NAME

Bio::Phylo::Unparsers::Nexus - Serializer used by Bio::Phylo::IO, no serviceable parts inside

DESCRIPTION

This module turns a Bio::Phylo::Matrices::Matrix object into a nexus formatted matrix. It is called by the Bio::Phylo::IO facade, don't call it directly. You can pass the following additional arguments to the unparse call:

        # an array reference of matrix, forest and taxa objects:
        -phylo => [ $block1, $block2 ]
        
        # the arguments that can be passed for matrix objects, 
        # refer to Bio::Phylo::Matrices::Matrix::to_nexus:
        -matrix_args => {}

        # the arguments that can be passed for forest objects, 
        # refer to Bio::Phylo::Forest::to_nexus:
        -forest_args => {}

        # the arguments that can be passed for taxa objects, 
        # refer to Bio::Phylo::Taxa::to_nexus:
        -taxa_args => {}        
        
        OR:
        
        # for backward compatibility:
        -phylo => $matrix       

INHERITED METHODS

Bio::Phylo::Unparsers::Nexus inherits from one or more superclasses. This means that objects of class Bio::Phylo::Unparsers::Nexus 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::Unparsers::Nexus 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 nexus serializer is called by the Bio::Phylo::IO object.

Bio::Phylo::Manual

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

REVISION

 $Id: Nexus.pm 843 2009-03-04 23:50:27Z rvos $