File Coverage

Bio/Factory/TreeFactoryI.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::Factory::TreeFactoryI
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::Factory::TreeFactoryI - Factory Interface for getting and writing trees
17             from/to a data stream
18              
19             =head1 SYNOPSIS
20              
21             # get a $factory from somewhere Bio::TreeIO likely
22             my $treeio = Bio::TreeIO->new(-format => 'newick', #this is phylip/newick format
23             -file => 'file.tre');
24             my $treeout = Bio::TreeIO->new(-format => 'nexus',
25             -file => ">file.nexus");
26              
27             # convert tree formats from newick/phylip to nexus
28             while(my $tree = $treeio->next_tree) {
29             $treeout->write_tree($tree);
30             }
31              
32             =head1 DESCRIPTION
33              
34             This interface describes the minimal functions needed to get and write
35             trees from a data stream. It is implemented by the L factory.
36              
37             =head1 FEEDBACK
38              
39             =head2 Mailing Lists
40              
41             User feedback is an integral part of the evolution of this and other
42             Bioperl modules. Send your comments and suggestions preferably to
43             the Bioperl mailing list. Your participation is much appreciated.
44              
45             bioperl-l@bioperl.org - General discussion
46             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
47              
48             =head2 Support
49              
50             Please direct usage questions or support issues to the mailing list:
51              
52             I
53              
54             rather than to the module maintainer directly. Many experienced and
55             reponsive experts will be able look at the problem and quickly
56             address it. Please include a thorough description of the problem
57             with code and data examples if at all possible.
58              
59             =head2 Reporting Bugs
60              
61             Report bugs to the Bioperl bug tracking system to help us keep track
62             of the bugs and their resolution. Bug reports can be submitted via the
63             web:
64              
65             https://github.com/bioperl/bioperl-live/issues
66              
67             =head1 AUTHOR - Jason Stajich
68              
69             Email jason@bioperl.org
70              
71             =head1 APPENDIX
72              
73             The rest of the documentation details each of the object methods.
74             Internal methods are usually preceded with a _
75              
76             =cut
77              
78              
79             # Let the code begin...
80              
81              
82             package Bio::Factory::TreeFactoryI;
83 23     23   105 use strict;
  23         25  
  23         649  
84              
85 23     23   77 use base qw(Bio::Root::RootI);
  23         25  
  23         2262  
86              
87             =head2 next_tree
88              
89             Title : next_tree
90             Usage : my $tree = $factory->next_tree;
91             Function: Get a tree from the factory
92             Returns : L
93             Args : none
94              
95             =cut
96              
97             sub next_tree{
98 0     0 1   my ($self,@args) = @_;
99 0           $self->throw_not_implemented();
100             }
101              
102             =head2 write_tree
103              
104             Title : write_tree
105             Usage : $treeio->write_tree($tree);
106             Function: Writes a tree onto the stream
107             Returns : none
108             Args : L
109              
110              
111             =cut
112              
113             sub write_tree{
114 0     0 1   my ($self,@args) = @_;
115 0           $self->throw_not_implemented();
116             }
117              
118             1;