Hmmm ... I thought there would be more activity on this thread. No-one seems to be actively working on it, so here's the code I used to get my timings.

#!/usr/bin/perl
#
#    multi-string-match.pl <FName>
#
#    Grind through a set of strings, and keep only the ones that don't
+ contain
#    any of the others as a substring.  FName is a file containing a l
+ist of 
#    strings, and if null, we'll use our test data.
#
#    Inspired by perlmonks node 906020, and the Knuth-Morris-Pratt alg
+orithm.
#
use strict;
use warnings;
use feature ':5.10';

# function is 10.67 chars wide, so need to round up, or we can't find 
+partials 
# (previous state will linger, so we can't find 'em!)
my $hashwidth = 11;

# our alphabet
my %xlat = (A=>1, C=>2, G=>3, T=>4, N=>0);

my @unique;
my @candidates;
my %MatchKeys;

my $fname = shift;
open my $FH, '<', $fname or die;
@candidates = <$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 } @candida
+tes;

my (@keypath, $t); #, @chars, @keypath);

my $cnt_dup=0;
CANDIDATE:
while ($t = shift @candidates) {
    my $h = 0;
    my $keywidth=0;
    @keypath=();
    my $rMatchKeys = \%MatchKeys;
    my $fl_partial=-1;
    my $l = length($t);
    while ($keywidth < $l) {
        $h = hash(substr($t,$keywidth,1), $h);
        ++$keywidth;
        if ($keywidth % $hashwidth == 0) {
            push @keypath, $h;
        }

        if ($fl_partial < 0) {
            # No current partial match
            if (exists $MatchKeys{$h}) {
                $rMatchKeys = $$rMatchKeys{$h};
                $fl_partial = $keywidth;
            }
        }
        else {
            if ( ($keywidth - $fl_partial) % $hashwidth == 0 ) {
                $rMatchKeys = exists($$rMatchKeys{$h}) ? $$rMatchKeys{
+$h} : undef;
            }
            elsif (exists($$rMatchKeys{REM}) and exists($$rMatchKeys{R
+EM}{$h})) {
                ++$cnt_dup;
                next CANDIDATE;
            }
        }
    }
    my $ar = [ $h, $keywidth % $hashwidth ];

    ### Add the path to %MatchKeys
    $rMatchKeys = \%MatchKeys;
    while (my $r = shift @keypath) {
        $$rMatchKeys{$r} = { } if !exists $$rMatchKeys{$r};
        $rMatchKeys = $$rMatchKeys{$r};
    }
    $$rMatchKeys{REM} = { } if !exists $$rMatchKeys{REM};
    if (exists($$rMatchKeys{REM}{$$ar[0]})
    and $$ar[1] == $$rMatchKeys{REM}{$$ar[0]}) {
        ++$cnt_dup;
        next CANDIDATE;
    }
    $$rMatchKeys{REM}{$$ar[0]} = $$ar[1];
    push @unique, $t;
}
my $end = time - $start;
print scalar(@unique), " unique items\n";
print "$cnt_dup rejected.\n";
print "$end seconds.\n";

sub hash {
    my ($curchar, $prevhash) = @_;
    $prevhash = ($prevhash * 8 + $xlat{$curchar}) & 0xffffffff;
}
[download]

...roboticus

When your only tool is a hammer, all problems look like your thumb.

I used this generator to create a 10000 string file where the first 5000 string are just randomly generated and the other 5000 are random substring extracted from the first 5000. Thus, you'd expect at most 5000 unique strings with a very slight possibility of there being fewer:

#! perl -slw
use strict;

sub rndStr{ join'', @_[ map{ rand $#_ } 1 .. shift ] }

our $N //= 10e3;

my $halfN = $N >> 1;

my @data; $#data = $N;

$data[ $_ ] = rndStr( 200 +int( rand 200 ), 'A', 'C', 'G', 'T', 'N' )
    for 0 .. $halfN;

$data[ $_ + $halfN ] = substr(
    $data[ $_ ], 10, 10 + int( rand( length( $data[ $_ ] ) - 20 ) )
) for 0 .. $halfN;

print for @data;
__END__
C:\test> 906020-gen -N=10e3 > 906020.10e3
[download]

When I run your code on this file it misses some dups:

C:\test>906020-robo 906020.10e3
5551 unique items
4450 rejected.
5 seconds.
[download]

---

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

BrowserUk:

Thanks, I'll dig into it tomorrow and see if I can find out what's going wrong.

Update: I've confirmed the error (20110531) but haven't isolated it yet.

...roboticus

When your only tool is a hammer, all problems look like your thumb.

I gave it a try to test your code. There are substrings among the output, but did not figure out why. It seems there are bugs within it. Nice code though!

yifangt:

Without an example of a case you're having trouble with, what do you expect me to do with your bug report? Provide a case that gives invalid results, and I can take a look at it.

...roboticus

When your only tool is a hammer, all problems look like your thumb.