note
roboticus
<p>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.</p>
<c>
#!/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 list of
# strings, and if null, we'll use our test data.
#
# Inspired by perlmonks node 906020, and the Knuth-Morris-Pratt algorithm.
#
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 } @candidates;
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($$rMatchKeys{REM}{$h})) {
++$cnt_dup;
next CANDIDATE;
}
}
}
my $ar = [ $h, $keywidth % $hashwidth ];
### Add the path to %MatchKeys
$rMatchKeys = \%MatchKeys;
while (my $r = shift @keypath) {
$$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;
}
</c>
<p>...[roboticus]</p>
<p><i>When your only tool is a hammer, all problems look like your thumb.</i></p>
906020
906085