# 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;

     my $self = shift;
    $self->SUPER::_initialize(@_);
    my ($print_count,$style,$order_by) = $self->_rearrange([qw(PRINT_COUNT 
							       BOOTSTRAP_STYLE
							       ORDER_BY)],
					  @_);
    $self->print_tree_count($print_count || 0);
    $self->bootstrap_style($style || $DefaultBootstrapStyle);
    $self->order_by($order_by) if defined $order_by;
    return;

   my ($self) = @_;
   local $/ = ";\n";
   return unless $_ = $self->_readline;
   s/[\r\n]//gs;
   my $score;
   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;
   if( s/^\s*\[([^\]]+)\]// ) {
       my $match = $1;
       $match =~ s/\s//g;
       $match =~ s/lh\=//;
       if( $match =~ /([-\d\.+]+)/ ) {
	   $score = $1;
       }
   }

   $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 ';' ) {
	   my $tree = $self->_eventHandler->end_document($chars);
	   $tree->score($score) if defined $score;
	   return $tree;
       } 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("internal node, 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 ( $ch eq ',' ) {
	   if( length($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;
		   $chars = '';		   
	       } else { 
		   $self->debug("leaf 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 = 0;
	   if( $lastevent ne ')' ) {
	       $leafstatus = 1;
	   }
	   $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;

   my ($self,@trees) = @_;  
   my $orderby = $self->order_by;
   my $bootstrap_style = $self->bootstrap_style;
   if( $self->print_tree_count ){ 
       $self->_print(sprintf(" %d\n",scalar @trees));
   }
   my $nl = $self->newline_each_node;
   foreach my $tree( @trees ) {
       my @data = _write_tree_Helper($tree->get_root_node,
				     $bootstrap_style,
				     $orderby,
				     $nl);
       if( $nl ) {
	   chomp($data[-1]);# remove last newline
	   $self->_print(join(",\n", @data), ";\n");
       } else {
	   $self->_print(join(',', @data), ";\n");
       }
   }
   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return;

    my ($node,$style,$orderby,$nl) = @_;
    $style = '' unless defined $style;
    return () if (!defined $node);

    my @data;
    foreach my $n ( $node->each_Descendent($orderby) ) {
	push @data, _write_tree_Helper($n,$style,$orderby,$nl);
    }
    
    # let's explicitly write out the bootstrap if we've got it
    my $id = $node->id_output;
    my $bs = $node->bootstrap; # bs better not have any spaces?
    $bs =~ s/\s+//g if defined $bs;
    my $bl = $node->branch_length;
    if( @data ) {
	if( $nl ) {
	    $data[0] = "(\n" . $data[0];
	    $data[-1] .= ")\n";
	} else {
	    $data[0] = "(" . $data[0];
	    $data[-1] .= ")";
	}

	if( $node->is_Leaf ) { 
	    $node->debug("node is a leaf!  This is unexpected...");

	    $id ||= '';
	    if( ! defined $bl || ! length($bl) ||
		($style && $style =~ /nobranchlength/i) ) {
		$data[-1] .= $id;
	    } elsif( defined $bl && length($bl) ) { 
		$data[-1] .= "$id:$bl";
	    } else { 
		$data[-1] .= $id;
	    }
	} else { 
	    if( ! defined $bl || ! length($bl) ||
		($style && $style =~ /nobranchlength/i) ) {
		
		if( defined $id || defined $bs ) {
		    $data[-1] .= defined $bs ? $bs : $id;
		}
	    } elsif( $style =~ /molphy/i ) {
		if( defined $id ) {
		    $data[-1] .= $id;
		}
		if( $bl =~ /\#/) {
		    $data[-1] .= $bl;
		} else { 
		    $data[-1] .= ":$bl";
		}
		if( defined $bs ) { 
		    $data[-1] .= "[$bs]";
		}
	    } else {
		# traditional style of 
		# ((A:1,B:2)81:3);   where 3 is internal node branch length
		#                    and 81 is bootstrap/node label
		if( defined $bs || defined $id ) {
		    $data[-1] .= defined $bs ? "$bs:$bl" : "$id:$bl";
		} elsif( $bl =~ /\#/ ) {
		    $data[-1] .= $bl;
		} else { 
		    $data[-1] .= ":$bl"; 
		}
	    }
	}
    } elsif( defined $id || defined $bl ) {
	my $str;
	$id ||= '';
	if( ! defined $bl || ! length($bl) ||
	    ($style && $style =~ /nobranchlength/i) ) {
	    $str = $id;
	} elsif( defined $bl && length($bl) ) { 
	    $str = "$id:$bl";
	} else { 
	    $str = $id;
	}
	push @data, $str;
    }
    return @data;

    my $self = shift;
    return $self->{'_print_tree_count'} = shift if @_;
    return $self->{'_print_tree_count'} || 0;

    my $self = shift;
    my $val = shift;
    if( defined $val ) {

	if( $val !~ /^nobranchlength|molphy|traditional/i ) {
	    $self->warn("requested an unknown bootstrap style $val, expect one of nobranchlength,molphy,traditional, not updating value.  Default is $DefaultBootstrapStyle\n");
	} else { 
	    $self->{'_bootstrap_style'} = $val;
	}
    }
    return $self->{'_bootstrap_style'} || $DefaultBootstrapStyle;

    my $self = shift;

    return $self->{'order_by'} = shift if @_;
    return $self->{'order_by'};

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  http://bugzilla.open-bio.org/

 Title   : new
 Args    : -print_count     => boolean  default is false
           -bootstrap_style => set the bootstrap style (one of nobranchlength,
							molphy, traditional)
           -order_by        => set the order by sort method 
                               (see Bio::Node::Node::each_Descendent() )