static int parse_args(struct config *cfg, char **host, char **port, int argc, char **argv) {
char c, *host_str;
memset(cfg, 0, sizeof(struct config));
cfg->threads = 2;
cfg->connections = 10;
cfg->duration = 10;
cfg->timeout = SOCKET_TIMEOUT_MS;
while ((c = getopt_long(argc, argv, "t:c:d:T:Lrv?", longopts, NULL)) != -1) {
switch (c) {
case 't':
if (scan_metric(optarg, &cfg->threads)) return -1;
break;
case 'c':
if (scan_metric(optarg, &cfg->connections)) return -1;
break;
case 'd':
if (scan_time(optarg, &cfg->duration)) return -1;
break;
case 'L':
cfg->latency = true;
break;
case 'T':
if (scan_time(optarg, &cfg->timeout)) return -1;
cfg->timeout *= 1000;
break;
case 'v':
printf("wrk-nonsense %s [%s] ", VERSION, aeGetApiName());
printf("Copyright (C) 2012 Will Glozer (hackt up by Forrest L Norvell)\n");
break;
case 'r':
fprintf(stderr, "wrk 2.0.0+ uses -d instead of -r\n");
case 'h':
case '?':
case ':':
default:
return -1;
}
}
if (!cfg->threads || !cfg->duration) return -1;
if (!cfg->connections || cfg->connections < cfg->threads) {
fprintf(stderr, "number of connections must be >= threads\n");
return -1;
}
if (argc > 1 && optind < argc) {
host_str = strdup(argv[optind]);
*host = strsep(&host_str, ":");
*port = host_str;
}
return 0;
}
static int parse_supertcp(struct ftpparse *f, char *p[], int l[],
unsigned int count)
{
unsigned long mon;
unsigned long day;
unsigned long year;
unsigned long hour;
unsigned long min;
unsigned long sec;
int mtimetype;
uint64 size=0; /* optional, dirs */
int x;
int dir=0;
/* CMT <DIR> 11-21-94 10:17 */
/* DESIGN1.DOC 11264 05-11-95 14:20 */
if (count<4) return 0;
x=scan_time(p[3],l[3],&hour,&min,&sec,&mtimetype);
if (x!=l[3]) return 0;
x=get_ulong(p[2],l[2],&mon);
if (x!=2 || p[2][x]!='-') return 0;
x++;
x+=get_ulong(p[2]+x,l[2]-x,&day);
if (x!=5 || p[2][x]!='-') return 0;
x++;
x+=get_ulong(p[2]+x,l[2]-x,&year);
if ((x!=8 && x!=10) || p[2][x]!=' ') return 0;
if (!fix_year(&year)) return 0;
if (my_byte_equal(p[1],5,"<DIR>"))
dir=1;
else {
x=get_uint64(p[1],l[1],&size);
if (!x || p[1][x]!=' ') return 0;
}
f->name=p[0];
f->namelen=l[0];
f->size=size;
if (!dir)
f->sizetype=FTPPARSE_SIZE_BINARY;
utcdate2tai (&f->mtime,year,mon,day,hour,min,sec);
f->mtimetype=mtimetype;
if (dir) f->flagtrycwd=1;
else f->flagtryretr=1;
return 1;
}
/**
Create a record of a speeding incident
and scan the relevant data from the file pointer fp,
in this format:
2/3/2005 3:45 87.6 JJJ 472
@param fp file pointer to read from
@return pointer to newly created speeding incident
*/
Speeding * scan_speeding( FILE *fp )
{
Speeding * new_speeding = (Speeding *)malloc(sizeof(Speeding));
if( new_speeding != NULL ) {
if( ( scan_date( &new_speeding->date, fp ))
&&( scan_time( &new_speeding->time, fp ))
&& fscanf( fp,"%lf", &new_speeding->speed )
&& fgets( new_speeding->plate, MAX_PLATE, fp )) {
return( new_speeding );
}
else {
free( new_speeding );
}
}
return( NULL );
}
void ElutionPeakDetection::detectElutionPeaks_(MassTrace & mt, std::vector<MassTrace> & single_mtraces)
{
std::vector<DoubleReal> rts, ints;
for (MassTrace::const_iterator c_it = mt.begin(); c_it != mt.end(); ++c_it)
{
rts.push_back(c_it->getRT());
ints.push_back(c_it->getIntensity());
}
std::vector<DoubleReal> smoothed_data;
LowessSmoothing lowess_smooth;
Param lowess_params;
// use dynamically computed window sizes
// Size win_size = mt.getFWHMScansNum();
// use one global window size for all mass traces to smooth
DoubleReal scan_time(mt.getScanTime());
Size win_size = std::ceil(chrom_fwhm_ / scan_time);
// std::cout << "win_size elution: " << scan_time << " " << win_size << std::endl;
// if there is no previous FWHM estimation... do it now
// if (win_size == 0)
// {
// mt.estimateFWHM(false); // estimate FWHM
// win_size = mt.getFWHMScansNum();
// }
lowess_params.setValue("window_size", win_size);
lowess_smooth.setParameters(lowess_params);
lowess_smooth.smoothData(rts, ints, smoothed_data);
mt.setSmoothedIntensities(smoothed_data);
// debug intensities
// Size i = 0;
// std::cout << "*****" << std::endl;
// for (MassTrace::const_iterator mt_it = mt.begin(); mt_it != mt.end(); ++mt_it)
// {
// std::cout << mt_it->getIntensity() << " " << smoothed_data[i] << std::endl;
// ++i;
// }
//std::cout << "*****" << std::endl;
std::vector<Size> maxes, mins;
// mt.findLocalExtrema(win_size / 2, maxes, mins);
findLocalExtrema(mt, win_size/2, maxes, mins);
// if only one maximum exists: finished!
if (maxes.size() == 1)
{
bool pw_ok = true;
bool snr_ok = true;
// check mass trace filter criteria (if enabled)
if (pw_filtering_ == "fixed")
{
DoubleReal act_fwhm(mt.estimateFWHM(true));
// std::cout << "act_fwhm: " << act_fwhm << " ";
if (act_fwhm < min_fwhm_ || act_fwhm > max_fwhm_)
{
pw_ok = false;
}
// std::cout << pw_ok << std::endl;
}
if (mt_snr_filtering_)
{
if (computeApexSNR(mt) < chrom_peak_snr_)
{
snr_ok = false;
}
}
if (pw_ok && snr_ok)
{
mt.updateSmoothedMaxRT();
if (pw_filtering_ != "fixed")
{
mt.estimateFWHM(true);
}
// check for minimum/maximum trace length
// DoubleReal mt_length(std::fabs(mt.rbegin()->getRT() - mt.begin()->getRT()));
// if ((mt_length >= min_trace_length_) && (mt_length <= max_trace_length_))
// if (mt_quality >= 1.2)
// {
#ifdef _OPENMP
#pragma omp critical
#endif
single_mtraces.push_back(mt);
}
}
else if (maxes.empty())
{
return;
}
else // split mt to subtraces
{
MassTrace::const_iterator cp_it = mt.begin();
Size last_idx(0);
for (Size min_idx = 0; min_idx < mins.size(); ++min_idx)
{
// copy subtrace between cp_it and splitpoint
std::vector<PeakType> tmp_mt;
std::vector<DoubleReal> smoothed_tmp;
while (last_idx <= mins[min_idx])
{
tmp_mt.push_back(*cp_it);
smoothed_tmp.push_back(mt.getSmoothedIntensities()[last_idx]);
++cp_it;
++last_idx;
}
// check if
// if (tmp_mt.size() >= win_size / 2)
// {
DoubleReal scantime(mt.getScanTime());
MassTrace new_mt(tmp_mt, scantime);
// copy smoothed ints
new_mt.setSmoothedIntensities(smoothed_tmp);
// check filter criteria
bool pw_ok = true;
bool snr_ok = true;
// check mass trace filter criteria (if enabled)
if (pw_filtering_ == "fixed")
{
DoubleReal act_fwhm(new_mt.estimateFWHM(true));
// std::cout << "act_fwhm: " << act_fwhm << " ";
if (act_fwhm < min_fwhm_ || act_fwhm > max_fwhm_)
{
pw_ok = false;
}
// std::cout << pw_ok << std::endl;
}
if (mt_snr_filtering_)
{
if (computeApexSNR(mt) < chrom_peak_snr_)
{
snr_ok = false;
}
}
if (pw_ok && snr_ok)
{
// set label of subtrace
String tr_num;
std::stringstream read_in;
read_in << (min_idx + 1);
tr_num = "." + read_in.str();
new_mt.setLabel(mt.getLabel() + tr_num);
//new_mt.updateWeightedMeanRT();
new_mt.updateSmoothedMaxRT();
//new_mt.updateSmoothedWeightedMeanRT();
new_mt.updateWeightedMeanMZ();
new_mt.updateWeightedMZsd();
if (pw_filtering_ != "fixed")
{
new_mt.estimateFWHM(true);
}
// DoubleReal mt_quality(computeApexSNR(new_mt));
// DoubleReal new_mt_length(std::fabs(new_mt.rbegin()->getRT() - new_mt.begin()->getRT()));
// if ((new_mt_length >= min_trace_length_) && (new_mt_length <= max_trace_length_))
//{
#ifdef _OPENMP
#pragma omp critical
#endif
single_mtraces.push_back(new_mt);
}
// }
}
// don't forget the trailing trace
std::vector<PeakType> tmp_mt;
std::vector<DoubleReal> smoothed_tmp;
while (last_idx < mt.getSize())
{
tmp_mt.push_back(*cp_it);
smoothed_tmp.push_back(mt.getSmoothedIntensities()[last_idx]);
++cp_it;
++last_idx;
}
// if (tmp_mt.size() >= win_size / 2)
// {
DoubleReal scantime(mt.getScanTime());
MassTrace new_mt(tmp_mt, scantime);
// copy smoothed ints
new_mt.setSmoothedIntensities(smoothed_tmp);
// check filter criteria
bool pw_ok = true;
bool snr_ok = true;
// check mass trace filter criteria (if enabled)
if (pw_filtering_ == "fixed")
{
DoubleReal act_fwhm(new_mt.estimateFWHM(true));
// std::cout << "act_fwhm: " << act_fwhm << " ";
if (act_fwhm < min_fwhm_ || act_fwhm > max_fwhm_)
{
pw_ok = false;
}
// std::cout << pw_ok << std::endl;
}
if (mt_snr_filtering_)
{
if (computeApexSNR(mt) < chrom_peak_snr_)
{
snr_ok = false;
}
}
if (pw_ok && snr_ok)
{
// set label of subtrace
String tr_num;
std::stringstream read_in;
read_in << (mins.size() + 1);
tr_num = "." + read_in.str();
new_mt.setLabel(mt.getLabel() + tr_num);
new_mt.updateSmoothedMaxRT();
new_mt.updateWeightedMeanMZ();
new_mt.updateWeightedMZsd();
if (pw_filtering_ != "fixed")
{
new_mt.estimateFWHM(true);
}
// DoubleReal mt_quality(computeApexSNR(new_mt));
// DoubleReal mt_length(std::fabs(new_mt.rbegin()->getRT() - new_mt.begin()->getRT()));
// if ((mt_length >= min_trace_length_) && (mt_length <= max_trace_length_))
// {
#ifdef _OPENMP
#pragma omp critical
#endif
single_mtraces.push_back(new_mt);
}
// }
}
return;
}
/* another bright re-invention of a broken wheel from the people, who
* made an art of it.
*/
static int
parse_os2(struct ftpparse *f, char *p[], int l[],
unsigned int count)
{
/* 0 DIR 04-11-95 16:26 ADDRESS
* 612 A 07-28-95 16:45 air_tra1.bag
* 310992 06-28-94 09:56 INSTALL.EXE
*/
unsigned long mon;
unsigned long day;
unsigned long year;
unsigned long hour;
unsigned long min;
unsigned long sec;
int mtimetype;
uint64 size;
int x;
unsigned int i;
int dir=0;
if (count<4) return 0;
x=get_uint64(p[0],l[0],&size);
if (!x || p[0][x]!=' ') return 0;
for (i=1; i<count-2; i++) {
x=get_ulong(p[i],l[i],&mon);
if (!x) continue;
if (x!=2 || p[i][x]!='-') return 0;
mon-=1;
x++;
x+=get_ulong(p[i]+x,l[i]-x,&day);
if (x!=5 || p[i][x]!='-') return 0;
x++;
x+=get_ulong(p[i]+x,l[i]-x,&year);
if (x!=8 || p[i][x]!=' ') return 0;
if (!fix_year(&year)) return 0;
break;
}
if (i>1)
if (my_byte_equal(p[i-1],3,"DIR"))
dir=1;
i++;
if (i==count) return 0;
x=scan_time(p[i],l[i],&hour,&min,&sec,&mtimetype);
if (x!=l[i]) return 0;
i++;
if (i==count) return 0;
f->name=p[i];
f->namelen=l[i];
if (dir) {
f->flagtrycwd=1;
} else {
f->flagtryretr=1;
f->sizetype=FTPPARSE_SIZE_BINARY;
f->size=size;
}
utcdate2tai (&f->mtime,year,mon,day,hour,min,sec);
f->mtimetype=mtimetype;
return 1;
}
static int
parse_unix(struct ftpparse *f, char *buf, int len,
char *p[], int l[], unsigned int count)
{
/* the horror ... */
/* this list has been taken from Daniel Bernsteins ftpparse.c */
/* UNIX-style listing, without inum and without blocks */
/* "-rw-r--r-- 1 root other 531 Jan 29 03:26 README" */
/* "dr-xr-xr-x 2 root other 512 Apr 8 1994 etc" */
/* "dr-xr-xr-x 2 root 512 Apr 8 1994 etc" */
/* "lrwxrwxrwx 1 root other 7 Jan 25 00:17 bin -> usr/bin" */
/* Also produced by Microsoft's FTP servers for Windows: */
/* "---------- 1 owner group 1803128 Jul 10 10:18 ls-lR.Z" */
/* "d--------- 1 owner group 0 May 9 19:45 Softlib" */
/* Also WFTPD for MSDOS: */
/* "-rwxrwxrwx 1 noone nogroup 322 Aug 19 1996 message.ftp" */
/* Also NetWare: */
/* "d [R----F--] supervisor 512 Jan 16 18:53 login" */
/* "- [R----F--] rhesus 214059 Oct 20 15:27 cx.exe" */
/* Also NetPresenz for the Mac: */
/* "-------r-- 326 1391972 1392298 Nov 22 1995 MegaPhone.sit" */
/* "drwxrwxr-x folder 2 May 10 1996 network" */
/*restructured: */
/* -PERM 1 user group 531 Jan 29 03:26 README */
/* dPERM 2 user group 512 Apr 8 1994 etc */
/* dPERM 2 user 512 Apr 8 1994 etc */
/* lPERM 1 user group 7 Jan 25 00:17 bin -> usr/bin */
/* -PERM 1 user group 1803128 Jul 10 10:18 ls-lR.Z */
/* dPERM 1 user group 0 May 9 19:45 Softlib */
/* -PERM 1 user group 322 Aug 19 1996 message.ftp */
/* d [R----F--] user 512 Jan 16 18:53 login */
/* - [R----F--] user 214059 Oct 20 15:27 cx.exe */
/* -PERM 326 NUMB NUMBER Nov 22 1995 MegaPhone.sit */
/* dPERM folder 2 May 10 1996 network */
/* handled as: */
/* dPERM folder 2 May 10 1996 network */
/* 0 1 2 3 4 5 6 7 8 */
/* note the date system: MON DAY [YEAR|TIME] */
int mon=-1; /* keep gcc quiet */
unsigned long day;
unsigned long year;
unsigned long hour;
unsigned long min;
unsigned long sec;
uint64 size;
int flagtrycwd=0;
int flagtryretr=0;
unsigned int i;
int x;
int mtimetype;
int may_have_size=0;
switch(p[0][0]) {
case 'd': flagtrycwd=1; break;
case '-': flagtryretr=1; break;
case 'l': flagtryretr=flagtrycwd=1; break;
}
i=3;
if (l[1]==6 && my_byte_equal(p[1],l[1],"folder"))
i=2;
x=get_uint64(p[i],l[i],&size);
if (x==l[i]) may_have_size=1;
i++;
while (i<count) {
mon=get_month(p[i],l[i]);
if (-1==mon) {
/* may be size */
x=get_uint64(p[i],l[i],&size);
if (x==l[i]) may_have_size=1;
}
i++;
if (-1!=mon) break;
}
if (i==count) return 0;
x=get_ulong(p[i],l[i],&day);
if (!x) return 0;
if (p[i][x]!=' ') return 0;
if (++i==count) return 0;
x=get_ulong(p[i],l[i],&year);
if (!x) return 0;
if (p[i][x]==':') {
x=scan_time(p[i],l[i],&hour,&min,&sec,&mtimetype);
if (x!=l[i]) return 0;
year=guess_year(mon,day);
} else {
mtimetype=FTPPARSE_MTIME_REMOTEDAY;
hour=min=sec=0;
/* may be this case: */
/* - [-RWCE-F-] mlm 11820 Feb 3 93 12:00 drivers.doc */
if (i+2<count) {
x=scan_time(p[i+1],l[i+1],&hour,&min,&sec,&mtimetype);
if (x!=l[i+1]) {
hour=min=sec=0;
mtimetype=FTPPARSE_MTIME_REMOTEDAY;
} else
i++;
}
if (!fix_year(&year)) return 0;
}
if (++i==count) return 0;
/* note: dosplit eats spaces - but we need them here. So go back. */
f->name=p[i];
f->namelen=buf+len-p[i];
/* "-rwxrwxrwx 1 noone nogroup 322 Aug 19 1996 message.ftp" */
/* "-rwxrwxrwx 1 noone nogroup 322 Aug 19 1996 spacy" */
/* but: */
/* "d [R----F--] supervisor 512 Jan 16 18:53 login" */
if (p[0][1]!=' ') {
while (f->name[-2]==' ') {
f->name--;
f->namelen++;
}
}
if (may_have_size) {
f->sizetype=FTPPARSE_SIZE_BINARY;
f->size=size;
}
f->flagtryretr=flagtryretr;
f->flagtrycwd=flagtrycwd;
utcdate2tai (&f->mtime,year,mon,day,hour,min,sec);
f->mtimetype=mtimetype;
f->format=FTPPARSE_FORMAT_LS; /* for programs dealing with symlinks */
if ('l'==*buf) {
unsigned int j;
for (j=1;j<f->namelen-4;j++) /* 1, -4: no empty names, please */
if (f->name[j]==' '
&& f->name[j+1]=='-'
&& f->name[j+2]=='>'
&& f->name[j+3]==' ') {
f->symlink=f->name+j+4;
f->symlinklen=f->namelen-j-4;
f->namelen=j;
break;
}
}
return 1;
}
static int parse_multinet(struct ftpparse *f, char *p[], int l[],
unsigned int count)
{
/* "CORE.DIR;1 1 8-SEP-1996 16:09 [SYSTEM] (RWE,RWE,RE,RE)" */
/* "[VMSSERV.FILES]ALARM.DIR;1 1/3 5-MAR-1993 18:09:" */
int mon;
unsigned long day;
unsigned long year;
unsigned long hour;
unsigned long min;
unsigned long sec;
int mtimetype;
int x;
char *q;
int m;
if (count<4) return 0;
q=p[2];
m=l[2];
x=get_ulong(q,m,&day);
if (!x || x>2 || day>31) return 0;
if (q[x] != '-') return 0;
q+=x+1;
m-=x+1;
mon=get_month(q,m);
if (-1==mon) return 0;
if (q[3]!='-') return 0;
q+=4;
if (m<5) return 0;
m-=4;
x=get_ulong(q,m,&year);
if (!x || q[x]!=' ') return 0;
if (!fix_year(&year)) return 0;
x=scan_time(p[3],l[3],&hour,&min,&sec,&mtimetype);
if (x!=l[3]) return 0;
f->mtimetype = mtimetype;;
utcdate2tai (&f->mtime,year,mon,day,hour,min,sec);
for (x=0;x<l[0];x++)
if (p[0][x]==';')
break;
if (x>4)
if (p[0][x-4]=='.'
&& p[0][x-3]=='D'
&& p[0][x-2]=='I'
&& p[0][x-1]=='R') {
x-=4;
f->flagtrycwd=1;
}
if (!f->flagtrycwd)
f->flagtryretr=1;
f->namelen=x;
f->name=p[0];
if (f->name[0]=='[') {
/* [dir]file.maybe */
unsigned int y;
for (y=1;y<f->namelen;y++)
if (f->name[y]==']')
break;
if (y!=f->namelen) y++; /* skip ] */
if (y!=f->namelen) {
f->name+=y;
f->namelen-=y;
}
}
return 1;
}
/* note the mon-day-year! */
static int
parse_msdos(struct ftpparse *f, char *buf, unsigned int len)
{
unsigned int pos,start;
unsigned int state;
unsigned long mon;
unsigned long day;
unsigned long year;
unsigned long hour;
unsigned long min;
unsigned long sec;
int mtimetype;
unsigned int x;
uint64 size=0;
unsigned int flagtrycwd=0;
unsigned int flagtryretr=0;
int maxspaces=0; /* to keep leading spaces before dir/file name */
for (state=start=pos=0;pos<len;pos++) {
switch(state) {
case 0: /* month */
if ('-'==buf[pos]) {
state++;
if (pos==start) return 0;
if (get_ulong(buf+start,pos-start,&mon)!=pos-start) return 0;
start=pos+1;
}
break;
case 1: /* day */
if ('-'==buf[pos]) {
state++;
if (pos==start) return 0;
if (get_ulong(buf+start,pos-start,&day)!=pos-start) return 0;
start=pos+1;
}
break;
case 2: /* year */
if (' '==buf[pos]) {
state++;
if (pos-start!=2 && pos-start!=4) return 0;
if (get_ulong(buf+start,pos-start,&year)!=pos-start) return 0;
start=pos+1;
if (!fix_year(&year)) return 0;
}
break;
case 3: /* spaces */
if (' ' == buf[pos]) continue;
state++;
start=pos;
/* FALL THROUGH */
case 4: /* time */
x=scan_time(buf+start,len-pos,&hour,&min,&sec,&mtimetype);
if (!x) return 0;
pos+=x;
if (pos==len) return 0;
state++;
break;
case 5: /* spaces */
if (' ' == buf[pos]) continue;
state++;
start=pos;
/* FALL THROUGH */
case 6: /* <DIR> or length */
if (' ' == buf[pos]) {
if (get_uint64(buf+start,pos-start,&size)!=pos-start) {
if (pos-start < 5
|| !my_byte_equal(buf+start,5,"<DIR>"))
return 0;
flagtrycwd=1;
maxspaces=10;
} else {
flagtryretr=1;
maxspaces=1;
}
state++;
start=pos;
}
break;
case 7: /* spaces */
if (' ' == buf[pos])
if (--maxspaces)
continue;
state++;
start=pos;
/* FALL THROUGH */
case 8: /* file / dir name */
f->name=buf+start;
f->namelen=len-pos;
f->flagtrycwd=flagtrycwd;
f->flagtryretr=flagtryretr;
f->mtimetype=mtimetype;
if (flagtryretr) {
f->size=size;
f->sizetype=FTPPARSE_SIZE_BINARY;
}
if (!fix_year(&year)) return 0;
utcdate2tai(&f->mtime,year,mon-1,day,hour,min,sec);
return 1;
}
}
return 0;
}
