/usr/share/perl5/Bio/TreeIO/nexml.pm is in libbio-perl-perl 1.6.924-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 | #
# BioPerl module for Bio::TreeIO::nexml
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chase Miller <chmille4@gmail.com>
#
# Copyright Chase Miller
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::TreeIO::nexml - A TreeIO driver module for parsing NeXML tree files
=head1 SYNOPSIS
use Bio::TreeIO;
my $in = Bio::TreeIO->new(-file => 'data.nexml' -format => 'Nexml');
while( my $tree = $in->next_tree ) {
}
=head1 DESCRIPTION
This is a driver module for parsing tree data in a NeXML format. For
more information on NeXML, visit L<http://www.nexml.org>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Chase Miller
Email chmille4@gmail.com
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::TreeIO::nexml;
use strict;
use lib '../..';
use Bio::Event::EventGeneratorI;
use IO::String;
use Bio::Nexml::Factory;
use Bio::Phylo::IO qw (parse unparse);
use base qw(Bio::TreeIO);
sub _initialize {
my $self = shift;
$self->SUPER::_initialize(@_);
$self->{_doc} = undef;
}
=head2 next_tree
Title : next_tree
Usage : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : L<Bio::Tree::TreeI>
Args : none
=cut
sub next_tree {
my ($self) = @_;
unless ( $self->{'_parsed'} ) {
$self->_parse;
}
return $self->{'_trees'}->[ $self->{'_treeiter'}++ ];
}
=head2 doc
Title : doc
Usage : $treeio->doc
Function: Returns the biophylo nexml document object
Returns : Bio::Phylo::Project
Args : none or Bio::Phylo::Project object
=cut
sub doc {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_doc'} = $value;
}
return $obj->{'_doc'};
}
=head2 rewind
Title : rewind
Usage : $treeio->rewind
Function: Resets the stream
Returns : none
Args : none
=cut
sub rewind {
my $self = shift;
$self->{'_treeiter'} = 0;
}
sub _parse {
my ($self) = @_;
$self->{'_parsed'} = 1;
$self->{'_treeiter'} = 0;
my $fac = Bio::Nexml::Factory->new();
$self->doc(parse(
'-file' => $self->{'_file'},
'-format' => 'nexml',
'-as_project' => '1'
));
$self->{'_trees'} = $fac->create_bperl_tree($self);
}
=head2 write_tree
Title : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : L<Bio::Tree::TreeI>
=cut
sub write_tree {
my ($self, $bp_tree) = @_;
my $fac = Bio::Nexml::Factory->new();
my $taxa = $fac->create_bphylo_taxa($bp_tree);
my ($tree) = $fac->create_bphylo_tree($bp_tree, $taxa);
my $forest = Bio::Phylo::Factory->create_forest();
$self->doc(Bio::Phylo::Factory->create_project());
$forest->set_taxa($taxa);
$forest->insert($tree);
$self->doc->insert($forest);
my $ret = $self->_print($self->doc->to_xml());
$self->flush;
return $ret;
}
1;
|