use Perl

• substr(A,B,1) (Score:2)

  by Matts (1087)

  This will be what kills it. Looking for single chars in a string with perl is painful. There's no nice way around it, except perhaps to do a pre-split into an array, but then look at what you've got - an array of SVs - the overhead is huge.
  
  You *might* be able to make it faster with a regexp. But basically doing anything character by character in perl is very slow.
  
  (it's also one of the main reasons that XML::SAX::PurePerl is so slow)
  • Re: (Score:1)

    by Alias (5735)

    (it's also one of the main reasons that XML::SAX::PurePerl is so slow)

    Ditto with PPI...
    
    I managed to compensate by applying a regex if the character I see suggests I can read ahead a fair way.
    
    You might be able to abuse the regex engine for this though...
    
    s/./something;$1/e
    
• You can double the speed (more or less) (Score:1)

  by runrig (3385)

  In the alignment.pl code, nearly all the time is spent in the 'compute f matrix' loop. Pre-splitting the strings to arrays saved a few seconds (and took nearly no time). Using @_ directly instead of assigning to lexicals in the score and max subroutines (and using the ?: operator to write one line functions) saved a few more seconds (the python didn't seem quite fair to compare since it has named parameters, so you save the assignment).

  There was also a lot of array indexing, so pre-assigning the first leve
  • Re: (Score:1)

    by runrig (3385)

    And I don't know if it saved any time, but replacing the C-style for loops with perly 1..$n style ones made at least that part more readable.
• 4x (Score:1)

  by ChrisDolan (2855)

  Interestingly, 97% of the alignment.pl time is spent in the creation of the f-matrix.
  
  At the expense of some readability, I sped alignment.pl up by a factor of four (96 sec to 23 sec on my iMac G5 with perl5.8.6). You can view my modified code [chrisdolan.net] at your peril. The substr was not in fact the biggest cost -- I was surprised that changing to m/\G(.)/cg didn't save any time. The biggest win (about 40% time decrease) was unrolling the subroutines, of course, which is what some of the other languages may be doing