#! perl -slw
use strict;
use vars qw[$N];
use Benchmark::Timer; my $T= new Benchmark::Timer;
$|++;

$N ||= 10; # The number of random permutations of each string to analyse.

##my $start-seq = <STARTS>;
## No need to count frequencies just to build any array.
##my @bases = split//, $start_seq;

# Simulate the above two lines for testing
my @bases = map{ qw[A C G T N][ rand 5 ] } 1..50_000;


my $perms_count = 0;
for( 1 .. $N ) {
    # Pick our first random 7 char string
    my $sub7= join'', @bases[ map{ rand @bases } 1 .. 7 ];

    my $count = @bases - 7;         # No. of 7 chars string to match against.

    $T->start( 'search' );

    while( $count-- ) {
        printf "\r%d", $count;
    #   print 'Checking: ', $sub7;

        #Unroll the match loop
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';

        # Drop the first char and tack a new one on the end.
        $sub7 = substr( $sub7, 1 ) . $bases[ rand @bases ];
    }
    $T->stop( 'search' );
}

print 'Found: ', $perms_count, ' matches in';

$T->report;


##</code><code>##

#! perl -slw
use strict;

sub p{
    my @a = split '', shift;
    while( @_ ) {
        my @c= split '', shift;
        my @b=();
        for my $c ( @c ) {
            push @b, $_ . $c for @a ;
        }
        @a = @b;
    }
    return @a;
}

my @combs = (
    p( 'NT', 'GCATN', 'NG', 'NC', 'NG', 'NT', 'NG' ),
    p( 'NG', 'NT', 'NG', 'NC', 'NG', 'GCATN', 'NT' ),
    p( 'NA', 'GCATN', 'NC', 'NG', 'NC', 'NA', 'NC' ),
    p( 'NC', 'NA', 'NC', 'NG', 'NC', 'GCATN', 'NA' ),
);

my %seen; @seen{ @combs } = ();

print "The number of unique 7-char sequences that can be matched by the regexes is:",
    scalar keys %seen;