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Summary

Bio::TreeIO::nhx - TreeIO implementation for parsing
Newick/New Hampshire eXtendend (NHX) format.

Package variables

Included modules

Inherit

Bio::TreeIO

Synopsis

  # do not use this module directly
  use Bio::TreeIO;
  my $treeio = new Bio::TreeIO(-format => 'nhx', -file => 'tree.dnd');
  my $tree = $treeio->next_tree;

Description

This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format.

Methods

Methods description

 Title   : next_tree
 Usage   : my $tree = $treeio->next_tree
 Function: Gets the next tree in the stream
 Returns : Bio::Tree::TreeI
 Args    : none

 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Write a tree out to data stream in nhx format
 Returns : none
 Args    : Bio::Tree::TreeI object

Methods code

sub _initialize {

  my($self, %args) = @_;
  $args{-nodetype} ||= 'Bio::Tree::NodeNHX';
  $self->SUPER::_initialize(%args);

}

sub _write_tree_Helper {

    my ($node) = @_;
    return () unless defined $node;

    my @data;
    
    foreach my $n ( $node->each_Descendent() ) {
	push @data, _write_tree_Helper($n);
    }
        
    if( @data > 1 ) {
	$data[0] = "(" . $data[0];
	$data[-1] .= ")";
	$data[-1] .= ":". $node->branch_length if $node->branch_length;	
	# this is to not print out an empty NHX for the root node which is 
	# a convience for how we get a handle to the whole tree
	if( $node->ancestor || $node->id || defined $node->branch_length ) {
	    $data[-1] .= '[' . 
		join(":", "&&NHX", 
		     map { "$_=" .join(',',$node->get_tag_values($_)) } 
		     $node->get_all_tags() ) . ']';
	}
    } else { 
	push @data, $node->to_string; # a leaf
    }
    return @data;
}


1;

}

sub next_tree {

    my ($self) = @_;
    local $/ = ";\n";
    return unless $_ = $self->_readline;
    s/\s+//g;
    $self->debug("entry is $_\n");
    my $chars = '';
    $self->_eventHandler->start_document;
    my ($prev_event,$lastevent) = ('','');
    my @ch = split(//, $_);
    foreach my $ch  (@ch) {
	if( $ch eq ';' ) { 	   
	    $self->_eventHandler->in_element('node') && 
		$self->_eventHandler->end_element( {'Name' => 'node'});
	    return $self->_eventHandler->end_document;
	} elsif ($ch eq '[') {
	    if ( length $chars ) {
		if ( $lastevent eq ':' ) {
		    $self->_eventHandler->start_element( { Name => 'branch_length' } );
		    $self->_eventHandler->characters($chars);
		    $self->_eventHandler->end_element( { Name => 'branch_length' });
		    $lastevent = $prev_event;
		} else {
		    $self->debug("id with no branchlength is $chars\n");
		    $self->_eventHandler->start_element( { 'Name' => 'node' } );
		    $self->_eventHandler->start_element( { 'Name' => 'id' } );
		    $self->_eventHandler->characters($chars);
		    $self->_eventHandler->end_element( { 'Name' => 'id' } );		   
		}
	    } else {
		$self->_eventHandler->start_element( { Name => 'node' } );
	    }
	    my $leafstatus = ( $lastevent ne ')' ) ? 1 : 0;
	    $self->_eventHandler->start_element({'Name' => 'leaf'});
	    $self->_eventHandler->characters($leafstatus);
	    $self->_eventHandler->end_element({'Name' => 'leaf'});	   
	    $chars = '';
	    
	    $self->_eventHandler->start_element( { Name => 'nhx_tag' });
	} elsif( $ch eq '(' ) {
	    $chars = '';
	    $self->_eventHandler->start_element( {'Name' => 'tree'} );
	} elsif($ch eq ')' ) {
	    if( length $chars ) {
		if( $lastevent eq ':') {
		    unless ($self->_eventHandler->within_element('nhx_tag')) {
			$self->_eventHandler->start_element( { 'Name' => 'branch_length'});
			$self->_eventHandler->characters($chars);
			$self->_eventHandler->end_element( {'Name' => 'branch_length'});
		    } else {
			$self->throw("malformed input; end of node ) before ] found");
		    }
		} else { 
		    $self->debug("id with no branchlength is $chars\n");
		    $self->_eventHandler->start_element( { 'Name' => 'node' } );
		    $self->_eventHandler->start_element( { 'Name' => 'id' } );
		    $self->_eventHandler->characters($chars);
		    $self->_eventHandler->end_element( { 'Name' => 'id' } );
		}

	    } elsif ( $lastevent ne ']' ) {
		$self->_eventHandler->start_element( {'Name' => 'node'} );
	    }
	    my $leafstatus = ( $lastevent ne ')' ) ? 1 : 0;
	    $self->_eventHandler->start_element({'Name' => 'leaf'});
	    $self->_eventHandler->characters($leafstatus);
	    $self->_eventHandler->end_element({'Name' => 'leaf'});	   
	    
	    $self->_eventHandler->end_element( {'Name' => 'node'} );
	    $self->_eventHandler->end_element( {'Name' => 'tree'} );
	    $chars = '';
	} elsif ( $ch eq ',' ) {
	    if( length $chars ) {
		if( $lastevent eq ':' ) {
		    $self->_eventHandler->start_element( { 'Name' => 'branch_length'});
		    $self->_eventHandler->characters($chars);
		    $self->_eventHandler->end_element( {'Name' => 'branch_length'});
		    $lastevent = $prev_event;
		} else { 
		    $self->debug("id with no branchlength is $chars\n");
		    $self->_eventHandler->start_element( { 'Name' => 'node' } );
		    $self->_eventHandler->start_element( { 'Name' => 'id' } );
		    $self->_eventHandler->characters($chars);
		    $self->_eventHandler->end_element( { 'Name' => 'id' } );
		}   
	    } elsif ( $lastevent ne ']' ) {
		$self->_eventHandler->start_element( { 'Name' => 'node' } );
	    }
	    $self->_eventHandler->end_element( {'Name' => 'node'} );
	    $chars = '';
	} elsif( $ch eq ':' ) {
	    if ($self->_eventHandler->within_element('nhx_tag')) {
		if ($lastevent eq '=') {
		    $self->_eventHandler->start_element( { Name => 'tag_value' } );
		    $self->_eventHandler->characters($chars);
		    $self->_eventHandler->end_element( { Name => 'tag_value' } );
		    $chars = '';
		} else {
		    if ($chars eq '&&NHX') {
			$chars = ''; # get rid of &&NHX:
		    } else {
			$self->throw("Unrecognized, non\&\& NHX string: >>$chars<<");
		    }
		}
	    } elsif ($lastevent ne ']') {
		$self->debug("id with a branchlength coming is $chars\n");
		$self->_eventHandler->start_element( { 'Name' => 'node' } );
		$self->_eventHandler->start_element( { 'Name' => 'id' } );
		$self->_eventHandler->characters($chars);
		$self->_eventHandler->end_element( { 'Name' => 'id' } );
		$chars = '';
	    }
	} elsif ( $ch eq '=' ) {
	    if ($self->_eventHandler->within_element('nhx_tag')) {
		$self->_eventHandler->start_element( { Name => 'tag_name' } );
		$self->_eventHandler->characters($chars);
		$self->_eventHandler->end_element( { Name => 'tag_name' } );
		$chars = '';
	    } else {
		$chars .= $ch;
	    }
	} elsif ( $ch eq ']' ) {
	    if ($self->_eventHandler->within_element('nhx_tag') && $lastevent eq '=') {
		$self->_eventHandler->start_element( { Name => 'tag_value' } );
		$self->_eventHandler->characters($chars);
		$self->_eventHandler->end_element( { Name => 'tag_value' } );
		$chars = '';
		$self->_eventHandler->end_element( { Name => 'nhx_tag' } );
	    } else {
		$chars .= $ch;
		next;
	    }
	} else { 	   
	    $chars .= $ch;
	    next;
	}
	$prev_event = $lastevent;
	$lastevent = $ch;
    }       
    return undef;

}

sub write_tree {

    my ($self,@trees) = @_;
   foreach my $tree ( @trees ) {
       my @data = _write_tree_Helper($tree->get_root_node);
       if($data[-1] !~ /\)$/ ) {
	   $data[0] = "(".$data[0];
	   $data[-1] .= ")";
       }
       $self->_print(join(',', @data), ";\n");
   }
   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return;

}

General documentation

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Describe contact details here

Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _