########################################################################

use FIG;
my $fig = new FIG;
use Sim;

# usage: fast_blastp BlastParms

my $parms = (@ARGV > 0) ? join(" ",@ARGV) : "";

$/ = "\n>";
while (defined($_ = <STDIN>))
{
    chomp;
    $/ = "\n";
    if ($_ =~ /^>?(\S+)[^\n]*\n(.*)/s)
    {
	my $id = $1;
	my $seq = $2;
#	print STDERR "processing $id\n";
	$seq =~ s/\s//gs;
	my @sims = $fig->dsims($id,$seq,500,0.1,undef,$parms);
	foreach my $sim (@sims)
	{
	    print join("\t",($sim->id1,$sim->id2,$sim->iden,$sim->b1,$sim->e1,$sim->ln1,
			     $sim->b2,$sim->e2,$sim->ln2,$sim->psc,$sim->bsc,$sim->nbsc)),"\n";
	}
    }
    $/ = "\n>";
}