use Bio::Factory::EMBOSS;
  # get an EMBOSS application object from the EMBOSS factory
  $factory = new Bio::Factory::EMBOSS
  $application = $factory->program('embossversion');
  # run the application with an optional hash containing parameters
  $result = $application->run(); # returns a string or creates a file
  print $result . "\n";

  $water = $factory->program('water');

  # here is an example of running the application
  # water can compare 1 seq against 1->many sequences
  # in a database using Smith-Waterman
  my $seq_to_test; # this would have a seq here
  my @seqs_to_check; # this would be a list of seqs to compare 
                     # (could be just 1)
  my $wateroutfile = 'out.water';
  $water->run({ '-sequencea' => $seq_to_test,
              '-seqall'    => \@seqs_to_check,
              '-gapopen'   => '10.0',
              '-gapextend' => '0.5',
              '-outfile'   => $wateroutfile});
  # now you might want to get the alignment
  use Bio::AlignIO;
  my $alnin = new Bio::AlignIO(-format => 'emboss',
			       -file   => $wateroutfile);

  while( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
  }

  my($class, $args) = @_;
  my $self = $class->SUPER::new();  
  $self->{ '_attributes' } = $args;

  $self->name($self->{ '_attributes' }->{'name'});
  delete $self->{ '_attributes' }->{'name'};

  $self->descr($self->{ '_attributes' }->{'documentation'});
  delete $self->{ '_attributes' }->{'documentation'};

  $self->group($self->{ '_attributes' }->{'groups'});
  delete $self->{ '_attributes' }->{'groups'};

  $self->{'_io'} = new Bio::Root::IO('-verbose' => $self->verbose);
  return $self;

    my ($self, $input) = @_;
    $self->{'_io'}->_io_cleanup();
    # test input
    print Dumper($input) if $self->verbose > 0;
    $self->_acd2input($input);

    # collect the options into a string 
    my $option_string = '';
    foreach my $attr (keys %{$input}) {
	my $attr_name = substr($attr, 1) if substr($attr, 0, 1) =~ /\W/;
	
	my $array = 0;
	
	if( defined $input->{$attr} && ref($input->{$attr}) ) {

	    my (@pieces);
	    
	    if( $array = (ref($input->{$attr}) =~ /array/i) ) {
		foreach my $s ( @{$input->{$attr}} ) {
		    @pieces = @{$input->{$attr}};
		}
	    } else {
		@pieces = ($input->{$attr});
	    }
	    if( $pieces[0]->isa('Bio::PrimarySeqI') ) {
		require Bio::SeqIO;
		my ($tfh,$tempfile) = $self->{'_io'}->tempfile();
		my $out = new Bio::SeqIO(-format => 'fasta',
					 -fh     => $tfh);
		foreach my $seq ( @pieces ) {
			$out->write_seq($seq);
		    }
		$out->close();
		$input->{$attr} = $tempfile;
	    } elsif( $pieces[0]->isa('Bio::Align::AlignI') ) {
		require Bio::AlignIO;
		my ($tfh,$tempfile) = $self->{'_io'}->tempfile();
		my $out = new Bio::AlignIO(-format => 'msf',
					   -fh     => $tfh);
		foreach my $p ( @pieces ) {
		    $out->write_aln($p);
		}
		$input->{$attr} = $tempfile;
	    }
	}
	# ADD: validate the values against acd
	
	$self->debug("Input attr: ". $attr_name. " => ". 
		     %{$input}->{$attr}. "\n"); 
	$option_string .= " " . $attr;
	$option_string .= " ". %{$input}->{$attr} 
	   if %{$input}->{$attr};
    }

    my $runstring = join (' ', $self->name, $option_string, '-auto');
    print STDERR "Command line: ", $runstring, "\n" if $self->verbose > 0;
    return `$runstring`;

    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'_name'} = $value;
    }
    return $self->{'_name'};

    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'_descr'} = $value;
    }
    return $self->{'_descr'};

    my ($self,$value) = @_;
    if (defined $value) {
	my ($group, $subgroup) = split ':', $value;
	$self->{'_group'} = $group;
	$self->{'_subgroup'} = $subgroup;
    }
    return $self->{'_group'};

    my ($self) = @_;
    return $self->{'_subgroup'};

    my ($self, $input) = @_;
    # match acd attributes against the input
    foreach my $attr (keys %{$self->{'_attributes'}}) {
	$self->debug( "ACD Attr: |". $attr. "|\n");
	my $input_value = '';
	my $input_key = '';
	$input_key = 1, $input_value = %{$input}->{"-$attr"} if defined %{$input}->{"-$attr"};
#	my $input_name = substr($input_value, 1) if substr($input_value, 0, 1) =~ /\W/;
	$self->debug("--------------$input_value, $attr\n") if $input_key;

#	 $self->throw('Attribute [$attr] not set') if 
#	     defined %{$self}->{'_attributes'}->{$attr_name}->{optional} and $input_value ;
#	 
#	 $self->throw('Attribute [$attr] not set')
#	     if ( %{$self}->{'_attributes'}->{$attr}->{optional} eq 'N' and defined %{$input}->{$attr_name} and %{$input}->{$attr_name} eq '' ) or 
#		 
##
#		 ( %{$self}->{'_attributes'}->{$attr}->{required} eq 'Y' and not exists %{$input}->{$attr_name})  ;
    }

  bioperl-l@bioperl.org                         - General discussion
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  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

 Title   : _acd2input
 Usage   : $embossfactory->_acd2input()
 Function: compares ACD file requirements to input hash
 Returns : 
 Throws  : if requirements are not met 
 Args    : None