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 = '0.212650';
10 17     17   3581777 use strict;
  17         203  
  17         522  
11 17     17   108 use warnings;
  17         35  
  17         502  
12              
13 17     17   7204 use Bio::MUST::Core::Types;
  17         65  
  17         755  
14 17     17   19956 use Bio::MUST::Core::SeqId;
  17         106  
  17         1160  
15 17     17   11111 use Bio::MUST::Core::Seq;
  17         72  
  17         839  
16 17     17   10762 use Bio::MUST::Core::SeqMask;
  17         75  
  17         778  
17 17     17   11002 use Bio::MUST::Core::SeqMask::Pmsf;
  17         77  
  17         822  
18 17     17   11448 use Bio::MUST::Core::SeqMask::Profiles;
  17         80  
  17         801  
19 17     17   162 use Bio::MUST::Core::IdList;
  17         40  
  17         423  
20 17     17   10076 use Bio::MUST::Core::IdMapper;
  17         74  
  17         768  
21 17     17   189 use Bio::MUST::Core::Ali;
  17         39  
  17         430  
22 17     17   11343 use Bio::MUST::Core::Ali::Stash;
  17         66  
  17         666  
23 17     17   8771 use Bio::MUST::Core::Ali::Temporary;
  17         78  
  17         741  
24 17     17   9771 use Bio::MUST::Core::Tree;
  17         81  
  17         772  
25 17     17   10387 use Bio::MUST::Core::Tree::Forest;
  17         66  
  17         734  
26 17     17   14235 use Bio::MUST::Core::Taxonomy;
  17         104  
  17         905  
27 17     17   10871 use Bio::MUST::Core::GeneticCode::Factory;
  17         82  
  17         790  
28 17     17   10039 use Bio::MUST::Core::PostPred;
  17         124  
  17         959  
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 0.212650
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