Beefy Boxes and Bandwidth Generously Provided by pair Networks
Don't ask to ask, just ask

comment on

( #3333=superdoc: print w/replies, xml ) Need Help??
I came up with an algorithm inspired by bzip's algorithm of generating all substrings and then sorting them. I tried yours on a list of 20 strings of 1000 chars, and it ran in 153 seconds. Mine ran in 0.67 seconds, yielding the same results. 30 strings of 3000 chars runs in 20.3 seconds on mine; scaling up from there starts to get painful, but I would guess the OP's requirement of 300 strings of 3000 chars would run in under an hour, if it had plenty of memory (there will be 900,000 strings averaging 1500 chars in length).

Give it a whirl.

use warnings; use strict; use Time::HiRes; if (@ARGV == 0) { print "Finds longest matching substring between any pair of test s +trings\n"; print "in the given file. Pairs of lines are expected with the fir +st of a\n"; print "pair being the string name and the second the test string." +; exit (1); } my $minmatch = 4; my $startTime = [Time::HiRes::gettimeofday ()]; my @strings; while (<>) { chomp(my $label = $_); chomp(my $string = <>); # Compute all substrings push @strings, map [substr($string, $_), $label, $_], 0..(length($st +ring) - $minmatch); } print "Loaded. Sorting...\n"; @strings = sort {$a->[0] cmp $b->[0]} @strings; print "Sorted. Finding matches...\n"; # Now walk through the list. The best match for each string will be th +e # previous or next element in the list that is not from the original s +ubstring, # so for each entry, just look for the next one. See how many initial +letters # match and track the best matches my @matchdata = (0); # (length, index1-into-strings, index2-into-strin +gs) for my $i1 (0..($#strings - 1)) { my $i2 = $i1 + 1; ++$i2 while $i2 <= $#strings and $strings[$i2][1] eq $strings[$i1][1 +]; next if $i2 > $#strings; my ($common) = map length, ($strings[$i1][0] ^ $strings[$i2][0]) =~ +/^(\0*)/; if ($common > $matchdata[0]) { @matchdata = ($common, [$i1, $i2]); } elsif ($common == $matchdata[0]) { push @matchdata, [$i1, $i2]; } } print "Best match: $matchdata[0] chars\n"; for my $i (@matchdata[1..$#matchdata]) { print "$strings[$i->[0]][1] starting at $strings[$i->[0]][2]" . " and $strings[$i->[1]][1] starting at $strings[$i->[1]][2]\n"; } print "Completed in " . Time::HiRes::tv_interval ($startTime) . "\n";
A test-data generating program follows
use warnings; use strict; my ($howmany, $howlong) = (20, 1000); # Generate $howmany strings of $howlong characters for my $s (1..$howmany) { print "'String $s'\n"; my $str = ''; $str .= (qw(A C G T))[rand 4] for 1..$howlong; print "$str\n"; }

Caution: Contents may have been coded under pressure.

In reply to Re^3: Fast common substring matching by Roy Johnson
in thread Fast common substring matching by GrandFather

Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":

  • Are you posting in the right place? Check out Where do I post X? to know for sure.
  • Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
    <code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>
  • Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
  • Want more info? How to link or How to display code and escape characters are good places to start.
Log In?

What's my password?
Create A New User
Domain Nodelet?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others drinking their drinks and smoking their pipes about the Monastery: (2)
As of 2023-02-09 01:44 GMT
Find Nodes?
    Voting Booth?
    I prefer not to run the latest version of Perl because:

    Results (44 votes). Check out past polls.