1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
|
#
# Module for Bio::PhyloNetwork::TreeFactory
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Gabriel Cardona <gabriel(dot)cardona(at)uib(dot)es>
#
# Copyright Gabriel Cardona
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::PhyloNetwork::TreeFactory - Module to sequentially generate
Phylogenetic Trees
=head1 SYNOPSIS
use strict;
use warnings;
use Bio::PhyloNetwork;
use Bio::PhyloNetwork::TreeFactory;
# Will generate sequentially all the 15 binary phylogetic
# trees with 4 leaves
my $factory=Bio::PhyloNetwork::TreeFactory->new(-numleaves=>4);
my @nets;
while (my $net=$factory->next_network()) {
push @nets,$net;
print "".(scalar @nets).": ".$net->eNewick()."\n";
}
=head1 DESCRIPTION
Sequentially builds a (binary) phylogenetic tree each time
next_network is called.
=head1 AUTHOR
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es
=head1 SEE ALSO
L<Bio::PhyloNetwork>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
=cut
package Bio::PhyloNetwork::TreeFactory;
use strict;
use warnings;
use base qw(Bio::Root::Root);
use Bio::PhyloNetwork;
=head2 new
Title : new
Usage : my $factory = new Bio::PhyloNetwork::TreeFactory();
Function: Creates a new Bio::PhyloNetwork::TreeFactory
Returns : Bio::PhyloNetwork::RandomFactory
Args : -numleaves => integer
OR
-leaves => reference to an array (of leaves names)
Returns a Bio::PhyloNetwork::TreeFactory object. Such an object will
sequentially create binary phylogenetic trees
each time next_network is called.
If the parameter -leaves=E<gt>\@leaves is given, then the set of leaves of
these networks will be @leaves. If it is given the parameter
-numleaves=E<gt>$numleaves, then the set of leaves will be "l1"..."l$numleaves".
=cut
sub new {
my ($pkg,@args)=@_;
my $self=$pkg->SUPER::new(@args);
my ($leavesR,$numleaves,$numhybrids)=
$self->_rearrange([qw(LEAVES
NUMLEAVES
NUMHYBRIDS)],@args);
my @leaves;
if ((! defined $leavesR) && (defined $numleaves)) {
@leaves=map {"l$_"} (1..$numleaves);
$leavesR=\@leaves;
}
if (! defined $leavesR) {
$self->throw("No leaves set neither numleaves given");
}
@leaves=@$leavesR;
$self->{leaves}=$leavesR;
$numleaves=@leaves;
$self->{numleaves}=$numleaves;
if ($numleaves > 2) {
my @leavesparent=@leaves;
my $newleaf=pop @leavesparent;
$self->{newleaf}=$newleaf;
$self->{parent}=
new($pkg,-leaves=>\@leavesparent);
my $oldnet=$self->{parent}->next_network();
$self->{oldnet}=$oldnet;
my @candidates=$oldnet->nodes();
$self->{candidates}=\@candidates;
}
$self->{index}=0;
bless($self,$pkg);
}
=head2 next_network
Title : next_network
Usage : my $net=$factory->next_network()
Function: returns a tree
Returns : Bio::PhyloNetwork
Args : none
=cut
sub next_network {
my ($self)=@_;
my $n=$self->{numleaves};
if ($self->{numleaves} == 2) {
if ($self->{index} == 0) {
my $graph=Graph::Directed->new();
$graph->add_edges("t0",$self->{leaves}->[0],"t0",$self->{leaves}->[1]);
my $net=Bio::PhyloNetwork->new(-graph=>$graph);
$self->{index}++;
return $net;
}
else {
return 0;
}
}
else {
if ($self->{index} == (scalar @{$self->{candidates}})) {
my $oldnet=$self->{parent}->next_network();
if (! $oldnet) {
return 0;
}
$self->{oldnet}=$oldnet;
my @candidates=$oldnet->nodes();
$self->{candidates}=\@candidates;
$self->{index}=0;
}
my $graph=$self->{oldnet}->{graph}->copy();
my $u=$self->{candidates}->[$self->{index}];
foreach my $w ($graph->predecessors($u)) {
$graph->delete_edge($w,$u);
$graph->add_edge($w,"t$n");
}
$graph->add_edge("t$n",$u);
$graph->add_edge("t$n",$self->{newleaf});
my $net=Bio::PhyloNetwork->new(-graph=>$graph);
$self->{index}++;
return $net;
}
}
1;
|
