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Summary

Bio::TreeIO::newick - TreeIO implementation for parsing
Newick/New Hampshire/PHYLIP format.

Package variables

Included modules

Inherit

Bio::TreeIO

Synopsis

  # do not use this module directly
  use Bio::TreeIO;
  my $treeio = new Bio::TreeIO(-format => 'newick', 
                               -file => 't/data/LOAD_Ccd1.dnd');
  my $tree = $treeio->next_tree;

Description

This module handles parsing and writing of Newick/PHYLIP/New Hampshire 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 newick/phylip format
 Returns : none
 Args    : Bio::Tree::TreeI object

Methods code

sub _write_tree_Helper {

    my ($node) = @_;
    return () if (!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] .= ")";
	# let's explicitly write out the bootstrap if we've got it
	my $b;
	if( defined ($b = $node->bootstrap) ) {
	    $data[-1] .= $b;
	} elsif( defined ($b = $node->id) ) {
	    $data[-1] .= $b;
	}
	$data[-1] .= ":". $node->branch_length if( $node->branch_length);
	
    } else {
	if( defined $node->id || defined $node->branch_length ) { 
	    push @data, sprintf("%s%s",
				defined $node->id ? $node->id : '', 
				defined $node->branch_length ? ":" .
				$node->branch_length : '');
	}
    }
    return @data;
}


1;

}

sub next_tree {

   my ($self) = @_;
   local $/ = ";\n";
   return unless $_ = $self->_readline;
#   s/\s+//g;
   my $despace = sub {my $dirty = shift; $dirty =~ s/\s+//gs; return $dirty};
   my $dequote = sub {my $dirty = shift; $dirty =~ s/^"?\s*(.+?)\s*"?$/$1/; return $dirty};
   s/([^"]*)(".+?")([^"]*)/$despace->($1) . $dequote->($2) . $despace->($3)/egsx;
   $self->debug("entry is $_\n");
#   my $empty = chr(20);
 
   # replace empty labels with a tag
#   s/\(,/\($empty,/ig;
#   s/,,/,$empty,/ig;
#   s/,,/,/ig;
#   s/,\)/,$empty\)/ig;
#   s/\"/\'/ig;

   my $chars = '';
   $self->_eventHandler->start_document;
   my ($prev_event,$lastevent,$id) = ('','','');
   foreach my $ch ( split(//,$_) ) {
       if( $ch eq ';' ) { 	   
	   return $self->_eventHandler->end_document;
       } elsif( $ch eq '(' ) {
	   $chars = '';
	   $self->_eventHandler->start_element( {'Name' => 'tree'} );
       } elsif($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' } );
		   $id = $chars;
	       }
	       my $leafstatus = 0;
	       if( $lastevent ne ')' ) {
		   $leafstatus = 1;
	       }

	       $self->_eventHandler->start_element({'Name' => 'leaf'});
	       $self->_eventHandler->characters($leafstatus);
	       $self->_eventHandler->end_element({'Name' => 'leaf'});
	       $id = '';
	   } else {
	       $self->_eventHandler->start_element( {'Name' => 'node'} );
	   }

	   $self->_eventHandler->end_element( {'Name' => 'node'} );
	   $self->_eventHandler->end_element( {'Name' => 'tree'} );
	   $chars = '';
       } elsif ( $ch eq ',' ) {
	   if( $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;
		   $chars = '';		   
	       } 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' } );
		   $id = $chars;
	       }
	   } 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'});
	   $self->_eventHandler->end_element( {'Name' => 'node'} );
	   $chars = '';
	   $id    = '';
       } elsif( $ch eq ':' ) {
	   $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' } );	   
	   $id = $chars;
	   $chars = '';
       } 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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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _