NAME

Bio::Phylo::Parsers::Nexml - Parser used by Bio::Phylo::IO, no serviceable parts inside

DESCRIPTION

This module parses nexml data. It is called by the Bio::Phylo::IO facade, don't call it directly. In addition to parsing from files, handles or strings (which are specified by the -file, -handle and -string arguments) this parser can also parse xml directly from a url (-url => $phylows_output), provided you have LWP installed.

INHERITED METHODS

Bio::Phylo::Parsers::Nexml inherits from one or more superclasses. This means that objects of class Bio::Phylo::Parsers::Nexml also "do" the methods from the superclasses in addition to the ones implemented in this class. Below is the documentation for those additional methods, organized by superclass.

SUPERCLASS Bio::Phylo::IO

Bio::Phylo::Parsers::Nexml inherits from superclass Bio::Phylo::IO. Below are the public methods (if any) from this superclass.

parse()

Parses a file or string.

Type    : Class method
Title   : parse
Usage   : my $obj = Bio::Phylo::IO->parse(%options);
Function: Creates (file) handle, 
          instantiates appropriate parser.
Returns : A Bio::Phylo::* object
Args    : -file    => (path),
           or
          -string  => (scalar),
          -format  => (description format),
          -(other) => (parser specific options)
Comments: The parse method makes assumptions about 
          the capabilities of Bio::Phylo::Parsers::* 
          modules: i) their names match those of the
          -format => (blah) arguments, insofar that 
          ucfirst(blah) . '.pm' is an existing module; 
          ii) the modules implement a _from_handle, 
          or a _from_string method. Exceptions are 
          thrown if either assumption is violated. 
          
          If @ARGV contains even key/value pairs such
          as "format newick file <filename>" (note: no
          dashes) these will be prepended to @_, for
          one-liners.          

unparse()

Unparses object(s) to a string.

Type    : Class method
Title   : unparse
Usage   : my $string = Bio::Phylo::IO->unparse(
              %options
          );
Function: Turns Bio::Phylo object into a 
          string according to specified format.
Returns : SCALAR
Args    : -phylo   => (Bio::Phylo object),
          -format  => (description format),
          -(other) => (parser specific options)

SEE ALSO

Bio::Phylo::IO

The nexml parser is called by the Bio::Phylo::IO object. Look there to learn how to parse nexml (or any other data Bio::Phylo supports).

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

http://www.nexml.org

For more information about the nexml data standard, visit http://www.nexml.org

REVISION

$Id: Nexml.pm 844 2009-03-05 00:07:26Z rvos $