# Build a Promoterwise alignment factory
  my @params = ('-s'=>1,'-query_start'=>10,'-dymem'=>1);
  my  $factory = Bio::Tools::Run::Promoterwise->new(@params);

  my (@fp)= $factory->run($seq1,$seq2);

  # each feature pair is a group of hsps
  foreach my $fp(@fp){
    print "Hit Length: ".$fp->feature1->length."\n";
    print "Hit Start: ".$fp->feature1->start."\n";
    print "Hit End: ".$fp->feature1->end."\n";
    print "Hsps: \n";
    my @first_hsp = $fp->feature1->sub_SeqFeature;
    my @second_hsp = $fp->feature2->sub_SeqFeature;
    for ($i..$#first_hsp){
      print $first_hsp[$i]->seq." ".$second_hsp[$i]->seq."\n";
    }
  }
  print "end: ". $fp->feature2->start."\t".$fp->feature2->end."\n";

  #Available parameters include:
  #( S T U V QUERY_START QUERY_END TARGET_START
  #TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT
  #LHREJECT LHMAX DYMEM KBYTE DYCACHE)
  #For an explanation of these parameters, please see documentation
  #from the Wise package.

    @PROMOTERWISE_PARAMS = qw( S T U V QUERY_START QUERY_END TARGET_START
                           TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT
                           LHREJECT LHMAX DYMEM KBYTE DYCACHE);
			   

    @OTHER_SWITCHES = qw(SILENT QUIET ERROROFFSTD);

    # Authorize attribute fields
    foreach my $attr ( @PROMOTERWISE_PARAMS, @PROMOTERWISE_SWITCHES,
                       @OTHER_SWITCHES) { $OK_FIELD{$attr}++;

    return 'promoterwise';

    return Bio::Root::IO->catfile($ENV{WISEDIR},"/src/bin/") if $ENV{WISEDIR};

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

  my ($attr, $value);
  while (@args) {
    $attr =   shift @args;
    $value =  shift @args;
    next if( $attr =~ /^-/ ); # don't want named parameters
    $self->$attr($value);
  }
  return $self;

    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr} = shift if @_;
    return $self->{$attr};

    my ($self) = @_;

    return undef unless $self->executable;
    my $prog = $self->executable;
    my $string = `$prog -version`;
    $string =~ /(Version *)/i;
    return $1 || undef;

    my ($self, $seq1, $seq2)=@_;
    my ($attr, $value, $switch);
    $self->io->_io_cleanup();
# Create input file pointer
    my ($infile1,$infile2)= $self->_setinput($seq1, $seq2);
    if (!($infile1 && $infile2))
        {$self->throw("Bad input data (sequences need an id ) ");}


# run promoterwise 
    my @fp = $self->_run($infile1,$infile2);
    return @fp;

    my ($self,$infile1,$infile2) = @_;
    my $instring;
    $self->debug( "Program ".$self->executable."\n");
    unless ( $self->executable ) {
	$self->throw("Cannot run Promoterwise unless the executable is found.".
                     " Check your environment variables or make sure ". 
                     "promoterwise is in your path.");
    }
    my $paramstring = $self->_setparams;
    
    my $commandstring = $self->executable." $infile1 $infile2 $paramstring";
    # this is to capture STDERR messages which leak out when you run programs
    # with open(FH, "... |");
    if( ( $self->silent && $self->quiet) &&
	($^O !~ /os2|dos|MSWin32|amigaos/) ) {
	# yeah, like promoterwise is really going to run on Windows...
	$commandstring .= ' -quiet -silent -erroroffstd  2> /dev/null';
    }
    $self->debug( "promoterwise command = $commandstring");
    open(PW, "$commandstring |") || 
        $self->throw( "Promoterwise call ($commandstring) crashed: $?\n ");
    my $pw_parser = Bio::Tools::Promoterwise->new(-fh=>\*PW,
                                                  -query1_seq=>$self->_query1_seq,
                                                  -query2_seq=>$self->_query2_seq);
    my @fp;
    while (my $fp = $pw_parser->next_result){
        push @fp,$fp;
    }

    return @fp;

    my ($self, $seq1, $seq2) = @_;
    my ($tfh1,$tfh2,$outfile1,$outfile2);

    $self->throw("calling with not enough arguments") unless $seq1 && $seq2;

    # Not going to set _query_pep/_subject_dna_seq 
    # if you pass in a filename

    unless( ref($seq1) ) {
	unless( -e $seq1 ) {
	    $self->throw("Sequence1 is not a Bio::PrimarySeqI object nor file\n");
	}
    	$outfile1 = $seq1;
    } 
    else { 
	($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
	my $out1 = Bio::SeqIO->new('-fh'     => $tfh1,
				   '-format' => 'fasta');
	$out1->write_seq($seq1);
	$self->_query1_seq($seq1);
	# Make sure you close things - this is what creates
	# Out of filehandle errors 
	close($tfh1);
	undef $tfh1;
    }
    unless( ref($seq2) ) {
    	unless( -e $seq2 ) { 
	    $self->throw("Sequence2 is not a Bio::PrimarySeqI object nor file\n");    
	}
	$outfile2 = $seq2;	
    } 
    else { 
    	($tfh2,$outfile2) = $self->io->tempfile(-dir=>$self->tempdir);
	my $out2 = Bio::SeqIO->new('-fh'     => $tfh2, 
				   '-format' => 'fasta');
    	$out2->write_seq($seq2);

	$self->_query2_seq($seq2);
	# Make sure you close things - this is what creates
	# Out of filehandle errors 
	close($tfh2);
	undef $tfh2;
    }
    return ($outfile1,$outfile2);

    my ($self) = @_;
    my $param_string;
    foreach my $attr(@PROMOTERWISE_PARAMS){
        my $value = $self->$attr();
        next unless (defined $value);
        my $attr_key = ' -'.(lc $attr);
        $param_string .= $attr_key.' '.$value;
    }
    foreach my $attr(@PROMOTERWISE_SWITCHES){
        my $value = $self->$attr();
        next unless (defined $value);
        my $attr_key = ' -'.(lc $attr);
        $param_string .=$attr_key;
    }

    $param_string = $param_string." -hitoutput tab"; #specify the output option
    return $param_string;

  my ($self,$seq) = @_;
  if(defined $seq){
    $self->{'_query1_seq'} = $seq;
  }
  return $self->{'_query1_seq'};

  my ($self,$seq) = @_;
  if(defined $seq){
    $self->{'_query2_seq'} = $seq;
  }
  return $self->{'_query2_seq'};
}
1;

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  http://redmine.open-bio.org/projects/bioperl/

 Title   :  _query_pep_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the query sequence
 Example :
 Returns :  
 Args    :

 Title   :  _subject_dna_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the subject sequence
 Example :
 Returns :

 Args    :