Bio/TreeIO/nhx.pm

   1 #
   2 # BioPerl module for Bio::TreeIO::nhx
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Aaron Mackey <amackey@virginia.edu>
   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::TreeIO::nhx - TreeIO implementation for parsing
  17     Newick/New Hampshire eXtendend (NHX) format.
  18
  19 =head1 SYNOPSIS
  20
  21   # do not use this module directly
  22   use Bio::TreeIO;
  23   my $treeio = Bio::TreeIO->new(-format => 'nhx', -file => 'tree.dnd');
  24   my $tree = $treeio->next_tree;
  25
  26 =head1 DESCRIPTION
  27
  28 This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this and other
  35 Bioperl modules. Send your comments and suggestions preferably to the
  36 Bioperl mailing list.  Your participation is much appreciated.
  37
  38   bioperl-l@bioperl.org                  - General discussion
  39   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  40
  41 =head2 Support
  42
  43 Please direct usage questions or support issues to the mailing list:
  44
  45 I<bioperl-l@bioperl.org>
  46
  47 rather than to the module maintainer directly. Many experienced and
  48 reponsive experts will be able look at the problem and quickly
  49 address it. Please include a thorough description of the problem
  50 with code and data examples if at all possible.
  51
  52 =head2 Reporting Bugs
  53
  54 Report bugs to the Bioperl bug tracking system to help us keep track
  55 of the bugs and their resolution. Bug reports can be submitted viax the
  56 web:
  57
  58   https://github.com/bioperl/bioperl-live/issues
  59
  60 =head1 AUTHOR - Aaron Mackey
  61
  62 Email amackey-at-virginia.edu
  63
  64 =head1 CONTRIBUTORS
  65
  66 Email jason-at-bioperl-dot-org
  67
  68 =head1 APPENDIX
  69
  70 The rest of the documentation details each of the object methods.
  71 Internal methods are usually preceded with a _
  72
  73 =cut
  74
  75
  76 # Let the code begin...
  77
  78
  79 package Bio::TreeIO::nhx;
  80 use strict;
  81
  82 # Object preamble - inherits from Bio::Root::Root
  83
  84 use Bio::Tree::NodeNHX;
  85 use Bio::Event::EventGeneratorI;
  86 #use XML::Handler::Subs;
  87
  88 use base qw(Bio::TreeIO::newick);
  89
  90 sub _initialize {
  91   my($self, %args) = @_;
  92   $args{-nodetype} ||= 'Bio::Tree::NodeNHX';
  93   $self->SUPER::_initialize(%args);
  94 }
  95
  96 sub _node_as_string {
  97   my $self = shift;
  98   my $node = shift;
  99   my $params = shift;
 100
 101   my $label_stringbuffer = $self->SUPER::_node_as_string($node,$params);
 102
 103   my @tags = $node->get_all_tags;
 104   if( scalar(@tags) > 0 ) {
 105     @tags = sort @tags;
 106     $label_stringbuffer .= '[' .
 107       join(":", "&&NHX",
 108            map { "$_=" .join(',',$node->get_tag_values($_)) }
 109            @tags ) . ']';
 110   }
 111   return $label_stringbuffer;
 112 }
 113
 114 1;