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Summary

Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing

Package variables

Included modules

Inherit

Bio::TreeIO

Synopsis

  use Bio::TreeIO;
  my $in = new Bio::TreeIO(-file => 'input', -format => 'newick');
  my $out = new Bio::TreeIO(-file => '>output', -format => 'tabtree');

  while( my $tree = $in->next_tree ) {
      $out->write_tree($tree);
  }

Description

This is a made up format just for outputting trees as an ASCII drawing.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::TreeIO::tabtree();
 Function: Builds a new Bio::TreeIO::tabtree object 
 Returns : Bio::TreeIO::tabtree
 Args    :

 Title   : next_tree
 Usage   : 
 Function: Sorry not possible with this format
 Returns : none
 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 ($node,$depth) = @_;
    return () if (!defined $node);

    my @data;
    my @d = $node->each_Descendent();

    push @data,sprintf("%s%s","\t"x$depth,
		       $node->to_string);
    if( @d ) {
	my $c = 0;
	foreach my $n ( @d ) {
	    push @data, _write_tree_Helper($n,$depth+1);
	}
    }

    return @data;

}

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

}

sub next_tree {

    $_[0]->throw("Sorry the format 'tabtree' can only be used as an output format at this time");
}

1;

}

sub write_tree {

   my ($self,$tree) = @_;      
   my @data = _write_tree_Helper($tree->get_root_node,0);
   $self->_print(join("\n", @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 _