File Coverage

Bio/Tree/NodeNHX.pm
Criterion Covered Total %
statement 28 38 73.6
branch 13 16 81.2
condition 4 9 44.4
subroutine 6 6 100.0
pod 3 3 100.0
total 54 72 75.0


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Tree::NodeNHX
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Aaron Mackey
7             #
8             # Copyright Aaron Mackey
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::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
17              
18             =head1 SYNOPSIS
19              
20             use Bio::Tree::NodeNHX;
21             my $nodeA = Bio::Tree::NodeNHX->new();
22             my $nodeL = Bio::Tree::NodeNHX->new();
23             my $nodeR = Bio::Tree::NodeNHX->new();
24              
25             my $node = Bio::Tree::NodeNHX->new();
26             $node->add_Descendents($nodeL);
27             $node->add_Descendents($nodeR);
28              
29             print "node is not a leaf \n" if( $node->is_leaf);
30              
31             =head1 DESCRIPTION
32              
33             Makes a Tree Node with NHX tags, suitable for building a Tree. See
34             L for a full list of functionality.
35              
36             =head1 FEEDBACK
37              
38             =head2 Mailing Lists
39              
40             User feedback is an integral part of the evolution of this and other
41             Bioperl modules. Send your comments and suggestions preferably to
42             the Bioperl mailing list. Your participation is much appreciated.
43              
44             bioperl-l@bioperl.org - General discussion
45             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
46              
47             =head2 Support
48              
49             Please direct usage questions or support issues to the mailing list:
50              
51             I
52              
53             rather than to the module maintainer directly. Many experienced and
54             reponsive experts will be able look at the problem and quickly
55             address it. Please include a thorough description of the problem
56             with code and data examples if at all possible.
57              
58             =head2 Reporting Bugs
59              
60             Report bugs to the Bioperl bug tracking system to help us keep track
61             of the bugs and their resolution. Bug reports can be submitted via
62             the web:
63              
64             https://github.com/bioperl/bioperl-live/issues
65              
66             =head1 AUTHOR - Aaron Mackey
67              
68             Email amackey@virginia.edu
69              
70             =head1 CONTRIBUTORS
71              
72             The NHX (New Hampshire eXtended) format was created by Chris Zmasek,
73             and is described at:
74              
75             http://sourceforge.net/projects/forester-atv/
76              
77             =head1 APPENDIX
78              
79             The rest of the documentation details each of the object methods.
80             Internal methods are usually preceded with a _
81              
82             =cut
83              
84              
85             # Let the code begin...
86              
87             package Bio::Tree::NodeNHX;
88 5     5   16 use strict;
  5         4  
  5         132  
89              
90              
91 5     5   15 use base qw(Bio::Tree::Node);
  5         6  
  5         1957  
92              
93             =head2 new
94              
95             Title : new
96             Usage : my $obj = Bio::Tree::NodeNHX->new();
97             Function: Builds a new Bio::Tree::NodeNHX object
98             Returns : Bio::Tree::NodeNHX
99             Args : -left => pointer to Left descendent (optional)
100             -right => pointer to Right descenent (optional)
101             -branch_length => branch length [integer] (optional)
102             -bootstrap => bootstrap value (string)
103             -description => description of node
104             -id => unique id for node
105             -nhx => hashref of NHX tags and values
106              
107             =cut
108              
109             sub new {
110 550     550 1 969 my($class,@args) = @_;
111              
112 550         1167 my $self = $class->SUPER::new(@args);
113 550         1212 my ($nhx) = $self->_rearrange([qw(NHX)], @args);
114 550         957 $self->nhx_tag($nhx);
115 550         1021 return $self;
116             }
117              
118             sub DESTROY {
119 549     549   381 my ($self) = @_;
120             # try to insure that everything is cleaned up
121 549         677 $self->SUPER::DESTROY();
122 549 50 33     3118 if( defined $self->{'_desc'} &&
123             ref($self->{'_desc'}) =~ /ARRAY/i ) {
124 0         0 while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
  0         0  
125 0         0 $node->{'_ancestor'} = undef; # insure no circular references
126 0         0 $node->DESTROY();
127 0         0 $node = undef;
128             }
129 0         0 $self->{'_desc'} = {};
130             }
131             }
132              
133             sub to_string{
134 2492     2492 1 1798 my ($self) = @_;
135 2492         2927 my @tags = $self->get_all_tags;
136 2492         2061 my $tagstr = '';
137 2492 100       3438 if( scalar(@tags) > 0 ) {
138             $tagstr = '[' . join(":", "&&NHX",
139 2269         1852 map { "$_=" .join(',',
  3473         5073  
140             $self->get_tag_values($_))}
141             @tags ) . ']';
142             }
143 2492 100       3446 return sprintf("%s%s%s",
    100          
144             defined $self->id ? $self->id : '',
145             defined $self->branch_length ? ':' .
146             $self->branch_length : ' ',
147             $tagstr);
148             }
149              
150             =head2 nhx_tag
151              
152             Title : nhx_tag
153             Usage : my $tag = $nodenhx->nhx_tag(%tags);
154             Function: Set tag-value pairs for NHX nodes
155             Returns : none
156             Args : hashref to update the tags/value pairs
157             OR
158             with a scalar value update the bootstrap value by default
159              
160              
161             =cut
162              
163             sub nhx_tag {
164 550     550 1 452 my ($self, $tags) = @_;
165 550 100 66     2473 if (defined $tags && (ref($tags) =~ /HASH/i)) {
    50 33        
166 478         1349 while( my ($tag,$val) = each %$tags ) {
167 778 50       934 if( ref($val) =~ /ARRAY/i ) {
168 0         0 for my $v ( @$val ) {
169 0         0 $self->add_tag_value($tag,$v);
170             }
171             } else {
172 778         1152 $self->add_tag_value($tag,$val);
173             }
174             }
175 478 100       788 if (exists $tags->{'B'}) {
176 135         229 $self->bootstrap($tags->{'B'});
177             }
178             } elsif (defined $tags and ! ref ($tags)) {
179 0           $self->debug( "here with $tags\n");
180             # bootstrap by default
181 0           $self->bootstrap($tags);
182             }
183             }
184              
185             1;