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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:45:45 2015

Filename/Users/ap13/perl5/lib/perl5/Bio/Location/CoordinatePolicyI.pm
StatementsExecuted 5 statements in 124µs
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11116µs28µsBio::Location::CoordinatePolicyI::::BEGIN@84Bio::Location::CoordinatePolicyI::BEGIN@84
1118µs68µsBio::Location::CoordinatePolicyI::::BEGIN@86Bio::Location::CoordinatePolicyI::BEGIN@86
0000s0sBio::Location::CoordinatePolicyI::::endBio::Location::CoordinatePolicyI::end
0000s0sBio::Location::CoordinatePolicyI::::startBio::Location::CoordinatePolicyI::start
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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
15Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing
16a 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
31Objects implementing this interface are used by Bio::LocationI
32implementing objects to determine integer-valued coordinates when
33asked for it. While this may seem trivial for simple locations, there
34are different ways to do it for fuzzy or compound (split)
35locations. Classes implementing this interface implement a certain
36policy, like 'always widest range', 'always smallest range', 'mean for
37BETWEEN locations', etc. By installing a different policy object in a
38Location object, the behaviour of coordinate computation can be changed
39on-the-fly, and with a single line of code client-side.
40
41=head1 FEEDBACK
42
43User feedback is an integral part of the evolution of this and other
44Bioperl modules. Send your comments and suggestions preferably to one
45of 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
52Please direct usage questions or support issues to the mailing list:
53
54I<bioperl-l@bioperl.org>
55
56rather than to the module maintainer directly. Many experienced and
57reponsive experts will be able look at the problem and quickly
58address it. Please include a thorough description of the problem
59with code and data examples if at all possible.
60
61=head2 Reporting Bugs
62
63Report bugs to the Bioperl bug tracking system to help us keep track
64the bugs and their resolution. Bug reports can be submitted via the
65web:
66
67 https://github.com/bioperl/bioperl-live/issues
68
69=head1 AUTHOR - Hilmar Lapp, Jason Stajich
70
71Email hlapp@gmx.net, jason@bioperl.org
72
73=head1 APPENDIX
74
75The rest of the documentation details each of the object
76methods. Internal methods are usually preceded with a _
77
78=cut
79
80# Let the code begin...
81
82
83package Bio::Location::CoordinatePolicyI;
84232µs241µs
# spent 28µs (16+13) within Bio::Location::CoordinatePolicyI::BEGIN@84 which was called: # once (16µs+13µs) by base::import at line 84
use strict;
# spent 28µs making 1 call to Bio::Location::CoordinatePolicyI::BEGIN@84 # spent 13µs making 1 call to strict::import
85
86290µs268µs
# spent 68µs (8+60) within Bio::Location::CoordinatePolicyI::BEGIN@86 which was called: # once (8µs+60µs) by base::import at line 86
use base qw(Bio::Root::RootI);
# 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
99sub 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
115sub end {
116 my ($self) = @_;
117 $self->throw_not_implemented();
118}
119
12012µs1;