if (!$d->[$x][$y][0] && !$d->[$x][$y][1] && !$d->[$x][$y][2]) {
for (my $u=$x; $u>0; $u--) { unshift @ra, $sa[$u-1]; }
for (my $v=$y; $v>0; $v--) { unshift @rb, $sb[$v-1]; }
while (scalar(@ra)
while (scalar(@rb)
while (scalar(@rc) # print out the answer
$i++; # global variable
$scr = 0; # score for each alignment
print "
Alignment: $i
Sa:";
foreach my $x (@ra) { print " $x"; }
print "
Sb:";
foreach my $y (@rb) { print " $y"; }
print "
Scr";
foreach my $z (@rc) {
if ($z eq '.') {
print " .";
} else {
printf '%4d', $z;
$scr += $z;
}
}
print " = $scr
";
}