
condition n/a
subroutine 2 8 25.0
pod 6 6 100.0
total 14 32 43.7


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Map::RelativeI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Sendu Bala
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
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://github.com/bioperl/bioperl-live/issues
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 9     9   43 use strict;
  9         10  
  9         239  
78              
79 9     9   28 use base qw(Bio::Root::RootI);
  9         10  
  9         1507  
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 0     0 1   my $self = shift;
94 0           $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 0     0 1   my $self = shift;
115 0           $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 0     0 1   my $self = shift;
133 0           $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 0     0 1   my $self = shift;
152 0           $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 0     0 1   my $self = shift;
171 0           $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 0     0 1   my $self = shift;
188 0           $self->throw_not_implemented();
189             }
190              
191             1;