/ 
Bio-Phylo-0.01
River stage two • 8 direct dependents • 17 total dependents
/ Bio::Phylo::Parsers::Newick

NAME

Bio::Phylo::Parsers::Newick - A library for parsing phylogenetic trees in Newick format.

SYNOPSIS

my $newick = new Bio::Phylo::Parsers::Newick;
my $trees = $newick->parse(-file => 'tree.dnd', -format => 'newick');

DESCRIPTION

This module parses tree descriptions in parenthetical format.

CONSTRUCTOR

new()
Type    : Constructor
Title   : new
Usage   : my $newick = new Bio::Phylo::Parsers::Newick;
Function: Initializes a Bio::Phylo::Parsers::Newick object.
Returns : A Bio::Phylo::Parsers::Newick object.
Args    : none.

PARSER

from_both(%options), from_handle, from_string
Type    : Wrapper
Title   : from_both(%options)
Usage   : $newick->from_both(%options);
Function: Extracts trees from file, sends strings to _parse_string()
Returns : Bio::Phylo::Trees
Args    : -handle => (\*FH) or -string => (scalar).
Comments:
_parse_string($string)
Type    : Parser
Title   : _parse_string($string)
Usage   : my $tree = $newick->_parse_string($string);
Function: Creates a populated Bio::Phylo::Trees::Tree object from a newick
          string.
Returns : A Bio::Phylo::Trees::Tree object.
Args    : $string = a newick tree description
_nodelabels($string)
Type    : Internal method.
Title   : _nodelabels($string)
Usage   : my $labelled = $newick->_nodelabels($string);
Function: Returns a newick string with labelled nodes
Returns : SCALAR
Args    : $string = a newick tree description

CONTAINER

container
Type    : Internal method
Title   : container
Usage   : $newick->container;
Function:
Returns : SCALAR
Args    :
container_type
Type    : Internal method
Title   : container_type
Usage   : $newick->container_type;
Function:
Returns : SCALAR
Args    :

AUTHOR

Rutger Vos, <rvosa@sfu.ca>

BUGS

Please report any bugs or feature requests to bug-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.