Bio/Tree/NodeNHX.pm

   1 #
   2 # BioPerl module for Bio::Tree::NodeNHX
   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::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<Bio::Tree::Node> 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<bioperl-l@bioperl.org>
  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 use strict;
  89
  90
  91 use base qw(Bio::Tree::Node);
  92
  93 =head2 new
  94
  95  Title   : new
  96  Usage   : my $obj = Bio::Tree::NodeNHX->new();
  97  Function: Builds a new Bio::Tree::NodeNHX object
  98  Returns : Bio::Tree::NodeNHX
  99  Args    : -left          => pointer to Left descendent (optional)
 100            -right         => pointer to Right descenent (optional)
 101            -branch_length => branch length [integer] (optional)
 102            -bootstrap     => bootstrap value (string)
 103            -description   => description of node
 104            -id            => unique id for node
 105            -nhx           => hashref of NHX tags and values
 106
 107 =cut
 108
 109 sub new {
 110   my($class,@args) = @_;
 111
 112   my $self = $class->SUPER::new(@args);
 113   my ($nhx) = $self->_rearrange([qw(NHX)], @args);
 114   $self->nhx_tag($nhx);
 115   return $self;
 116 }
 117
 118 sub DESTROY {
 119     my ($self) = @_;
 120     # try to insure that everything is cleaned up
 121     $self->SUPER::DESTROY();
 122     if( defined $self->{'_desc'} &&
 123         ref($self->{'_desc'}) =~ /ARRAY/i ) {
 124         while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
 125             $node->{'_ancestor'} = undef; # insure no circular references
 126             $node->DESTROY();
 127             $node = undef;
 128         }
 129         $self->{'_desc'} = {};
 130     }
 131 }
 132
 133 sub to_string{
 134    my ($self) = @_;
 135    my @tags = $self->get_all_tags;
 136    my $tagstr = '';
 137    if( scalar(@tags) > 0 ) {
 138        $tagstr = '[' . join(":", "&&NHX",
 139                             map { "$_=" .join(',',
 140                                               $self->get_tag_values($_))}
 141                             @tags ) . ']';
 142    }
 143    return sprintf("%s%s%s",
 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 = $nodenhx->nhx_tag(%tags);
 154  Function: Set tag-value pairs for NHX nodes
 155  Returns : none
 156  Args    : hashref to update the tags/value pairs
 157            OR
 158            with a scalar value update the bootstrap value by default
 159
 160
 161 =cut
 162
 163 sub nhx_tag {
 164     my ($self, $tags) = @_;
 165     if (defined $tags && (ref($tags) =~ /HASH/i)) {
 166         while( my ($tag,$val) = each %$tags ) {
 167             if( ref($val) =~ /ARRAY/i ) {
 168                 for my $v ( @$val ) {
 169                     $self->add_tag_value($tag,$v);
 170                 }
 171             } else {
 172                 $self->add_tag_value($tag,$val);
 173             }
 174         }
 175         if (exists $tags->{'B'}) {
 176             $self->bootstrap($tags->{'B'});
 177         }
 178     } elsif (defined $tags and ! ref ($tags)) {
 179         $self->debug( "here with $tags\n");
 180         # bootstrap by default
 181         $self->bootstrap($tags);
 182     }
 183 }
 184
 185 1;