Summary

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

Package variables

Inherit

Bio::TreeIO

Synopsis

  use Bio::TreeIO;
  my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick');
  my $out = Bio::TreeIO->new(-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 = Bio::TreeIO::tabtree->new();
 Function: Builds a new Bio::TreeIO::tabtree object 
 Returns : Bio::TreeIO::tabtree
 Args    :

 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

 Title   : next_tree
 Usage   : 
 Function: Sorry not possible with this format
 Returns : none
 Args    : none

Methods code

sub new {

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

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

}

sub write_tree {

   my ($self,$tree) = @_;      
   my $line = _write_tree_Helper($tree->get_root_node,"");
   $self->_print($line. "\n");   
   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return;

}

sub _write_tree_Helper {

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

    my @d = $node->each_Descendent();
    my $line = "";
    my ($i,$lastchild) = (0,scalar @d - 1);
    for my $n ( @d ) {
	if( $n->is_Leaf ) {
	    $line .= sprintf("%s|\n %s\\-%s\n",
			     $indent,$indent,$n->id || '');
	} else { 
	    $line .= sprintf("$indent|  %s\n",( $n->id ? 
					       sprintf("(%s)",$n->id) : ''));
	}
	my $new_indent = $indent . (($i == $lastchild) ? "| " : "  ");
	if( $n != $node ) {
	    # avoid the unlikely case of cycles
	    $line .= _write_tree_Helper($n,$new_indent);	
	}
    }
    return $line;

}

sub next_tree {

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

1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

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

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

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

Email jason@bioperl.org

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