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 = '0.212670';
10 17     17   3533151 use strict;
  17         204  
  17         548  
11 17     17   99 use warnings;
  17         29  
  17         504  
12              
13 17     17   7356 use Bio::MUST::Core::Types;
  17         64  
  17         706  
14 17     17   19497 use Bio::MUST::Core::SeqId;
  17         102  
  17         1157  
15 17     17   11023 use Bio::MUST::Core::Seq;
  17         73  
  17         771  
16 17     17   10939 use Bio::MUST::Core::SeqMask;
  17         75  
  17         745  
17 17     17   10611 use Bio::MUST::Core::SeqMask::Pmsf;
  17         75  
  17         742  
18 17     17   11715 use Bio::MUST::Core::SeqMask::Profiles;
  17         75  
  17         752  
19 17     17   178 use Bio::MUST::Core::IdList;
  17         46  
  17         423  
20 17     17   9794 use Bio::MUST::Core::IdMapper;
  17         73  
  17         759  
21 17     17   156 use Bio::MUST::Core::Ali;
  17         37  
  17         423  
22 17     17   10992 use Bio::MUST::Core::Ali::Stash;
  17         61  
  17         660  
23 17     17   8902 use Bio::MUST::Core::Ali::Temporary;
  17         63  
  17         678  
24 17     17   9257 use Bio::MUST::Core::Tree;
  17         70  
  17         767  
25 17     17   10076 use Bio::MUST::Core::Tree::Forest;
  17         68  
  17         797  
26 17     17   13323 use Bio::MUST::Core::Taxonomy;
  17         112  
  17         858  
27 17     17   10662 use Bio::MUST::Core::GeneticCode::Factory;
  17         92  
  17         730  
28 17     17   10382 use Bio::MUST::Core::PostPred;
  17         79  
  17         954  
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 0.212670
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