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1 # $Id: NodeNHX.pm,v 1.5.2.1 2003/09/14 19:00:35 jason Exp $
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2 #
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3 # BioPerl module for Bio::Tree::NodeNHX
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4 #
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5 # Cared for by Aaron Mackey <amackey@virginia.edu>
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6 #
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7 # Copyright Aaron Mackey
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Tree::NodeNHX;
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20 my $nodeA = new Bio::Tree::NodeNHX();
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21 my $nodeL = new Bio::Tree::NodeNHX();
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22 my $nodeR = new Bio::Tree::NodeNHX();
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23
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24 my $node = new Bio::Tree::NodeNHX();
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25 $node->add_Descendents($nodeL);
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26 $node->add_Descendents($nodeR);
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27
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28 print "node is not a leaf \n" if( $node->is_leaf);
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29
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30 =head1 DESCRIPTION
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31
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32 Makes a Tree Node with NHX tags, suitable for building a Tree. See
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33 L<Bio::Tree::Node> for a full list of functionality.
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34
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35 =head1 FEEDBACK
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36
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37 =head2 Mailing Lists
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38
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39 User feedback is an integral part of the evolution of this and other
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40 Bioperl modules. Send your comments and suggestions preferably to
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41 the Bioperl mailing list. Your participation is much appreciated.
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42
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43 bioperl-l@bioperl.org - General discussion
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44 http://bioperl.org/MailList.shtml - About the mailing lists
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45
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46 =head2 Reporting Bugs
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47
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48 Report bugs to the Bioperl bug tracking system to help us keep track
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49 of the bugs and their resolution. Bug reports can be submitted via
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50 the web:
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51
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52 http://bugzilla.bioperl.org/
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53
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54 =head1 AUTHOR - Aaron Mackey
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55
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56 Email amackey@virginia.edu
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57
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58 =head1 CONTRIBUTORS
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59
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60 The NHX (New Hampshire eXtended) format was created by Chris Zmasek,
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61 and is described at:
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62
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63 http://www.genetics.wustl.edu/eddy/forester/NHX.html
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64
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65 =head1 APPENDIX
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66
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67 The rest of the documentation details each of the object methods.
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68 Internal methods are usually preceded with a _
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69
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70 =cut
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71
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72
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73 # Let the code begin...
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74
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75 package Bio::Tree::NodeNHX;
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76 use vars qw(@ISA);
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77 use strict;
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78
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79 use Bio::Tree::Node;
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80
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81 @ISA = qw(Bio::Tree::Node);
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82
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83 =head2 new
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84
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85 Title : new
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86 Usage : my $obj = new Bio::Tree::NodeNHX();
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87 Function: Builds a new Bio::Tree::NodeNHX object
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88 Returns : Bio::Tree::NodeNHX
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89 Args : -left => pointer to Left descendent (optional)
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90 -right => pointer to Right descenent (optional)
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91 -branch_length => branch length [integer] (optional)
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92 -bootstrap => value bootstrap value (string)
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93 -description => description of node
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94 -id => unique id for node
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95 -nhx => hashref of NHX tags and values
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96
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97 =cut
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98
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99 sub new {
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100 my($class,@args) = @_;
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101
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102 my $self = $class->SUPER::new(@args);
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103 my ($nhx) = $self->_rearrange([qw(NHX)], @args);
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104 $self->nhx_tag($nhx);
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105 return $self;
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106 }
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107
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108 sub DESTROY {
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109 my ($self) = @_;
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110 # try to insure that everything is cleaned up
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111 $self->SUPER::DESTROY();
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112 if( defined $self->{'_desc'} &&
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113 ref($self->{'_desc'}) =~ /ARRAY/i ) {
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114 while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
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115 $node->{'_ancestor'} = undef; # insure no circular references
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116 $node->DESTROY();
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117 $node = undef;
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118 }
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119 $self->{'_desc'} = {};
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120 }
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121 }
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122
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123 sub to_string{
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124 my ($self) = @_;
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125 return sprintf("%s%s%s",
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126 defined $self->id ? $self->id : '',
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127 defined $self->branch_length ? ':' .
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128 $self->branch_length : ' ',
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129 '[' . join(":", "&&NHX",
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130 map { "$_=" .join(',',
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131 $self->get_tag_values($_))}
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132 $self->get_all_tags() ) . ']'
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133 );
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134 }
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135
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136 =head2 nhx_tag
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137
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138 Title : nhx_tag
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139 Usage : my $tag = $nodenhx->nhx_tag(%tags);
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140 Function: Set tag-value pairs for NHX nodes
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141 Returns : none
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142 Args : hashref to update the tags/value pairs
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143 OR
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144 with a scalar value update the bootstrap value by default
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145
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146
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147 =cut
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148
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149 sub nhx_tag {
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150 my ($self, $tags) = @_;
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151 if (defined $tags && (ref($tags) =~ /HASH/i)) {
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152 while( my ($tag,$val) = each %$tags ) {
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153 if( ref($val) =~ /ARRAY/i ) {
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154 for my $v ( @$val ) {
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155 $self->add_tag_value($tag,$v);
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156 }
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157 } else {
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158 $self->add_tag_value($tag,$val);
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159 }
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160 }
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161 if (exists $tags->{'B'}) {
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162 $self->bootstrap($tags->{'B'});
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163 }
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164 } elsif (defined $tags and ! ref ($tags)) {
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165 print STDERR "here with $tags\n";
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166 # bootstrap by default
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167 $self->bootstrap($tags);
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168 }
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169 }
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170
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171 1;
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