File Coverage

Bio/Align/StatisticsI.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::Align::StatisticsI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Jason Stajich
7             #
8             # Copyright Jason Stajich
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::Align::StatisticsI - Calculate some statistics for an alignment
17              
18             =head1 SYNOPSIS
19              
20             Give standard usage here
21              
22             =head1 DESCRIPTION
23              
24             Describe the interface here
25              
26             =head1 FEEDBACK
27              
28             =head2 Mailing Lists
29              
30             User feedback is an integral part of the evolution of this and other
31             Bioperl modules. Send your comments and suggestions preferably to
32             the Bioperl mailing list. Your participation is much appreciated.
33              
34             bioperl-l@bioperl.org - General discussion
35             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
36              
37             =head2 Support
38              
39             Please direct usage questions or support issues to the mailing list:
40              
41             I
42              
43             rather than to the module maintainer directly. Many experienced and
44             reponsive experts will be able look at the problem and quickly
45             address it. Please include a thorough description of the problem
46             with code and data examples if at all possible.
47              
48             =head2 Reporting Bugs
49              
50             Report bugs to the Bioperl bug tracking system to help us keep track
51             of the bugs and their resolution. Bug reports can be submitted via the
52             web:
53              
54             https://github.com/bioperl/bioperl-live/issues
55              
56             =head1 AUTHOR - Jason Stajich
57              
58             Email jason@bioperl.org
59              
60             =head1 APPENDIX
61              
62             The rest of the documentation details each of the object methods.
63             Internal methods are usually preceded with a _
64              
65             =cut
66              
67              
68             # Let the code begin...
69              
70              
71             package Bio::Align::StatisticsI;
72 4     4   26 use strict;
  4         9  
  4         109  
73              
74              
75 4     4   17 use base qw(Bio::Root::RootI);
  4         6  
  4         410  
76              
77             =head2 distance
78              
79             Title : distance
80             Usage : my $distance_mat = $stats->distance(-align => $aln,
81             -method => $method);
82             Function: Calculates a distance matrix for all pairwise distances of
83             sequences in an alignment.
84             Returns : Array ref
85             Args : -align => Bio::Align::AlignI object
86             -method => String specifying specific distance method
87             (implementing class may assume a default)
88              
89             =cut
90              
91             sub distance{
92 0     0 1   my ($self,@args) = @_;
93 0           $self->throw_not_implemented();
94             }
95              
96             =head2 available_distance_methods
97              
98             Title : available_distance_methods
99             Usage : my @methods = $stats->available_distance_methods();
100             Function: Enumerates the possible distance methods
101             Returns : Array of strings
102             Args : none
103              
104              
105             =cut
106              
107             sub available_distance_methods{
108 0     0 1   my ($self,@args) = @_;
109 0           $self->throw_not_implemented();
110             }
111              
112             1;