--- Peter Vreman <[EMAIL PROTECTED]> wrote:
> >>
> >> --- Marco van de Voort <[EMAIL PROTECTED]> 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.
> >
> > Thanks, I've added it to the fpc repository so the source will not be
> lost
>
> For me the code didn't finish in a reasonable time. It spend too much time
> in moving ansistrings
> around. I have update the program to use a pchar instead of an ansistring
> so it finishes within
> reasonable time. The updated source can be found in:
>
>
http://svn.freepascal.org/svn/fpc/trunk/tests/bench/shootout/src/regexdna.pp
>
> But the code is a lot slower than gcc so there is still a lot of
> performance tuning to do:
>
> 100000 300000 500000
> fpascal 1.169 4.581 11.754
> gcc-2 1.033 3.078 5.111
Much, much faster than the original. There was an off-by-one error
that made the last line of the output incorrect.
{ The Computer Language Benchmarks Game
http://shootout.alioth.debian.org
contributed by Steve Fisher
modified by Peter Vreman
compile with
fpc -O3 regex-dna.pp
}
uses regexpr,strutils;
function replace_matches( const target: pchar; const repl: ansistring;
const str: ansistring; var dest: ansistring ): longint;
var
engine : tRegexprEngine;
count, index, size : longint;
pstart : pchar;
starti : longint;
begin
if not GenerateRegExprEngine( target, [], engine) then
begin
writeln( 'Failed to generate regex. engine for "',target,'".' );
halt(1)
end;
count := 0;
dest := '';
starti := 1;
pstart := pchar(str);
while starti <= length(str) do
begin
if RegExprPos(engine, pstart, index, size ) then
begin
inc(count);
dest := dest + Copy( str, starti, index) + repl;
inc(pstart,index+size);
inc(starti,index+size);
end
else
break
end;
DestroyRegExprEngine( engine );
dest:=dest+Copy( str, starti, length(str)-starti+1);
exit(count);
end;
function count_matches( target: pchar; const str: ansistring ): longint;
var
engine : tRegexprEngine;
pstart : pchar;
starti,
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;
pstart := pchar(str);
starti := 1;
while starti <= length(str) do
begin
if RegExprPos(engine, pstart, index, size ) then
begin
inc(count);
inc(pstart,index+size);
inc(starti,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;
inbuf : array[0..64*1024] of char;
begin
settextbuf(input,inbuf);
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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