Here's my solution, which I sent to the OP off list.
Funny how he never reported back with a summary, as
is the custom....
# operates on $_
sub find_subsequences
{
#local $_ = shift; # if you'd rather pass it.
my( $chars, $min_occurrences, $max_subseq_length, $results_ar ) =
@_;
$results_ar ||= [];
my @p; # a sliding window of positions at which pattern matches.
while ( /[$chars]/g )
{
push @p, pos() - 1; # since pos() is 1-based.
shift @p while @p > $min_occurrences; # slide the window
if ( @p == $min_occurrences )
{
my $len = $p[-1] - $p[0] + 1;
if ( $len <= $max_subseq_length )
{
my $subseq = substr $_, $p[0], $len;
push @$results_ar, [ $p[0], $subseq ];
}
}
}
$results_ar
}
# test
my @chars = qw( A T C G );
$_ = '';
for ( my $i = 0; $i < 10_000; $i++ )
{
$_ .= $chars[ rand @chars ];
}
use Tie::Array;
@Tie::ArrayPrint::ISA = qw( Tie::StdArray );
sub Tie::ArrayPrint::PUSH
{
my $self = shift;
@_ == 1 && ref($_[0]) eq 'ARRAY' and
print "\@ $_[0][0] ($_[0][1])\n";
push @$self, @_;
}
my @subseqs;
#tie @subseqs, 'Tie::ArrayPrint';
find_subsequences( join('',@chars[0,1]), 7, 12, [EMAIL PROTECTED] );
print scalar(@subseqs), " hits found.\n";
--
John Douglas Porter
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