/ 
bioperl-1.5.2_004-RCd
/ Bio::TreeIO::newick

NAME

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

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.

FEEDBACK

Mailing Lists

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

Reporting Bugs

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/

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

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

new

 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 L<Bio::Node::Node::each_Descendent()> )

next_tree

Title   : next_tree
Usage   : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : L<Bio::Tree::TreeI>
Args    : none

write_tree

Title   : write_tree
Usage   : $treeio->write_tree($tree);
Function: Write a tree out to data stream in newick/phylip format
Returns : none
Args    : L<Bio::Tree::TreeI> object
Title   : print_tree_count
Usage   : $obj->print_tree_count($newval)
Function: Get/Set flag for printing out the tree count (paml,protml way)
Returns : value of print_tree_count (a scalar)
Args    : on set, new value (a scalar or undef, optional)

bootstrap_style

Title   : bootstrap_style
Usage   : $obj->bootstrap_style($newval)
Function: A description of how bootstraps and branch lengths are
          written, as the ID part of the internal node or else in []
          in the branch length (Molphy-like; I am sure there is a
          better name for this but am not sure where to go for some
          sort of format documentation)

          If no branch lengths are requested then no bootstraps are usually
          written (unless someone REALLY wants this functionality...)

          Can take on strings which contain the possible values of
          'nobranchlength'   --> don't draw any branch lengths - this
                                 is helpful if you don't want to have to 
                                 go through and delete branch len on all nodes
          'molphy' --> draw bootstraps (100) like
                                 (A:0.11,B:0.22):0.33[100];
          'traditional' --> draw bootstraps (100) like
                                 (A:0.11,B:0.22)100:0.33;
Returns : value of bootstrap_style (a scalar)
Args    : on set, new value (a scalar or undef, optional)

order_by

Title   : order_by
Usage   : $obj->order_by($newval)
Function: Allow node order to be specified (typically "alpha")
          See L<Bio::Node::Node::each_Descendent()>
Returns : value of order_by (a scalar)
Args    : on set, new value (a scalar or undef, optional)