File Coverage

Bio/Location/CoordinatePolicyI.pm
Criterion Covered Total %
statement 6 10 60.0
branch n/a
condition n/a
subroutine 2 4 50.0
pod 2 2 100.0
total 10 16 62.5


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Location::CoordinatePolicyI
3             # Please direct questions and support issues to
4             #
5             # Cared for by Hilmar Lapp
6             # and Jason Stajich
7             #
8             # Copyright Hilmar Lapp, Jason Stajich
9             #
10             # You may distribute this module under the same terms as perl itself
11             # POD documentation - main docs before the code
12              
13             =head1 NAME
14              
15             Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing
16             a certain policy of computing integer-valued coordinates of a Location
17              
18             =head1 SYNOPSIS
19              
20             # get a location, e.g., from a SeqFeature
21             $location = $feature->location();
22             # examine its coordinate computation policy
23             print "Location of feature ", $feature->primary_tag(), " employs a ",
24             ref($location->coordinate_policy()),
25             " instance for coordinate computation\n";
26             # change the policy, e.g. because the user chose to do so
27             $location->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
28              
29             =head1 DESCRIPTION
30              
31             Objects implementing this interface are used by Bio::LocationI
32             implementing objects to determine integer-valued coordinates when
33             asked for it. While this may seem trivial for simple locations, there
34             are different ways to do it for fuzzy or compound (split)
35             locations. Classes implementing this interface implement a certain
36             policy, like 'always widest range', 'always smallest range', 'mean for
37             BETWEEN locations', etc. By installing a different policy object in a
38             Location object, the behaviour of coordinate computation can be changed
39             on-the-fly, and with a single line of code client-side.
40              
41             =head1 FEEDBACK
42              
43             User feedback is an integral part of the evolution of this and other
44             Bioperl modules. Send your comments and suggestions preferably to one
45             of the Bioperl mailing lists. Your participation is much appreciated.
46              
47             bioperl-l@bioperl.org - General discussion
48             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
49              
50             =head2 Support
51              
52             Please direct usage questions or support issues to the mailing list:
53              
54             I
55              
56             rather than to the module maintainer directly. Many experienced and
57             reponsive experts will be able look at the problem and quickly
58             address it. Please include a thorough description of the problem
59             with code and data examples if at all possible.
60              
61             =head2 Reporting Bugs
62              
63             Report bugs to the Bioperl bug tracking system to help us keep track
64             the bugs and their resolution. Bug reports can be submitted via the
65             web:
66              
67             https://github.com/bioperl/bioperl-live/issues
68              
69             =head1 AUTHOR - Hilmar Lapp, Jason Stajich
70              
71             Email hlapp@gmx.net, jason@bioperl.org
72              
73             =head1 APPENDIX
74              
75             The rest of the documentation details each of the object
76             methods. Internal methods are usually preceded with a _
77              
78             =cut
79              
80             # Let the code begin...
81              
82              
83             package Bio::Location::CoordinatePolicyI;
84 192     192   949 use strict;
  192         221  
  192         5025  
85              
86 192     192   749 use base qw(Bio::Root::RootI);
  192         195  
  192         19832  
87              
88             =head2 start
89              
90             Title : start
91             Usage : $start = $policy->start($location);
92             Function: Get the integer-valued start coordinate of the given location as
93             computed by this computation policy.
94             Returns : A positive integer number.
95             Args : A Bio::LocationI implementing object.
96              
97             =cut
98              
99             sub start {
100 0     0 1   my ($self) = @_;
101 0           $self->throw_not_implemented();
102             }
103              
104             =head2 end
105              
106             Title : end
107             Usage : $end = $policy->end($location);
108             Function: Get the integer-valued end coordinate of the given location as
109             computed by this computation policy.
110             Returns : A positive integer number.
111             Args : A Bio::LocationI implementing object.
112              
113             =cut
114              
115             sub end {
116 0     0 1   my ($self) = @_;
117 0           $self->throw_not_implemented();
118             }
119              
120             1;