# $Id: Nexus.pm 843 2009-03-04 23:50:27Z rvos $
package Bio::Phylo::Unparsers::Nexus;
use strict;
use Bio::Phylo::IO;
use Bio::Phylo::Util::CONSTANT qw(:objecttypes);
use Bio::Phylo::Util::Exceptions 'throw';
use vars qw(@ISA);
@ISA=qw(Bio::Phylo::IO);

=head1 NAME

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

=head1 DESCRIPTION

This module turns a L<Bio::Phylo::Matrices::Matrix> object into a nexus
formatted matrix. It is called by the L<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	

=begin comment

 Type    : Constructor
 Title   : _new
 Usage   : my $nex = Bio::Phylo::Unparsers::Nexus->_new;
 Function: Initializes a Bio::Phylo::Unparsers::Nexus object.
 Returns : A Bio::Phylo::Unparsers::Nexus object.
 Args    : none.

=end comment

=cut

sub _new {
    my $class = shift;
    my $self  = {};
    if (@_) {
        my %opts = @_;
        foreach my $key ( keys %opts ) {
            my $localkey = uc $key;
            $localkey =~ s/-//;
            unless ( ref $opts{$key} ) {
                $self->{$localkey} = uc $opts{$key};
            }
            else {
                $self->{$localkey} = $opts{$key};
            }
        }
    }
    bless $self, $class;
    return $self;
}

=begin comment

 Type    : Wrapper
 Title   : _to_string($matrix)
 Usage   : $nexus->_to_string($matrix);
 Function: Stringifies a matrix object into
           a nexus formatted table.
 Alias   :
 Returns : SCALAR
 Args    : Bio::Phylo::Matrices::Matrix;

=end comment

=cut

sub _to_string {
    my $self   = shift;
    my $blocks = $self->{'PHYLO'};
    my $nexus  = "#NEXUS\n";
    my $type;
    eval { $type = $blocks->_type  };

    # array?
    if ( $@ ) {
    	for my $block ( @$blocks ) {
    		eval { $type = $block->_type };
    		my %args;
    		if ( $type == _FOREST_ ) {
    			if ( exists $self->{'FOREST_ARGS'} ) {
    				%args = %{ $self->{'FOREST_ARGS'} };
    			}
    		}
    		elsif ( $type == _TAXA_ ) {
    			if ( exists $self->{'TAXA_ARGS'} ) {
    				%args = %{ $self->{'TAXA_ARGS'} };
    			}    			
    		}
    		elsif ( $type == _MATRIX_ ) {
    			if ( exists $self->{'MATRIX_ARGS'} ) {
    				%args = %{ $self->{'MATRIX_ARGS'} };
    			}     			
    		}
    		elsif ( $@ ) {
		    	throw 'ObjectMismatch' => "Can't unparse this object: $blocks";
    		}
    		$nexus .= $block->to_nexus(%args);
    	}
    }
    
    # matrix?
    elsif ( defined $type and $type == _MATRIX_ ) {
    	$nexus .= $blocks->to_nexus;
    }
    
    # wrong!
    else {
    	throw 'ObjectMismatch' => "Can't unparse this object: $blocks";
    }
    
    return $nexus;

}

# podinherit_insert_token
# podinherit_start_token_do_not_remove
# AUTOGENERATED pod created by /Users/rvosa/Applications/podinherit on Wed Mar  4 17:13:58 2009
# DO NOT EDIT the code below, rerun /Users/rvosa/Applications/podinherit instead.

=pod

=head1 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.

=head2 SUPERCLASS Bio::Phylo::IO

Bio::Phylo::Unparsers::Nexus inherits from superclass L<Bio::Phylo::IO>. 
Below are the public methods (if any) from this superclass.

=over

=item 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.          

=item 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)

=back

=cut

# podinherit_stop_token_do_not_remove

=head1 SEE ALSO

=over

=item L<Bio::Phylo::IO>

The nexus serializer is called by the L<Bio::Phylo::IO> object.

=item L<Bio::Phylo::Manual>

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

=back

=head1 REVISION

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

=cut

1;