File Coverage

blib/lib/Bio/MUST/Core.pm
Criterion Covered Total %
statement 54 54 100.0
branch n/a
condition n/a
subroutine 18 18 100.0
pod n/a
total 72 72 100.0


line stmt bran cond sub pod time code
1             package Bio::MUST::Core;
2             # ABSTRACT: Core classes and utilities for Bio::MUST
3             # CONTRIBUTOR: Catherine COLSON <ccolson@doct.uliege.be>
4             # CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
5             # CONTRIBUTOR: Raphael LEONARD <rleonard@doct.uliege.be>
6             # CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>
7             # CONTRIBUTOR: Loic MEUNIER <loic.meunier@doct.uliege.be>
8             # CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
9             $Bio::MUST::Core::VERSION = '0.212530';
10 17     17   3703586 use strict;
  17         188  
  17         537  
11 17     17   96 use warnings;
  17         47  
  17         479  
12              
13 17     17   8154 use Bio::MUST::Core::Types;
  17         60  
  17         750  
14 17     17   20275 use Bio::MUST::Core::SeqId;
  17         103  
  17         1152  
15 17     17   11646 use Bio::MUST::Core::Seq;
  17         72  
  17         802  
16 17     17   11819 use Bio::MUST::Core::SeqMask;
  17         79  
  17         785  
17 17     17   12274 use Bio::MUST::Core::SeqMask::Pmsf;
  17         77  
  17         806  
18 17     17   12830 use Bio::MUST::Core::SeqMask::Profiles;
  17         78  
  17         832  
19 17     17   176 use Bio::MUST::Core::IdList;
  17         41  
  17         447  
20 17     17   11188 use Bio::MUST::Core::IdMapper;
  17         69  
  17         792  
21 17     17   169 use Bio::MUST::Core::Ali;
  17         32  
  17         436  
22 17     17   12466 use Bio::MUST::Core::Ali::Stash;
  17         65  
  17         733  
23 17     17   10255 use Bio::MUST::Core::Ali::Temporary;
  17         67  
  17         757  
24 17     17   10595 use Bio::MUST::Core::Tree;
  17         77  
  17         866  
25 17     17   11903 use Bio::MUST::Core::Tree::Forest;
  17         77  
  17         798  
26 17     17   14417 use Bio::MUST::Core::Taxonomy;
  17         105  
  17         929  
27 17     17   11883 use Bio::MUST::Core::GeneticCode::Factory;
  17         78  
  17         786  
28 17     17   11301 use Bio::MUST::Core::PostPred;
  17         74  
  17         996  
29              
30             # TODO: switch to factory (see Bio::Phylo::Factory) to avoid 'use aliased'
31              
32             1;
33              
34             __END__
35              
36             =pod
37              
38             =head1 NAME
39              
40             Bio::MUST::Core - Core classes and utilities for Bio::MUST
41              
42             =head1 VERSION
43              
44             version 0.212530
45              
46             =head1 DESCRIPTION
47              
48             This distribution is the base of the C<Bio::MUST> module collection designed
49             for writing phylogenomic applications in Perl. Their main strength lies in
50             their transparent handling of the NCBI Taxonomy database (see
51             L<https://www.ncbi.nlm.nih.gov/taxonomy>), for example to automatically label
52             ancestral nodes in phylogenetic trees.
53              
54             C<Bio::MUST> classes do not need (and are not meant as a replacement for)
55             L<BioPerl>. In contrast, they depend on both L<Bio::LITE::Taxonomy> and
56             L<Bio::Phylo>, two non-BioPerl distribution for dealing with biological data.
57              
58             C<Bio::MUST> modules have been used in production since 2013 but are not yet
59             ready for wider adoption due to their lack of documentation. This should
60             improve over time. Meanwhile, adventurous users can have a look at the
61             L<Bio::MUST::Core::Ali> class which is already fully documented.
62              
63             =head1 AUTHOR
64              
65             Denis BAURAIN <denis.baurain@uliege.be>
66              
67             =head1 CONTRIBUTORS
68              
69             =for stopwords Catherine COLSON Arnaud DI FRANCO Raphael LEONARD Valerian LUPO Loic MEUNIER Mick VAN VLIERBERGHE
70              
71             =over 4
72              
73             =item *
74              
75             Catherine COLSON <ccolson@doct.uliege.be>
76              
77             =item *
78              
79             Arnaud DI FRANCO <arnaud.difranco@gmail.com>
80              
81             =item *
82              
83             Raphael LEONARD <rleonard@doct.uliege.be>
84              
85             =item *
86              
87             Valerian LUPO <valerian.lupo@doct.uliege.be>
88              
89             =item *
90              
91             Loic MEUNIER <loic.meunier@doct.uliege.be>
92              
93             =item *
94              
95             Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
96              
97             =back
98              
99             =head1 COPYRIGHT AND LICENSE
100              
101             This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.
102              
103             This is free software; you can redistribute it and/or modify it under
104             the same terms as the Perl 5 programming language system itself.
105              
106             =cut