#!/usr/bin/perl
#
#       multi-string-match_brute_force.pl <FName>
#
use strict;
use warnings;
use feature ':5.10';

my $fname = shift;
open my $FH, '<', $fname or die;
my @candidates = <$FH>;

@candidates =
        grep { /^[ACGTN]+$/ } # delete the comments
        map { s/^\s+//; s/\s+$//; $_ }
        @candidates;

my $start = time;
@candidates = sort { length($a) <=> length($b) || $a cmp $b } @candidates;
my @unique;
my $cnt_dup=0;
OUTER:
while (my $t = shift @candidates) {
        for my $u (@unique) {
                if ($t =~ /$u/) {
                        ++$cnt_dup;
                        next OUTER;
                }
        }
        push @unique, $t;
}
my $end = time - $start;

print scalar(@unique), " unique items.\n";
print "$cnt_dup rejected.\n";
print "$end seconds\n";