I've done some test
there are 5 version of revcom test
1. original
2. done bigger buffer
3 use tTextSrteam
4+ 5 in place of readln i've pass const string
6 only one set string variable
7 no move- I've rem MOVE procedure
I've repeat test in program, because time of test are vary (I don't know
why)
on FPC I use -OG3ru -XX - Xs parameters
Source attached
My conclusion:
1. on Linux MOVE implementation is very slow (or I make mistake in tests)
2. on win read via text file is two times slower than via handle, on
Linux is not so slowly (depends on pt. 1)
on win consume 50%, on Linux 80%
Results:
On Delphi+win+athlon2.8
readln 144696
readln +big buffer 146475
ttextStream 52767 <2 times faster
no read file 31106
no read file +big buffer 30935
no read file 30994
no set string 32243
no move 18353 <2 times faster
ttextStream 52306
readln +big buffer 146588
readln 144410
on FPC+win+athlon2.8 (the same machine)
readln 88309
readln +big buffer 88159
ttextStream 45789 <2 times faster
no read file 32341
no read file +big buffer 24045
no read file 23886
no set string 25246
no move 15031 <2 times faster
ttextStream 45425
readln +big buffer 88460
readln 87379
on FPC +linux gentoo+athlon 2.6
readln 76621
readln +big buffer 79921
ttextStream 73222 <no times faster
no read file 65700
no read file +big buffer 70429
no read file 75157
no set string 80239
no move 27527 <3 times faster
ttextStream 76936
readln +big buffer 77679
readln 78108
Darek
PS. Sorry for my English.
{ The Computer Language Shootout
http://shootout.alioth.debian.org/
Contributed by Marco van de Voort
}
unit revcom;
interface
uses textStream,cpu_timer;
procedure revRun(amem : integer);
procedure revrun2(amem : integer);
procedure revrun3(amem : integer);
procedure testrevrun;
implementation
//{$mode objfpc}
{$I-}
//uses system;
//Uses BaseUnix;
var lookupComplement : array[#0..#255] of char;
pa,
pb : text;
Const FASTAXLAT : array[0..11] of array[0..1] of char = (
( 'A', 'T' ), ( 'C', 'G' ),
( 'B', 'V' ), ( 'D', 'H' ),
( 'K', 'M' ), ( 'R', 'Y' ),
( 'a', 't' ), ( 'c', 'g' ),
( 'b', 'v' ), ( 'd', 'h' ),
( 'k', 'm' ), ( 'r', 'y' ));
BufferIncrement = 1024;
procedure flushbuffer(buffer:pchar;inbuf:integer);
var p,p2 : pchar;
c : char;
begin
if inbuf>0 then
begin
p:=buffer;
p2:[EMAIL PROTECTED];
while p<p2 do
begin
c:=lookupcomplement[p^];
p^:=lookupcomplement[p2^];
inc(p);
p2^:=c;
dec(p2);
end;
if p2=p then
p^:=lookupcomplement[p^];
p:=buffer;
while (inbuf > 60) do
begin
c := p[60];
p[60]:=#0;
writeln(pb,p);
p[60]:=c;
inc(p,60);
dec(inbuf,60);
end;
p[inbuf]:=#0;
writeln(pb,p);
end;
end;
(*
function FileOpenA(const FileName: ansistring): Integer;
{$IFNDEF WIN32}
begin
result:=fileopen(filename,mode);
{$ELSE}
begin
Result := Integer(CreateFileA(PChar(FileName), GENERIC_READ,
FILE_SHARE_READ or FILE_SHARE_WRITE, nil, OPEN_EXISTING,
FILE_ATTRIBUTE_NORMAL+FILE_FLAG_SEQUENTIAL_SCAN, 0));
{$ENDIF}
end;
*)
procedure revrun(amem :integer);
const rBufSize =1024;
var s : shortstring;
c : char;
buffersize,
bufferptr,
len : integer;
rBuf : pchar;
p :pchar;
sss : ansiString;
io : integer;
lll : integer;
hhh : integer;
// pa : tream;
begin
// hhh:=fileOpenA('revcomp-input.txt');
assign(pa,'revcomp-input.txt');
reset(pa);
assign(pb,'revcomp-output.txt');
rewrite(pb);
for c:=#0 to #255 do
lookupcomplement[c]:=c;
for len:=0 to high(FASTAXLAT) do
begin
lookupcomplement[FASTAXLAT[len][0]]:=upcase(FASTAXLAT[len][1]);
lookupcomplement[FASTAXLAT[len][1]]:=upcase(FASTAXLAT[len][0]);
end;
buffersize:=bufferincrement*amem;
bufferptr :=0;
// rBufSize:=1024;
getmem(p,buffersize);
// getMem(buf,rBufSize+1);
// lll:=170;
// while pa.readLN(s)>=0 do begin
// dec(lll);
// s:='GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA';
while not eof(pa) do begin
readln(pa,s);
// while (input.inoutFunc(input))=0 do
{
while readFile(hhh,buf^,rBufSIze,io,nil) and (io>0) do begin
}
{ pb:=input.bufferptr;
pc:=pb+input.buffersize;
while pb<pc do begin
pa:=pb;
while pb^>#19 do inc(pb);
move (buf,s[1],pb-pa);
s[0]:=char(pb-pa);
}
len:=length(s);
if (len>0) and (s[1]='>') then
begin
flushbuffer(p,bufferptr);
writeln(pb,s);
bufferptr:=0;
end
else
begin
if (bufferptr+len)>=buffersize then
begin
inc(buffersize,bufferincrement+2);
reallocmem(p,buffersize);
end;
move (s[1],p[bufferptr],len);
inc(bufferptr,len);
end;
// end;
end;
flushbuffer(p,bufferptr);
close(pb);
close(pa);
end;
procedure revrun2(amem : integer);
const rBufSize =1024;
var s : shortstring;
c : char;
buffersize,
bufferptr,
len : integer;
rBuf : pchar;
p :pchar;
sss : ansiString;
io : integer;
lll : integer;
hhh : integer;
pa : tTextStream;
begin
// hhh:=fileOpenA('revcomp-input.txt');
// assign(pa,'revcomp-input.txt');
// reset(pa);
pa:=tTextStream.create('revcomp-input.txt',0);
assign(pb,'revcomp-output1.txt');
rewrite(pb);
for c:=#0 to #255 do
lookupcomplement[c]:=c;
for len:=0 to high(FASTAXLAT) do
begin
lookupcomplement[FASTAXLAT[len][0]]:=upcase(FASTAXLAT[len][1]);
lookupcomplement[FASTAXLAT[len][1]]:=upcase(FASTAXLAT[len][0]);
end;
buffersize:=bufferincrement*amem;
bufferptr :=0;
// rBufSize:=1024;
getmem(p,buffersize);
// getMem(buf,rBufSize+1);
// lll:=170;
while pa.readLN(s)>=0 do begin
// dec(lll);
// s:='GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA';
// while not eof(pa) do begin
// readln(pa,s);
// while (input.inoutFunc(input))=0 do
{
while readFile(hhh,buf^,rBufSIze,io,nil) and (io>0) do begin
}
{ pb:=input.bufferptr;
pc:=pb+input.buffersize;
while pb<pc do begin
pa:=pb;
while pb^>#19 do inc(pb);
move (buf,s[1],pb-pa);
s[0]:=char(pb-pa);
}
len:=length(s);
if (len>0) and (s[1]='>') then
begin
flushbuffer(p,bufferptr);
writeln(pb,s);
bufferptr:=0;
end
else
begin
if (bufferptr+len)>=buffersize then
begin
inc(buffersize,bufferincrement+2);
reallocmem(p,buffersize);
end;
move (s[1],p[bufferptr],len);
inc(bufferptr,len);
end;
// end;
end;
flushbuffer(p,bufferptr);
close(pb);
pa.free;
// close(pa);
end;
procedure revrun3(amem : integer);
const rBufSize =1024;
var s : shortstring;
c : char;
buffersize,
bufferptr,
len : integer;
rBuf : pchar;
p :pchar;
sss : ansiString;
io : integer;
lll : integer;
hhh : integer;
pa : tTextStream;
begin
// hhh:=fileOpenA('revcomp-input.txt');
// assign(pa,'revcomp-input.txt');
// reset(pa);
pa:=tTextStream.create('revcomp-input.txt',0);
assign(pb,'revcomp-output3.txt');
rewrite(pb);
for c:=#0 to #255 do
lookupcomplement[c]:=c;
for len:=0 to high(FASTAXLAT) do
begin
lookupcomplement[FASTAXLAT[len][0]]:=upcase(FASTAXLAT[len][1]);
lookupcomplement[FASTAXLAT[len][1]]:=upcase(FASTAXLAT[len][0]);
end;
buffersize:=bufferincrement*amem;
bufferptr :=0;
// rBufSize:=1024;
getmem(p,buffersize);
// getMem(buf,rBufSize+1);
lll:=170;
// while pa.readLN(s)>=0 do begin
while lll>0 do begin
dec(lll);
if lll mod 40 =0 then s:='>cos tam '
else s:='GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA';
len:=length(s);
if (len>0) and (s[1]='>') then
begin
flushbuffer(p,bufferptr);
writeln(pb,s);
bufferptr:=0;
end
else
begin
if (bufferptr+len)>=buffersize then
begin
inc(buffersize,bufferincrement+2);
reallocmem(p,buffersize);
end;
move (s[1],p[bufferptr],len);
inc(bufferptr,len);
end;
// end;
end;
flushbuffer(p,bufferptr);
close(pb);
pa.free;
// close(pa);
end;
procedure revrun4(amem : integer);
const rBufSize =1024;
var s : shortstring;
s2 : shortString;
c : char;
buffersize,
bufferptr,
len : integer;
rBuf : pchar;
p :pchar;
sss : ansiString;
io : integer;
lll : integer;
hhh : integer;
pa : tTextStream;
begin
// hhh:=fileOpenA('revcomp-input.txt');
// assign(pa,'revcomp-input.txt');
// reset(pa);
pa:=tTextStream.create('revcomp-input.txt',0);
assign(pb,'revcomp-output3.txt');
rewrite(pb);
for c:=#0 to #255 do
lookupcomplement[c]:=c;
for len:=0 to high(FASTAXLAT) do
begin
lookupcomplement[FASTAXLAT[len][0]]:=upcase(FASTAXLAT[len][1]);
lookupcomplement[FASTAXLAT[len][1]]:=upcase(FASTAXLAT[len][0]);
end;
buffersize:=bufferincrement*amem;
bufferptr :=0;
// rBufSize:=1024;
getmem(p,buffersize);
// getMem(buf,rBufSize+1);
lll:=170;
// while pa.readLN(s)>=0 do begin
s:='GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA';
s2:='>cos tam ddddddddd';
while lll>0 do begin
dec(lll);
len:=length(s);
if ((len mod 40)=0 ) and (s2[1]='>') then
begin
flushbuffer(p,bufferptr);
writeln(pb,s);
bufferptr:=0;
end
else
begin
if (bufferptr+len)>=buffersize then
begin
inc(buffersize,bufferincrement+2);
reallocmem(p,buffersize);
end;
move (s[1],p[bufferptr],len);
inc(bufferptr,len);
end;
// end;
end;
flushbuffer(p,bufferptr);
close(pb);
pa.free;
// close(pa);
end;
procedure revrun5(amem : integer);
const rBufSize =1024;
var s : shortstring;
s2 : shortString;
c : char;
buffersize,
bufferptr,
len : integer;
rBuf : pchar;
p :pchar;
sss : ansiString;
io : integer;
lll : integer;
hhh : integer;
pa : tTextStream;
begin
// hhh:=fileOpenA('revcomp-input.txt');
// assign(pa,'revcomp-input.txt');
// reset(pa);
pa:=tTextStream.create('revcomp-input.txt',0);
assign(pb,'revcomp-output3.txt');
rewrite(pb);
for c:=#0 to #255 do
lookupcomplement[c]:=c;
for len:=0 to high(FASTAXLAT) do
begin
lookupcomplement[FASTAXLAT[len][0]]:=upcase(FASTAXLAT[len][1]);
lookupcomplement[FASTAXLAT[len][1]]:=upcase(FASTAXLAT[len][0]);
end;
buffersize:=bufferincrement*amem;
bufferptr :=0;
// rBufSize:=1024;
getmem(p,buffersize);
// getMem(buf,rBufSize+1);
lll:=170;
// while pa.readLN(s)>=0 do begin
s:='GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA';
s2:='>cos tam ddddddddd';
while lll>0 do begin
dec(lll);
len:=length(s);
if ((len mod 40)=0 ) and (s2[1]='>') then
begin
flushbuffer(p,bufferptr);
writeln(pb,s);
bufferptr:=0;
end
else
begin
if (bufferptr+len)>=buffersize then
begin
inc(buffersize,bufferincrement+2);
reallocmem(p,buffersize);
end;
// move (s[1],p[bufferptr],len);
inc(bufferptr,len);
end;
// end;
end;
flushbuffer(p,bufferptr);
close(pb);
pa.free;
// close(pa);
end;
procedure testRevRun;
var
i,nn : integer;
pp : text;
aa : int64;
begin
assign(pp,'result.txt');
rewrite(pp);
nn:=100;
fillchar(lookupComplement,sizeof(lookupComplement),1);
aa:=clock;
for i:= 1 to nn do revRun(4);
aa:=clock-aa;
writeln(pp,' readln ',aa);
aa:=clock;
for i:= 1 to nn do revRun(44);
aa:=clock-aa;
writeln(pp,' readln +big buffer ',aa);
aa:=clock;
for i:= 1 to nn do revRun2(4);
aa:=clock-aa;
writeln(pp,' ttextStream ',aa);
aa:=clock;
for i:= 1 to nn do revRun3(4);
aa:=clock-aa;
writeln(pp,' no read file ',aa);
aa:=clock;
for i:= 1 to nn do revRun3(4);
aa:=clock-aa;
writeln(pp,' no read file +big buffer ',aa);
aa:=clock;
for i:= 1 to nn do revRun3(4);
aa:=clock-aa;
writeln(pp,' no read file ',aa);
aa:=clock;
for i:= 1 to nn do revRun4(4);
aa:=clock-aa;
writeln(pp,' no set string ',aa);
aa:=clock;
for i:= 1 to nn do revRun5(4);
aa:=clock-aa;
writeln(pp,' no move ',aa);
aa:=clock;
for i:= 1 to nn do revRun2(4);
aa:=clock-aa;
writeln(pp,' ttextStream ',aa);
aa:=clock;
for i:= 1 to nn do revRun(44);
aa:=clock-aa;
writeln(pp,' readln +big buffer ',aa);
aa:=clock;
for i:= 1 to nn do revRun(4);
aa:=clock-aa;
writeln(pp,' readln ',aa);
close(pp);
end;
begin
// run;
end.
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