File Coverage

Bio/Location/NarrowestCoordPolicy.pm
Criterion Covered Total %
statement 17 17 100.0
branch 2 4 50.0
condition n/a
subroutine 5 5 100.0
pod 3 3 100.0
total 27 29 93.1


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Location::NarrowestCoordPolicy
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Hilmar Lapp
7             # and Jason Stajich
8             #
9             # Copyright Hilmar Lapp, Jason Stajich
10             #
11             # You may distribute this module under the same terms as perl itself
12             # POD documentation - main docs before the code
13              
14             =head1 NAME
15              
16             Bio::Location::NarrowestCoordPolicy - class implementing
17             Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
18              
19             =head1 SYNOPSIS
20              
21             See Bio::Location::CoordinatePolicyI
22              
23             =head1 DESCRIPTION
24              
25             CoordinatePolicyI implementing objects are used by Bio::LocationI
26             implementing objects to determine integer-valued coordinates when
27             asked for it.
28              
29             This class will compute the coordinates such that always the narrowest possible
30             range is returned, but by using some common sense. This means that e.g.
31             locations like "E5..100" (start before position 5) will return 5 as start
32             (returned values have to be positive integers).
33              
34             =head1 FEEDBACK
35              
36             User feedback is an integral part of the evolution of this and other
37             Bioperl modules. Send your comments and suggestions preferably to one
38             of the Bioperl mailing lists. Your participation is much appreciated.
39              
40             bioperl-l@bioperl.org - General discussion
41             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
42              
43             =head2 Support
44              
45             Please direct usage questions or support issues to the mailing list:
46              
47             I
48              
49             rather than to the module maintainer directly. Many experienced and
50             reponsive experts will be able look at the problem and quickly
51             address it. Please include a thorough description of the problem
52             with code and data examples if at all possible.
53              
54             =head2 Reporting Bugs
55              
56             Report bugs to the Bioperl bug tracking system to help us keep track
57             the bugs and their resolution. Bug reports can be submitted via the
58             web:
59              
60             https://github.com/bioperl/bioperl-live/issues
61              
62             =head1 AUTHOR - Hilmar Lapp, Jason Stajich
63              
64             Email Ehlapp-at-gmx.netE, Ejason@bioperl.orgE
65              
66             =head1 APPENDIX
67              
68             The rest of the documentation details each of the object
69             methods. Internal methods are usually preceded with a _
70              
71             =cut
72              
73             # Let the code begin...
74              
75              
76             package Bio::Location::NarrowestCoordPolicy;
77 1     1   1067 use strict;
  1         1  
  1         28  
78              
79              
80 1     1   3 use base qw(Bio::Root::Root Bio::Location::CoordinatePolicyI);
  1         1  
  1         190  
81              
82             sub new {
83 1     1 1 2 my ($class, @args) = @_;
84 1         6 my $self = $class->SUPER::new(@args);
85              
86 1         3 return $self;
87             }
88              
89              
90             =head2 start
91              
92             Title : start
93             Usage : $start = $policy->start($location);
94             Function: Get the integer-valued start coordinate of the given location as
95             computed by this computation policy.
96             Returns : A positive integer number.
97             Args : A Bio::LocationI implementing object.
98              
99             =cut
100              
101             sub start {
102 3     3 1 1 my ($self,$loc) = @_;
103              
104             # For performance reasons we don't check that it's indeed a Bio::LocationI
105             # object. Hopefully, Location-object programmers are smart enough.
106 3         6 my $pos = $loc->max_start();
107             # if max is not defined or equals 0 we resort to min
108 3 50       5 $pos = $loc->min_start() if(! $pos);
109 3         9 return $pos;
110             }
111              
112             =head2 end
113              
114             Title : end
115             Usage : $end = $policy->end($location);
116             Function: Get the integer-valued end coordinate of the given location as
117             computed by this computation policy.
118             Returns : A positive integer number.
119             Args : A Bio::LocationI implementing object.
120              
121             =cut
122              
123             sub end {
124 3     3 1 3 my ($self,$loc) = @_;
125              
126             # For performance reasons we don't check that it's indeed a Bio::LocationI
127             # object. Hopefully, Location-object programmers are smart enough.
128 3         4 my $pos = $loc->min_end();
129             # if min is not defined or equals 0 we resort to max
130 3 50       6 $pos = $loc->max_end() if(! $pos);
131 3         6 return $pos;
132             }
133              
134             1;
135