Bio/Tree/NodeNHX.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Tree::NodeNHX
   4 #
   5 # Cared for by Aaron Mackey <amackey@virginia.edu>
   6 #
   7 # Copyright Aaron Mackey
   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::NodeNHX - A Simple Tree Node with support for NHX tags
  16
  17 =head1 SYNOPSIS
  18
  19     use Bio::Tree::NodeNHX;
  20     my $nodeA = Bio::Tree::NodeNHX->new();
  21     my $nodeL = Bio::Tree::NodeNHX->new();
  22     my $nodeR = Bio::Tree::NodeNHX->new();
  23
  24     my $node = Bio::Tree::NodeNHX->new();
  25     $node->add_Descendents($nodeL);
  26     $node->add_Descendents($nodeR);
  27
  28     print "node is not a leaf \n" if( $node->is_leaf);
  29
  30 =head1 DESCRIPTION
  31
  32 Makes a Tree Node with NHX tags, suitable for building a Tree.  See
  33 L<Bio::Tree::Node> for a full list of functionality.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to
  41 the Bioperl mailing list.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Reporting Bugs
  47
  48 Report bugs to the Bioperl bug tracking system to help us keep track
  49 of the bugs and their resolution. Bug reports can be submitted via
  50 the web:
  51
  52   http://bugzilla.open-bio.org/
  53
  54 =head1 AUTHOR - Aaron Mackey
  55
  56 Email amackey@virginia.edu
  57
  58 =head1 CONTRIBUTORS
  59
  60 The NHX (New Hampshire eXtended) format was created by Chris Zmasek,
  61 and is described at:
  62
  63   http://www.genetics.wustl.edu/eddy/forester/NHX.html
  64
  65 =head1 APPENDIX
  66
  67 The rest of the documentation details each of the object methods.
  68 Internal methods are usually preceded with a _
  69
  70 =cut
  71
  72
  73 # Let the code begin...
  74
  75 package Bio::Tree::NodeNHX;
  76 use strict;
  77
  78
  79 use base qw(Bio::Tree::Node);
  80
  81 =head2 new
  82
  83  Title   : new
  84  Usage   : my $obj = Bio::Tree::NodeNHX->new();
  85  Function: Builds a new Bio::Tree::NodeNHX object
  86  Returns : Bio::Tree::NodeNHX
  87  Args    : -left          => pointer to Left descendent (optional)
  88            -right         => pointer to Right descenent (optional)
  89            -branch_length => branch length [integer] (optional)
  90            -bootstrap     => bootstrap value (string)
  91            -description   => description of node
  92            -id            => unique id for node
  93            -nhx           => hashref of NHX tags and values
  94
  95 =cut
  96
  97 sub new {
  98   my($class,@args) = @_;
  99
 100   my $self = $class->SUPER::new(@args);
 101   my ($nhx) = $self->_rearrange([qw(NHX)], @args);
 102   $self->nhx_tag($nhx);
 103   return $self;
 104 }
 105
 106 sub DESTROY {
 107     my ($self) = @_;
 108     # try to insure that everything is cleaned up
 109     $self->SUPER::DESTROY();
 110     if( defined $self->{'_desc'} &&
 111         ref($self->{'_desc'}) =~ /ARRAY/i ) {
 112         while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
 113             $node->{'_ancestor'} = undef; # insure no circular references
 114             $node->DESTROY();
 115             $node = undef;
 116         }
 117         $self->{'_desc'} = {};
 118     }
 119 }
 120
 121 sub to_string{
 122    my ($self) = @_;
 123    my @tags = $self->get_all_tags;
 124    my $tagstr = '';
 125    if( @tags ) {
 126        $tagstr = '[' . join(":", "&&NHX",
 127                             map { "$_=" .join(',',
 128                                               $self->get_tag_values($_))}
 129                             @tags ) . ']';
 130    }
 131    return sprintf("%s%s%s",
 132                   defined $self->id ? $self->id : '',
 133                   defined $self->branch_length ? ':' .
 134                   $self->branch_length : ' ',
 135                   $tagstr);
 136 }
 137
 138 =head2 nhx_tag
 139
 140  Title   : nhx_tag
 141  Usage   : my $tag = $nodenhx->nhx_tag(%tags);
 142  Function: Set tag-value pairs for NHX nodes
 143  Returns : none
 144  Args    : hashref to update the tags/value pairs
 145            OR
 146            with a scalar value update the bootstrap value by default
 147
 148
 149 =cut
 150
 151 sub nhx_tag {
 152     my ($self, $tags) = @_;
 153     if (defined $tags && (ref($tags) =~ /HASH/i)) {
 154         while( my ($tag,$val) = each %$tags ) {
 155             if( ref($val) =~ /ARRAY/i ) {
 156                 for my $v ( @$val ) {
 157                     $self->add_tag_value($tag,$v);
 158                 }
 159             } else {
 160                 $self->add_tag_value($tag,$val);
 161             }
 162         }
 163         if (exists $tags->{'B'}) {
 164             $self->bootstrap($tags->{'B'});
 165         }
 166     } elsif (defined $tags and ! ref ($tags)) {
 167         $self->debug( "here with $tags\n");
 168         # bootstrap by default
 169         $self->bootstrap($tags);
 170     }
 171 }
 172
 173 1;