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 = new Bio::Tree::NodeNHX();
  21     my $nodeL = new Bio::Tree::NodeNHX();
  22     my $nodeR = new Bio::Tree::NodeNHX();
  23
  24     my $node = new Bio::Tree::NodeNHX();
  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/MailList.shtml  - 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.bioperl.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 vars qw(@ISA);
  77 use strict;
  78
  79 use Bio::Tree::Node;
  80
  81 @ISA = qw(Bio::Tree::Node);
  82
  83 =head2 new
  84
  85  Title   : new
  86  Usage   : my $obj = new Bio::Tree::NodeNHX();
  87  Function: Builds a new Bio::Tree::NodeNHX object
  88  Returns : Bio::Tree::NodeNHX
  89  Args    : -left          => pointer to Left descendent (optional)
  90            -right         => pointer to Right descenent (optional)
  91            -branch_length => branch length [integer] (optional)
  92            -bootstrap     => bootstrap value (string)
  93            -description   => description of node
  94            -id            => unique id for node
  95            -nhx           => hashref of NHX tags and values
  96
  97 =cut
  98
  99 sub new {
 100   my($class,@args) = @_;
 101
 102   my $self = $class->SUPER::new(@args);
 103   my ($nhx) = $self->_rearrange([qw(NHX)], @args);
 104   $self->nhx_tag($nhx);
 105   return $self;
 106 }
 107
 108 sub DESTROY {
 109     my ($self) = @_;
 110     # try to insure that everything is cleaned up
 111     $self->SUPER::DESTROY();
 112     if( defined $self->{'_desc'} &&
 113         ref($self->{'_desc'}) =~ /ARRAY/i ) {
 114         while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
 115             $node->{'_ancestor'} = undef; # insure no circular references
 116             $node->DESTROY();
 117             $node = undef;
 118         }
 119         $self->{'_desc'} = {};
 120     }
 121 }
 122
 123 sub to_string{
 124    my ($self) = @_;
 125    my @tags = $self->get_all_tags;
 126    my $tagstr = '';
 127    if( @tags ) {
 128        $tagstr = '[' . join(":", "&&NHX",
 129                             map { "$_=" .join(',',
 130                                               $self->get_tag_values($_))}
 131                             @tags ) . ']';
 132    }
 133    return sprintf("%s%s%s",
 134                   defined $self->id ? $self->id : '',
 135                   defined $self->branch_length ? ':' .
 136                   $self->branch_length : ' ',
 137                   $tagstr);
 138 }
 139
 140 =head2 nhx_tag
 141
 142  Title   : nhx_tag
 143  Usage   : my $tag = $nodenhx->nhx_tag(%tags);
 144  Function: Set tag-value pairs for NHX nodes
 145  Returns : none
 146  Args    : hashref to update the tags/value pairs
 147            OR
 148            with a scalar value update the bootstrap value by default
 149
 150
 151 =cut
 152
 153 sub nhx_tag {
 154     my ($self, $tags) = @_;
 155     if (defined $tags && (ref($tags) =~ /HASH/i)) {
 156         while( my ($tag,$val) = each %$tags ) {
 157             if( ref($val) =~ /ARRAY/i ) {
 158                 for my $v ( @$val ) {
 159                     $self->add_tag_value($tag,$v);
 160                 }
 161             } else {
 162                 $self->add_tag_value($tag,$val);
 163             }
 164         }
 165         if (exists $tags->{'B'}) {
 166             $self->bootstrap($tags->{'B'});
 167         }
 168     } elsif (defined $tags and ! ref ($tags)) {
 169         print STDERR "here with $tags\n";
 170         # bootstrap by default
 171         $self->bootstrap($tags);
 172     }
 173 }
 174
 175 1;