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1 | # | ||||
2 | # BioPerl module for Bio::Location::CoordinatePolicyI | ||||
3 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
4 | # | ||||
5 | # Cared for by Hilmar Lapp <hlapp@gmx.net> | ||||
6 | # and Jason Stajich <jason@bioperl.org> | ||||
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<bioperl-l@bioperl.org> | ||||
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 | 2 | 32µs | 2 | 41µs | # spent 28µs (16+13) within Bio::Location::CoordinatePolicyI::BEGIN@84 which was called:
# once (16µs+13µs) by base::import at line 84 # spent 28µs making 1 call to Bio::Location::CoordinatePolicyI::BEGIN@84
# spent 13µs making 1 call to strict::import |
85 | |||||
86 | 2 | 90µs | 2 | 68µs | # spent 68µs (8+60) within Bio::Location::CoordinatePolicyI::BEGIN@86 which was called:
# once (8µs+60µs) by base::import at line 86 # spent 68µs making 1 call to Bio::Location::CoordinatePolicyI::BEGIN@86
# spent 60µs making 1 call to base::import, recursion: max depth 2, sum of overlapping time 60µs |
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 | my ($self) = @_; | ||||
101 | $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 | my ($self) = @_; | ||||
117 | $self->throw_not_implemented(); | ||||
118 | } | ||||
119 | |||||
120 | 1 | 2µs | 1; |