|
0
|
1 # $Id: TreeI.pm,v 1.11.2.1 2003/09/14 20:21:10 jason Exp $
|
|
|
2 #
|
|
|
3 # BioPerl module for Bio::Tree::TreeI
|
|
|
4 #
|
|
|
5 # Cared for by Jason Stajich <jason@bioperl.org>
|
|
|
6 #
|
|
|
7 # Copyright Jason Stajich
|
|
|
8 #
|
|
|
9 # You may distribute this module under the same terms as perl itself
|
|
|
10
|
|
|
11 # POD documentation - main docs before the code
|
|
|
12
|
|
|
13 =head1 NAME
|
|
|
14
|
|
|
15 Bio::Tree::TreeI - A Tree object suitable for lots of things, designed
|
|
|
16 originally for Phylogenetic Trees.
|
|
|
17
|
|
|
18 =head1 SYNOPSIS
|
|
|
19
|
|
|
20 # get a Bio::Tree::TreeI somehow
|
|
|
21 # like from a TreeIO
|
|
|
22 my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'treefile.dnd');
|
|
|
23 my $tree = $treeio->next_tree;
|
|
|
24 my @nodes = $tree->get_nodes;
|
|
|
25 my @leaves = $tree->get_leaf_nodes;
|
|
|
26 my $root = $tree->get_root_node;
|
|
|
27
|
|
|
28 =head1 DESCRIPTION
|
|
|
29
|
|
|
30 This object holds a pointer to the Root of a Tree which is a
|
|
|
31 Bio::Tree::NodeI.
|
|
|
32
|
|
|
33 =head1 FEEDBACK
|
|
|
34
|
|
|
35 =head2 Mailing Lists
|
|
|
36
|
|
|
37 User feedback is an integral part of the evolution of this and other
|
|
|
38 Bioperl modules. Send your comments and suggestions preferably to
|
|
|
39 the Bioperl mailing list. Your participation is much appreciated.
|
|
|
40
|
|
|
41 bioperl-l@bioperl.org - General discussion
|
|
|
42 http://bioperl.org/MailList.shtml - About the mailing lists
|
|
|
43
|
|
|
44 =head2 Reporting Bugs
|
|
|
45
|
|
|
46 Report bugs to the Bioperl bug tracking system to help us keep track
|
|
|
47 of the bugs and their resolution. Bug reports can be submitted via
|
|
|
48 the web:
|
|
|
49
|
|
|
50 http://bugzilla.bioperl.org/
|
|
|
51
|
|
|
52 =head1 AUTHOR - Jason Stajich
|
|
|
53
|
|
|
54 Email jason@bioperl.org
|
|
|
55
|
|
|
56 =head1 CONTRIBUTORS
|
|
|
57
|
|
|
58 Aaron Mackey amackey@virginia.edu
|
|
|
59 Elia Stupka, elia@fugu-sg.org
|
|
|
60
|
|
|
61 =head1 APPENDIX
|
|
|
62
|
|
|
63 The rest of the documentation details each of the object methods.
|
|
|
64 Internal methods are usually preceded with a _
|
|
|
65
|
|
|
66 =cut
|
|
|
67
|
|
|
68
|
|
|
69 # Let the code begin...
|
|
|
70
|
|
|
71
|
|
|
72 package Bio::Tree::TreeI;
|
|
|
73 use Bio::Tree::NodeI;
|
|
|
74 use vars qw(@ISA);
|
|
|
75 use strict;
|
|
|
76
|
|
|
77 @ISA = qw(Bio::Tree::NodeI);
|
|
|
78
|
|
|
79 =head2 get_nodes
|
|
|
80
|
|
|
81 Title : get_nodes
|
|
|
82 Usage : my @nodes = $tree->get_nodes()
|
|
|
83 Function: Return list of Tree::NodeI objects
|
|
|
84 Returns : array of Tree::NodeI objects
|
|
|
85 Args : (named values) hash with one value
|
|
|
86 order => 'b|breadth' first order or 'd|depth' first order
|
|
|
87
|
|
|
88 =cut
|
|
|
89
|
|
|
90 sub get_nodes{
|
|
|
91 my ($self) = @_;
|
|
|
92 $self->throw_not_implemented();
|
|
|
93 }
|
|
|
94
|
|
|
95 =head2 get_root_node
|
|
|
96
|
|
|
97 Title : get_root_node
|
|
|
98 Usage : my $node = $tree->get_root_node();
|
|
|
99 Function: Get the Top Node in the tree, in this implementation
|
|
|
100 Trees only have one top node.
|
|
|
101 Returns : Bio::Tree::NodeI object
|
|
|
102 Args : none
|
|
|
103
|
|
|
104 =cut
|
|
|
105
|
|
|
106 sub get_root_node{
|
|
|
107 my ($self) = @_;
|
|
|
108 $self->throw_not_implemented();
|
|
|
109 }
|
|
|
110
|
|
|
111 =head2 number_nodes
|
|
|
112
|
|
|
113 Title : number_nodes
|
|
|
114 Usage : my $size = $tree->number_nodes
|
|
|
115 Function: Returns the number of nodes
|
|
|
116 Example :
|
|
|
117 Returns :
|
|
|
118 Args :
|
|
|
119
|
|
|
120
|
|
|
121 =cut
|
|
|
122
|
|
|
123 sub number_nodes{
|
|
|
124 my ($self) = @_;
|
|
|
125 my $root = $self->get_root_node;
|
|
|
126 if( defined $root && $root->isa('Bio::Tree::NodeI')) {
|
|
|
127 return $root->descendent_count;
|
|
|
128 }
|
|
|
129 return 0;
|
|
|
130 }
|
|
|
131
|
|
|
132 =head2 total_branch_length
|
|
|
133
|
|
|
134 Title : total_branch_length
|
|
|
135 Usage : my $size = $tree->total_branch_length
|
|
|
136 Function: Returns the sum of the length of all branches
|
|
|
137 Returns : integer
|
|
|
138 Args : none
|
|
|
139
|
|
|
140 =cut
|
|
|
141
|
|
|
142 sub total_branch_length {
|
|
|
143 my ($self) = @_;
|
|
|
144 $self->throw_not_implemented();
|
|
|
145 }
|
|
|
146
|
|
|
147 =head2 height
|
|
|
148
|
|
|
149 Title : height
|
|
|
150 Usage : my $height = $tree->height
|
|
|
151 Function: Gets the height of tree - this LOG_2($number_nodes)
|
|
|
152 WARNING: this is only true for strict binary trees. The TreeIO
|
|
|
153 system is capable of building non-binary trees, for which this
|
|
|
154 method will currently return an incorrect value!!
|
|
|
155 Returns : integer
|
|
|
156 Args : none
|
|
|
157
|
|
|
158 =cut
|
|
|
159
|
|
|
160 sub height{
|
|
|
161 my ($self) = @_;
|
|
|
162 my $nodect = $self->number_nodes;
|
|
|
163 return 0 if( ! $nodect );
|
|
|
164 return log($nodect) / log(2);
|
|
|
165 }
|
|
|
166
|
|
|
167 =head2 id
|
|
|
168
|
|
|
169 Title : id
|
|
|
170 Usage : my $id = $tree->id();
|
|
|
171 Function: An id value for the tree
|
|
|
172 Returns : scalar
|
|
|
173 Args :
|
|
|
174
|
|
|
175
|
|
|
176 =cut
|
|
|
177
|
|
|
178 sub id{
|
|
|
179 my ($self,@args) = @_;
|
|
|
180 $self->throw_not_implemented();
|
|
|
181 }
|
|
|
182
|
|
|
183 =head2 score
|
|
|
184
|
|
|
185 Title : score
|
|
|
186 Usage : $obj->score($newval)
|
|
|
187 Function: Sets the associated score with this tree
|
|
|
188 This is a generic slot which is probably best used
|
|
|
189 for log likelihood or other overall tree score
|
|
|
190 Returns : value of score
|
|
|
191 Args : newvalue (optional)
|
|
|
192
|
|
|
193
|
|
|
194 =cut
|
|
|
195
|
|
|
196 sub score{
|
|
|
197 my ($self,$value) = @_;
|
|
|
198 $self->throw_not_implemented();
|
|
|
199 }
|
|
|
200
|
|
|
201 =head2 get_leaf_nodes
|
|
|
202
|
|
|
203 Title : get_leaf_nodes
|
|
|
204 Usage : my @leaves = $tree->get_leaf_nodes()
|
|
|
205 Function: Returns the leaves (tips) of the tree
|
|
|
206 Returns : Array of Bio::Tree::NodeI objects
|
|
|
207 Args : none
|
|
|
208
|
|
|
209
|
|
|
210 =cut
|
|
|
211
|
|
|
212 sub get_leaf_nodes{
|
|
|
213 my ($self) = @_;
|
|
|
214 return grep { $_->is_Leaf() } $self->get_nodes(-sortby => 'creation');
|
|
|
215 }
|
|
|
216
|
|
|
217
|
|
|
218 1;
|
