Bio::TreeIO tabtree
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Summary
Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing
Package variables
No package variables defined.
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
newDescriptionCode
write_treeDescriptionCode
_write_tree_Helper
No description
Code
next_treeDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::TreeIO::tabtree->new();
Function: Builds a new Bio::TreeIO::tabtree object
Returns : Bio::TreeIO::tabtree
Args :
write_treecodeprevnextTop
 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
next_treecodeprevnextTop
 Title   : next_tree
Usage :
Function: Sorry not possible with this format
Returns : none
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
}
write_treedescriptionprevnextTop
sub write_tree {
   my ($self,$tree) = @_;      
   my $line = _write_tree_Helper($tree->get_root_node,"");
   $self->_print($line. "\n");   
   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return;
}
_write_tree_HelperdescriptionprevnextTop
sub _write_tree_Helper {
    my ($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;
}
next_treedescriptionprevnextTop
sub next_tree {
    $_[0]->throw("Sorry the format 'tabtree' can only be used as an output format at this time");
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _