[fpc-pascal] FPC now 3rd in shootout

[S. Fisher]

--- Marco van de Voort <marcov at stack.nl> wrote:

> > http://shootout.alioth.debian.org/gp4/benchmark.php?test=all&lang=all
> > 
> > The reason is that D's mean degraded from 1.40 to 1.43.  I wonder how
> > that could happen.
> 
> They change often. Clean is also quite variable. I assume the differences
> are simply in the magnitude of the uncertainty of the measuring.

I submitted this regex-dna program on 2007-10-31.  It's still in limbo:
neither accepted nor rejected.

{ The Computer Language Benchmarks Game
  http://shootout.alioth.debian.org

  contributed by Steve Fisher

  compile with
  fpc -O3 regex-dna.pp
}

uses regexpr, strutils;

function replace_matches( const target: pchar;  const repl: pchar;
                const str: ansistring;  var dest: ansistring ): longint;
var
  engine : tRegexprEngine;
  substr : ansistring;
  count, index, size : longint;
begin
  if not GenerateRegExprEngine( target, [], engine) then
  begin
    writeln( 'Failed to generate regex. engine for "',target,'".' );
    halt(1)
  end;
  count := 0;
  dest := '';
  substr := str;
  while length(substr) > 0 do
  begin
    if RegExprPos(engine, pchar(substr), index, size ) then
    begin
      count += 1;
      dest += ansiLeftStr( substr, index) + repl;
      substr := ansiRightStr(substr,length(substr)-index-size);
    end
    else
      break
  end;
  DestroyRegExprEngine( engine );
  dest += substr;
  exit(count)
end;

function count_matches( target: pchar; const str: ansistring ): longint;
var
  engine : tRegexprEngine;
  substr : ansistring;
  count, index, size : longint;
begin
  if not GenerateRegExprEngine( target, [ref_caseinsensitive], engine) then
  begin
    writeln( 'Failed to generate regex. engine for "',target,'".' );
    halt(1)
  end;
  count := 0;
  substr := str;
  while length(substr) > 0 do
  begin
    if RegExprPos(engine, pchar(substr), index, size ) then
    begin
      count += 1;
      substr := ansiRightStr(substr,length(substr)-index-size);
    end
    else
      break
  end;
  DestroyRegExprEngine( engine );
  exit(count)
end;

const
  patterns : array[1..9] of pchar =
    (
      '(agggtaaa)|(tttaccct)',
      '([cgt]gggtaaa)|(tttaccc[acg])',
      '(a[act]ggtaaa)|(tttacc[agt]t)',
      '(ag[act]gtaaa)|(tttac[agt]ct)',
      '(agg[act]taaa)|(ttta[agt]cct)',
      '(aggg[acg]aaa)|(ttt[cgt]ccct)',
      '(agggt[cgt]aa)|(tt[acg]accct)',
      '(agggta[cgt]a)|(t[acg]taccct)',
      '(agggtaa[cgt])|([acg]ttaccct)'
    );
  replacements : array[1..11,1..2] of pchar =
  (  
    ('B', '(c|g|t)'), ('D', '(a|g|t)'), ('H', '(a|c|t)'), ('K', '(g|t)'),
    ('M', '(a|c)'), ('N', '(a|c|g|t)'), ('R', '(a|g)'), ('S', '(c|t)'),
    ('V', '(a|c|g)'), ('W', '(a|t)'), ('Y', '(c|t)')
  );


var
  pattern : pchar;
  sequence, new_seq : ansiString;
  line, tmp: string[255];
  letter, repl : pchar;
  i, count, init_length, clean_length, reps : longint;

begin
  sequence := '';
  init_length := 0;
  while not eof do
  begin
    readln( line );
    init_length += length( line ) + 1;
    if line[1] <> '>' then
      sequence := sequence + line;
  end;
  clean_length := length(sequence);

  for i := low(patterns) to high(patterns) do
  begin
    pattern := patterns[i];
    count := count_matches( pattern, sequence );
    tmp := delChars( delChars(pattern,'('), ')' );
    writeln( tmp, ' ', count);
  end;

  
  //  Replace.
  for i := low(replacements) to high(replacements) do
  begin
    letter := replacements[i][1];  repl := replacements[i][2];
    reps := replace_matches(letter,repl,sequence,new_seq);
    sequence := new_seq;
  end;


  writeln;
  writeln( init_length );
  writeln( clean_length );
  writeln( length(sequence) );
end.


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